1
|
Yu T, Nie J, Zang H, Zeng Z, Yang Y. Peanut-based Rotation Stabilized Diazotrophic Communities and Increased Subsequent Wheat Yield. MICROBIAL ECOLOGY 2023; 86:2447-2460. [PMID: 37296336 DOI: 10.1007/s00248-023-02254-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 06/05/2023] [Indexed: 06/12/2023]
Abstract
The introduction of legumes into rotations can improve nitrogen use efficiency and crop yield; however, its microbial mechanism involved remains unclear. This study aimed to explore the temporal impact of peanut introduction on microorganisms related to nitrogen metabolism in rotation systems. In this study, the dynamics of diazotrophic communities in two crop seasons and wheat yields of two rotation systems: winter wheat - summer maize (WM) and spring peanut → winter wheat - summer maize (PWM) in the North China Plain were investigated. Our results showed that peanut introduction increased wheat yield and biomass by 11.6% (p < 0.05) and 8.9%, respectively. Lower Chao1 and Shannon indexes of the diazotrophic communities were detected in soils that sampling in June compared with those sampling in September, although no difference was found between WM and PWM. Principal co-ordinates analysis (PCoA) showed that rotation system significantly changed the diazotrophic community structures (PERMANOVA; p < 0.05). Compared with WM, the genera of Azotobacter, Skermanella, Azohydromonas, Rhodomicrobium, Azospirillum, Unclassified_f_Opitutaceae, and Unclassified_f_Rhodospirillaceae were significantly enriched (p < 0.05) in PWM. Furthermore, rotation system and sampling time significantly influenced soil properties, which significantly correlated with the top 15 genera in relative abundance. Partial least squares path modeling (PLS-PM) analysis further showed that the diazotrophic community diversity (alpha- and beta-diversity) and soil properties (pH, SOC and TN) significantly affected wheat yield. In conclusion, legume inclusion has the potential to stabilize diazotrophic community structure at the temporal scales and increase subsequent crop yield.
Collapse
Affiliation(s)
- Taobing Yu
- College of Agronomy and Biotechnology, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Jiangwen Nie
- College of Agronomy and Biotechnology, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Huadong Zang
- College of Agronomy and Biotechnology, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Zhaohai Zeng
- College of Agronomy and Biotechnology, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Yadong Yang
- College of Agronomy and Biotechnology, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China.
| |
Collapse
|
2
|
Cenčič Predikaka T, Mastnak T, Svoljšak Jerman M, Finšgar M. Ex situ bioremediation of diesel fuel-contaminated soil in two different climates. INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2023; 25:1881-1889. [PMID: 37125609 DOI: 10.1080/15226514.2023.2204165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
The petroleum industry is often faced with accidental spills and discharges that pollute valuable natural resources such as soil. The purpose of this study was to assess bioremediation potential of an on-site landfarming unit (LU), a highly economical solution that complies with the zero-waste policy, for bioremediation of the contaminated soil after an actual diesel fuel leakage in a fuel depot. The first aim was to evaluate the effects of different climates on hydrocarbon bioremediation. For this reason, a part of the contaminated soil was moved from the initial location with a sub-Mediterranean climate to an LU at another location with a temperate continental climate. Our results demonstrated that remediation in sub-Mediterranean climate is less effective than the remediation in a temperate continental climate. The second aim of this study was to evaluate the effect of different plant species on the microbial population during bioremediation. For that purpose, 365-day monitoring of phospholipid fatty acids (PLFA) was performed. Our results support the hypothesis that plant-assisted bioremediation can diminish toxic effects of diesel-polluted soil and that the changes in plant species during bioremediation cause changes in the microbial population.
Collapse
Affiliation(s)
- Tjaša Cenčič Predikaka
- Institute for Chemistry, Ecology, Measurements and Analytics, IKEMA d.o.o, Lovrenc na Dravskem polju, Slovenia
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Maribor, Slovenia
| | - Tinkara Mastnak
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Maribor, Slovenia
| | | | - Matjaž Finšgar
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Maribor, Slovenia
| |
Collapse
|
3
|
Papik J, Strejcek M, Musilova L, Guritz R, Leewis MC, Leigh MB, Uhlik O. Legacy Effects of Phytoremediation on Plant-Associated Prokaryotic Communities in Remediated Subarctic Soil Historically Contaminated with Petroleum Hydrocarbons. Microbiol Spectr 2023; 11:e0444822. [PMID: 36975310 PMCID: PMC10100700 DOI: 10.1128/spectrum.04448-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 02/17/2023] [Indexed: 03/29/2023] Open
Abstract
Phytoremediation of petroleum hydrocarbons in subarctic regions relies on the successful establishment of plants that stimulate petroleum-degrading microorganisms, which can be challenging due to the extreme climate, limited nutrients, and difficulties in maintaining sites in remote locations. A long-term phytoremediation experiment was initiated in Alaska in 1995 with the introduction of grasses and/or fertilizer to petroleum hydrocarbon (PHC)-contaminated soils that were subsequently left unmanaged. In 2011, the PHC concentrations were below detection limits in all soils tested and the originally planted grasses had been replaced by volunteer plant species that had colonized the site. Here, we sought to understand how the original treatments influenced the structure of prokaryotic communities associated with plant species that colonized the soils and to assess the interactions between the rhizospheric and endophytic communities of the colonizing vegetation 20 years after the experiment was established. Metataxonomic analysis performed using 16S rRNA gene sequencing revealed that the original type of contaminated soil and phytoremediation strategy influenced the structure of both rhizospheric and endophytic communities of colonizing plants, even 20 years after the treatments were applied and following the disappearance of the originally planted grasses. Our findings demonstrate that the choice of initial phytoremediation strategy drove the succession of microorganisms associated with the colonizing vegetation. The outcome of this study provides new insight into the establishment of plant-associated microbial communities during secondary succession of subarctic areas previously contaminated by PHCs and indicates that the strategies for restoring these ecosystems influence the plant-associated microbiota in the long term. IMPORTANCE Subarctic ecosystems provide key services to local communities, yet they are threatened by pollution caused by spills and disposal of petroleum waste. Finding solutions for the remediation and restoration of subarctic soils is valuable for reasons related to human and ecosystem health, as well as environmental justice. This study provides novel insight into the long-term succession of soil and plant-associated microbiota in subarctic soils that had been historically contaminated with different sources of PHCs and subjected to distinct phytoremediation strategies. We provide evidence that even after the successful removal of PHCs and the occurrence of secondary succession, the fingerprint of the original source of contamination and the initial choice of remediation strategy can be detected as a microbial legacy in the rhizosphere, roots, and shoots of volunteer vegetation even 2 decades after the contamination had occurred. Such information needs to be borne in mind when designing and applying restoration approaches for PHC-contaminated soils in subarctic ecosystems.
Collapse
Affiliation(s)
- Jakub Papik
- University of Chemistry, and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Michal Strejcek
- University of Chemistry, and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Lucie Musilova
- University of Chemistry, and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Rodney Guritz
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, Alaska, USA
- Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, Alaska, USA
| | - Mary-Cathrine Leewis
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, Alaska, USA
- Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, Alaska, USA
- Agriculture and Agri-Food Canada, Quebec, Quebec, Canada
| | - Mary Beth Leigh
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, Alaska, USA
- Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, Alaska, USA
| | - Ondrej Uhlik
- University of Chemistry, and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| |
Collapse
|
4
|
Banister RB, Schwarz MT, Fine M, Ritchie KB, Muller EM. Instability and Stasis Among the Microbiome of Seagrass Leaves, Roots and Rhizomes, and Nearby Sediments Within a Natural pH Gradient. MICROBIAL ECOLOGY 2022; 84:703-716. [PMID: 34596709 PMCID: PMC9622545 DOI: 10.1007/s00248-021-01867-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 09/10/2021] [Indexed: 05/10/2023]
Abstract
Seagrass meadows are hotspots of biodiversity with considerable economic and ecological value. The health of seagrass ecosystems is influenced in part by the makeup and stability of their microbiome, but microbiome composition can be sensitive to environmental change such as nutrient availability, elevated temperatures, and reduced pH. The objective of the present study was to characterize the bacterial community of the leaves, bulk samples of roots and rhizomes, and proximal sediment of the seagrass species Cymodocea nodosa along the natural pH gradient of Levante Bay, Vulcano Island, Italy. The bacterial community was determined by characterizing the 16S rRNA amplicon sequencing and analyzing the operational taxonomic unit classification of bacterial DNA within samples. Statistical analyses were used to explore how life-long exposure to different pH/pCO2 conditions may be associated with significant differences in microbial communities, dominant bacterial classes, and microbial diversity within each plant section and sediment. The microbiome of C. nodosa significantly differed among all sample types and site-specific differences were detected within sediment and root/rhizome microbial communities, but not the leaves. These results show that C. nodosa leaves have a consistent microbial community even across a pH range of 8.15 to 6.05. The ability for C. nodosa to regulate and maintain microbial structure may indicate a semblance of resilience within these vital ecosystems under projected changes in environmental conditions such as ocean acidification.
Collapse
Affiliation(s)
- Raymond B Banister
- Mote Marine Laboratory, Coral Health and Disease Program, Sarasota, FL, USA.
- Institute for Global Ecology, Florida Institute of Technology, 150, W University Blvd, Melbourne, FL, 32901, USA.
| | - Melbert T Schwarz
- Mote Marine Laboratory, Coral Health and Disease Program, Sarasota, FL, USA
| | - Maoz Fine
- The Goodman Faculty of Life Sciences, Bar-Ilan University, 52900, Ramat Gan, Israel
- The Interuniversity Institute for Marine Science, P.O.B. 469, 88103, Eilat, Israel
| | - Kim B Ritchie
- Department of Natural Sciences, University of South Carolina Beaufort, 801, Carteret St., Beaufort, SC, 29906, USA
| | - Erinn M Muller
- Mote Marine Laboratory, Coral Health and Disease Program, Sarasota, FL, USA
| |
Collapse
|
5
|
Kracmarova M, Uhlik O, Strejcek M, Szakova J, Cerny J, Balik J, Tlustos P, Kohout P, Demnerova K, Stiborova H. Soil microbial communities following 20 years of fertilization and crop rotation practices in the Czech Republic. ENVIRONMENTAL MICROBIOME 2022; 17:13. [PMID: 35346385 PMCID: PMC8962459 DOI: 10.1186/s40793-022-00406-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 03/08/2022] [Indexed: 05/25/2023]
Abstract
BACKGROUND Although fertilization and crop rotation practices are commonly used worldwide in agriculture to maximize crop yields, their long-term effect on the structures of soil microorganisms is still poorly understood. This study investigated the long-term impact of fertilization and crop rotation on soil microbial diversity and the microbial community structure in four different locations with three soil types. Since 1996, manure (MF; 330 kg N/ha), sewage sludge (SF; 330 and SF3x; 990 kg N/ha), and NPK (NPK; 330 kg N/ha) fertilizers were periodically applied to the soils classified as chernozem, luvisol and cambisol, which are among the most abundant or fertile soils used for agricultural purposes in the world. In these soils, potato (Solanum tuberosum L.), winter wheat (Triticum aestivum L.), and spring barley (Hordeum vulgare L.) were rotated every three years. RESULTS Soil chemistry, which was significantly associated with location, fertilization, crop rotation, and the interaction of fertilization and location, was the dominant driver of soil microbial communities, both prokaryotic and fungal. A direct effect of long-term crop rotation and fertilization on the structure of their communities was confirmed, although there was no evidence of their influence on microbial diversity. Fungal and bacterial communities responded differently to fertilization treatments; prokaryotic communities were only significantly different from the control soil (CF) in soils treated with MF and SF3x, while fungal communities differed across all treatments. Indicator genera were identified for different treatments. These taxa were either specific for their decomposition activities or fungal plant pathogens. Sequential rotation of the three crops restricted the growth of several of the indicator plant pathogens. CONCLUSIONS Long-term fertilization and crop rotation significantly altered microbial community structure in the soil. While fertilization affected soil microorganisms mainly through changes in nutrient profile, crop rotations lead to the attraction and repulsion of specific plant pathogens. Such changes in soil microbial communities need to be considered when planning soil management.
Collapse
Affiliation(s)
- Martina Kracmarova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28, Prague 6, Czech Republic.
| | - Ondrej Uhlik
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28, Prague 6, Czech Republic
| | - Michal Strejcek
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28, Prague 6, Czech Republic
| | - Jirina Szakova
- Department of Agro-Environmental Chemistry and Plant Nutrition, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 21, Prague - Suchdol, Czech Republic
| | - Jindrich Cerny
- Department of Agro-Environmental Chemistry and Plant Nutrition, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 21, Prague - Suchdol, Czech Republic
| | - Jiri Balik
- Department of Agro-Environmental Chemistry and Plant Nutrition, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 21, Prague - Suchdol, Czech Republic
| | - Pavel Tlustos
- Department of Agro-Environmental Chemistry and Plant Nutrition, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 21, Prague - Suchdol, Czech Republic
| | - Petr Kohout
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Videnska 1083, 142 20, Praha 4, Czech Republic
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Vinicna 5, 128 44, Praha 2, Czech Republic
| | - Katerina Demnerova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28, Prague 6, Czech Republic
| | - Hana Stiborova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28, Prague 6, Czech Republic.
| |
Collapse
|
6
|
Yang J, Duan Y, Guo Y, Li Z, Ni X, Zhang J, Awasthi MK, Li H. Grass waste utilization to alter aggregate-related carbon chemical composition and fungal community structure in apple orchard. CHEMOSPHERE 2022; 287:132404. [PMID: 34597634 DOI: 10.1016/j.chemosphere.2021.132404] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 08/30/2021] [Accepted: 09/27/2021] [Indexed: 06/13/2023]
Abstract
The grass-waste management model affects soil organic carbon (SOC) and the microorganism community structure; however, studies on the relationship between the fungal community structure and the SOC chemical component at the aggregate level are poor. Solid-state 13C NMR and 18 S rDNA methods were used to evaluate the relationship between the SOC chemical composition and fungal community abundance at the aggregate level. Grass mulching significantly increased the percentage of labile carbon O-alkyl C (5.19%-11.79%) and decreased the instability of SOC (1.38-0.69). Microaggregates contained higher alkyl C (33.77%) and lower aromatic C (18.31%), and the A/O-A ratio (1.03) was higher than that of macroaggregates (0.89-0.96). Ascomycota, Basidiomycota and Mortierellomycota dominated the fungal community at the phylum level, and their abundance increased after grass mulching. Microaggregates supported more microbial diversity and richness and were rich in the Ascomycota (36.69%-67.49%) phylum, while LM aggregates were rich in Basidiomycota (5.62%-39.84%). We proved that changes in the O-alkyl C, carbonyl C, aromatic C and alkyl C of SOC chemical components were closely connected to fungal community composition, which together explained the change in fungal composition by 63.81%-71.99% among aggregates. We concluded that alterations in the chemical form of organic carbon were closely related to a change in the soil fungal community. This connection has a positive impact on soil nutrient utilization and SOC conversion in fruit-grass composite ecosystems and promotes the understanding of the relationship between the soil microbial community and nutrient cycling during long-term grass waste utilization.
Collapse
Affiliation(s)
- Jianfeng Yang
- College of Natural Resources and Environment, Northwest A&F University, No.3 Taicheng Road, Yangling, Shaanxi, 712100, China; Key Laboratory of Plant Nutrition and the Agro-Environment in Northwest China, Ministry of Agriculture and Rural Affairs, China
| | - Yumin Duan
- College of Natural Resources and Environment, Northwest A&F University, No.3 Taicheng Road, Yangling, Shaanxi, 712100, China; Key Laboratory of Plant Nutrition and the Agro-Environment in Northwest China, Ministry of Agriculture and Rural Affairs, China
| | - Yaru Guo
- College of Natural Resources and Environment, Northwest A&F University, No.3 Taicheng Road, Yangling, Shaanxi, 712100, China; Key Laboratory of Plant Nutrition and the Agro-Environment in Northwest China, Ministry of Agriculture and Rural Affairs, China
| | - Zelin Li
- College of Natural Resources and Environment, Northwest A&F University, No.3 Taicheng Road, Yangling, Shaanxi, 712100, China; Key Laboratory of Plant Nutrition and the Agro-Environment in Northwest China, Ministry of Agriculture and Rural Affairs, China
| | - Xinhua Ni
- College of Natural Resources and Environment, Northwest A&F University, No.3 Taicheng Road, Yangling, Shaanxi, 712100, China; Key Laboratory of Plant Nutrition and the Agro-Environment in Northwest China, Ministry of Agriculture and Rural Affairs, China
| | - Jiatao Zhang
- College of Natural Resources and Environment, Northwest A&F University, No.3 Taicheng Road, Yangling, Shaanxi, 712100, China; Key Laboratory of Plant Nutrition and the Agro-Environment in Northwest China, Ministry of Agriculture and Rural Affairs, China
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, No.3 Taicheng Road, Yangling, Shaanxi, 712100, China; Key Laboratory of Plant Nutrition and the Agro-Environment in Northwest China, Ministry of Agriculture and Rural Affairs, China.
| | - Huike Li
- College of Natural Resources and Environment, Northwest A&F University, No.3 Taicheng Road, Yangling, Shaanxi, 712100, China; Key Laboratory of Plant Nutrition and the Agro-Environment in Northwest China, Ministry of Agriculture and Rural Affairs, China.
| |
Collapse
|
7
|
Ezazi R, Ahmadzadeh M, Majidian S, Stefani E, Pindo M, Donati C. Responses of cucumber (Cucumis sativus L.) rhizosphere microbial community to some agronomic management practices. FEMS Microbiol Ecol 2021; 97:6325168. [PMID: 34289042 DOI: 10.1093/femsec/fiab107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 07/19/2021] [Indexed: 11/14/2022] Open
Abstract
The microbial communities associated to the rhizosphere (the rhizomicrobiome) have a substantial impact on plant growth and yield. Understanding the effects of agricultural management on the rhizomicrobiome is very important for selecting efficient practices. By sequencing the V4 region of 16S rRNA for bacteria and the ITS1 regions and fungi, we investigated the influences of agronomic practices, including cucumber grafting on cucurbit hybrid (Cucurbita moschata × C. maxima), cucumber-garlic intercropping, and treatment with fungicide iprodione-carbendazim on cucumber rhizosphere microbial communities during plant growth. Soil dehydrogenase activity (DHA) and plant vegetative parameters were assessed as an indicator of overall soil microbial activity. We found that both treatments and growth stage induced significant shifts in microbial community structure. Grafting had the highest number of differentially abundant OTUs compared to control samples, followed by intercropping and fungicide treatment, while plant development stage affected both alpha and beta diversities indices and composition of the rhizomicrobiome. DHA was more dependent on plant growth stages than on treatments. Among the assessed factors, grafting and plant developmental stage resulted in the greatest changes in the microbial community composition. Grafting also increased the plant growth parameters, suggesting that this method should be further investigated in vegetable production systems.
Collapse
Affiliation(s)
- Robab Ezazi
- Department of Plant Protection, College of Agriculture and Natural Resources, University of Tehran, Daneshkadeh Ave., Karaj, Iran, Postal code: 31587-77871
| | - Masoud Ahmadzadeh
- Department of Plant Protection, College of Agriculture and Natural Resources, University of Tehran, Daneshkadeh Ave., Karaj, Iran, Postal code: 31587-77871
| | - Sina Majidian
- School of Electrical Engineering, Iran university of science and technology, Narmak, Hengam street, Tehran, Iran, Postal code: 16846-13114
| | - Erika Stefani
- Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, Via Mach 1, 38010 San Michele all'Adige (TN) - Italy
| | - Massimo Pindo
- Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, Via Mach 1, 38010 San Michele all'Adige (TN) - Italy
| | - Claudio Donati
- Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, Via Mach 1, 38010 San Michele all'Adige (TN) - Italy
| |
Collapse
|
8
|
Gan CD, Jia YB, Yang JY. Remediation of fluoride contaminated soil with nano-hydroxyapatite amendment: Response of soil fluoride bioavailability and microbial communities. JOURNAL OF HAZARDOUS MATERIALS 2021; 405:124694. [PMID: 33278725 DOI: 10.1016/j.jhazmat.2020.124694] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 11/16/2020] [Accepted: 11/23/2020] [Indexed: 06/12/2023]
Abstract
Nano-hydroxyapatite (NHAP), possessing high defluoridation capacity, has been widely used to remove fluoride (F) from polluted water, but little is known about how it affects the bioavailability and toxicity of soil F towards plants. Here, the impact of NHAP (2% w/w) amendment on immobilization, speciation and accumulation of F was studied in a soil-plant system. The results revealed that the NHAP amendment worked effectively to reduce levels of water-soluble F (37.3%-87.8%) and increase available P (76.6%-147%). X-ray photoelectron spectroscopy analysis indicated that the formation of insoluble CaF2 and the ion exchange of F- with OH- into NHAP might be involved in the mechanism of F immobilization and soil pH elevation. Exposure to NHAP significantly decreased the abundance of Cyanobacteria in tested soils, and Gemmatimonadetes abundance in bulk soil was significantly higher than that in rhizosphere soil at 1,000 mg kg-1 F spiked level. Additionally, NHAP amendment decreased F accumulation in wheat shoots (9.10%-18.7%) and roots (3.88%-22.4%), which could mainly be attributed to the reduction of soil bioavailable F and the supplement of Ca from NHAP. These results suggest that NHAP could be a promising amendment to be applied to acidic soil contaminated with F.
Collapse
Affiliation(s)
- Chun-Dan Gan
- College of Architecture and Environment, Sichuan University, Chengdu 610065, China; Yibin Institute of Industrial Technology, Sichuan University Yibin Park, Yibin 644000, China
| | - Yan-Bo Jia
- Hangzhou Institute for Food and Drug Control, Hangzhou 310022, China
| | - Jin-Yan Yang
- College of Architecture and Environment, Sichuan University, Chengdu 610065, China; Yibin Institute of Industrial Technology, Sichuan University Yibin Park, Yibin 644000, China.
| |
Collapse
|
9
|
Adamczyk M, Rüthi J, Frey B. Root exudates increase soil respiration and alter microbial community structure in alpine permafrost and active layer soils. Environ Microbiol 2021; 23:2152-2168. [PMID: 33393203 DOI: 10.1111/1462-2920.15383] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 12/22/2020] [Accepted: 12/29/2020] [Indexed: 12/15/2022]
Abstract
Due to climate warming, alpine ecosystems are changing rapidly. Ongoing upward migrations of plants and thus an increase of easily decomposable substrates will strongly affect the soil microbiome. To understand how belowground communities will respond to such changes, we set up an incubation experiment with permafrost and active soil layers from northern (NW) and southern (SE) slopes of a mountain ridge on Muot da Barba Peider in the Swiss Alps and incubated them with or without artificial root exudates (AREs) at two temperatures, 4°C or 15°C. The addition of AREs resulted in elevated respiration across all soil types. Bacterial and fungal alpha diversity decreased significantly, coinciding with strong shifts in microbial community structure in ARE-treated soils. These shifts in bacterial community structure were driven by an increased abundance of fast-growing copiotrophic taxa. Fungal communities were predominantly affected by AREs in SE active layer soils and shifted towards fast-growing opportunistic yeast. In contrast, in the colder NW facing active layer and permafrost soils fungal communities were more influenced by temperature changes. These findings demonstrate the sensitivity of soil microbial communities in high alpine ecosystems to climate change and how shifts in these communities may lead to functional changes impacting biogeochemical processes.
Collapse
Affiliation(s)
- Magdalene Adamczyk
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, Birmensdorf, 8903, Switzerland
| | - Joel Rüthi
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, Birmensdorf, 8903, Switzerland
| | - Beat Frey
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, Birmensdorf, 8903, Switzerland
| |
Collapse
|
10
|
Lopez-Echartea E, Strejcek M, Mukherjee S, Uhlik O, Yrjälä K. Bacterial succession in oil-contaminated soil under phytoremediation with poplars. CHEMOSPHERE 2020; 243:125242. [PMID: 31995861 DOI: 10.1016/j.chemosphere.2019.125242] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 10/13/2019] [Accepted: 10/26/2019] [Indexed: 05/18/2023]
Abstract
Petroleum hydrocarbons (PHCs) continue to be among the most common pollutants in soil worldwide. Phytoremediation has become a sustainable way of dealing with PHC contamination. We conducted the off-site phytoremediation of PHC-polluted soil from an oil tanker truck accident, where poplars were used for the phytoremediation of the oil-polluted soil in a boreal climate during a seven-year treatment. The succession of bacterial communities over the entire phytoremediation process was monitored using microbial ecological tools relying on high-throughput 16S rRNA gene sequencing. Upon the successful depletion of PHCs from soil, endophytic communities were analyzed in order to assess the complete plant-associated microbiome after the ecological recovery. The rhizosphere-associated soil exhibited different bacterial dynamics than unplanted soil, but both soils experienced succession of bacteria over time, with diversity being negatively correlated with PHC concentration. In the relatively short growing season in North Europe, seasonal variations in environmental conditions were identified that contributed to the dynamics of bacterial communities. Overall, our study proved that phytoremediation using poplar trees can be used to assist in the removal of PHCs from soils in boreal climate conditions and provides new insight into the succession patterns of bacterial communities associated with these plants.
Collapse
Affiliation(s)
- Eglantina Lopez-Echartea
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Michal Strejcek
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Shinjini Mukherjee
- KU Leuven, Laboratory of Aquatic Ecology, Evolution and Conservation, Leuven, Belgium
| | - Ondrej Uhlik
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Kim Yrjälä
- University of Helsinki, Department of Forest Sciences, Helsinki, Finland; Zhejiang A&F University, State Key Laboratory of Subtropical Silviculture, Zhejiang, China.
| |
Collapse
|
11
|
Terzaghi E, Vergani L, Mapelli F, Borin S, Raspa G, Zanardini E, Morosini C, Anelli S, Nastasio P, Sale VM, Armiraglio S, Di Guardo A. Rhizoremediation of weathered PCBs in a heavily contaminated agricultural soil: Results of a biostimulation trial in semi field conditions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 686:484-496. [PMID: 31185397 DOI: 10.1016/j.scitotenv.2019.05.458] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 05/28/2019] [Accepted: 05/30/2019] [Indexed: 05/18/2023]
Abstract
This paper describes the results of a rhizoremediation greenhouse experiment planned to select the best plant species and soil management for the bioremediation of weathered polychlorinated biphenyls (PCBs). We evaluated the ability of different plant species to stimulate activity and diversity of the soil microbial community leading to the reduction of PCB concentrations in a heavily contaminated soil (at mg kg-1 dw level), of the national priority site for remediation (SIN) "Brescia-Caffaro" in Italy. Biostimulation was determined in large size (6kg) pots, to reflect semi-field conditions with a soil/root volume ratio larger than in most rhizoremediation experiments present in the literature. In total, 10 treatments were tested in triplicates comparing 7 plant species (grass and trees) and 5 soil/cultivation conditions (i.e., only one plant species, plant consociation, redox cycle, compost or ammonium thiosulfate addition) with the appropriate unplanted controls. After 18months of biostimulation the overall reduction of total PCBs varied between 14 and 20%. Microbial analysis revealed a shift in the microbial community structure over time and showed that all the planted treatments significantly enhanced microbial hydrolytic activity and the abundance of bacterial populations, including potential PCB degraders, in the soil surrounding plant roots. The plant species most effective in reducing the contaminant concentrations were Festuca arundinacea cultivated adding compost or in consociation with Cucurbita pepo ssp. pepo and Medicago sativa cultivated with Rhizobium spp. and mycorrhizal fungi; they reduced total PCB concentrations of about 20% and showed the significant depletion of a high number of PCB congeners (29, 37 and 23, respectively, out of the 79 measured). Our results suggest that these plant species are particularly efficient in increasing soil PCB bioavailability and in stimulating microbial degradation. They could be used in field rhizoremediation strategies to enhance the natural attenuation process and reduce PCB levels in historically contaminated sites.
Collapse
Affiliation(s)
- Elisa Terzaghi
- DiSAT, University of Insubria, Via Valleggio 11, Como, Italy
| | | | | | - Sara Borin
- DeFENS, University of Milan, Via Celoria 2, Milan, Italy
| | - Giuseppe Raspa
- DCEME, Sapienza University of Rome, Via Eudossiana 18, Rome, Italy
| | | | | | | | | | | | - Stefano Armiraglio
- Municipality of Brescia - Museum of Natural Sciences, Via Ozanam 4, Brescia, Italy
| | | |
Collapse
|
12
|
Liang SX, Xi X, Ding L, Chen Q, Liu W. Immobilization Mechanism of Nano-Hydroxyapatite on Lead in the Ryegrass Rhizosphere Soil Under Root Confinement. BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2019; 103:330-335. [PMID: 31263937 DOI: 10.1007/s00128-019-02665-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 06/19/2019] [Indexed: 06/09/2023]
Abstract
The immobilization effect and mechanism of nano-hydroxyapatite(NHAP) on Pb in the ryegrass rhizosphere soil were studied by root-bag experiment. The speciation analysis results revealed that the residual Pb concentrations in the rhizosphere soil significantly increased after NHAP application. The acid-soluble and reducible Pb concentrations significantly decreased, indicating that NHAP had obviously immobilized Pb. Meanwhile, NHAP significantly promoted the secretion of tartaric acid from ryegrass roots, resulting the rhizosphere soil pH had been below that of the control group. This helped to relieve the stress of Pb on ryegrass, also promoted the dissolution of NHAP, resulting the formation of stable precipitation with more Pb ions. NHAP increased the rhizosphere soil pH by 0.03 to 0.17, which promoted the conversion of Pb to non-utilizable bioavailability. The total Pb mass balance indicated only a very small proportion Pb transferred to the shoots through ryegrass roots. The formation of pyromorphite by Pband NHAP in soil was accordingly to interpret the dominant mechanism for Pb immobilization.
Collapse
Affiliation(s)
- Shu-Xuan Liang
- College of Chemistry and Environmental Science, Hebei University; Key Laboratory of Analytical Science of Hebei Province, Baoding, P. R. China.
| | - Xiaocan Xi
- College of Chemistry and Environmental Science, Hebei University; Key Laboratory of Analytical Science of Hebei Province, Baoding, P. R. China
| | - Ling Ding
- College of Chemistry and Environmental Science, Hebei University; Key Laboratory of Analytical Science of Hebei Province, Baoding, P. R. China
| | - Qiusheng Chen
- Tianjin Institute of Agricultural Quality Standard and Testing Technology, Tianjin, 300381, P. R. China
| | - Wei Liu
- College of Chemistry and Environmental Science, Hebei University; Key Laboratory of Analytical Science of Hebei Province, Baoding, P. R. China.
| |
Collapse
|
13
|
Liu JL, Yao J, Wang F, Min N, Gu JH, Li ZF, Sunahara G, Duran R, Solevic-Knudsen T, Hudson-Edwards KA, Alakangas L. Bacterial diversity in typical abandoned multi-contaminated nonferrous metal(loid) tailings during natural attenuation. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 247:98-107. [PMID: 30669085 DOI: 10.1016/j.envpol.2018.12.045] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 12/08/2018] [Accepted: 12/15/2018] [Indexed: 06/09/2023]
Abstract
Abandoned nonferrous metal(loid) tailings sites are anthropogenic, and represent unique and extreme ecological niches for microbial communities. Tailings contain elevated and toxic content of metal(loid)s that had negative effects on local human health and regional ecosystems. Microbial communities in these typical tailings undergoing natural attenuation are often very poorly examined. The diversity and inferred functions of bacterial communities were examined at seven nonferrous metal(loid) tailings sites in Guangxi (China), which were abandoned between 3 and 31 years ago. The acidity of the tailings sites rose over 31 years of site inactivity. Desulfurivibrio, which were always coupled with sulfur/sulfide oxidation to dissimilate the reduction of nitrate/nitrite, were specific in tailings with 3 years abandonment. However, genus beneficial to plant growth (Rhizobium), and iron/sulfur-oxidizing bacteria and metal(loid)-related genera (Acidiferrobacter and Acidithiobacillus) were specific within tailings abandoned for 23 years or more. The increased abundance of acid-generating iron/sulfur-oxidizing and metal(loid)-related bacteria and specific bacterial communities during the natural attenuation could provide new insights for understanding microbial ecosystem functioning in mine tailings. OTUs related to Sulfuriferula, Bacillus, Sulfurifustis, Gaiella, and Thiobacillus genera were the main contributors differentiating the bacterial communities between the different tailing sites. Multiple correlation analyses between bacterial communities and geochemical parameters indicated that pH, TOC, TN, As, Pb, and Cu were the main drivers influencing the bacterial community structures. PICRUSt functional exploration revealed that the main functions were related to DNA repair and recombination, important functions for bacterial adaptation to cope with the multi-contamination of tailings. Such information provides new insights to guide future metagenomic studies for the identification of key functions beyond metal-transformation/resistance. As well, our results offers novel outlooks for the management of bacterial communities during natural attenuation of multi-contaminated nonferrous metal(loid) tailings sites.
Collapse
Affiliation(s)
- Jian-Li Liu
- School of Energy and Environment Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Jun Yao
- School of Water Resource and Environment Engineering, China University of Geosciences (Beijing), 100083, China.
| | - Fei Wang
- School of Energy and Environment Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Ning Min
- School of Water Resource and Environment Engineering, China University of Geosciences (Beijing), 100083, China
| | - Ji-Hai Gu
- School of Water Resource and Environment Engineering, China University of Geosciences (Beijing), 100083, China
| | - Zi-Fu Li
- School of Energy and Environment Engineering, University of Science and Technology Beijing, Beijing, 100083, China.
| | - Geoffrey Sunahara
- School of Water Resource and Environment Engineering, China University of Geosciences (Beijing), 100083, China; Department of Natural Resource Sciences, McGill University, Montreal, Quebec, H9X3V9, Canada
| | - Robert Duran
- School of Water Resource and Environment Engineering, China University of Geosciences (Beijing), 100083, China; Equipe Environnement et Microbiologie, MELODY Group, Université de Pau et des Pays de l'Adour, E2S-UPPA, IPREM UMR CNRS 5254, BP 1155, 64013, Pau Cedex, France
| | - Tatjana Solevic-Knudsen
- Institute of Chemistry, Technology and Metallurgy, University of Belgrade, Njegoseva 12, PO Box 473, 11001, Belgrade, Serbia
| | - Karen A Hudson-Edwards
- Environment & Sustainability Institute and Camborne School of Mines, University of Exeter, Penryn, Cornwall, TR10 9DF, UK
| | - Lena Alakangas
- Department of Chemical Engineering and Geosciences, Luleå University of Technology, SE-97187 Luleå, Sweden
| |
Collapse
|
14
|
Singer E, Bonnette J, Kenaley SC, Woyke T, Juenger TE. Plant compartment and genetic variation drive microbiome composition in switchgrass roots. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:185-195. [PMID: 30537406 PMCID: PMC6850097 DOI: 10.1111/1758-2229.12727] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 11/28/2018] [Accepted: 12/04/2018] [Indexed: 05/05/2023]
Abstract
Switchgrass (Panicum virgatum) is a promising biofuel crop native to the United States with genotypes that are adapted to a wide range of distinct ecosystems. Various plants have been shown to undergo symbioses with plant growth-promoting bacteria and fungi, however, plant-associated microbial communities of switchgrass have not been extensively studied to date. We present 16S ribosomal RNA gene and internal transcribed spacer (ITS) data of rhizosphere and root endosphere compartments of four switchgrass genotypes to test the hypothesis that host selection of its root microbiota prevails after transfer to non-native soil. We show that differences in bacterial, archaeal and fungal community composition and diversity are strongly driven by plant compartment and switchgrass genotypes and ecotypes. Plant-associated microbiota show an enrichment in Alphaproteobacteria and Actinobacteria as well as Sordariales and Pleosporales compared with the surrounding soil. Root associated compartments display low-complexity communities dominated and enriched in Actinobacteria, in particular Streptomyces, in the lowland genotypes, and in Alphaproteobacteria, specifically Sphingobium, in the upland genotypes. Our comprehensive root analysis serves as a snapshot of host-specific bacterial and fungal associations of switchgrass in the field and confirms that host-selected microbiomes persist after transfer to non-native soil.
Collapse
Affiliation(s)
- Esther Singer
- Department of Energy Joint Genome InstituteWalnut CreekCAUSA
| | - Jason Bonnette
- Department of Integrative Biology, University of Texas AustinAustinTXUSA
| | - Shawn C. Kenaley
- School of Integrative Plant Science, Cornell UniversityIthacaNYUSA
| | - Tanja Woyke
- Department of Energy Joint Genome InstituteWalnut CreekCAUSA
| | - Thomas E. Juenger
- Department of Integrative Biology, University of Texas AustinAustinTXUSA
| |
Collapse
|
15
|
The Effects of Different Lead Pollution Levels on Soil Microbial Quantities and Metabolic Function with/without Salix integra Thunb. Planting. FORESTS 2019. [DOI: 10.3390/f10020077] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Background and Objectives: Salix integra Thunb., a fast-growing woody species, has been used in phytoremediation in recent years. It has the potential to accumulate high amounts of lead (Pb) in its growth, however, its effects on soil microbial community structure and function during its phytoextraction processes are not well understood, especially at different pollution levels. Materials and Methods: In our study, we set unplanted and planted Salix integra in areas with four levels of Pb treatments (0, 500, 1000, and 1500 mg/kg). After six months of planting, the rhizospheric soil, bulk soil, and unplanted soil were collected. Soil properties and microbes participating in nitrogen and phosphorus cycling were measured, following standard methods. Microbial metabolic functions were assessed using a Biolog-ECO microplate. Results: The bacteria (nitrogen-fixing bacteria, ammonifying bacteria, inorganic phosphorus-solubilizing bacteria, and nitrosobacteria) all increased in the 500 mg/kg treatment and decreased in the 1500 mg/kg treatment compared with the 0 mg/kg treatment, especially in rhizospheric soil. The microbial metabolisms decreased along with the increase of Pb levels, with the exception of the rhizospheric soil with a 500 mg/kg treatment. The metabolic patterns were relative to the pollution levels. The utilization of carbohydrates was decreased, and of amino acids or fatty acids was increased, in the 500 mg/kg treatment, while the opposite occurred in the 1500 mg/kg treatment. The values of soil properties, microbial quantities, and metabolic activities were higher in rhizospheric than bulk soil, while the differences between bulk and unplanted soil were different among the different Pb treatments. The soil properties had little effect on the microbial quantities and metabolic activities. Conclusions: S. integra planting and Pb levels had an interactive effect on the microbial community. In general, S. integra planting promoted microbial quantities and metabolic activity in rhizospheric soil. Lower Pb pollution increased microbial quantities and promoted the utilization of amino acids or fatty acids, while higher Pb concentrations decreased microbial quantities and metabolic activities, and promoted the utilization of carbohydrates.
Collapse
|
16
|
O’Brien FJM, Dumont MG, Webb JS, Poppy GM. Rhizosphere Bacterial Communities Differ According to Fertilizer Regimes and Cabbage ( Brassica oleracea var. capitata L.) Harvest Time, but Not Aphid Herbivory. Front Microbiol 2018; 9:1620. [PMID: 30083141 PMCID: PMC6064718 DOI: 10.3389/fmicb.2018.01620] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 06/28/2018] [Indexed: 11/16/2022] Open
Abstract
Rhizosphere microbial communities are known to be highly diverse and strongly dependent on various attributes of the host plant, such as species, nutritional status, and growth stage. High-throughput 16S rRNA gene amplicon sequencing has been used to characterize the rhizosphere bacterial community of many important crop species, but this is the first study to date to characterize the bacterial and archaeal community of Brassica oleracea var. capitata. The study also tested the response of the bacterial community to fertilizer type (organic or synthetic) and N dosage (high or low), in addition to plant age (9 or 12 weeks) and aphid (Myzus persicae) herbivory (present/absent). The impact of aboveground herbivory on belowground microbial communities has received little attention in the literature, and since the type (organic or mineral) and amount of fertilizer applications are known to affect M. percicae populations, these treatments were applied at agricultural rates to test for synergistic effects on the soil bacterial community. Fertilizer type and plant growth were found to result in significantly different rhizosphere bacterial communities, while there was no effect of aphid herbivory. Several operational taxonomic units were identified as varying significantly in abundance between the treatment groups and age cohorts. These included members of the S-oxidizing genus Thiobacillus, which was significantly more abundant in organically fertilized 12-week-old cabbages, and the N-fixing cyanobacteria Phormidium, which appeared to decline in synthetically fertilized soils relative to controls. These responses may be an effect of accumulating root-derived glucosinolates in the B. oleracea rhizosphere and increased N-availability, respectively.
Collapse
Affiliation(s)
- Flora J. M. O’Brien
- Biological Sciences, University of Southampton, Southampton, United Kingdom
- NIAB EMR, East Malling, United Kingdom
| | - Marc G. Dumont
- Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Jeremy S. Webb
- Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Guy M. Poppy
- Biological Sciences, University of Southampton, Southampton, United Kingdom
| |
Collapse
|
17
|
Hu Y, Dou X, Li J, Li F. Impervious Surfaces Alter Soil Bacterial Communities in Urban Areas: A Case Study in Beijing, China. Front Microbiol 2018; 9:226. [PMID: 29545776 PMCID: PMC5839015 DOI: 10.3389/fmicb.2018.00226] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Accepted: 01/30/2018] [Indexed: 12/20/2022] Open
Abstract
The rapid expansion of urbanization has caused land cover change, especially the increasing area of impervious surfaces. Such alterations have significant effects on the soil ecosystem by impeding the exchange of gasses, water, and materials between soil and the atmosphere. It is unclear whether impervious surfaces have any effects on soil bacterial diversity and community composition. In the present study, we conducted an investigation of bacterial communities across five typical land cover types, including impervious surfaces (concrete), permeable pavement (bricks with round holes), shrub coverage (Buxus megistophylla Levl.), lawns (Festuca elata Keng ex E. Alexeev), and roadside trees (Sophora japonica Linn.) in Beijing, to explore the response of bacteria to impervious surfaces. The soil bacterial communities were addressed by high-throughput sequencing of the bacterial 16S rRNA gene. We found that Proteobacteria, Actinobacteria, Acidobacteria, Bacteroidetes, Chloroflexi, and Firmicutes were the predominant phyla in urban soils. Soil from impervious surfaces presented a lower bacterial diversity, and differed greatly from other types of land cover. Soil bacterial diversity was predominantly affected by Zn, dissolved organic carbon (DOC), and soil moisture content (SMC). The composition of the bacterial community was similar under shrub coverage, roadside trees, and lawns, but different from beneath impervious surfaces and permeable pavement. Variance partitioning analysis showed that edaphic properties contributed to 12% of the bacterial community variation, heavy metal pollution explained 3.6% of the variation, and interaction between the two explained 33% of the variance. Together, our data indicate that impervious surfaces induced changes in bacterial community composition and decrease of bacterial diversity. Interactions between edaphic properties and heavy metals were here found to change the composition of the bacterial community and diversity across areas with different types of land cover, and soil properties play a more important role than heavy metals.
Collapse
Affiliation(s)
- Yinhong Hu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaolin Dou
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Juanyong Li
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation and Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Feng Li
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
18
|
Gallart M, Adair KL, Love J, Meason DF, Clinton PW, Xue J, Turnbull MH. Host Genotype and Nitrogen Form Shape the Root Microbiome of Pinus radiata. MICROBIAL ECOLOGY 2018; 75:419-433. [PMID: 28875273 DOI: 10.1007/s00248-017-1055-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 08/22/2017] [Indexed: 05/10/2023]
Abstract
A central challenge in community ecology is understanding the role that phenotypic variation among genotypes plays in structuring host-associated communities. While recent studies have investigated the relationship between plant genotype and the composition of soil microbial communities, the effect of genotype-by-environment interactions on the plant microbiome remains unclear. In this study, we assessed the influence of tree genetics (G), nitrogen (N) form and genotype-by-environment interaction (G x N) on the composition of the root microbiome. Rhizosphere communities (bacteria and fungi) and root-associated fungi (including ectomycorrhizal and saprotrophic guilds) were characterised in two genotypes of Pinus radiata with contrasting physiological responses to exogenous organic or inorganic N supply. Genotype-specific responses to N form influenced the composition of the root microbiome. Specifically, (1) diversity and composition of rhizosphere bacterial and root-associated fungal communities differed between genotypes that had distinct responses to N form, (2) shifts in the relative abundance of individual taxa were driven by the main effects of N form or host genotype and (3) the root microbiome of the P. radiata genotype with the most divergent growth responses to organic and inorganic N was most sensitive to differences in N form. Our results show that intraspecific variation in tree response to N form has significant consequences for the root microbiome of P. radiata, demonstrating the importance of genotype-by-environment interactions in shaping host-associated communities.
Collapse
Affiliation(s)
- Marta Gallart
- Centre for Integrative Ecology, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
| | - Karen L Adair
- Centre for Integrative Ecology, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Department of Entomology, Cornell University, Ithaca, NY, USA
| | - Jonathan Love
- Centre for Integrative Ecology, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, Umeå, Sweden
| | | | | | | | - Matthew H Turnbull
- Centre for Integrative Ecology, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| |
Collapse
|
19
|
Vergani L, Mapelli F, Marasco R, Crotti E, Fusi M, Di Guardo A, Armiraglio S, Daffonchio D, Borin S. Bacteria Associated to Plants Naturally Selected in a Historical PCB Polluted Soil Show Potential to Sustain Natural Attenuation. Front Microbiol 2017; 8:1385. [PMID: 28790991 PMCID: PMC5524726 DOI: 10.3389/fmicb.2017.01385] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 07/10/2017] [Indexed: 11/13/2022] Open
Abstract
The exploitation of the association between plants and microorganisms is a promising approach able to boost natural attenuation processes for soil clean-up in vast polluted areas characterized by mixed chemical contamination. We aimed to explore the selection of root-associated bacterial communities driven by different plant species spontaneously established in abandoned agricultural soils within a historical polluted site in north Italy. The site is highly contaminated by chlorinated persistent organic pollutants, mainly constituted by polychlorobiphenyls (PCBs), together with heavy metals and metalloids, in variable concentrations and uneven distribution. The overall structure of the non-vegetated and root-associated soil fractions bacterial communities was described by high-throughput sequencing of the 16S rRNA gene, and a collection of 165 rhizobacterial isolates able to use biphenyl as unique carbon source was assayed for plant growth promotion (PGP) traits and bioremediation potential. The results showed that the recruitment of specific bacterial communities in the root-associated soil fractions was driven by both soil fractions and plant species, explaining 21 and 18% of the total bacterial microbiome variation, respectively. PCR-based detection in the soil metagenome of bacterial bphA gene, encoding for the biphenyl dioxygenase α subunit, indicated that the soil in the site possesses metabolic traits linked to PCB degradation. Biphenyl-utilizing bacteria isolated from the rhizosphere of the three different plant species showed low phylogenetic diversity and well represented functional traits, in terms of PGP and bioremediation potential. On average, 72% of the strains harbored the bphA gene and/or displayed catechol 2,3-dioxygenase activity, involved in aromatic ring cleavage. PGP traits, including 1-aminocyclopropane-1-carboxylic acid deaminase activity potentially associated to plant stress tolerance induction, were widely distributed among the isolates according to in vitro assays. PGP tested in vivo on tomato plants using eleven selected bacterial isolates, confirmed the promotion and protection potential of the rhizosphere bacteria. Different spontaneous plant species naturally selected in a historical chronically polluted site showed to determine the enrichment of peculiar bacterial communities in the soil fractions associated to the roots. All the rhizosphere communities, nevertheless, hosted bacteria with degradation/detoxification and PGP potential, putatively sustaining the natural attenuation process.
Collapse
Affiliation(s)
- Lorenzo Vergani
- Department of Food, Environmental and Nutritional Sciences, University of MilanMilan, Italy
| | - Francesca Mapelli
- Department of Food, Environmental and Nutritional Sciences, University of MilanMilan, Italy
| | - Ramona Marasco
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and TechnologyThuwal, Saudi Arabia
| | - Elena Crotti
- Department of Food, Environmental and Nutritional Sciences, University of MilanMilan, Italy
| | - Marco Fusi
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and TechnologyThuwal, Saudi Arabia
| | - Antonio Di Guardo
- Department of Science and High Technology, University of InsubriaComo, Italy
| | | | - Daniele Daffonchio
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and TechnologyThuwal, Saudi Arabia
| | - Sara Borin
- Department of Food, Environmental and Nutritional Sciences, University of MilanMilan, Italy
| |
Collapse
|
20
|
Yang W, Zhang T, Lin S, Ni W. Distance-dependent varieties of microbial community structure and metabolic functions in the rhizosphere of Sedum alfredii Hance during phytoextraction of a cadmium-contaminated soil. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:14234-14248. [PMID: 28421524 DOI: 10.1007/s11356-017-9007-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 04/07/2017] [Indexed: 06/07/2023]
Abstract
The recovery of microbial community and activities is crucial to the remediation of contaminated soils. Distance-dependent variations of microbial community composition and metabolic characteristics in the rhizospheric soil of hyperaccumulator during phytoextraction are poorly understood. A 12-month phytoextraction experiment with Sedum alfredii in a Cd-contaminated soil was conducted. A pre-stratified rhizobox was used for separating sub-layer rhizospheric (0-2, 2-4, 4-6, 6-8, 8-10 mm from the root mat)/bulk soils. Soil microbial structure and function were analyzed by phospholipid fatty acid (PLFA) and MicroResp™ methods. The concentrations of total and specified PLFA biomarkers and the utilization rates for the 14 substrates (organic carbon) in the 0-2-mm sub-layer rhizospheric soil were significantly increased, as well as decreased with the increase in the distance from the root mat. Microbial structure measured by the ratios of different groups of PLFAs such as fungal/bacterial, monounsaturated/saturated, ratios of Gram-positive to Gram-negative (GP/GN) bacterial, and cyclopropyl/monoenoic precursors and 19:0 cyclo/18:1ω7c were significantly changed in the 0-2-mm soil. The PLFA contents and substrate utilization rates were negatively correlated with pH and total, acid-soluble, and reducible fractions of Cd, while positively correlated with labile carbon. The dynamics of microbial community were likely due to root exudates and Cd uptake by S. alfredii. This study revealed the stimulations and gradient changes of rhizosphere microbial community through phytoextraction, as reduced Cd concentration, pH, and increased labile carbons are due to the microbial community responses.
Collapse
Affiliation(s)
- Wenhao Yang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
- College of Environmental and Resource Sciences, Key Laboratory of Agricultural Resource and Environment of Zhejiang Province, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Taoxiang Zhang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Sen Lin
- College of Environmental and Resource Sciences, Key Laboratory of Agricultural Resource and Environment of Zhejiang Province, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Wuzhong Ni
- College of Environmental and Resource Sciences, Key Laboratory of Agricultural Resource and Environment of Zhejiang Province, Zhejiang University, Hangzhou, 310058, People's Republic of China.
| |
Collapse
|
21
|
Effects of Liquid Organic Fertilizers on Plant Growth and Rhizosphere Soil Characteristics of Chrysanthemum. SUSTAINABILITY 2017. [DOI: 10.3390/su9050841] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
|
22
|
Garoutte A, Cardenas E, Tiedje J, Howe A. Methodologies for probing the metatranscriptome of grassland soil. J Microbiol Methods 2016; 131:122-129. [PMID: 27793585 DOI: 10.1016/j.mimet.2016.10.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 10/21/2016] [Accepted: 10/21/2016] [Indexed: 10/20/2022]
Abstract
Metatranscriptomics provides an opportunity to identify active microbes and expressed genes in complex soil communities in response to particular conditions. Currently, there are a limited number of soil metatranscriptome studies to provide guidance for using this approach in this challenging matrix. Hence, we evaluated the technical challenges of applying soil metatranscriptomics to a highly diverse, low activity natural system. We used a non-targeted rRNA removal approach, duplex nuclease specific (DSN) normalization, to generate a metatranscriptomic library from field collected soil supporting a perennial grass, Miscanthus x giganteus (a biofuel crop), and evaluated its ability to provide insight into its active community members and their expressed protein-coding genes. We also evaluated various bioinformatics approaches for analyzing our soil metatranscriptome, including annotation of unassembled transcripts, de novo assembly, and aligning reads to known genomes. Further, we evaluated various databases for their ability to provide annotations for our metatranscriptome. Overall, our results emphasize that low activity, highly genetically diverse and relatively stable microbiomes, like soil, requires very deep sequencing to sample the transcriptome beyond the common core functions. We identified several key areas that metatranscriptomic analyses will benefit from including increased rRNA removal, assembly of short read transcripts, and more relevant reference bases while providing a priority set of expressed genes for functional assessment.
Collapse
Affiliation(s)
- Aaron Garoutte
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States.
| | - Erick Cardenas
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - James Tiedje
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States; Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | - Adina Howe
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States; Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, Iowa, United States
| |
Collapse
|
23
|
Musilova L, Ridl J, Polivkova M, Macek T, Uhlik O. Effects of Secondary Plant Metabolites on Microbial Populations: Changes in Community Structure and Metabolic Activity in Contaminated Environments. Int J Mol Sci 2016; 17:E1205. [PMID: 27483244 PMCID: PMC5000603 DOI: 10.3390/ijms17081205] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 06/20/2016] [Accepted: 07/15/2016] [Indexed: 12/19/2022] Open
Abstract
Secondary plant metabolites (SPMEs) play an important role in plant survival in the environment and serve to establish ecological relationships between plants and other organisms. Communication between plants and microorganisms via SPMEs contained in root exudates or derived from litter decomposition is an example of this phenomenon. In this review, the general aspects of rhizodeposition together with the significance of terpenes and phenolic compounds are discussed in detail. We focus specifically on the effect of SPMEs on microbial community structure and metabolic activity in environments contaminated by polychlorinated biphenyls (PCBs) and polyaromatic hydrocarbons (PAHs). Furthermore, a section is devoted to a complex effect of plants and/or their metabolites contained in litter on bioremediation of contaminated sites. New insights are introduced from a study evaluating the effects of SPMEs derived during decomposition of grapefruit peel, lemon peel, and pears on bacterial communities and their ability to degrade PCBs in a long-term contaminated soil. The presented review supports the "secondary compound hypothesis" and demonstrates the potential of SPMEs for increasing the effectiveness of bioremediation processes.
Collapse
Affiliation(s)
- Lucie Musilova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague, Technicka 3, 166 28 Prague, Czech Republic.
| | - Jakub Ridl
- Department of Genomics and Bioinformatics, Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic.
| | - Marketa Polivkova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague, Technicka 3, 166 28 Prague, Czech Republic.
| | - Tomas Macek
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague, Technicka 3, 166 28 Prague, Czech Republic.
| | - Ondrej Uhlik
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague, Technicka 3, 166 28 Prague, Czech Republic.
| |
Collapse
|