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Huang S, Yu J, Hou D, Yue H, Zhang D, Li Y, Lyu J, Jin L, Jin N. Response of soil microbial community diversity to continuous cucumber cropping in facilities along the Yellow River irrigation area. PLoS One 2023; 18:e0289772. [PMID: 37566624 PMCID: PMC10420343 DOI: 10.1371/journal.pone.0289772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 07/26/2023] [Indexed: 08/13/2023] Open
Abstract
Cucumber is an important cash crop; however, continuous cropping obstacles readily occur within the intensive production processes of facility horticulture. This study aimed to determine the effects of continuous cropping on soil quality and the microbial community in the rhizosphere soil of cucumbers. Rhizosphere soil of cucumber planted continuously for 4, 8, and 12 years was investigated, and soil that was not continuously planted was used as the control. Soil physicochemical properties, enzyme activity, microbial diversity, and richness were determined. The results showed that with the increase in continuous cropping years (0, 4, 8, and 12 years), soil total salt content continuously increased, while the pH value significantly decreased. Compared with the control, soil organic matter, alkali-hydrolyzed nitrogen, available phosphorus, available potassium, and nitrate nitrogen contents increased significantly after 4 and 8 years of continuous cropping. Spearman correlation analysis showed that pH was negatively correlated with sucrase or sucrose and available phosphorus was positively correlated with alkaline phosphatase. Compared with the control, the diversity and abundance of bacterial and fungal communities in cucumber rhizosphere soil decreased after 4 and 12 years of continuous cropping. Continuous cropping led to a significant increase in the richness of the dominant phylum of cucumber rhizosphere soil. Principal coordinates analysis showed that, compared with the control, the soil microbial community structure was significantly separated after 4, 8, and 12 years of continuous cropping, and the microbial community structure was most similar after 4 and 8 years of continuous cropping. In addition, redundancy analysis showed that pH was the main driver of soil microbial dominance. In conclusion, continuous cropping of cucumber along the Yellow River irrigation area has led to the deterioration of soil nutrients and microbial communities in that region. This experiment provides a theoretical foundation for addressing the challenges associated with continuous cropping in cucumber cultivation.
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Affiliation(s)
- Shuchao Huang
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Jihua Yu
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Dong Hou
- Vegetable Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, China
| | - Hongzhong Yue
- Vegetable Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, China
| | - Dongqin Zhang
- Vegetable Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, China
| | - Yali Li
- Vegetable Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, China
| | - Jian Lyu
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Li Jin
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Ning Jin
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
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Azeem M, Arockiam Jeyasundar PGS, Ali A, Riaz L, Khan KS, Hussain Q, Kareem HA, Abbas F, Latif A, Majrashi A, Ali EF, Li R, Shaheen SM, Li G, Zhang Z, Zhu YG. Cow bone-derived biochar enhances microbial biomass and alters bacterial community composition and diversity in a smelter contaminated soil. ENVIRONMENTAL RESEARCH 2023; 216:114278. [PMID: 36115420 DOI: 10.1016/j.envres.2022.114278] [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: 05/08/2022] [Revised: 08/24/2022] [Accepted: 09/02/2022] [Indexed: 06/15/2023]
Abstract
Bone waste could be utilized as a potential amendment for remediation of smelter-contaminated soils. Nevertheless, the influences of cow bone-derived biochar (CB) on soil microbial biomass and microbial community composition in multi-metal contaminated mining soils are still not clearly documented. Hence, the cow bone was used as feedstock material for biochar preparation and pyrolyzed at two temperatures such as 500 °C (CB500) and 800 °C (CB800), and added to a smelter soil at the dosage of 0 (unamended control), 2.5, 5, and 10% (w/w); then, the soil treatments were cultivated by maize. The CB effect on soil biochemical attributes and response of soil microbial biomass, bacterial communities, and diversity indices were examined after harvesting maize. Addition of CB enhanced total nutrient contents (i.e., total nitrogen up to 26% and total phosphorus P up to 27%) and the nutrients availability (i.e., NH4 up to 50%; NO3 up to 31%; Olsen P up to 48%; extractable K up to 18%; dissolved organic carbon up to 74%) in the treated soil, as compared to the control. The CB500 application revealed higher microbial biomass C (up to 66%), P (up to 41%), and bacterial gene abundance (up to 76%) than the control. However, comparatively a lower microbial biomass nitrogen and diversity indices were observed in the biochar (both with CB500 and CB800) treated soils than in the unamended soils. At the phylum level, the highest dose (10% of CB500 and CB800 resulted in contrasting effects on the Proteobacteria diversity. The CB50010 favored the Pseudomonas abundance (up to 793%), Saccharibacteria (583%), Parcubacteria (138%), Actinobacteria (65%), and Firmicutes (48%) microbial communities, while CB80010 favored the Saccharibacteria (386%), Proteobacteria (12%) and Acidobacteria (11%), as compared to the control. These results imply that CB500 and CB800 have a remarkable impact on microbial biomass and bacterial diversity in smelter contaminated soils. Particularly, CB500 was found to be suitable for enhancing microbial biomass, bacterial growth of specific phylum, and diversity, which can be useful for bioremediation of mining soils.
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Affiliation(s)
- Muhammad Azeem
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China; Zhejiang Key Lab of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo, 315830, China; College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, China; Institute of Soil and Environmental Sciences, Pir Mehr Ali Shah Arid Agriculture University Rawalpindi, Punjab, 46300, Pakistan
| | | | - Amjad Ali
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, China
| | - Luqman Riaz
- Department of Environmental Sciences, University of Narowal, 51750, Punjab, Pakistan
| | - Khalid S Khan
- Institute of Soil and Environmental Sciences, Pir Mehr Ali Shah Arid Agriculture University Rawalpindi, Punjab, 46300, Pakistan
| | - Qaiser Hussain
- Institute of Soil and Environmental Sciences, Pir Mehr Ali Shah Arid Agriculture University Rawalpindi, Punjab, 46300, Pakistan
| | - Hafiz A Kareem
- College of Grassland Agriculture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Fakhar Abbas
- College of Environmental Science and Engineering, Zhongkai Agriculture and Engineering University, Guangzhou, China
| | - Abdul Latif
- Barani Agricultural Research Institute, Chakwal, Punjab, 48800, Pakistan
| | - Ali Majrashi
- Department of Biology, College of Science, Taif University, P.O. Box 11099, Taif, 21944, Saudi Arabia
| | - Esmat F Ali
- Department of Biology, College of Science, Taif University, P.O. Box 11099, Taif, 21944, Saudi Arabia
| | - Ronghua Li
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Sabry M Shaheen
- University of Wuppertal, School of Architecture and Civil Engineering, Institute of Foundation Engineering, Water- and Waste-Management, Laboratory of Soil- and Groundwater-Management, Pauluskirchstraße 7, 42285, Wuppertal, Germany; King Abdulaziz University, Faculty of Meteorology, Environment, and Arid Land Agriculture, Department of Arid Land Agriculture, 21589, Jeddah, Saudi Arabia; University of Kafrelsheikh, Faculty of Agriculture, Department of Soil and Water Sciences, 33516, Kafr El-Sheikh, Egypt.
| | - Gang Li
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China; Zhejiang Key Lab of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo, 315830, China
| | - Zenqqiang Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China; Zhejiang Key Lab of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo, 315830, China.
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Abstract
The concept of one health highlights that human health is not isolated but connected to the health of animals, plants and environments. In this Review, we demonstrate that soils are a cornerstone of one health and serve as a source and reservoir of pathogens, beneficial microorganisms and the overall microbial diversity in a wide range of organisms and ecosystems. We list more than 40 soil microbiome functions that either directly or indirectly contribute to soil, plant, animal and human health. We identify microorganisms that are shared between different one health compartments and show that soil, plant and human microbiomes are perhaps more interconnected than previously thought. Our Review further evaluates soil microbial contributions to one health in the light of dysbiosis and global change and demonstrates that microbial diversity is generally positively associated with one health. Finally, we present future challenges in one health research and formulate recommendations for practice and evaluation.
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Affiliation(s)
- Samiran Banerjee
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, USA.
| | - Marcel G A van der Heijden
- Plant-Soil Interactions Group, Agroscope, Zurich, Switzerland. .,Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland.
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Wang C, Ma H, Feng Z, Yan Z, Song B, Wang J, Zheng Y, Hao W, Zhang W, Yao M, Wang Y. Integrated organic and inorganic fertilization and reduced irrigation altered prokaryotic microbial community and diversity in different compartments of wheat root zone contributing to improved nitrogen uptake and wheat yield. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 842:156952. [PMID: 35752240 DOI: 10.1016/j.scitotenv.2022.156952] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/18/2022] [Accepted: 06/20/2022] [Indexed: 06/15/2023]
Abstract
The effect of long-term water and integrated fertilization on prokaryotic microorganisms and their regulation for crop nutrient uptake remains unknown. Therefore, the impact of soil water and integrated fertilization after eight years on prokaryotic microbial communities in different compartments of root zone and their association with wheat nitrogen (N) absorption and yield were investigated. The results showed that compared with fertilization treatments (F), water regimes (W) more drastically modulated the prokaryotic microbial community structure and diversity in bulk soil, rhizosphere and endosphere. The increase of irrigation improved the prokaryotic diversity in the rhizosphere and endosphere while decreased the diversity in the bulk soil. Application of organic fertilizers significantly improved soil organic matter (SOM) and nutrient contents, increased rhizosphere and endophytic prokaryotic microbial diversity, and elevated the relative abundance of aerobic ammonia oxidation and nitrification-related functional microorganisms in rhizosphere and endosphere. Increasing irrigation elevated the relative abundance of functional microorganisms related to aerobic ammonia oxidation and nitrification in the rhizosphere and endosphere. Soil water content (SWC) and NH4+-N as well as NO3--N were key predictors of prokaryotic microbial community composition under W and F treatments, respectively. Appropriate application of irrigation and organic fertilizers increased the relative abundance of some beneficial bacteria such as Flavobacterium. Water and fertilization treatments regulated the prokaryotic microbial communities of bulk soil, rhizosphere and endosphere by altering SWC and SOM, and provided evidence for the modulation of prokaryotic microorganisms to promote nitrogen uptake and wheat yield under long-term irrigation and fertilization. Conclusively, the addition of organic manure (50 %) with inorganic fertilizers (50 %) and reduced amount of irrigation (pre-sowing and jointing-period irrigation) decreased the application amount of chemical fertilizers and water, while increased SOM and nutrient content, improved prokaryotic diversity, and changed prokaryotic microbial community structure in the wheat root zone, resulting in enhanced nutrient uptake and wheat yield.
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Affiliation(s)
- Chao Wang
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Haiyang Ma
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Key Laboratory of Tropical Crops Nutrition of Hainan Province, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China
| | - Zhihan Feng
- Engineering Research Center of Soil Remediation of Fujian Province University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhenxing Yan
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Bolong Song
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jialong Wang
- Engineering Research Center of Soil Remediation of Fujian Province University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuyin Zheng
- Engineering Research Center of Soil Remediation of Fujian Province University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Weiping Hao
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wenying Zhang
- Institute of Dryland Farming, Hebei Academy of Agriculture and Forestry Sciences, Hengshui 053000, China.
| | - Minjie Yao
- Engineering Research Center of Soil Remediation of Fujian Province University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Yaosheng Wang
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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5
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Practices and Barriers to Sustainable Urban Agriculture: A Case Study of Louisville, Kentucky. URBAN SCIENCE 2021. [DOI: 10.3390/urbansci5040092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
As urban populations increase, there is growing interest in developing innovative technologies, sustainable urban farming practices, policy measures, and other strategies to address key barriers in urban agriculture that impede improved food security and sustained urban livelihoods. We surveyed forty urban farmers and gardeners (growers) in Louisville, Kentucky, for base-level information to assess their agricultural practices and the various factors or key barriers that could influence such practices. Secondary objectives were identifying areas where practices could be improved, and identifying opportunities for research, outreach, and incentives for urban growers to transition to more sustainable and higher-yielding practices. The majority of these urban growers were white females, were more diverse than Kentucky farmers, and attained a higher degree of education than Kentucky residents as a whole. Most were engaged in urban agriculture for non-commercial reasons, and 11% were full-time urban growers operating farms for profit. Smaller farms were less likely to be operated for profit or have farm certifications than medium-sized or larger farms (Chi-squared = 14.459, p = 0.042). We found no significant differences among farm sizes in terms of whether growers rented or owned the land they were on (Chi-squared = 9.094, p = 0.168). The most common sustainable practices recorded were composting (60%), crop rotation (54%), polyculture (54%), organic farming (49%), and low or no-till (46%). The least common practices were alley cropping (5%), plasticulture (3%), and hydroponics (3%). Small farms were less likely to use crop rotation than medium-sized or large farms (Chi-squared = 13.548, p = 0.003), and farms responding to the survey in the latter part of the data collection were less likely to use compost than expected based on responses from the early part of data collection (Chi-shared = 5.972, p = 0.014). Challenges faced by these growers included limited space, accessibility to farm certification, presence of pests and diseases, and lack of record keeping and soil testing for fertility and contamination. Our study documents the need for more farm certification, education, outreach, training, research, investment, innovative ideas and solutions, collaboration among stakeholders, and better access to land through favorable urban policies and local support.
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Tan B, Li Y, Liu T, Tan X, He Y, You X, Leong KH, Liu C, Li L. Response of Plant Rhizosphere Microenvironment to Water Management in Soil- and Substrate-Based Controlled Environment Agriculture (CEA) Systems: A Review. FRONTIERS IN PLANT SCIENCE 2021; 12:691651. [PMID: 34456936 PMCID: PMC8385539 DOI: 10.3389/fpls.2021.691651] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 07/16/2021] [Indexed: 05/06/2023]
Abstract
As natural agroecology deteriorates, controlled environment agriculture (CEA) systems become the backup support for coping with future resource consumption and potential food crises. Compared with natural agroecology, most of the environmental parameters of the CEA system rely on manual management. Such a system is dependent and fragile and prone to degradation, which includes harmful bacteria proliferation and productivity decline. Proper water management is significant for constructing a stabilized rhizosphere microenvironment. It has been proved that water is an efficient tool for changing the availability of nutrients, plant physiological processes, and microbial communities within. However, for CEA issues, relevant research is lacking at present. The article reviews the interactive mechanism between water management and rhizosphere microenvironments from the perspectives of physicochemical properties, physiological processes, and microbiology in CEA systems. We presented a synthesis of relevant research on water-root-microbes interplay, which aimed to provide detailed references to the conceptualization, research, diagnosis, and troubleshooting for CEA systems, and attempted to give suggestions for the construction of a high-tech artificial agricultural ecology.
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Affiliation(s)
- Bo Tan
- State Key Laboratory of Hydraulics and Mountain River Engineering, College of Water Resource and Hydropower, Sichuan University, Chengdu, China
| | - Yihan Li
- State Key Laboratory of Hydraulics and Mountain River Engineering, College of Water Resource and Hydropower, Sichuan University, Chengdu, China
| | - Tiegang Liu
- State Key Laboratory of Hydraulics and Mountain River Engineering, College of Water Resource and Hydropower, Sichuan University, Chengdu, China
| | - Xiao Tan
- State Key Laboratory of Hydraulics and Mountain River Engineering, College of Water Resource and Hydropower, Sichuan University, Chengdu, China
| | - Yuxin He
- State Key Laboratory of Hydraulics and Mountain River Engineering, College of Water Resource and Hydropower, Sichuan University, Chengdu, China
| | - Xueji You
- Department of Hydraulic Engineering, College of Civil Engineering, Tongji University, Shanghai, China
- Department of Civil, Architectural and Environmental Engineering, The University of Texas at Austin, Austin, TX, United States
| | - Kah Hon Leong
- Department of Environmental Engineering, Faculty of Engineering and Green Technology, Universiti Tunku Abdul Rahman, Kampar, Malaysia
| | - Chao Liu
- State Key Laboratory of Hydraulics and Mountain River Engineering, College of Water Resource and Hydropower, Sichuan University, Chengdu, China
- *Correspondence: Chao Liu,
| | - Longguo Li
- State Key Laboratory of Hydraulics and Mountain River Engineering, College of Water Resource and Hydropower, Sichuan University, Chengdu, China
- Longguo Li,
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7
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Maphuhla NG, Lewu FB, Oyedeji OO. The Effects of Physicochemical Parameters on Analysed Soil Enzyme Activity from Alice Landfill Site. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 18:ijerph18010221. [PMID: 33396701 PMCID: PMC7795255 DOI: 10.3390/ijerph18010221] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/12/2020] [Accepted: 12/19/2020] [Indexed: 11/28/2022]
Abstract
The soil pollution as a product of xenobiotics, industrial action, agricultural chemicals, or inappropriate disposal of waste can change the natural environment of soil indices and trigger life-threatening situations. Soil enzyme activity is the suitable bio-indicator or parameter for monitoring soil pollution due to their sensitivity that quickly responds to any soil disturbances. Also, they are known to play an essential role in maintaining soil health and a quality environment. This study aimed to determine the levels of enzyme activity in soil from polluted and unpolluted sites and study the relationship between the physicochemical properties and soil enzyme activity to manage soil pollution. Four selected enzymes (Urease, Invertase, Catalase, and Phosphatase) were examined for their activity from forty samples using the assay method for 24 h; the colorimetry spectrophotometer measured their activity. The obtained data revealed that Invertase activity was a predominant enzyme in all soil samples. Whereas, the urease activity had obtained in low amounts for all collection sites, especially on Site A1. Soil pH had discovered to range between 5.8 and 8.51, moisture content values recorded to vary from 0.12% to 9.09%, and soil organic carbon recorded to fluctuate between 0.08% and 1.54%. Urease and phosphatase activity correlated positively with all soil physicochemical properties except for moisture content, which correlated negatively (r = −0.297; p ≥ 0.05). The invertase activity negatively associated all soil physicochemical properties, excluding the moisture content that correlated positively and significantly with invertase activity. We noted that the dumpsite soil contains low enzyme activity levels, which might attribute to the type of waste disposed off. Also, only the phosphatase activity reported correlating positively with all examined physicochemical parameters entirely.
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Affiliation(s)
- Nontobeko Gloria Maphuhla
- Department of Chemistry, Faculty of Science and Agriculture, University of Fort Hare, Private Bag X1314, Alice 5700, South Africa
- Correspondence: or (N.G.M.); (O.O.O.)
| | - Francis Bayo Lewu
- Department of Agriculture, Faculty of Applied Sciences, Cape Peninsula University of Technology, Wellington Campus, P.O. Box X8, Wellington 7655, Western Cape, South Africa;
| | - Opeoluwa Oyehan Oyedeji
- Department of Chemistry, Faculty of Science and Agriculture, University of Fort Hare, Private Bag X1314, Alice 5700, South Africa
- Correspondence: or (N.G.M.); (O.O.O.)
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Salomon MJ, Watts-Williams SJ, McLaughlin MJ, Cavagnaro TR. Urban soil health: A city-wide survey of chemical and biological properties of urban agriculture soils. JOURNAL OF CLEANER PRODUCTION 2020; 275:122900. [PMID: 32834569 PMCID: PMC7362792 DOI: 10.1016/j.jclepro.2020.122900] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 05/19/2020] [Accepted: 06/15/2020] [Indexed: 06/11/2023]
Abstract
The integration of urban green spaces into modern city planning is seen as a promising tool to offset the drawbacks of ever-expanding cities. Urban agriculture is a common method to implement such strategies and to increase urban sustainability with a special focus on food security. Due to their location, urban farms are highly influenced by past and present anthropogenic activities which can threaten both soil health and food safety. This study includes 12 urban agriculture sites in the metropolitan area of Adelaide, Australia. It is the first of its kind to focus on soil health in urban agriculture systems with a further emphasis on mycorrhizal fungi. Descriptive information about each site, the biodiversity of the selected plots and soil samples from different depths and locations were collected and analysed for chemical and biological parameters. Seven metals, total and plant-available (Colwell) phosphorus and available nitrogen were measured in soils. A glasshouse bioassay was also conducted to determine the abundance of beneficial arbuscular mycorrhizal fungi in the soils and the change of root colonization after inoculation with the mycorrhizal fungus Rhizophagus irregularis. Results showed a generally high biodiversity of plants that correlated with site activity (commercial or community garden) and which could potentially be used for urban biodiversity conservation. Metal concentrations in soils were below national guidelines levels for all samples, although sites with previous industrial history showed elevated levels when compared to sites without industrial history. The use of raised beds with introduced soils eliminated differences in previous land-use history, thereby providing a good option to support cleaner production. Gardening soils were considered highly fertile, with plant-available (Colwell) P concentrations exceeding recommended levels for most horticultural crops, while soils were adequately supplied with nitrogen. Most plant nutrients were derived from freely available urban waste streams and integrated via composting. Various urban waste streams could be used to counter-act imbalanced soil nutrients. Arbuscular mycorrhizal fungi were present in all sites, indicating that the practiced soil management is sustainable from a microbial perspective. Given their important role in supporting plant nutrition, and potential to reduce the need for external nutrient inputs, they provide an important focal point for achieving clean and sustainable urban food production. The results were incorporated into a framework for the management of urban soil health.
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Affiliation(s)
- M J Salomon
- The Waite Research Institute and the School of Agriculture, Food and Wine, The University of Adelaide, Waite Campus, PMB1 Glen Osmond, SA, 5064, Australia
| | - S J Watts-Williams
- The Waite Research Institute and the School of Agriculture, Food and Wine, The University of Adelaide, Waite Campus, PMB1 Glen Osmond, SA, 5064, Australia
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Adelaide, Glen Osmond, South Australia, Australia
| | - M J McLaughlin
- The Waite Research Institute and the School of Agriculture, Food and Wine, The University of Adelaide, Waite Campus, PMB1 Glen Osmond, SA, 5064, Australia
| | - T R Cavagnaro
- The Waite Research Institute and the School of Agriculture, Food and Wine, The University of Adelaide, Waite Campus, PMB1 Glen Osmond, SA, 5064, Australia
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9
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Islam W, Noman A, Naveed H, Huang Z, Chen HYH. Role of environmental factors in shaping the soil microbiome. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:41225-41247. [PMID: 32829437 DOI: 10.1007/s11356-020-10471-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 08/10/2020] [Indexed: 05/09/2023]
Abstract
The soil microbiome comprises one of the most important and complex components of all terrestrial ecosystems as it harbors millions of microbes including bacteria, fungi, archaea, viruses, and protozoa. Together, these microbes and environmental factors contribute to shaping the soil microbiome, both spatially and temporally. Recent advances in genomic and metagenomic analyses have enabled a more comprehensive elucidation of the soil microbiome. However, most studies have described major modulators such as fungi and bacteria while overlooking other soil microbes. This review encompasses all known microbes that may exist in a particular soil microbiome by describing their occurrence, abundance, diversity, distribution, communication, and functions. Finally, we examined the role of several abiotic factors involved in the shaping of the soil microbiome.
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Affiliation(s)
- Waqar Islam
- Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, 350007, China
- Institute of Geography, Fujian Normal University, Fuzhou, 350007, China
- Faculty of Natural Resources Management, Lakehead University, 955 Oliver Rd, Thunder Bay, ON, P7B 5E1, Canada
| | - Ali Noman
- Department of Botany, Government College University, Faisalabad, 38000, Pakistan
| | - Hassan Naveed
- College of Life Science, Leshan Normal University, Leshan, 614004, Sichuan, China
| | - Zhiqun Huang
- Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, 350007, China.
- Institute of Geography, Fujian Normal University, Fuzhou, 350007, China.
| | - Han Y H Chen
- Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, 350007, China.
- Institute of Geography, Fujian Normal University, Fuzhou, 350007, China.
- Faculty of Natural Resources Management, Lakehead University, 955 Oliver Rd, Thunder Bay, ON, P7B 5E1, Canada.
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10
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Successional Variation in the Soil Microbial Community in Odaesan National Park, Korea. SUSTAINABILITY 2020. [DOI: 10.3390/su12114795] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Succession is defined as variation in ecological communities caused by environmental changes. Environmental succession can be caused by rapid environmental changes, but in many cases, it is slowly caused by climate change or constant low-intensity disturbances. Odaesan National Park is a well-preserved forest located in the Taebaek mountain range in South Korea. The forest in this national park is progressing from a mixed-wood forest to a broad-leaved forest. In this study, microbial community composition was investigated using 454 sequencing of soil samples collected from 13 different locations in Odaesan National Park. We assessed whether microbial communities are affected by changes in environmental factors such as water content (WC), nutrient availability (total carbon (TC) and total nitrogen (TN)) and pH caused by forest succession. WC, TC, TN and pH significantly differed between the successional stages of the forest. The WC, TC and TN of the forest soils tended to increase as succession progressed, while pH tended to decrease. In both successional stages, the bacterial genus Pseudolabrys was the most abundant, followed by Afipia and Bradyrhizobium. In addition, the fungal genus Saitozyma showed the highest abundance in the forest soils. Microbial community composition changed according to forest successional stage and soil properties (WC, TC, TN, and pH). Furthermore, network analysis of both bacterial and fungal taxa revealed strong relationships of the microbial community depending on the soil properties affected by forest succession.
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Changes in soil taxonomic and functional diversity resulting from gamma irradiation. Sci Rep 2019; 9:7894. [PMID: 31133738 PMCID: PMC6536540 DOI: 10.1038/s41598-019-44441-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 04/05/2019] [Indexed: 12/30/2022] Open
Abstract
Little is known of the effects of ionizing radiation exposure on soil biota. We exposed soil microcosms to weekly bursts of 60Co gamma radiation over six weeks, at three levels of exposure (0.1 kGy/hr/wk [low], 1 kGy/hr/wk [medium] and 3 kGy/hr/wk [high]). Soil DNA was extracted, and shotgun metagenomes were sequenced and characterised using MG-RAST. We hypothesized that with increasing radiation exposure there would be a decrease in both taxonomic and functional diversity. While bacterial diversity decreased, diversity of fungi and algae unexpectedly increased, perhaps because of release from competition. Despite the decrease in diversity of bacteria and of biota overall, functional gene diversity of algae, bacteria, fungi and total biota increased. Cycles of radiation exposure may increase the range of gene functional strategies viable in soil, a novel ecological example of the effects of stressors or disturbance events promoting some aspects of diversity. Moreover, repeated density-independent population crashes followed by population expansion may allow lottery effects, promoting coexistence. Radiation exposure produced large overall changes in community composition. Our study suggests several potential novel radiation-tolerant groups: in addition to Deinococcus-Thermus, which reached up to 20% relative abundance in the metagenome, the phyla Chloroflexi (bacteria), Chytridiomycota (fungi) and Nanoarcheota (archaea) may be considered as radiation-tolerant.
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Igalavithana AD, Farooq M, Kim KH, Lee YH, Qayyum MF, Al-Wabel MI, Lee SS, Ok YS. Determining soil quality in urban agricultural regions by soil enzyme-based index. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2017; 39:1531-1544. [PMID: 28653083 DOI: 10.1007/s10653-017-9998-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 06/09/2017] [Indexed: 06/07/2023]
Abstract
Urban agricultural soils are highly variable, and careful selection of sensitive indicators is needed for the assessment of soil quality. This study is proposed to develop an index based on soil enzyme activities for assessing the quality of urban agricultural soils. Top soils were collected from urban agricultural areas of Korea, and soil chemical properties, texture, microbial fatty acids, and enzyme activities were determined. The soils belonged to five textural classes with the highest frequency of sandy loam. There was no clear correlation between the soil chemical properties and soil microbial properties. Principal component analysis (PCA) and factor analysis were applied to microbial groups for identification of microbial community variation in soils. Two soil groups, namely group 1 (G1) and group 2 (G2), based on microbial community abundance were examined by PCA, and those were more prominent in factor analysis. The G1 soils showed higher microbial community abundance than G2 soils. The canonical discriminant analysis was applied to the enzyme activities of sandy loam soil to develop an index, and the index validation was confirmed using the unused soils and published data. The high-quality soils in published literature assigned the high valued index. Microbial fatty acids and soil enzyme activities can be suitable indicators for soil quality evaluation of urban agricultural soils.
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Affiliation(s)
- Avanthi Deshani Igalavithana
- Korea Biochar Research Center and School of Natural Resources and Environmental Science, Kangwon National University, Chuncheon, 24341, Korea
| | - Muhammad Farooq
- Department of Agronomy, University of Agriculture, Faisalabad, 38040, Pakistan
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6001, Australia
| | - Kye-Hoon Kim
- Department of Environmental Horticulture, University of Seoul, Seoul, 08826, Korea
| | - Young-Han Lee
- Division of Plant Environmental Research, Gyeogsangnam-do Agricultural Research and Extension Services, Jinju, 52773, Korea
| | - Muhammad Farooq Qayyum
- Department of Soil Science, Faculty of Agricultural Science and Technology, Bahauddin Zakariya University, Multan, Pakistan
| | - Mohammad I Al-Wabel
- Soil Sciences Department, College of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia
| | - Sang Soo Lee
- Korea Biochar Research Center and School of Natural Resources and Environmental Science, Kangwon National University, Chuncheon, 24341, Korea
| | - Yong Sik Ok
- Korea Biochar Research Center and School of Natural Resources and Environmental Science, Kangwon National University, Chuncheon, 24341, Korea.
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