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Lancaster E, Winston R, Martin J, Lee J. Urban stormwater green infrastructure: Evaluating the public health service role of bioretention using microbial source tracking and bacterial community analyses. WATER RESEARCH 2024; 259:121818. [PMID: 38815337 DOI: 10.1016/j.watres.2024.121818] [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: 02/12/2024] [Revised: 04/30/2024] [Accepted: 05/20/2024] [Indexed: 06/01/2024]
Abstract
Bioretention cells (BRCs) control stormwater flow on-site during precipitation, reducing runoff and improving water quality through chemical, physical, and biological processes. While BRCs are effective in these aspects, they provide habitats for wildlife and may face microbial hazards from fecal shedding, posing a potential threat to human health and the nearby environment. However, limited knowledge exists regarding the ability to control microbial hazards (e.g., beyond using typical indicator bacteria) through stormwater biofiltration. Therefore, the purpose of this study is to characterize changes in the bacterial community of urban stormwater undergoing bioretention treatment, with the goal of assessing the public health implications of these green infrastructure solutions. Samples from BRC inflow and outflow in Columbus, Ohio, were collected post-heavy storms from October 2021 to March 2022. Conventional culture-based E. coli monitoring and microbial source tracking (MST) were conducted to identify major fecal contamination extent and its sources (i.e., human, canine, avian, and ruminant). Droplet digital polymerase chain reaction (ddPCR) was utilized to quantify the level of host-associated fecal contamination in addition to three antibiotic resistant genes (ARGs): tetracycline resistance gene (tetQ), sulfonamide resistance gene (sul1), and Klebsiella pneumoniae carbapenemase resistance gene (blaKPC). Subsequently, 16S rRNA gene sequencing was conducted to characterize bacterial community differences between stormwater BRC inflow and outflow. Untreated urban stormwater reflects anthropogenic contamination, suggesting it as a potential source of contamination to waterbodies and urban environments. When comparing inlet and outlet BRC samples, urban stormwater treated via biofiltration did not increase microbial hazards, and changes in bacterial taxa and alpha diversity were negligible. Beta diversity results reveal a significant shift in bacterial community structure, while simultaneously enhancing the water quality (i.e., reduction of metals, total suspended solids, total nitrogen) of urban stormwater. Significant correlations were found between the bacterial community diversity of urban stormwater with fecal contamination (e.g. dog) and ARG (sul1), rainfall intensity, and water quality (hardness, total phosphorous). The study concludes that bioretention technology can sustainably maintain urban microbial water quality without posing additional public health risks, making it a viable green infrastructure solution for heavy rainfall events exacerbated by climate change.
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Affiliation(s)
- Emma Lancaster
- Division of Environmental Health Sciences, College of Public Health, The Ohio State University, Columbus, OH, USA; Environmental Sciences Graduate Program, The Ohio State University, Columbus, OH, USA
| | - Ryan Winston
- Environmental Sciences Graduate Program, The Ohio State University, Columbus, OH, USA; Department of Food, Agricultural, and Biological Engineering, The Ohio State University, Columbus, OH, USA; Department of Civil, Environmental, and Geodetic Engineering, The Ohio State University, Columbus, OH, USA
| | - Jay Martin
- Department of Food, Agricultural, and Biological Engineering, The Ohio State University, Columbus, OH, USA; Sustainability Institute, The Ohio State University, Columbus, OH, USA
| | - Jiyoung Lee
- Division of Environmental Health Sciences, College of Public Health, The Ohio State University, Columbus, OH, USA; Environmental Sciences Graduate Program, The Ohio State University, Columbus, OH, USA; Department of Food Science & Technology, The Ohio State University, Columbus, OH, USA; Infectious Diseases Institute, The Ohio State University, Columbus, OH, USA.
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2
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Ye J, Zhu Y, Chen H, Tang J, Zhao X, Sun X, Zhang J, Chen Y, Guo Y, Fang N, Tan Y, Zhang T. Land use, stratified wastewater and sediment, and microplastic attribute factors jointly influence the microplastic prevalence and bacterial colonization patterns in sewer habitats. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 918:170653. [PMID: 38331294 DOI: 10.1016/j.scitotenv.2024.170653] [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: 10/31/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 02/10/2024]
Abstract
The capacity of microplastics to harbor and propagate bacteria has been the focus of attention over the last decade. Such microplastic-supported bacterial colonization behavior in the municipal sewer system could be a critical ecological link influencing the biogeochemical activities and risks in receiving waters in urban areas, given the alarming microplastic loads discharged there. This study conducted a large-scale survey covering a wide range of residential and industrial catchments in Shanghai, China. We aimed to assess the microplastic prevalence and bacterial colonization patterns in different sewer habitats and to explore the role of land use, stratified wastewater and sediment, and microplastic attributes in shaping the patterns. We found that the sewer system formed a temporal but pronounced microplastic pool, with land use playing a significant role in the variability of microplastic prevalence. Industrial sewers contained a high abundance of microplastics with large particle sizes, diverse polymer compositions, and shapes. However, while there was a spatial discrepancy between urban and suburban areas in the abundance of microplastics in residential sewers, their predominant polymer and shape types were simple, i.e., polyethylene terephthalate (PET) and fibers. Sewer habitat characteristics, particularly the stratified wastewater and sediment determined microbial colonization patterns. The latter acted as a long-term sink for microplastics and supported the high growth of colonizers. In contrast, the wastewater plastisphere presented novel niches, hosting communities with a marked proportion of unique bacterial genera after colonization. Besides, statistics showed a highly positive and dense co-occurrence network of the plastisphere communities, especially those from the industrial sewer sediment, with enhanced metabolic activity, cellular processes and systems, and increased human pathogenic potential. Findings indicated a coarse and uncertain effect of the selective pressure of microplastic attributes on plastisphere community structure differentiation.
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Affiliation(s)
- Jianfeng Ye
- School of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai 200092, China
| | - Yi Zhu
- School of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai 200092, China
| | - Hao Chen
- Science and Technology Innovation Center for Eco-environmental Protection, Shanghai Investigation, Design & Research Institute Co., Ltd., Shanghai 200050, China; YANGTZE Eco-Environment Engineering Research Center, Three Gorges Corporation, Beijing 100038, China.
| | - Jianfei Tang
- College of Engineering, Shanghai Polytechnic University, Shanghai 201209, China
| | - Xin Zhao
- Shanghai Water Engineering Design and Research Institute Co., Ltd., Shanghai 200333, China
| | - Xiaonan Sun
- College of Environment, Hohai University, 210098, China
| | - Jinxu Zhang
- School of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai 200092, China
| | - Yu Chen
- School of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai 200092, China
| | - Yali Guo
- Science and Technology Innovation Center for Eco-environmental Protection, Shanghai Investigation, Design & Research Institute Co., Ltd., Shanghai 200050, China; YANGTZE Eco-Environment Engineering Research Center, Three Gorges Corporation, Beijing 100038, China
| | - Ning Fang
- Science and Technology Innovation Center for Eco-environmental Protection, Shanghai Investigation, Design & Research Institute Co., Ltd., Shanghai 200050, China; YANGTZE Eco-Environment Engineering Research Center, Three Gorges Corporation, Beijing 100038, China
| | - Yaqin Tan
- Science and Technology Innovation Center for Eco-environmental Protection, Shanghai Investigation, Design & Research Institute Co., Ltd., Shanghai 200050, China; YANGTZE Eco-Environment Engineering Research Center, Three Gorges Corporation, Beijing 100038, China
| | - Ting Zhang
- Science and Technology Innovation Center for Eco-environmental Protection, Shanghai Investigation, Design & Research Institute Co., Ltd., Shanghai 200050, China; YANGTZE Eco-Environment Engineering Research Center, Three Gorges Corporation, Beijing 100038, China
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3
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Beaver RC, Neufeld JD. Microbial ecology of the deep terrestrial subsurface. THE ISME JOURNAL 2024; 18:wrae091. [PMID: 38780093 PMCID: PMC11170664 DOI: 10.1093/ismejo/wrae091] [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: 11/01/2023] [Revised: 03/04/2024] [Accepted: 05/22/2024] [Indexed: 05/25/2024]
Abstract
The terrestrial subsurface hosts microbial communities that, collectively, are predicted to comprise as many microbial cells as global surface soils. Although initially thought to be associated with deposited organic matter, deep subsurface microbial communities are supported by chemolithoautotrophic primary production, with hydrogen serving as an important source of electrons. Despite recent progress, relatively little is known about the deep terrestrial subsurface compared to more commonly studied environments. Understanding the composition of deep terrestrial subsurface microbial communities and the factors that influence them is of importance because of human-associated activities including long-term storage of used nuclear fuel, carbon capture, and storage of hydrogen for use as an energy vector. In addition to identifying deep subsurface microorganisms, recent research focuses on identifying the roles of microorganisms in subsurface communities, as well as elucidating myriad interactions-syntrophic, episymbiotic, and viral-that occur among community members. In recent years, entirely new groups of microorganisms (i.e. candidate phyla radiation bacteria and Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoloarchaeota, Nanoarchaeota archaea) have been discovered in deep terrestrial subsurface environments, suggesting that much remains unknown about this biosphere. This review explores the historical context for deep terrestrial subsurface microbial ecology and highlights recent discoveries that shape current ecological understanding of this poorly explored microbial habitat. Additionally, we highlight the need for multifaceted experimental approaches to observe phenomena such as cryptic cycles, complex interactions, and episymbiosis, which may not be apparent when using single approaches in isolation, but are nonetheless critical to advancing our understanding of this deep biosphere.
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Affiliation(s)
- Rachel C Beaver
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Josh D Neufeld
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
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Verrone V, Gupta A, Laloo AE, Dubey RK, Hamid NAA, Swarup S. Organic matter stability and lability in terrestrial and aquatic ecosystems: A chemical and microbial perspective. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167757. [PMID: 37852479 DOI: 10.1016/j.scitotenv.2023.167757] [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: 07/18/2023] [Revised: 10/06/2023] [Accepted: 10/10/2023] [Indexed: 10/20/2023]
Abstract
Terrestrial and aquatic ecosystems have specific carbon fingerprints and sequestration potential, due to the intrinsic properties of the organic matter (OM), mineral content, environmental conditions, and microbial community composition and functions. A small variation in the OM pool can imbalance the carbon dynamics that ultimately affect the climate and functionality of each ecosystem, at regional and global scales. Here, we review the factors that continuously contribute to carbon stability and lability, with particular attention to the OM formation and nature, as well as the microbial activities that drive OM aggregation, degradation and eventually greenhouse gas emissions. We identified that in both aquatic and terrestrial ecosystems, microbial attributes (i.e., carbon metabolism, carbon use efficiency, necromass, enzymatic activities) play a pivotal role in transforming the carbon stock and yet they are far from being completely characterised and not often included in carbon estimations. Therefore, future research must focus on the integration of microbial components into carbon mapping and models, as well as on translating molecular-scaled studies into practical approaches. These strategies will improve carbon management and restoration across ecosystems and contribute to overcome current climate challenges.
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Affiliation(s)
- Valeria Verrone
- National University of Singapore Environmental Research Institute, National University of Singapore,117411, Singapore
| | - Abhishek Gupta
- Singapore Centre of Environmental Engineering and Life Sciences, National University of Singapore, Singapore.
| | - Andrew Elohim Laloo
- National University of Singapore Environmental Research Institute, National University of Singapore,117411, Singapore; Singapore Centre of Environmental Engineering and Life Sciences, National University of Singapore, Singapore
| | - Rama Kant Dubey
- National University of Singapore Environmental Research Institute, National University of Singapore,117411, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore; Department of Biotechnology, GLA University, Mathura, Uttar Pradesh 281406, India
| | - Nur Ashikin Abdul Hamid
- National University of Singapore Environmental Research Institute, National University of Singapore,117411, Singapore
| | - Sanjay Swarup
- National University of Singapore Environmental Research Institute, National University of Singapore,117411, Singapore; Singapore Centre of Environmental Engineering and Life Sciences, National University of Singapore, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
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5
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Bassani I, Bellini R, Vizzarro A, Coti C, Pozzovivo V, Barbieri D, Pirri CF, Verga F, Menin B. Biogeochemical characterization of four depleted gas reservoirs for conversion into underground hydrogen storage. Environ Microbiol 2023; 25:3683-3702. [PMID: 37964633 DOI: 10.1111/1462-2920.16538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 10/31/2023] [Indexed: 11/16/2023]
Abstract
Depleted gas reservoirs are a valuable option for underground hydrogen storage (UHS). However, different classes of microorganisms, which are capable of using free H2 as a reducing agent for their metabolism, inhabit deep underground formations and can potentially affect the storage. This study integrates metagenomics based on Illumina-NGS sequencing of bacterial and archaeal 16S rRNA and dsrB and mcrA functional genes to unveil the composition and the variability of indigenous microbial populations of four Italian depleted reservoirs. The obtained mcrA sequences allow us to implement the existing taxonomic database for mcrA gene sequences with newly classified sequences obtained from the Italian gas reservoirs. Moreover, the KEGG and COG predictive functional annotation was used to highlight the metabolic pathways potentially associated with hydrogenotrophic metabolisms. The analyses revealed the specificity of each reservoir microbial community, and taxonomic and functional data highlighted the presence of an enriched number of taxa, whose activity depends on both reservoir hydrochemical composition and nutrient availability, of potential relevance in the context of UHS. This study is the very first to address the profiling of the microbial population and allowed us to perform a preliminary assessment of UHS feasibility in Italy.
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Affiliation(s)
- Ilaria Bassani
- Centre for Sustainable Future Technologies, Fondazione Istituto Italiano di Tecnologia, Turin, Italy
| | - Ruggero Bellini
- Centre for Sustainable Future Technologies, Fondazione Istituto Italiano di Tecnologia, Turin, Italy
| | - Arianna Vizzarro
- Centre for Sustainable Future Technologies, Fondazione Istituto Italiano di Tecnologia, Turin, Italy
| | | | | | | | - Candido Fabrizio Pirri
- Centre for Sustainable Future Technologies, Fondazione Istituto Italiano di Tecnologia, Turin, Italy
- Department of Applied Science and Technology, Politecnico di Torino, Turin, Italy
| | - Francesca Verga
- Department of Applied Science and Technology, Politecnico di Torino, Turin, Italy
| | - Barbara Menin
- Centre for Sustainable Future Technologies, Fondazione Istituto Italiano di Tecnologia, Turin, Italy
- National Research Council, Institute of Agricultural Biology and Biotechnology (CNR-IBBA), Milan, Italy
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Hernandez-Becerra N, Cliffe L, Xiu W, Boothman C, Lloyd JR, Nixon SL. New microbiological insights from the Bowland shale highlight heterogeneity of the hydraulically fractured shale microbiome. ENVIRONMENTAL MICROBIOME 2023; 18:14. [PMID: 36855215 PMCID: PMC9972762 DOI: 10.1186/s40793-023-00465-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 01/11/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Hydraulically fractured shales offer a window into the deep biosphere, where hydraulic fracturing creates new microbial ecosystems kilometers beneath the surface of the Earth. Studying the microbial communities from flowback fluids that are assumed to inhabit these environments provides insights into their ecophysiology, and in particular their ability to survive in these extreme environments as well as their influence on site operation e.g. via problematic biofouling processes and/or biocorrosion. Over the past decade, research on fractured shale microbiology has focused on wells in North America, with a few additional reported studies conducted in China. To extend the knowledge in this area, we characterized the geochemistry and microbial ecology of two exploratory shale gas wells in the Bowland Shale, UK. We then employed a meta-analysis approach to compare geochemical and 16S rRNA gene sequencing data from our study site with previously published research from geographically distinct formations spanning China, Canada and the USA. RESULTS Our findings revealed that fluids recovered from exploratory wells in the Bowland are characterized by moderate salinity and high microbial diversity. The microbial community was dominated by lineages known to degrade hydrocarbons, including members of Shewanellaceae, Marinobacteraceae, Halomonadaceae and Pseudomonadaceae. Moreover, UK fractured shale communities lacked the usually dominant Halanaerobium lineages. From our meta-analysis, we infer that chloride concentrations play a dominant role in controlling microbial community composition. Spatio-temporal trends were also apparent, with different shale formations giving rise to communities of distinct diversity and composition. CONCLUSIONS These findings highlight an unexpected level of compositional heterogeneity across fractured shale formations, which is not only relevant to inform management practices but also provides insight into the ability of diverse microbial consortia to tolerate the extreme conditions characteristic of the engineered deep subsurface.
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Affiliation(s)
- Natali Hernandez-Becerra
- Williamson Research Centre for Molecular Environmental Science, Department of Earth and Environmental Sciences, The University of Manchester, Manchester, UK
| | - Lisa Cliffe
- Williamson Research Centre for Molecular Environmental Science, Department of Earth and Environmental Sciences, The University of Manchester, Manchester, UK
- Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
| | - Wei Xiu
- Williamson Research Centre for Molecular Environmental Science, Department of Earth and Environmental Sciences, The University of Manchester, Manchester, UK
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences (Beijing), Beijing, China
| | - Christopher Boothman
- Williamson Research Centre for Molecular Environmental Science, Department of Earth and Environmental Sciences, The University of Manchester, Manchester, UK
| | - Jonathan R Lloyd
- Williamson Research Centre for Molecular Environmental Science, Department of Earth and Environmental Sciences, The University of Manchester, Manchester, UK
| | - Sophie L Nixon
- Williamson Research Centre for Molecular Environmental Science, Department of Earth and Environmental Sciences, The University of Manchester, Manchester, UK.
- Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK.
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7
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Mullis MM, Selwyn JD, Kevorkian R, Tague ED, Castro HF, Campagna SR, Lloyd KG, Reese BK. Microbial survival mechanisms within serpentinizing Mariana forearc sediments. FEMS Microbiol Ecol 2023; 99:6985003. [PMID: 36631299 DOI: 10.1093/femsec/fiad003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 12/07/2022] [Accepted: 01/10/2023] [Indexed: 01/13/2023] Open
Abstract
Marine deep subsurface sediment is often a microbial environment under energy-limited conditions. However, microbial life has been found to persist and even thrive in deep subsurface environments. The Mariana forearc represents an ideal location for determining how microbial life can withstand extreme conditions including pH 10-12.5 and depleted nutrients. The International Ocean Discovery Program Expedition 366 to the Mariana Convergent Margin sampled three serpentinizing seamounts located along the Mariana forearc chain with elevated concentrations of methane, hydrogen, and sulfide. Across all three seamount summits, the most abundant transcripts were for cellular maintenance such as cell wall and membrane repair, and the most abundant metabolic pathways were the Entner-Doudoroff pathway and tricarboxylic acid cycle. At flank samples, sulfur cycling involving taurine assimilation dominated the metatranscriptomes. The in situ activity of these pathways was supported by the detection of their metabolic intermediates. All samples had transcripts from all three domains of Bacteria, Archaea, and Eukarya, dominated by Burkholderiales, Deinococcales, and Pseudomonales, as well as the fungal group Opisthokonta. All samples contained transcripts for aerobic methane oxidation (pmoABC) and denitrification (nirKS). The Mariana forearc microbial communities show activity not only consistent with basic survival mechanisms, but also coupled metabolic reactions.
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Affiliation(s)
- Megan M Mullis
- Life Sciences Department, Texas A&M University - Corpus Christi, Corpus Christi, TX, United States.,Dauphin Island Sea Lab, Mobile, AL, United States
| | - Jason D Selwyn
- Life Sciences Department, Texas A&M University - Corpus Christi, Corpus Christi, TX, United States
| | - Richard Kevorkian
- Microbiology Department, University of Tennessee, Knoxville, TN, United States
| | - Eric D Tague
- Microbiology Department, University of Tennessee, Knoxville, TN, United States
| | - Hector F Castro
- Microbiology Department, University of Tennessee, Knoxville, TN, United States.,Chemistry Department, UTK Biological and Small Molecule Mass Spectrometry Core, Knoxville, TN, United States
| | - Shawn R Campagna
- Microbiology Department, University of Tennessee, Knoxville, TN, United States.,Chemistry Department, UTK Biological and Small Molecule Mass Spectrometry Core, Knoxville, TN, United States
| | - Karen G Lloyd
- Microbiology Department, University of Tennessee, Knoxville, TN, United States
| | - Brandi Kiel Reese
- Dauphin Island Sea Lab, Mobile, AL, United States.,Marine Sciences Department, University of South Alabama, Mobile, AL, United States
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Mills M, Lee S, Mollenkopf D, Wittum T, Sullivan SMP, Lee J. Comparison of environmental microbiomes in an antibiotic resistance-polluted urban river highlights periphyton and fish gut communities as reservoirs of concern. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 851:158042. [PMID: 35973543 DOI: 10.1016/j.scitotenv.2022.158042] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 06/15/2023]
Abstract
Natural waterways near urban areas are heavily impacted by anthropogenic activities, including their microbial communities. A contaminant of growing public health concern in rivers is antibiotic resistant genes (ARGs), which can spread between neighboring bacteria and increase the potential for transmission of AR bacteria to animals and humans. To identify the matrices of most concern for AR, we compared ARG burdens and microbial community structures between sample types from the Scioto River Watershed, Ohio, the United States, from 2017 to 2018. Five environmental matrices (water, sediment, periphyton, detritus, and fish gut) were collected from 26 river sites. Due to our focus on clinically relevant ARGs, three carbapenem resistance genes (blaKPC, blaNDM, and blaOXA-48) were quantified via DropletDigital™ PCR. At a subset of nine urbanized sites, we conducted16S rRNA gene sequencing and functional gene predictions. Carbapenem resistance genes were quantified from all matrices, with blaKPC being the most detected (88 % of samples), followed by blaNDM (64 %) and blaOXA-48 (23 %). Fish gut samples showed higher concentrations of blaKPC and blaNDM than any other matrix, indicating potential ARG bioaccumulation, and risk of broader dissemination through aquatic and nearshore food webs. Periphyton had higher concentrations of blaNDM than water, sediment, or detritus. Microbial community analysis identified differences by sample type in community diversity and structure. Sediment samples had the most diverse microbial communities, and detritus, the least. Spearman correlations did not reveal significant relationships between the concentrations of the monitored ARGs and microbial community diversity. However, several differentially abundant taxa and microbial functions were identified by sample type that is definitive of these matrices' roles in the river ecosystem and habitat type. In summary, the fish gut and periphyton are a concern as AR reservoirs due to their relatively high concentration of carbapenem resistance genes, diverse microbial communities, and natural functions that promote AR.
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Affiliation(s)
- Molly Mills
- Division of Environmental Health Sciences, College of Public Health, The Ohio State University, Columbus, OH, USA; Environmental Sciences Graduate Program, The Ohio State University, Columbus, OH, USA
| | - Seungjun Lee
- Department of Food Science and Nutrition, Pukyong National University, Busan, Republic of Korea
| | - Dixie Mollenkopf
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH, USA
| | - Thomas Wittum
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH, USA; Infectious Diseases Institute, The Ohio State University, Columbus, OH, USA
| | - S Mažeika Patricio Sullivan
- Schiermeier Olentangy River Wetland Research Park, School of Environment and Natural Resources, The Ohio State University, Columbus, OH 43210, USA
| | - Jiyoung Lee
- Division of Environmental Health Sciences, College of Public Health, The Ohio State University, Columbus, OH, USA; Environmental Sciences Graduate Program, The Ohio State University, Columbus, OH, USA; Infectious Diseases Institute, The Ohio State University, Columbus, OH, USA; Department of Food Science & Technology, The Ohio State University, Columbus, OH, USA.
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9
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Abdulsada Z, Kibbee R, Princz J, DeRosa M, Örmeci B. Transformation of Silver Nanoparticles (AgNPs) during Lime Treatment of Wastewater Sludge and Their Impact on Soil Bacteria. NANOMATERIALS 2021; 11:nano11092330. [PMID: 34578645 PMCID: PMC8465233 DOI: 10.3390/nano11092330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 11/16/2022]
Abstract
This study investigated the impact of lime stabilization on the fate and transformation of AgNPs. It also evaluated the changes in the population and diversity of the five most relevant bacterial phyla in soil after applying lime-stabilized sludge containing AgNPs. The study was performed by spiking an environmentally relevant concentration of AgNPs (2 mg AgNPs/g TS) in sludge, applying lime stabilization to increase pH to above 12 for two hours, and applying lime-treated sludge to soil samples. Transmission electron microscopy (TEM) and energy-dispersive X-ray spectroscopy (EDS) were used to investigate the morphological and compositional changes of AgNPs during lime stabilization. After the application of lime stabilized sludge to the soil, soil samples were periodically analyzed for total genomic DNA and changes in bacterial phyla diversity using quantitative polymerase chain reaction (qPCR). The results showed that lime treatment effectively removed AgNPs from the aqueous phase, and AgNPs were deposited on the lime molecules. The results revealed that AgNPs did not significantly impact the presence and diversity of the assessed phyla in the soil. However, lime stabilized sludge with AgNPs affected the abundance of each phylum over time. No significant effects on the soil total organic carbon (TOC), heterotrophic plate count (HPC), and percentage of the live cells were observed.
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Affiliation(s)
- Zainab Abdulsada
- Department of Civil and Environmental Engineering, Carleton University, Ottawa, ON K1S 5B6, Canada; (Z.A.); (R.K.)
- Department of Environmental Engineering, University of Baghdad, Karrada, Al-Jadriya, Baghdad, Iraq
| | - Richard Kibbee
- Department of Civil and Environmental Engineering, Carleton University, Ottawa, ON K1S 5B6, Canada; (Z.A.); (R.K.)
| | - Juliska Princz
- Environment and Climate Change Canada, 335 River Road South, Ottawa, ON K1V 1C7, Canada;
| | - Maria DeRosa
- Department of Chemistry, Carleton University, Ottawa, ON K1S 5B6, Canada;
| | - Banu Örmeci
- Department of Civil and Environmental Engineering, Carleton University, Ottawa, ON K1S 5B6, Canada; (Z.A.); (R.K.)
- Correspondence: ; Tel.: +1-613-520-2600 (ext. 4144)
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10
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Sanz JL, Rodriguez N, Escudero C, Carrizo D, Amils R. Biological production of H 2 , CH 4 and CO 2 in the deep subsurface of the Iberian Pyrite Belt. Environ Microbiol 2021; 23:3913-3922. [PMID: 33973338 DOI: 10.1111/1462-2920.15561] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/29/2021] [Accepted: 05/01/2021] [Indexed: 11/26/2022]
Abstract
Most of the terrestrial deep subsurfaces are oligotrophic environments in which some gases, mainly H2 , CH4 and CO2 , play an important role as energy and/or carbon sources. In this work, we assessed their biotic and abiotic origin in samples from subsurface hard-rock cores of the Iberian Pyrite Belt (IPB) at three different depths (414, 497 and 520 m). One set of samples was sterilized (abiotic control) and all samples were incubated under anaerobic conditions. Our results showed that H2 , CH4 and CO2 remained low and constant in the sterilized controls while their levels were 4, 4.1 and 2.5 times higher respectively, in the unsterilized samples compared to the abiotic controls. The δ13 CCH4 -values measured in the samples (range -31.2 to -43.0 ‰) reveals carbon isotopic signatures that are within the range for biological methane production. Possible microorganisms responsible for the biotic production of the gases were assessed by CARD-FISH. The analysis of sequenced genomes of detected microorganisms within the subsurface of the IPB allowed to identify possible metabolic activities involved in H2 (Rhodoplanes, Shewanella and Desulfosporosinus), CH4 (Methanobacteriales) and CO2 production. The obtained results suggest that part of the H2 , CH4 and CO2 detected in the deep subsurface has a biological origin.
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Affiliation(s)
- Jose L Sanz
- Molecular Biology Department, Universidad Autónoma de Madrid, Madrid, Spain
| | - Nuria Rodriguez
- Centro de Astrobiología (INTA-CSIC), Torrejón de Ardoz, 28850, Spain
| | - Cristina Escudero
- Centro de Astrobiología (INTA-CSIC), Torrejón de Ardoz, 28850, Spain.,Centro de Biología Molecular Severo Ochoa (UAM-CSIC), Universidad Autónoma de Madrid, Madrid, 28049, Spain
| | - Daniel Carrizo
- Centro de Astrobiología (INTA-CSIC), Torrejón de Ardoz, 28850, Spain
| | - Ricardo Amils
- Centro de Astrobiología (INTA-CSIC), Torrejón de Ardoz, 28850, Spain.,Centro de Biología Molecular Severo Ochoa (UAM-CSIC), Universidad Autónoma de Madrid, Madrid, 28049, Spain
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11
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Zhang C, Zhao Z, Dong S, Zhou D. Simultaneous elimination of amoxicillin and antibiotic resistance genes in activated sludge process: Contributions of easy-to-biodegrade food. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 764:142907. [PMID: 33757248 DOI: 10.1016/j.scitotenv.2020.142907] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 10/02/2020] [Accepted: 10/03/2020] [Indexed: 06/12/2023]
Abstract
Antibiotics are continuously released into aquatic environments and ecosystems where they accumulate, which increases risks from the transmission of antibiotic resistance genes (ARGs). However, it is difficult to completely remove antibiotics by conventional biological methods, and during such treatment, ARGs may spread via the activated sludge process. Easy-to-biodegrade food have been reported to improve the removal of toxic pollutants, and therefore, this study investigated whether such co-substrates may also decrease the abundance of ARGs and their transferal. This study investigated amoxicillin (AMO) degradation using 0-100 mg/L acetate sodium as co-substrate in a sequencing biological reactor. Proteobacteria, Bacteroidetes, and Actinobacteria were identified as dominant phyla for AMO removal and mineralization. Furthermore, acetate addition increased the abundances of adeF and mdsC as efflux resistance genes, which improved microbial resistance, the coping ability of AMO toxicity, and the repair of the damage from AMO. As a result, acetate addition contributed to almost 100% AMO removal and stabilized the chemical oxygen demand (~20 mg/L) in effluents when the influent AMO fluctuated from 20 to 100 mg/L. Moreover, the total abundance of ARGs decreased by approximately ~30%, and the proportion of the most dominant antibiotic resistance bacteria Proteobacteria decreased by ~9%. The total abundance of plasmids that encode ARGs decreased by as much as ~30%, implying that the ARG spreading risks were alleviated. In summary, easy-to-biodegrade food contributed to the simultaneous elimination of antibiotics and ARGs in an activated sludge process.
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Affiliation(s)
- Chongjun Zhang
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun 130021, China; Jilin Provincial Key Laboratory of Water Resources and Environment, Jilin University, Changchun 130021, China; Engineering Lab for Water Pollution Control and Resources Recovery of Jilin Province, School of Environment, Northeast Normal University, Changchun 130117, China
| | - Zhiquan Zhao
- Engineering Lab for Water Pollution Control and Resources Recovery of Jilin Province, School of Environment, Northeast Normal University, Changchun 130117, China
| | - Shuangshi Dong
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun 130021, China; Jilin Provincial Key Laboratory of Water Resources and Environment, Jilin University, Changchun 130021, China
| | - Dandan Zhou
- Engineering Lab for Water Pollution Control and Resources Recovery of Jilin Province, School of Environment, Northeast Normal University, Changchun 130117, China.
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12
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Yang Y, Ashworth AJ, Durso LM, Savin M, DeBruyn JM, Cook K, Moore PA, Owens PR. Do Long-Term Conservation Pasture Management Practices Influence Microbial Diversity and Antimicrobial Resistant Genes in Runoff? Front Microbiol 2021; 12:617066. [PMID: 33897633 PMCID: PMC8060697 DOI: 10.3389/fmicb.2021.617066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 03/15/2021] [Indexed: 12/02/2022] Open
Abstract
Runoff from land-applied manure and poultry litter is one mechanism by which manure-borne bacteria are transported over large distances in the environment. There is a global concern that antimicrobial resistant (AMR) genes may be transmitted through the food chain from animal manures to soil to surface water. However, details are lacking on the ecology of AMR genes in water runoff as well as how conservation management practices may affect the runoff microbiome or minimize the movement of AMR genes. The aim of this study was to identify microbial community structure and diversity in water runoff following 14-years of poultry litter and cattle manure deposition and to evaluate the amount of AMR genes under five conventional and conservation pasture management strategies. Since 2004, all watersheds received annual poultry litter at a rate of 5.6 Mg ha−1 and were consistently managed. Surface runoff samples were collected from each watershed from 2018 to 2019, characterized using Illumina 16S rRNA gene amplicon sequencing and enumerated for four AMR-associated genes (ermB, sulI, intlI, and blactx-m-32) using quantitative PCR. Overall, long-term pasture management influenced water microbial community structure, with effects differing by year (p < 0.05). Bacterial richness (Chao1 index) was influenced by pasture management, with the lowest richness occurring in the control (nearby non-agricultural water source) and the greatest under fields that were hayed (no cattle presence). Runoff bacterial richness in watersheds increased following poultry litter applications, indicating poultry litter is a possible source of bacteria and altered runoff community structure. The blactx-m-32 gene was not detected in any surface water sample. The remaining three AMR genes were absent in the non-agricultural control, but present in agricultural samples. However, there was no impact (p > 0.05) from pasture management on the abundance of these genes, indicating both conventional and conservation practices have similar ecologies for these targets; however, there was a greater detection of sulI genes from runoff in continuously grazed systems in 2019, with hay being lowest in 2019. Results illustrate that the edge of field buffer strips may increase bacterial richness in water runoff, but these changes in richness do not greatly impact target AMR genes in the United States largest land-use category.
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Affiliation(s)
- Yichao Yang
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, United States
| | - Amanda J Ashworth
- USDA-ARS, Poultry Production and Product Safety Research Unit, Fayetteville, AR, United States
| | - Lisa M Durso
- USDA-ARS, Agroecosystem Management Research Unit, Lincoln, NE, United States
| | - Mary Savin
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, United States
| | - Jennifer M DeBruyn
- Department of Biosystems Engineering & Soil Science, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Kimberly Cook
- USDA-ARS, Nutrition, Food Safety/Quality, Office of National Programs, Beltsville, MD, United States
| | - Philip A Moore
- USDA-ARS, Poultry Production and Product Safety Research Unit, Fayetteville, AR, United States
| | - Phillip R Owens
- USDA-ARS, Dale Bumpers Small Farms Research Center, Booneville, AR, United States
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13
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Murphy TR, Xiao R, Hamilton-Brehm SD. Hybrid genome de novo assembly with methylome analysis of the anaerobic thermophilic subsurface bacterium Thermanaerosceptrum fracticalcis strain DRI-13 T. BMC Genomics 2021; 22:209. [PMID: 33757423 PMCID: PMC7988955 DOI: 10.1186/s12864-021-07535-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 03/15/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND There is a dearth of sequenced and closed microbial genomes from environments that exceed > 500 m below level terrestrial surface. Coupled with even fewer cultured isolates, study and understanding of how life endures in the extreme oligotrophic subsurface environments is greatly hindered. Using a de novo hybrid assembly of Illumina and Oxford Nanopore sequences we produced a circular genome with corresponding methylome profile of the recently characterized thermophilic, anaerobic, and fumarate-respiring subsurface bacterium, Thermanaerosceptrum fracticalcis, strain DRI-13T to understand how this microorganism survives the deep subsurface. RESULTS The hybrid assembly produced a single circular genome of 3.8 Mb in length with an overall GC content of 45%. Out of the total 4022 annotated genes, 3884 are protein coding, 87 are RNA encoding genes, and the remaining 51 genes were associated with regulatory features of the genome including riboswitches and T-box leader sequences. Approximately 24% of the protein coding genes were hypothetical. Analysis of strain DRI-13T genome revealed: 1) energy conservation by bifurcation hydrogenase when growing on fumarate, 2) four novel bacterial prophages, 3) methylation profile including 76.4% N6-methyladenine and 3.81% 5-methylcytosine corresponding to novel DNA methyltransferase motifs. As well a cluster of 45 genes of unknown protein families that have enriched DNA mCpG proximal to the transcription start sites, and 4) discovery of a putative core of bacteriophage exclusion (BREX) genes surrounded by hypothetical proteins, with predicted functions as helicases, nucleases, and exonucleases. CONCLUSIONS The de novo hybrid assembly of strain DRI-13T genome has provided a more contiguous and accurate view of the subsurface bacterium T. fracticalcis, strain DRI-13T. This genome analysis reveals a physiological focus supporting syntrophy, non-homologous double stranded DNA repair, mobility/adherence/chemotaxis, unique methylome profile/recognized motifs, and a BREX defense system. The key to microbial subsurface survival may not rest on genetic diversity, but rather through specific syntrophy niches and novel methylation strategies.
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Affiliation(s)
- Trevor R Murphy
- Department of Microbiology, Southern Illinois University Carbondale, Carbondale, IL, USA
| | - Rui Xiao
- Department of Microbiology, Southern Illinois University Carbondale, Carbondale, IL, USA
| | - Scott D Hamilton-Brehm
- Department of Microbiology, Southern Illinois University Carbondale, Carbondale, IL, USA.
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14
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The Oral Bacterial Community in Melanophryniscus admirabilis (Admirable Red-Belly Toads): Implications for Conservation. Microorganisms 2021; 9:microorganisms9020220. [PMID: 33499099 PMCID: PMC7912307 DOI: 10.3390/microorganisms9020220] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/11/2021] [Accepted: 01/18/2021] [Indexed: 12/14/2022] Open
Abstract
Melanophryniscus admirabilis (admirable red-belly toad) is a microendemic and critically endangered species found exclusively along 700 m of the Forqueta River, in a fragment of the Atlantic Forest of southern Brazil. One of the greatest concerns regarding the conservation of this species is the extensive use of pesticides in areas surrounding their natural habitat. In recent years, the adaptation and persistence of animal species in human-impacted environments have been associated with microbiota. Therefore, the present study aimed to characterize the oral bacterial community of wild M. admirabilis and to address the question of how this community might contribute to this toad’s adaptation in the anthropogenic environment as well as its general metabolic capabilities. A total of 11 oral samples collected from wild M. admirabilis were characterized and analyzed via high-throughput sequencing. Fragments of the 16S rRNA variable region 4 (V4) were amplified, and sequencing was conducted using an Ion Personal Genome Machine (PGM) System with 316 chips. A total of 181,350 sequences were obtained, resulting in 16 phyla, 34 classes, 39 orders, and 77 families. Proteobacteria dominated (53%) the oral microbiota of toads, followed by Firmicutes (18%), Bacteroidetes (17%), and Actinobacteria (5%). No significant differences in microbial community profile from among the samples were reported, which suggests that the low dietary diversity observed in this population may directly influence the bacterial composition. Inferences of microbiome function were performed using PICRUSt2 software. Important pathways (e.g., xenobiotic degradation pathways for pesticides and aromatic phenolic compounds) were detected, which suggests that the bacterial communities may serve important roles in M. admirabilis health and survival in the anthropogenic environment. Overall, our results have important implications for the conservation and management of this microendemic and critically endangered species.
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15
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Getahun A, Kiros S, Muleta D, Assefa F. Genetic and metabolic diversities of rhizobacteria isolated from degraded soil of Ethiopia. Heliyon 2020; 6:e05697. [PMID: 33367126 PMCID: PMC7749386 DOI: 10.1016/j.heliyon.2020.e05697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 10/03/2020] [Accepted: 12/07/2020] [Indexed: 11/25/2022] Open
Abstract
Genetic and metabolic diversities of rhizobacteria are the fundamental sources for their adaptation to cope with abiotic and biotic stresses in order to enhance growth and health of plants in the soil. Thus, this study was initiated to assess the genetic and metabolic diversities of rhizobacteria isolated from plants grown in degraded soil through BOX-PCR and partial sequencing of 16S rRNA genes. A total of eighty isolates were recovered and subjected to phenotypic profiling of carbohydrate and amino acid utilization, BOX PCR and 16S rRNA profiling. The phenotypic profiling showed remarkable metabolic versatility with Ochrobactrum spp, Pseudomonas spp and Klebsiella spp, and BOX-PCR showed greater discriminatory power for fingerprinting of rhizobacterial isolates with high degree of polymorphism. Bacillus spp showed the highest Simpson's diversity Index. The 16S rRNA genes sequence assigned the rhizobacteria to phyla Proteobacteria with Gammaproteobacteria and Alphaproteobacteria classes and Firmicutes with Bacilli class. The data also showed that the most dominant species were Pseudomonas and Ochrobactrum. Genetic and metabolic diversities of the rhizobacterial isolates reveal the potential of these microbes for plant growth improvement under water deficient soil after testing other inoculant traits.
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Affiliation(s)
| | - Solomon Kiros
- AddisAbaba Institute of Technology, Addis Ababa University, Ethiopia
| | - Diriba Muleta
- College of Natural Sciences, Addis Ababa University, Ethiopia
- Corresponding author.
| | - Fassil Assefa
- College of Natural Sciences, Addis Ababa University, Ethiopia
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16
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Jin P, Ren B, Wang XC, Jin X, Shi X. Mechanism of microbial metabolic responses and ecological system conversion under different nitrogen conditions in sewers. WATER RESEARCH 2020; 186:116312. [PMID: 32846381 DOI: 10.1016/j.watres.2020.116312] [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: 10/03/2019] [Revised: 08/13/2020] [Accepted: 08/17/2020] [Indexed: 06/11/2023]
Abstract
Nitrogen plays a central role in the sewer ecosystem, and the bioconversion of nitrogen can significantly affect bioreactions in sewers. However, the mechanisms underlying the involvement of nitrogen-associated pollutants in sewer ecosystems remain unknown. In this study, the effects of two typical nitrogen ratios (organic/inorganic nitrogen: 7/3 (Group A) and 3/7 (Group B)) on carbon, nitrogen, and sulfur bioconversions were investigated in a pilot sewer. The distribution of amino acids, such as proline, glycine and methionine, was significantly different between Groups A and B, and carbon-associated communities (based on 16S rRNA gene copies) were more prevalent in Group A, while sulfur and nitrogen-associated communities were more prevalent in Group B. To explore the effect of nitrogen on microbial response mechanisms, metagenomics-based methods were used to investigate the roles of amino acids involved in carbon, nitrogen, and sulfur bioconversion in sewers. Proline, glycine, and tyrosine in Group A promoted the expression of genes associated with cell membrane transport and increased the rate of protein synthesis, which stimulated the enrichment of carbon-associated communities. The transmembrane transport of higher concentrations of alanine and methionine in Group B was essential for cell metabolism and nutrient transport, thereby enriching nitrogen and sulfur-associated communities. In this investigation, insights into carbon, nitrogen and sulfur bioconversions in sewer ecosystems were revealed, significantly improving the understanding of the sewer ecosystem within a community context.
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Affiliation(s)
- Pengkang Jin
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi Province, 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi Province, 710055, China
| | - Bo Ren
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi Province, 710055, China
| | - Xiaochang C Wang
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi Province, 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi Province, 710055, China
| | - Xin Jin
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi Province, 710055, China; Northwest China Key Laboratory of Water Resources and Environment Ecology, Xi'an University of Architecture and Technology, Xi'an, Shaanxi Province, 710055, China
| | - Xuan Shi
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi Province, 710055, China; Northwest China Key Laboratory of Water Resources and Environment Ecology, Xi'an University of Architecture and Technology, Xi'an, Shaanxi Province, 710055, China.
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17
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Mącik M, Gryta A, Sas-Paszt L, Frąc M. The Status of Soil Microbiome as Affected by the Application of Phosphorus Biofertilizer: Fertilizer Enriched with Beneficial Bacterial Strains. Int J Mol Sci 2020; 21:E8003. [PMID: 33121206 PMCID: PMC7663420 DOI: 10.3390/ijms21218003] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/21/2020] [Accepted: 10/23/2020] [Indexed: 01/05/2023] Open
Abstract
Regarding the unfavourable changes in agroecosystems resulting from the excessive application of mineral fertilizers, biopreparations containing live microorganisms are gaining increasing attention. We assumed that the application of phosphorus mineral fertilizer enriched with strains of beneficial microorganisms contribute to favourable changes in enzymatic activity and in the genetic and functional diversity of microbial populations inhabiting degraded soils. Therefore, in field experiments conditions, the effects of phosphorus fertilizer enriched with bacterial strains on the status of soil microbiome in two chemically degraded soil types (Brunic Arenosol - BA and Abruptic Luvisol - AL) were investigated. The field experiments included treatments with an optimal dose of phosphorus fertilizer (without microorganisms - FC), optimal dose of phosphorus fertilizer enriched with microorganisms including Paenibacillus polymyxa strain CHT114AB, Bacillus amyloliquefaciens strain AF75BB and Bacillus sp. strain CZP4/4 (FA100) and a dose of phosphorus fertilizer reduced by 40% and enriched with the above-mentioned bacteria (FA60). The analyzes performed included: the determination of the activity of the soil enzymes (protease, urease, acid phosphomonoesterase, β-glucosidase), the assessment of the functional diversity of microorganisms with the application of BIOLOGTM plates and the characterization of the genetic diversity of bacteria, archaea and fungi with multiplex terminal restriction fragment length polymorphism and next generation sequencing. The obtained results indicated that the application of phosphorus fertilizer enriched with microorganisms improved enzymatic activity, and the genetic and functional diversity of the soil microbial communities, however these effects were dependent on the soil type.
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Affiliation(s)
- Mateusz Mącik
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, 20-290 Lublin, Poland; (M.M.); (A.G.)
| | - Agata Gryta
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, 20-290 Lublin, Poland; (M.M.); (A.G.)
| | - Lidia Sas-Paszt
- Institute of Horticulture in Skierniewice, Pomologiczna 18, 96-100 Skierniewice, Poland;
| | - Magdalena Frąc
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, 20-290 Lublin, Poland; (M.M.); (A.G.)
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18
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Ntalli N, Adamski Z, Doula M, Monokrousos N. Nematicidal Amendments and Soil Remediation. PLANTS (BASEL, SWITZERLAND) 2020; 9:E429. [PMID: 32244565 PMCID: PMC7238745 DOI: 10.3390/plants9040429] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 03/03/2020] [Accepted: 03/21/2020] [Indexed: 12/20/2022]
Abstract
The intensification of agriculture has created concerns about soil degradation and toxicity of agricultural chemicals to non-target organisms. As a result, there is great urgency for discovering new ecofriendly tools for pest management and plant nutrition. Botanical matrices and their extracts and purified secondary metabolites have received much research interest, but time-consuming registration issues have slowed their adoption. In contrast, cultural practices such as use of plant matrices as soil amendments could be immediately used as plant protectants or organic fertilizers. Herein, we focus on some types of soil amendments of botanical origin and their utilization for nematicidal activity and enhancement of plant nutrition. The mode of action is discussed in terms of parasite control as well as plant growth stimulation.
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Affiliation(s)
- Nikoletta Ntalli
- Department of Pesticides Control and Phytopharmacy, Benaki Phytopathological Institute, 8 S. Delta Str., 14561 Athens, Greece
| | - Zbigniew Adamski
- Electron and Confocal Microscope Laboratory, Faculty of Biology, Adam Mickiewicz University in Poznań, 61-614 Poznań, Poland;
- Department of Animal Physiology and Development, Faculty of Biology, Adam Mickiewicz University in Poznań, ul. Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
| | - Maria Doula
- Laboratory of Non-Parasitic Diseases, Benaki Phytopathological Institute, 8 S. Delta Str., 14561 Athens, Greece;
| | - Nikolaos Monokrousos
- Laboratory of Molecular Ecology, International Hellenic University, 57001 Thessaloniki, Greece;
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19
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Hamdan HZ, Salam DA, Saikaly PE. Characterization of the microbial community diversity and composition of the coast of Lebanon: Potential for petroleum oil biodegradation. MARINE POLLUTION BULLETIN 2019; 149:110508. [PMID: 31425842 DOI: 10.1016/j.marpolbul.2019.110508] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 07/22/2019] [Accepted: 08/06/2019] [Indexed: 06/10/2023]
Abstract
In this study, the shoreline of Lebanon, which extends over 225 km along the eastern side of the Mediterranean Sea, was characterized for its sediment microbial community diversity and composition using 16S rRNA gene sequencing with Illumina MiSeq technology. Non-metric multidimensional scaling (NMDS) analysis showed no clear grouping among nearby sampled sites along the shoreline. Insignificant diversion between the wet and dry season microbial communities was observed along the coast at each sampling site. A high variation at the genus level was observed, with several novel genera identified at high relative abundance in certain locations, such as JTB255 marine benthic groups OTU_4 (5.4%) and OTU_60 (3.2%), and BD7-8 marine group OTU_5 (2.9%).
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Affiliation(s)
- Hamdan Z Hamdan
- Department of Civil and Environmental Engineering, Maroun Semaan Faculty of Engineering and Architecture, American University of Beirut, Beirut, Lebanon
| | - Darine A Salam
- Department of Civil and Environmental Engineering, Maroun Semaan Faculty of Engineering and Architecture, American University of Beirut, Beirut, Lebanon.
| | - Pascal E Saikaly
- Division of Biological and Environmental Sciences and Engineering, Water Desalination and Reuse Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
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20
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Igalavithana AD, Kim KH, Jung JM, Heo HS, Kwon EE, Tack FMG, Tsang DCW, Jeon YJ, Ok YS. Effect of biochars pyrolyzed in N 2 and CO 2, and feedstock on microbial community in metal(loid)s contaminated soils. ENVIRONMENT INTERNATIONAL 2019; 126:791-801. [PMID: 30903914 DOI: 10.1016/j.envint.2019.02.061] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 02/23/2019] [Accepted: 02/25/2019] [Indexed: 06/09/2023]
Abstract
Little is known about the effects of applying amendments on soil for immobilizing metal(loid)s on the soil microbial community. Alterations in the microbial community were examined after incubation of treated contaminated soils. One soil was contaminated with Pb and As, a second soil with Cd and Zn. Red pepper stalk (RPS) and biochars produced from RPS in either N2 atmosphere (RPSN) or CO2 atmosphere (RPSC) were applied at a rate of 2.5% to the two soils and incubated for 30 days. Bacterial communities of control and treated soils were characterized by sequencing 16S rRNA genes using the Illumina MiSeq sequencing. In both soils, bacterial richness increased in the amended soils, though somewhat differently between the treatments. Evenness values decreased significantly, and the final overall diversities were reduced. The neutralization of pH, reduced available concentrations of Pb or Cd, and supplementation of available carbon and surface area could be possible factors affecting the community changes. Biochar amendments caused the soil bacterial communities to become more similar than those in the not amended soils. The bacterial community structures at the phylum and genus levels showed that amendment addition might restore the normal bacterial community of soils, and cause soil bacterial communities in contaminated soils to normalize and stabilize.
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Affiliation(s)
- Avanthi Deshani Igalavithana
- Korea Biochar Research Center, O-Jeong Eco-Resilience Institute (OJERI), Division of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Kyoung-Ho Kim
- Department of Microbiology, College of Natural Science, Pukyong National University, 45 Yongso-ro, Nam-gu, Busan 608-737, Republic of Korea
| | - Jong-Min Jung
- Department of Environment and Energy, Sejong University, Seoul 05006, Republic of Korea
| | - Hye-Sook Heo
- Department of Microbiology, College of Natural Science, Pukyong National University, 45 Yongso-ro, Nam-gu, Busan 608-737, Republic of Korea
| | - Eilhann E Kwon
- Department of Environment and Energy, Sejong University, Seoul 05006, Republic of Korea
| | - Filip M G Tack
- Department of Green Chemistry and Technology, Ghent University, B-9000 Gent, Belgium
| | - Daniel C W Tsang
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Young Jae Jeon
- Department of Microbiology, College of Natural Science, Pukyong National University, 45 Yongso-ro, Nam-gu, Busan 608-737, Republic of Korea.
| | - Yong Sik Ok
- Korea Biochar Research Center, O-Jeong Eco-Resilience Institute (OJERI), Division of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea.
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21
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Lopez-Fernandez M, Åström M, Bertilsson S, Dopson M. Depth and Dissolved Organic Carbon Shape Microbial Communities in Surface Influenced but Not Ancient Saline Terrestrial Aquifers. Front Microbiol 2018; 9:2880. [PMID: 30538690 PMCID: PMC6277548 DOI: 10.3389/fmicb.2018.02880] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 11/09/2018] [Indexed: 12/31/2022] Open
Abstract
The continental deep biosphere is suggested to contain a substantial fraction of the earth's total biomass and microorganisms inhabiting this environment likely have a substantial impact on biogeochemical cycles. However, the deep microbial community is still largely unknown and can be influenced by parameters such as temperature, pressure, water residence times, and chemistry of the waters. In this study, 21 boreholes representing a range of deep continental groundwaters from the Äspö Hard Rock Laboratory were subjected to high-throughput 16S rRNA gene sequencing to characterize how the different water types influence the microbial communities. Geochemical parameters showed the stability of the waters and allowed their classification into three groups. These were (i) waters influenced by infiltration from the Baltic Sea with a "modern marine (MM)" signature, (ii) a "thoroughly mixed (TM)" water containing groundwaters of several origins, and (iii) deep "old saline (OS)" waters. Decreasing microbial cell numbers positively correlated with depth. In addition, there was a stronger positive correlation between increased cell numbers and dissolved organic carbon for the MM compared to the OS waters. This supported that the MM waters depend on organic carbon infiltration from the Baltic Sea while the ancient saline waters were fed by "geogases" such as carbon dioxide and hydrogen. The 16S rRNA gene relative abundance of the studied groundwaters revealed different microbial community compositions. Interestingly, the TM water showed the highest dissimilarity compared to the other two water types, potentially due to the several contrasting water types contributing to this groundwater. The main identified microbial phyla in the groundwaters were Gammaproteobacteria, unclassified sequences, Campylobacterota (formerly Epsilonproteobacteria), Patescibacteria, Deltaproteobacteria, and Alphaproteobacteria. Many of these taxa are suggested to mediate ferric iron and nitrate reduction, especially in the MM waters. This indicated that nitrate reduction may be a neglected but important process in the deep continental biosphere. In addition to the high number of unclassified sequences, almost 50% of the identified phyla were archaeal or bacterial candidate phyla. The percentage of unknown and candidate phyla increased with depth, pointing to the importance and necessity of further studies to characterize deep biosphere microbial populations.
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Affiliation(s)
| | - Mats Åström
- Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Stefan Bertilsson
- Limnology and Science for Life Laboratory, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
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Purkamo L, Bomberg M, Nyyssönen M, Ahonen L, Kukkonen I, Itävaara M. Response of Deep Subsurface Microbial Community to Different Carbon Sources and Electron Acceptors during ∼2 months Incubation in Microcosms. Front Microbiol 2017; 8:232. [PMID: 28265265 PMCID: PMC5316538 DOI: 10.3389/fmicb.2017.00232] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 02/02/2017] [Indexed: 11/13/2022] Open
Abstract
Acetate plays a key role as electron donor and acceptor and serves as carbon source in oligotrophic deep subsurface environments. It can be produced from inorganic carbon by acetogenic microbes or through breakdown of more complex organic matter. Acetate is an important molecule for sulfate reducers that are substantially present in several deep bedrock environments. Aceticlastic methanogens use acetate as an electron donor and/or a carbon source. The goal of this study was to shed light on carbon cycling and competition in microbial communities in fracture fluids of Finnish crystalline bedrock groundwater system. Fracture fluid was anaerobically collected from a fracture zone at 967 m depth of the Outokumpu Deep Drill Hole and amended with acetate, acetate + sulfate, sulfate only or left unamended as a control and incubated up to 68 days. The headspace atmosphere of microcosms consisted of 80% hydrogen and 20% CO2. We studied the changes in the microbial communities with community fingerprinting technique as well as high-throughput 16S rRNA gene amplicon sequencing. The amended microcosms hosted more diverse bacterial communities compared to the intrinsic fracture zone community and the control treatment without amendments. The majority of the bacterial populations enriched with acetate belonged to clostridial hydrogenotrophic thiosulfate reducers and Alphaproteobacteria affiliating with groups earlier found from subsurface and groundwater environments. We detected a slight increase in the number of sulfate reducers after the 68 days of incubation. The microbial community changed significantly during the experiment, but increase in specifically acetate-cycling microbial groups was not observed.
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Affiliation(s)
- Lotta Purkamo
- VTT Technical Research Centre of Finland Espoo, Finland
| | - Malin Bomberg
- VTT Technical Research Centre of Finland Espoo, Finland
| | | | | | - Ilmo Kukkonen
- Department of Physics, University of Helsinki Helsinki, Finland
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