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Zhang S, Cui T, Liu X, Zhan M, Song X, Xu Y, Yu R. Sludge biolysis pretreatment to reduce antibiotic resistance genes (ARGs): Insight into the relationship between potential ARGs hosts and BALOs' preferred prey. WATER RESEARCH 2024; 260:121949. [PMID: 38901315 DOI: 10.1016/j.watres.2024.121949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 06/05/2024] [Accepted: 06/14/2024] [Indexed: 06/22/2024]
Abstract
As an important reservoir of antibiotic resistance genes (ARGs), the sludge discharged from wastewater treatment plants is the key intermediate for ARG transport into the environment. Bdellovibrio-and-like organisms (BALOs) are predatory bacteria that are expected to attack antibiotic-resistant bacteria (ARB). In this study, the screened BALOs (C3 & D15) were mixed with the sludge for biolysis to achieve the satisfying removal efficiencies of six tet genes, two sul genes, and one mobile genetic element (intl 1). Among them, tet(Q) demonstrated the highest reduction rate in relative abundance at 87.3 ± 1.0 %, while tet(X) displayed the lowest of 11.7 ± 0.2 %. The microorganisms, including Longilinea, Methanobacterium, Acetobacterium, Sulfurimonas, allobaculum, Gaiella, AAP99, Ellin6067, Rhodoferax, Ferruginibacter and Thermomonas, were expected to play a dual role in the reduction of ARGs by serving as ARB and BALOs' preferred prey. Meanwhile, BALOs consortium improved ARGs reduction efficiency via the expansion of the prey profile. Additionally, BALOs decreased the relative abundance of not only pathogens (Shinella, Rickettsia, Burkholderia, Acinetobacter, Aeromonas, Clostridium, Klebsiella and Pseudomonas), but also the ARGs' host pathogens (Mycobacterium, Plesiocystis, Burkholderia, and Bacteroides). Therefore, the application of BALOs for sludge biolysis are promising to decrease the sludge's public health risks via limiting the spread of ARGs and pathogens into the environment.
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Affiliation(s)
- Siyuan Zhang
- Department of Environmental Science and Engineering, School of Energy and Environment, Wuxi Engineering Research Center of Taihu Lake Water Environment, Southeast University, Nanjing, Jiangsu, 210096, China; Key Laboratory of Environmental Medicine Engineering, Ministry of Education, Southeast University, Nanjing, Jiangsu, 210009, China
| | - Tingting Cui
- Department of Environmental Science and Engineering, School of Energy and Environment, Wuxi Engineering Research Center of Taihu Lake Water Environment, Southeast University, Nanjing, Jiangsu, 210096, China; Key Laboratory of Environmental Medicine Engineering, Ministry of Education, Southeast University, Nanjing, Jiangsu, 210009, China
| | - Xiaowen Liu
- Department of Environmental Science and Engineering, School of Energy and Environment, Wuxi Engineering Research Center of Taihu Lake Water Environment, Southeast University, Nanjing, Jiangsu, 210096, China; Key Laboratory of Environmental Medicine Engineering, Ministry of Education, Southeast University, Nanjing, Jiangsu, 210009, China
| | - Manjun Zhan
- Nanjing Research Institute of Environmental Protection, Nanjing Environmental Protection Bureau, Nanjing, Jiangsu, 210013, China
| | - Xin Song
- SUMEC Complete Equipment & Engineering CO. LTD, Nanjing 210018, China
| | - Yi Xu
- Nanjing No.1 Middle School, Nanjing, Jiangsu, 210013, China
| | - Ran Yu
- Department of Environmental Science and Engineering, School of Energy and Environment, Wuxi Engineering Research Center of Taihu Lake Water Environment, Southeast University, Nanjing, Jiangsu, 210096, China; Key Laboratory of Environmental Medicine Engineering, Ministry of Education, Southeast University, Nanjing, Jiangsu, 210009, China.
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2
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Cohen Y, Johnke J, Abed-Rabbo A, Pasternak Z, Chatzinotas A, Jurkevitch E. Unbalanced predatory communities and a lack of microbial degraders characterize the microbiota of a highly sewage-polluted Eastern-Mediterranean stream. FEMS Microbiol Ecol 2024; 100:fiae069. [PMID: 38684474 PMCID: PMC11099661 DOI: 10.1093/femsec/fiae069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 03/10/2024] [Accepted: 04/25/2024] [Indexed: 05/02/2024] Open
Abstract
Wastewater pollution of water resources takes a heavy toll on humans and on the environment. In highly polluted water bodies, self-purification is impaired, as the capacity of the riverine microbes to regenerate the ecosystem is overwhelmed. To date, information on the composition, dynamics and functions of the microbial communities in highly sewage-impacted rivers is limited, in particular in arid and semi-arid environments. In this year-long study of the highly sewage-impacted Al-Nar/Kidron stream in the Barr al-Khalil/Judean Desert east of Jerusalem, we show, using 16S and 18S rRNA gene-based community analysis and targeted qPCR, that both the bacterial and micro-eukaryotic communities, while abundant, exhibited low stability and diversity. Hydrolyzers of organics compounds, as well as nitrogen and phosphorus recyclers were lacking, pointing at reduced potential for regeneration. Furthermore, facultative bacterial predators were almost absent, and the obligate predators Bdellovibrio and like organisms were found at very low abundance. Finally, the micro-eukaryotic predatory community differed from those of other freshwater environments. The lack of essential biochemical functions may explain the stream's inability to self-purify, while the very low levels of bacterial predators and the disturbed assemblages of micro-eukaryote predators present in Al-Nar/Kidron may contribute to community instability and disfunction.
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Affiliation(s)
- Yossi Cohen
- Department of Plant Pathology and Microbiology, Institute of Environmental Sciences, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 76100, Israel
- Presently at DayTwo, Rehovot, Israel
| | - Julia Johnke
- Evolutionary Ecology and Genetics, Zoological Institute, University of Kiel, Kiel, Germany
| | | | - Zohar Pasternak
- Department of Plant Pathology and Microbiology, Institute of Environmental Sciences, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 76100, Israel
- Presently at the Division of Identification and Forensic Science, Israel Police, National Headquarters
| | - Antonis Chatzinotas
- Department of Applied Microbial Ecology, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
- Institute of Biology, Leipzig University, Talstrasse 33, 04103 Leipzig, Germany
- Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany
| | - Edouard Jurkevitch
- Department of Plant Pathology and Microbiology, Institute of Environmental Sciences, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 76100, Israel
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Zhang L, Guo L, Cui Z, Ju F. Exploiting predatory bacteria as biocontrol agents across ecosystems. Trends Microbiol 2024; 32:398-409. [PMID: 37951768 DOI: 10.1016/j.tim.2023.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 10/10/2023] [Accepted: 10/11/2023] [Indexed: 11/14/2023]
Abstract
Predatory bacteria have been increasingly known for their ubiquity in environments and great functional potentials in controlling unwanted microorganisms. Fundamental understanding of the predation mechanisms, population dynamics, and interaction patterns underlying bacterial predation is required for wise exploitation of predatory bacteria for enhancing ecoenvironmental, animal, and human health. Here, we review the recent achievements on applying predatory bacteria in different systems as biocontrol agents and living antibiotics as well as new findings in their phylogenetic diversity and predation mechanisms. We finally propose critical issues that deserve priority research and highlight the necessity to combine classic culture-based and advanced culture-independent approaches to push research frontiers of bacterial predation across ecosystems for promising biocontrol and therapy strategies towards a sustainable ecoenvironment and health.
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Affiliation(s)
- Lu Zhang
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang Province, China; Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, Zhejiang Province, China; Center of Synthetic Biology and Integrated Bioengineering, Westlake University, Hangzhou, Zhejiang Province, China; Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
| | - Lingyun Guo
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang Province, China; Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, Zhejiang Province, China; Center of Synthetic Biology and Integrated Bioengineering, Westlake University, Hangzhou, Zhejiang Province, China
| | - Zhongli Cui
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu Province, China
| | - Feng Ju
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang Province, China; Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, Zhejiang Province, China; Center of Synthetic Biology and Integrated Bioengineering, Westlake University, Hangzhou, Zhejiang Province, China; Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China.
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4
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Castellano-Hinojosa A, Gallardo-Altamirano MJ, González-Martínez A, González-López J. Novel insights into the impact of anticancer drugs on the performance and microbial communities of a continuous-flow aerobic granular sludge system. BIORESOURCE TECHNOLOGY 2024; 394:130195. [PMID: 38081471 DOI: 10.1016/j.biortech.2023.130195] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 12/08/2023] [Accepted: 12/09/2023] [Indexed: 02/04/2024]
Abstract
Anticancer drugs are frequently found in domestic wastewater, but knowledge of their impacts on wastewater treatment processes is limited. The effects of three levels of concentrations (low, medium, and high) of three anticancer drugs on physicochemical parameters and prokaryotic communities of a continuous-flow aerobic granular sludge (AGS) system were examined. Drugs at medium and high concentrations reduced the removal of total nitrogen and organic matter during the first 15 days of operation by approximately 15-20 % compared to a control, but these effects disappeared afterward. Removal efficiencies of drugs were in the range of 51.2-100 % depending on the concentration level. Drugs at medium and high concentrations reduced the abundance and diversity and altered the composition of prokaryotic communities. Specific taxa were linked to variations in performance parameters after the addition of the drugs. This study provides improved knowledge of the impacts of anticancer drugs in AGS systems operated in continuous-flow reactor.
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Affiliation(s)
- Antonio Castellano-Hinojosa
- Department of Microbiology, Institute of Water Research, University of Granada, C/Ramon y Cajal, 4, Granada 18071, Spain.
| | - Manuel J Gallardo-Altamirano
- Department of Microbiology, Institute of Water Research, University of Granada, C/Ramon y Cajal, 4, Granada 18071, Spain
| | - Alejandro González-Martínez
- Department of Microbiology, Institute of Water Research, University of Granada, C/Ramon y Cajal, 4, Granada 18071, Spain
| | - Jesús González-López
- Department of Microbiology, Institute of Water Research, University of Granada, C/Ramon y Cajal, 4, Granada 18071, Spain
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Liu R, Wei Z, Dong W, Wang R, Adams JM, Yang L, Krause SMB. Unraveling the impact of lanthanum on methane consuming microbial communities in rice field soils. Front Microbiol 2024; 15:1298154. [PMID: 38322316 PMCID: PMC10844099 DOI: 10.3389/fmicb.2024.1298154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 01/03/2024] [Indexed: 02/08/2024] Open
Abstract
The discovery of the lanthanide requiring enzymes in microbes was a significant scientific discovery that opened a whole new avenue of biotechnological research of this important group of metals. However, the ecological impact of lanthanides on microbial communities utilizing methane (CH4) remains largely unexplored. In this study, a laboratory microcosm model experiment was performed using rice field soils with different pH origins (5.76, 7.2, and 8.36) and different concentrations of La3+ in the form of lanthanum chloride (LaCl3). Results clearly showed that CH4 consumption was inhibited by the addition of La3+ but that the response depended on the soil origin and pH. 16S rRNA gene sequencing revealed the genus Methylobacter, Methylosarcina, and Methylocystis as key players in CH4 consumption under La3+ addition. We suggest that the soil microbiome involved in CH4 consumption can generally tolerate addition of high concentrations of La3+, and adjustments in community composition ensured ecosystem functionality over time. As La3+ concentrations increase, the way that the soil microbiome reacts may not only differ within the same environment but also vary when comparing different environments, underscoring the need for further research into this subject.
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Affiliation(s)
- Ruyan Liu
- School of Ecology and Environmental Sciences, East China Normal University, Shanghai, China
| | - Ziting Wei
- School of Ecology and Environmental Sciences, East China Normal University, Shanghai, China
| | - Wanying Dong
- School of Ecology and Environmental Sciences, East China Normal University, Shanghai, China
| | - Rui Wang
- School of Ecology and Environmental Sciences, East China Normal University, Shanghai, China
| | - Jonathan M. Adams
- School of Geographic and Oceanographic Sciences, Nanjing University, Nanjing, China
| | - Lin Yang
- School of Geographic and Oceanographic Sciences, Nanjing University, Nanjing, China
| | - Sascha M. B. Krause
- School of Ecology and Environmental Sciences, East China Normal University, Shanghai, China
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6
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Wu Z, Gao H, Chen Z, Su W, Jie Y, Zhu J, Yu R. Effect of predatory bacterial mixtures on biolysis of waste activated sludge to improve dewatering performance. ENVIRONMENTAL TECHNOLOGY 2023:1-32. [PMID: 38041588 DOI: 10.1080/09593330.2023.2291419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2023]
Abstract
The generation of surplus sludge during biological wastewater treatment has become a prevalent issue, necessitating the development of a dewatering approach that is efficient, economically feasible, and ecologically sound. Bdellovibrio-and-like organisms (BALOs) are obligatory parasitic bacteria that prey on an array of bacteria. In this study, different BALO strains were isolated and purified from waste activited sludge (WAS). Anti-predation host strains were applied to screen the BALO strains with different host-range to minimize the overlap of the biolysis prey spectrum. In addition, the BALO strains with different host preferences were mixed for sludge biolysis treatment efficiency comparison. The results indicated that the capillary suction time and the bound water content in the WAS treated with the mixed BALOs were significantly decreased by 25.9% ± 1.7% and 5.2% ± 1.2%, respectively, compared to those treated with the single BALO strain. The soluble chemical oxygen demand concentration in the mixed BALOs treated group was increased by 31.2% ± 0.7% than that treated with the single strain. The findings indicate that the mixed strains used in the treatment process resulted in a notable enhancement of both sludge dewatering performance and lysis degree. In addition, the abundance of Proteobacteria treated with the BALO mixtures decreased by 69.1% than the single strain treated one which demonstrated that the BALO mixture expanded the sludge host lysis spectrum. This study revealed the different effects of single and mixed strains on sludge community structure, suggesting that the BALO host range expansion is crucial to further improve sludge dewatering performances.
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Affiliation(s)
- Zeyu Wu
- Department of Environmental Science and Engineering, School of Energy and Environment, Southeast University, Nanjing, Jiangsu, China 210096
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, Southeast University, Nanjing, Jiangsu, China 210009
| | - Huan Gao
- Department of Environmental Science and Engineering, School of Energy and Environment, Southeast University, Nanjing, Jiangsu, China 210096
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, Southeast University, Nanjing, Jiangsu, China 210009
| | - Zhoukai Chen
- Department of Environmental Science and Engineering, School of Energy and Environment, Southeast University, Nanjing, Jiangsu, China 210096
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, Southeast University, Nanjing, Jiangsu, China 210009
- Hangzhou Planning and Design Academy, Hangzhou, Zhejiang, China, 310012
| | - Wenqiang Su
- Yang Zhong Bi Cheng Environmental Technology limited liability company, Yang Zhong, Jiangsu, China, 212200
| | - Yongfang Jie
- Yang Zhong Bi Cheng Environmental Technology limited liability company, Yang Zhong, Jiangsu, China, 212200
| | - Jian Zhu
- Yang Zhong Bi Cheng Environmental Technology limited liability company, Yang Zhong, Jiangsu, China, 212200
| | - Ran Yu
- Department of Environmental Science and Engineering, School of Energy and Environment, Southeast University, Nanjing, Jiangsu, China 210096
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, Southeast University, Nanjing, Jiangsu, China 210009
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7
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Mun W, Choi SY, Upatissa S, Mitchell RJ. Predatory bacteria as potential biofilm control and eradication agents in the food industry. Food Sci Biotechnol 2023; 32:1729-1743. [PMID: 37780591 PMCID: PMC10533476 DOI: 10.1007/s10068-023-01310-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 04/04/2023] [Accepted: 04/12/2023] [Indexed: 10/03/2023] Open
Abstract
Biofilms are a major concern within the food industry since they have the potential to reduce productivity in situ (within the field), impact food stability and storage, and cause downstream food poisoning. Within this review, predatory bacteria as potential biofilm control and eradication agents are discussed, with a particular emphasis on the intraperiplasmic Bdellovibrio-and-like organism (BALO) grouping. After providing a brief overview of predatory bacteria and their activities, focus is given to how BALOs fulfill four attributes that are essential for biocontrol agents to be successful in the food industry: (1) Broad spectrum activity against pathogens, both plant and human; (2) Activity against biofilms; (3) Safety towards humans and animals; and (4) Compatibility with food. As predatory bacteria possess all of these characteristics, they represent a novel form of biofilm biocontrol that is ripe for use within the food industry.
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Affiliation(s)
- Wonsik Mun
- School of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 South Korea
| | - Seong Yeol Choi
- School of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 South Korea
| | - Sumudu Upatissa
- School of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 South Korea
| | - Robert J. Mitchell
- School of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 South Korea
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Bai X, Dinkla IJT, Muyzer G. Shedding light on the total and active core microbiomes in slow sand filters for drinking water production. WATER RESEARCH 2023; 243:120404. [PMID: 37586176 DOI: 10.1016/j.watres.2023.120404] [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: 02/20/2023] [Revised: 07/01/2023] [Accepted: 07/23/2023] [Indexed: 08/18/2023]
Abstract
Slow sand filters (SSF) are widely used in the production of drinking water as a last barrier in the removal of pathogens. This removal mainly depends on the 'Schmutzdecke', a biofilm-like layer on the surface of the sand bed. Most previous studies focused on the total community as revealed by DNA analysis rather than on the active community, which may lead to an incorrect understanding of the SSF ecology. In the current study, we determined and compared the DNA- (total) and RNA-displayed (active) communities in the Schmutzdecke layer from 10 full-scale slow sand filters and further explored the SSF core microbiome in terms of both presence (DNA) and activity (RNA). Discrepancies were observed between the total and the active community, although there was a consistent grouping in the PCoA analysis. The DNA-displayed community may be somewhat inflated, while the RNA-displayed community could reveal low abundance (or rare) but active community members. The overall results imply that both DNA (presence) and RNA (activity) data should be considered to prevent the underestimation of organisms of functional importance but lower abundance. Microbial communities of studied mature Schmutzdecke were shaped by the influent water. Nevertheless, a core microbiome was shared by the mature Schmutzdeckes from independent filters, representing the dominant and consistent microbial community composition in slow sand filters. In the DNA samples, a total of 33 VSC families ('very strict core', with a relative abundance >0.1% and 100% prevalence) were observed across all filters. Among the RNA samples, there were 18 VSC families, including 16 families that overlapped with the DNA VSC families and 2 unique RNA VSC families. The core microbial community structure was influenced by the operational parameters, including the Schmutzdecke age and the sand size, and was less influenced by water flow. In addition, indicator organisms ('biomarkers') for the Schmutzdecke age, which show the longest duration that SSF can maintain a good operation, were observed in our study. The abundant presence of bacteria belonging to bacteriap25 and Caldilineaceae was associated with older Schmutzdeckes, revealing longer periods of stable operation performance of the filter, while the high abundance of bacteria belonging to Bdellovibrionaceae and Bryobacteraceae related to short periods of stable operation performance.
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Affiliation(s)
- Xi Bai
- Microbial Systems Ecology, Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 904, 1098, XH Amsterdam, the Netherlands
| | - Inez J T Dinkla
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911, MA Leeuwarden, the Netherlands
| | - Gerard Muyzer
- Microbial Systems Ecology, Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 904, 1098, XH Amsterdam, the Netherlands.
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9
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Scarim G, LaMartina EL, Venkiteshwaran K, Zitomer DH, Newton RJ, McNamara PJ. An inexpensive, reproducible method to quantify activated sludge foaming potential: Validation through lab-scale studies and year-long full-scale sampling campaign. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2023; 95:e10856. [PMID: 36949613 DOI: 10.1002/wer.10856] [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: 07/15/2022] [Revised: 02/15/2023] [Accepted: 03/19/2023] [Indexed: 06/18/2023]
Abstract
Activated sludge is a conventional treatment process for biochemical oxygen demand (BOD) and total suspended solids (TSS) removal at water resource recovery facilities (WRRFs). Foaming events are a common operational issue in activated sludge and can lead to decreased treatment efficiency, maintenance issues, and potential environmental health risks. Stable foaming events are caused by biological and chemical drivers (i.e., microbes and surfactants) during the aeration process. However, foaming events are difficult to predict and quantify. We present an inexpensive and easy-to-use method that can be applied at WRRFs to quantify foaming potential. Subsequently, the method was applied over a year-long full-scale study while data on microbial community composition and functional parameters associated with foaming potential were collected from activated sludge samples at South Shore Water Reclamation Facility (WRF) (Oak Creek, WI). Results from the development of the foaming potential method using linear alkylbenzene sulfonate (LAS) showed that the method was reproducible (relative standard deviation <20%) and able to capture changes in foam-inducing constituents. Using full-scale activated sludge samples, higher relative abundance values for the following genera were associated with foaming events: Zoogloea, Flavobacterium, Variovorax, and Bdellovibrio. This is the first report that Variovorx and Bdellovibrio relative abundance was correlated with foaming events in activated sludge. Furthermore, the foaming potential positively correlated (ρ = 0.24) with soluble total nitrogen. Characterizing foaming events through frequent sampling and monitoring of specific genera and functional parameters may allow for predictions and preemptive mitigation efforts to avoid negative consequences in the future. PRACTITIONER POINTS: A reproducible method to measure foaming potential in activated sludge is available. Genera Zoogloea, Flavobacterium, Variovorax, and Bdellovibrio correlated with foaming events. A year-long sampling campaign of activated sludge measuring foaming potential and microbial community composition was conducted at South Shore Water Reclamation Facility in Oak Creek, WI. More research at other facilities with this method is needed to understand links between microbes and foaming.
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Affiliation(s)
- Grace Scarim
- Department of Civil, Construction & Environmental Engineering, Marquette University, Milwaukee, Wisconsin, USA
| | - Emily Lou LaMartina
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Kaushik Venkiteshwaran
- Department of Civil, Construction & Environmental Engineering, Marquette University, Milwaukee, Wisconsin, USA
- Department of Civil, Coastal & Environmental Engineering, University of South Alabama, Mobile, Alabama, USA
| | - Daniel H Zitomer
- Department of Civil, Construction & Environmental Engineering, Marquette University, Milwaukee, Wisconsin, USA
| | - Ryan J Newton
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Patrick J McNamara
- Department of Civil, Construction & Environmental Engineering, Marquette University, Milwaukee, Wisconsin, USA
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10
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Active predation, phylogenetic diversity, and global prevalence of myxobacteria in wastewater treatment plants. THE ISME JOURNAL 2023; 17:671-681. [PMID: 36774445 PMCID: PMC9919749 DOI: 10.1038/s41396-023-01378-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 01/25/2023] [Accepted: 01/31/2023] [Indexed: 02/13/2023]
Abstract
The operation of modern wastewater treatment plants (WWTPs) is driven by activated sludge microbiota, a complex assemblage of trophically interacting microorganisms. Microbial predation is crucial to fundamental understanding of how biological interactions drive microbiome structuring and functioning of WWTPs. However, predatory bacteria have received little attention regarding their diversity, activity, and ecological function in activated sludge, limiting the exploitation of food web interactions for wastewater microbiome engineering. Here, by using rRNA-stable isotope probing of activated sludge microbiota with 13C-labeled prey bacteria, we uncovered diverse as-yet-uncultivated putative predatory bacteria that actively incorporated 13C-biomass. Myxobacteria, especially Haliangium and the mle1-27 clade, were found as the dominant active predators, refreshing conventional views based on a few predatory isolates of Bdellovibrionota from WWTPs. The identified predatory bacteria showed more selective predation on prey compared with the protists dominated by ciliates, providing in situ evidence for inter-domain predation behavior divergence in activated sludge. Putative predatory bacteria were tracked over a two-year microbiome monitoring effort at a local WWTP, revealing the predominance of Myxococcota (6.5 ± 1.3%) over Bdellovibrionota (1.0 ± 0.2%) lineages. Phylogenetic analysis unveiled highly diverse myxobacteria inhabiting activated sludge and suggested a habitat filtering effect in global WWTPs. Further mining of a global activated sludge microbiome dataset revealed the prevalence of Myxococcota (5.4 ± 0.1%) species and potential impacts of myxobacterial predation on process performance. Collectively, our findings provided unique insights into the predating activity, diversity, and prevalence of Myxococcota species in activated sludge, highlighting their links with wastewater treatment processes via trophic regulation of enteric and functional bacteria.
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Ibrahimi M, Loqman S, Jemo M, Hafidi M, Lemee L, Ouhdouch Y. The potential of facultative predatory Actinomycetota spp. and prospects in agricultural sustainability. Front Microbiol 2023; 13:1081815. [PMID: 36762097 PMCID: PMC9905845 DOI: 10.3389/fmicb.2022.1081815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 12/28/2022] [Indexed: 01/26/2023] Open
Abstract
Actinomycetota in the phylum of bacteria has been explored extensively as a source of antibiotics and secondary metabolites. In addition to acting as plant growth-promoting agents, they also possess the potential to control various plant pathogens; however, there are limited studies that report the facultative predatory ability of Actinomycetota spp. Furthermore, the mechanisms that underline predation are poorly understood. We assessed the diversity of strategies employed by predatory bacteria to attack and subsequently induce the cell lysing of their prey. We revisited the diversity and abundance of secondary metabolite molecules linked to the different predation strategies by bacteria species. We analyzed the pros and cons of the distinctive predation mechanisms and explored their potential for the development of new biocontrol agents. The facultative predatory behaviors diverge from group attack "wolfpack," cell-to-cell proximity "epibiotic," periplasmic penetration, and endobiotic invasion to degrade host-cellular content. The epibiotic represents the dominant facultative mode of predation, irrespective of the habitat origins. The wolfpack is the second-used approach among the Actinomycetota harboring predatory traits. The secondary molecules as chemical weapons engaged in the respective attacks were reviewed. We finally explored the use of predatory Actinomycetota as a new cost-effective and sustainable biocontrol agent against plant pathogens.
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Affiliation(s)
- Manar Ibrahimi
- Laboratory of Molecular Chemistry, Materials and Catalysis, Faculty of Sciences and Technics, Sultan Moulay Slimane University, Beni-Mellal, Morocco,Higher School of Technology Fkih Ben Salah, Sultan Moulay Slimane University, Fkih Ben Salah, Morocco
| | - Souad Loqman
- Laboratory of Microbiology and Virology, Faculty of Medicine and Pharmacy, Cadi Ayyad University, Marrakesh, Morocco
| | - Martin Jemo
- AgroBiosciences Program, Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco
| | - Mohamed Hafidi
- AgroBiosciences Program, Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco,Labelled Research Unit N°4 CNRST, Laboratory of Microbial Biotechnologies, Agrosciences and Environment (BioMAgE), Faculty of Sciences Semlalia, Cadi Ayyad University, Marrakesh, Morocco
| | - Laurent Lemee
- Institut de Chimie des Milieux et Matériaux de Poitiers (IC2MP–CNRS UMR 7285), Université de Poitiers, Poitiers, France
| | - Yedir Ouhdouch
- AgroBiosciences Program, Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco,Labelled Research Unit N°4 CNRST, Laboratory of Microbial Biotechnologies, Agrosciences and Environment (BioMAgE), Faculty of Sciences Semlalia, Cadi Ayyad University, Marrakesh, Morocco,*Correspondence: Yedir Ouhdouch,
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12
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Amancio Frutuoso FK, Ferreira Dos Santos A, da Silva França LL, Mendes Barros AR, Bezerra Dos Santos A. Influence of salt addition to stimulating biopolymers production in aerobic granular sludge systems. CHEMOSPHERE 2023; 311:137006. [PMID: 36330972 DOI: 10.1016/j.chemosphere.2022.137006] [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: 07/12/2022] [Revised: 09/27/2022] [Accepted: 10/23/2022] [Indexed: 06/16/2023]
Abstract
The influence of salt addition to stimulating biopolymers production in aerobic granular sludge (AGS) systems was evaluated. The control systems (R1: acetate and R2: propionate) initially obtained less accumulation of mixed liquor volatile suspended solids (MLVSS), indicating that the osmotic pressure in the salt-supplemented systems (R3: acetate and R4: propionate) contributed to biomass growth. However, the salt-supplemented systems collapsed between days 110 and 130 of operation. R3 and R4 showed better performance regarding nutrients removal due to the greater abundance of nitrifying and denitrifying bacteria and phosphate-accumulating organisms. Salt also contributed to the higher production of biopolymers such as alginate-like exopolymers (ALE) per gram of volatile suspended solids (VSS) (R1: 397 mgALE∙gVSS-1, R2: 140 mgALE∙gVSS-1, R3: 483 mgALE∙gVSS-1, R4: 311 mgALE∙gVSS-1). Amino acids like tyrosine and tryptophan were better identified in extracellular polymeric substances extract from salt-operated reactors. This study brings important results in the context of resource recovery by treating saline effluents.
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Affiliation(s)
| | - Amanda Ferreira Dos Santos
- Department of Hydraulic and Environmental Engineering, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | | | | | - André Bezerra Dos Santos
- Department of Hydraulic and Environmental Engineering, Federal University of Ceará, Fortaleza, Ceará, Brazil.
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13
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Sousa JMG, Louvado A, Coelho FJRC, Oliveira V, Oliveira H, Cleary DFR, Gomes NCM. In vitro study of the modulatory effects of heat-killed bacterial biomass on aquaculture bacterioplankton communities. Sci Rep 2022; 12:19699. [PMID: 36385260 PMCID: PMC9669034 DOI: 10.1038/s41598-022-23439-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/31/2022] [Indexed: 11/17/2022] Open
Abstract
Recent studies have shown that the addition of non-viable microbial biomass or their components (postbiotics) to fish feed can modulate the gut microbiome and positively influence fish health in aquaculture systems. However, no information was hitherto available on the use of non-viable microbial biomass to manipulate aquaculture bacterioplankton communities. To fill this gap, here we used an in vitro model to assess the effects of heat-killed biomasses of an antagonistic strain Pseudoalteromonas rubra SubTr2 and a non-antagonist strain Escherichia coli DH5α on bacterioplankton communities of a recirculating aquaculture system (RAS). Our results showed that these biomasses can have generalist and species-specific effects on aquaculture bacterioplankton structure and function. In addition, they enriched the abundance of bacterial predators, reduced bacterial load and potentially influenced nutrient cycling and pathogen development in aquaculture water. Despite its preliminary nature, for the first time, this study showed that heat-killed microbial biomass has potential application as an in situ modulator of bacterioplankton in aquaculture systems.
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Affiliation(s)
- J. M. G. Sousa
- grid.7311.40000000123236065CESAM-Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal
| | - A. Louvado
- grid.7311.40000000123236065CESAM-Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal
| | - F. J. R. C. Coelho
- grid.7311.40000000123236065CESAM-Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal
| | - V. Oliveira
- grid.7311.40000000123236065CESAM-Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal
| | - H. Oliveira
- grid.7311.40000000123236065CESAM-Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal
| | - D. F. R. Cleary
- grid.7311.40000000123236065CESAM-Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal
| | - N. C. M. Gomes
- grid.7311.40000000123236065CESAM-Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal
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14
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Liu F, Ji M, Xiao L, Wang X, Diao Y, Dan Y, Wang H, Sang W, Zhang Y. Organics composition and microbial analysis reveal the different roles of biochar and hydrochar in affecting methane oxidation from paddy soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 843:157036. [PMID: 35772551 DOI: 10.1016/j.scitotenv.2022.157036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 06/20/2022] [Accepted: 06/24/2022] [Indexed: 06/15/2023]
Abstract
Biochar and hydrochar, as valuable and eco-friendly soil remediation materials from greenwaste, have potential to enhance methane oxidation in paddy soil. But the mechanism of biomass carbon on the improvement of methane-oxidizing bacteria communities in paddy soil has not been adequately elucidated. In the present study, the effect of different-temperature rice straw-based biomass carbon (RB400, RB600, RH250 and RH300) on methane oxidation were investigated by analyzing the soil dissolved organic matter (DOM), physicochemical properties and changes in microbial community structure. The results of the 17-day incubation experiment showed that the methane oxidation rate increased under all types of biomass carbon in the first 6 days. The enhancement of methane oxidation rate was more pronounced for biochar compared to hydrochar, with RB600 being the most effective treatment. The result of excitation-emission matrix (EEM) fluorescence spectroscopy showed that less DOM were released from the soil in the biochar treatments compared to the hydrochar treatments and protein-like were detected only in the hydrochar group. Microbial analysis further showed that hydrochar inhibited the growth of Bacillus, Methylobacter, and Methylocystis, while RB600 significantly increased the relative abundance of methanotrophs (responsible for methane oxidation), such as Methylocystis and Methylobacter, which was consistent with their different effects on the methane oxidation rate. Moreover, from the analysis of principal component analysis (PCA) and canonical correspondence analysis (CCA), Methylobacter and Methylocystis were negatively respond to H/C of biomass carbon. The present study provides a deeper understanding of the effect of biomass carbon obtained by different processes on methane oxidation when applied to soil from the perspective of organic matter and microbial communities.
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Affiliation(s)
- Feihong Liu
- Textile Pollution Controlling Engineering Center of Ministry of Environmental Protection, College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
| | - Mengyuan Ji
- Department of Biology, University of Padua, 35131 Padova, Italy
| | - Lurui Xiao
- Textile Pollution Controlling Engineering Center of Ministry of Environmental Protection, College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
| | - Xiaoxia Wang
- Textile Pollution Controlling Engineering Center of Ministry of Environmental Protection, College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
| | - Yinzhu Diao
- Textile Pollution Controlling Engineering Center of Ministry of Environmental Protection, College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
| | - Yitong Dan
- Textile Pollution Controlling Engineering Center of Ministry of Environmental Protection, College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
| | - Huan Wang
- Textile Pollution Controlling Engineering Center of Ministry of Environmental Protection, College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
| | - Wenjing Sang
- Textile Pollution Controlling Engineering Center of Ministry of Environmental Protection, College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China.
| | - Yalei Zhang
- College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
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15
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Ezzedine JA, Janicot A, Rasconi S, Domaizon I, Jacquet S. Short-Term Dynamics of Bdellovibrio and Like Organisms in Lake Geneva in Response to a Simulated Climatic Extreme Event. MICROBIAL ECOLOGY 2022; 84:717-729. [PMID: 34623462 DOI: 10.1007/s00248-021-01875-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 09/18/2021] [Indexed: 06/13/2023]
Abstract
The short time-scale dynamics of three families of Bdellovibrio and like organisms (i.e. Bdellovibrionaceae, Peredibacteraceae, and Bacteriovoracaceae) were studied on the surface waters of Lake Geneva in summer. Using mesocosms deployed nearshore in July 2019, we simulated an extreme climatic event (an input of carbon from the watershed in response to runoff from the catchment, light reduction, and mixing in response to stormy conditions) and aimed to study the impact of both abiotic and biotic factors on their dynamics. The three families of Bdellovibrio and like organisms (BALOs) showed different dynamics during the experiment. Peredibacteraceae was the most abundant group, whereas Bacteriovoracaceae was the least abundant. Compared with the other two families, the abundance of Bdellovibrionaceae did not fluctuate, remaining relatively stable over time. Environmental variables only partially explained the dynamics of these families; in particular, temperature, pH, and chloride concentrations were positively correlated with Bacteriovoracaceae, Bdellovibrionaceae, and Peredibacteraceae abundance, respectively. Prokaryote-like particles (PLPs), such as those with high DNA content (HDNA), were strongly and positively correlated with Peredibacteraceae and Bacteriovoracaceae. In contrast, no relationships were found between Bdellovibrionaceae and PLP abundance, nor between the virus-like particles (VLPs) and the different BALOs. Overall, the experiment revealed that predation was stable in the face of the simulated climatic events. In addition, we observed that Peredibacteraceae and Bacteriovoracaceae share common traits, while Bdellovibrionaceae seems to constitute a distinct category.
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Affiliation(s)
- J A Ezzedine
- Université Savoie Mont-Blanc, INRAE, UMR CARRTEL, Thonon-les-Bains, France
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, CEA, INRAE, IRIG, Université Grenoble Alpes, Grenoble, France
| | - A Janicot
- Université Savoie Mont-Blanc, INRAE, UMR CARRTEL, Thonon-les-Bains, France
| | - S Rasconi
- Université Savoie Mont-Blanc, INRAE, UMR CARRTEL, Thonon-les-Bains, France
| | - I Domaizon
- Université Savoie Mont-Blanc, INRAE, UMR CARRTEL, Thonon-les-Bains, France
| | - S Jacquet
- Université Savoie Mont-Blanc, INRAE, UMR CARRTEL, Thonon-les-Bains, France.
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16
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Xue M, Gao H, Dong X, Zhan M, Yang G, Yu R. Promotion and mechanisms of Bdellovibrio sp. Y38 on membrane fouling alleviation in membrane bioreactor. ENVIRONMENTAL RESEARCH 2022; 212:113593. [PMID: 35660406 DOI: 10.1016/j.envres.2022.113593] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/17/2022] [Accepted: 05/29/2022] [Indexed: 06/15/2023]
Abstract
Membrane fouling is a major bottleneck limiting the widespread application of membrane bioreactors (MBR). In this study, Bdellovibrio sp. Y38, an obligate bacteriophage bacterium of Bdellovibrio-and-like organisms (BALOs), was enriched into highly concentrated culture medium (106-107 PFU/mL), and daily dosed into the MBR to investigate its effects on membrane fouling mitigation. The strain Y38 prolonged the membrane fouling cycle from 73 days to 90 days, indicating its membrane fouling alleviation potentials. The concentration of BALOs was increased 625 times higher than the control group after the whole operation, resulting in the concentration of chemical oxygen demand and nucleic acids in the liquid phase of the MBR system being significantly increased by 169.8 ± 1.5% and 126.7 ± 2.2%, respectively. The biomass growth rate was reduced by 27.2 ± 0.7% from day 0 to day 54. These results indicated the predation potential of Bdellovibrio sp. Y38 on the microorganisms in the sludge. The improvement of homogenized sludge and filtration and settling performance by the strain Y38 alleviated the membrane fouling. Compared with the control group, the macromolecular proteins in SMP and EPS were partially declined, and the polysaccharide in EPS decreased by 14.0 ± 3.9%, and the ratios of protein content to polysaccharide content (PN/PS) in SMP and EPS significantly increased by 35.6 ± 16.8% and 57.8 ± 6.1% at the middle stage, respectively, indicating the strain Y38 could alleviate membrane fouling by reducing and modifying SMP and EPS. Furthermore, the relative abundance of γ-proteobacteria decreased from 13.2% to 5.1% at the pre-middle stage, and Planctomycetes decreased from 1.5% to 0.8% at the end-stage, which were probably responsible for the membrane fouling mitigation. In addition, the strain Y38 had few impacts on the water treatment performance of MBR. There findings provide a promising strategy for in situ membrane pollution mitigation via exogenous additions of BALOs.
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Affiliation(s)
- Mengting Xue
- Department of Environmental Science and Engineering, School of Energy and Environment, Southeast University, Nanjing, Jiangsu, 210096, China; Key Laboratory of Environmental Medicine Engineering, Ministry of Education, Southeast University, Nanjing, Jiangsu, 210009, China
| | - Huan Gao
- Department of Environmental Science and Engineering, School of Energy and Environment, Southeast University, Nanjing, Jiangsu, 210096, China; Key Laboratory of Environmental Medicine Engineering, Ministry of Education, Southeast University, Nanjing, Jiangsu, 210009, China
| | - Xiaona Dong
- Department of Environmental Science and Engineering, School of Energy and Environment, Southeast University, Nanjing, Jiangsu, 210096, China; Key Laboratory of Environmental Medicine Engineering, Ministry of Education, Southeast University, Nanjing, Jiangsu, 210009, China
| | - Manjun Zhan
- Nanjing Research Institute of Environmental Protection, Nanjing Environmental Protection Bureau, Nanjing, Jiangsu, 210013, China
| | - Guangping Yang
- Nanjing Chinair Envir Sci-Tech Co., Ltd., Nanjing, Jiangsu, 210019, China
| | - Ran Yu
- Department of Environmental Science and Engineering, School of Energy and Environment, Southeast University, Nanjing, Jiangsu, 210096, China; Key Laboratory of Environmental Medicine Engineering, Ministry of Education, Southeast University, Nanjing, Jiangsu, 210009, China.
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17
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Ferreira Dos Santos A, Amancio Frutuoso FK, de Amorim de Carvalho C, Sousa Aguiar Lira VN, Mendes Barros AR, Bezerra Dos Santos A. Carbon source affects the resource recovery in aerobic granular sludge systems treating wastewater. BIORESOURCE TECHNOLOGY 2022; 357:127355. [PMID: 35609753 DOI: 10.1016/j.biortech.2022.127355] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
This study evaluated the influence of carbon sources on alginate-like exopolymers (ALE) and tryptophan (Trp) biosynthesis in the aerobic granular sludge (AGS). With acetate, the highest biopolymers levels, per gram of volatile suspended solids (VSS) (418.7 mgALE∙g-1 and 4.1 mgTrp∙gVSS-1), were found likely due to biomass loss throughout the operation, which resulted in lower sludge age (4-7 days) and shorter famine period. During granulation, encouraging results on ALE production were obtained with propionate (>250 mgALE∙gVSS-1), significantly higher than those found with glycerol, glucose, and sucrose. Regarding tryptophan production, propionate and glycerol proved to be good substrates, although the content was still lower than acetate (1.6 mgTrp∙gVSS-1). Granules fed with glucose showed the worst results compared to the other substrates (38.5 mgALE∙VSS-1 and 0.6 mgTrp∙gVSS-1) due to the filamentous microorganisms' abundance found. Therefore, this study provides insights to value the production of compounds of industrial interest in AGS systems.
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Affiliation(s)
- Amanda Ferreira Dos Santos
- Department of Hydraulic and Environmental Engineering, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | | | - Clara de Amorim de Carvalho
- Department of Hydraulic and Environmental Engineering, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | | | | | - André Bezerra Dos Santos
- Department of Hydraulic and Environmental Engineering, Federal University of Ceará, Fortaleza, Ceará, Brazil.
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18
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Reproducibility of Aerobic Granules in Treating Low-Strength and Low-C/N-Ratio Wastewater and Associated Microbial Community Structure. Processes (Basel) 2022. [DOI: 10.3390/pr10030444] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Long-term stability of the aerobic granular sludge system is essentially based on the microbial community structure of the biomass. In this study, the physicochemical and microbial characteristics of sludge and wastewater treatment performance were investigated regarding formation, maturation, and long-term maintenance of granules in two parallel sequencing batch reactors (SBR), R1 and R2, under identical conditions. The aim was to explore the linkage between microbial community structure of the aerobic granules, their long-term stability, as well as the reproducibility of granulation and long-term stability. The two reactors were operated with a COD concentration of 400 mg/L and a chemical oxygen demand to nitrogen (COD/N) ratio of 4:1 under anoxic–oxic conditions. It was found that although SVI30, sludge size, and distributions in R1 and R2 were different, aerobic granules were formed, and they maintained long-term stability in both reactors for 320 days, implying that a certain level of randomness of granulation does not affect the long-term stability and performance for COD and N removal. In addition, a significant reduction in the richness and diversity of microbial production was observed after the sludge was converted from inoculum or flocs to granules, but this did not negatively affect the performance of wastewater treatment. Among the predominant microbial species in aerobic granules, Zoogloea was identified as the most important bacteria present during the whole operation with the highest abundance, while Thauera was the important genus in the formation and maturation of the aerobic granules, but it cannot be maintained long-term due to the low food-to-microorganisms ratio (F/M) in the system. In addition, some species from Ohtaekwangia, Chryseobacterium, Taibaiella, and Tahibacter were found to proliferate strongly during long-term maintenance of aerobic granules. They may play an important role in the long-term stability of aerobic granules. These results demonstrate the reproducibility of granulation, the small influence of granulation on long-term stability, and the robustness of aerobic granulation for the removal of COD and N. Overall, our study contributes significantly to the understanding of microbial community structure for the long-term stability of aerobic granular sludge in the treatment of low-COD and low-COD/N-ratio wastewater in practice.
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19
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Ogundero A, Vignola M, Connelly S, Sloan WT. Validating Flow Cytometry as a Method for Quantifying Bdellovibrio Predatory Bacteria and Its Prey for Microbial Ecology. Microbiol Spectr 2022; 10:e0103321. [PMID: 35196816 PMCID: PMC8865432 DOI: 10.1128/spectrum.01033-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 01/31/2022] [Indexed: 12/19/2022] Open
Abstract
Bdellovibrio bacteriovorus is a predatory, Gram-negative bacteria that feeds on many pathogenic bacteria and has been investigated as a possible solution for mitigating biofilms in different fields. The application depends on more fundamental ecological studies into the dynamics between Bdellovibrio and their prey. To do so requires an accurate, reliable, and, preferably rapid, way of enumerating the cells. Flow cytometry (FCM) is potentially a rapid, accurate, and inexpensive tool for this, but it has yet to be validated in the enumeration of Bdellovibrio. In this study, we developed a protocol to measure the number of Bdellovibrio in samples of various densities using FCM and compared the results with those of other methods: optical density (OD), PFU assay (PFU), and quantitative PCR (qPCR). We observed a strong correlation between values obtained using FCM and PFU (ρ = 0.923) and FCM and qPCR (ρ = 0.987). Compared to optical density there was a much weaker correlation (ρ = 0.784), which was to be expected given the well-documented uncertainty in converting optical density (OD) to cell numbers. The FCM protocol was further validated by demonstrating its ability to distinguish and count mixed populations of Bdellovibrio and the prey Pseudomonas. Thus, the accuracy of FCM as well as its speed and reproducibility make it a suitable alternative for measuring Bdellovibrio cell numbers, especially where many samples are required to capture the dynamics of predator-prey interactions. IMPORTANCE The rise of antibiotic resistance and the unwanted growth of bacteria is a universally growing problem. Predatory bacteria can be used as a biological alternative to antibiotics because they grow by feeding on other bacteria. To apply this effectively requires further study and a deeper understanding of the forces that drive a prey population to elimination. Initially, such studies require more reliable methods to count these cells. Flow cytometry (FCM) is potentially a rapid, accurate, and inexpensive tool for this, but it has yet to be validated for predatory bacteria. This study develops a protocol to count the predatory bacteria Bdellovibrio bacteriovorus and its Pseudomonas prey using FCM and compare the results with those of other methods, demonstrating its ability for studies into B. bacteriovorus predation dynamics. This could lead to the use of B. bacteriovorus for killing bacterial biofilms in fields, such as drinking water and agriculture.
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Affiliation(s)
- Ayo Ogundero
- Infrastructure and Environment, School of Engineering, University of Glasgow, Glasgow, UK
| | - Marta Vignola
- Infrastructure and Environment, School of Engineering, University of Glasgow, Glasgow, UK
| | - Stephanie Connelly
- Infrastructure and Environment, School of Engineering, University of Glasgow, Glasgow, UK
| | - William T. Sloan
- Infrastructure and Environment, School of Engineering, University of Glasgow, Glasgow, UK
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20
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Jiang L, Zhang Y, Shen Q, Mao Y, Zhang Q, Ji F. The metabolic patterns of the complete nitrates removal in the biofilm denitrification systems supported by polymer and water-soluble carbon sources as the electron donors. BIORESOURCE TECHNOLOGY 2021; 342:126002. [PMID: 34852445 DOI: 10.1016/j.biortech.2021.126002] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/14/2021] [Accepted: 09/19/2021] [Indexed: 06/13/2023]
Abstract
In this study, two denitrification bio-filters adopted polycaprolactone (PCL) and sodium acetate (NaAc) as polymer and water-soluble carbon sources respectively. With the increasing influent nitrate concentrations, NaAc bio-filter always had shorter HRT to achieve complete nitrate removal. Furthermore, the optimal volumetric denitrification rate in NaAc bio-filter was 0.728 g N/(L·d), which was higher than 0.561 g N/(L·d) in PCL bio-filter. For nitrates removal, the costs of bio-filters supported by NaAc and PCL were 24.93 and 120.25 CNY/kg N respectively. Although Proteobacteria in PCL bio-filter was abundant with 83.98%, NaAc bio-filter had better denitrification performance, due to the appropriate ratio of nitrate removal microorganisms and organic matters degradation organisms. The total abundance value of the denitrification genera is NaAc (16.06%) < PCL (41.19%). However, PCL bio-filter had poor denitrification performance, due to the lower adequacy of PCL depolymerization enzymes and the low expression of the key genes for denitrification.
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Affiliation(s)
- Lei Jiang
- Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, PR China; College of Environment and Ecology, Chongqing University, Chongqing 400045, PR China
| | - Yifang Zhang
- North China Municipal Engineering Design and Research Institute, Tianjin 300381, PR China
| | - Qiushi Shen
- Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, PR China; College of Environment and Ecology, Chongqing University, Chongqing 400045, PR China
| | - Yuanxiang Mao
- Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, PR China; College of Environment and Ecology, Chongqing University, Chongqing 400045, PR China
| | - Qian Zhang
- Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, PR China; College of Environment and Ecology, Chongqing University, Chongqing 400045, PR China
| | - Fangying Ji
- Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, PR China; College of Environment and Ecology, Chongqing University, Chongqing 400045, PR China.
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21
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Mookherjee A, Jurkevitch E. Interactions between Bdellovibrio and like organisms and bacteria in biofilms: beyond predator-prey dynamics. Environ Microbiol 2021; 24:998-1011. [PMID: 34816563 DOI: 10.1111/1462-2920.15844] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/03/2021] [Accepted: 11/08/2021] [Indexed: 12/19/2022]
Abstract
Bdellovibrio and like organisms (BALOs) prey on Gram-negative bacteria in the planktonic phase as well as in biofilms, with the ability to reduce prey populations by orders of magnitude. During the last few years, evidence has mounted for a significant ecological role for BALOs, with important implications for our understanding of microbial community dynamics as well as for applications against pathogens, including drug-resistant pathogens, in medicine, agriculture and aquaculture, and in industrial settings for various uses. However, our understanding of biofilm predation by BALOs is still very fragmentary, including gaps in their effect on biofilm structure, on prey resistance, and on evolutionary outcomes of both predators and prey. Furthermore, their impact on biofilms has been shown to reach beyond predation, as they are reported to reduce biofilm structures of non-prey cells (including Gram-positive bacteria). Here, we review the available literature on BALOs in biofilms, extending known aspects to potential mechanisms employed by the predators to grow in biofilms. Within that context, we discuss the potential ecological significance and potential future utilization of the predatory and enzymatic possibilities offered by BALOs in medical, agricultural and environmental applications.
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Affiliation(s)
- Abhirup Mookherjee
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Institute of Environmental Sciences, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Edouard Jurkevitch
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Institute of Environmental Sciences, The Hebrew University of Jerusalem, Rehovot, Israel
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22
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Clagnan E, Brusetti L, Pioli S, Visigalli S, Turolla A, Jia M, Bargna M, Ficara E, Bergna G, Canziani R, Bellucci M. Microbial community and performance of a partial nitritation/anammox sequencing batch reactor treating textile wastewater. Heliyon 2021; 7:e08445. [PMID: 34901500 PMCID: PMC8637490 DOI: 10.1016/j.heliyon.2021.e08445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 10/25/2021] [Accepted: 11/17/2021] [Indexed: 01/04/2023] Open
Abstract
Implementation of onsite bioremediation technologies is essential for textile industries due to rising concerns in terms of water resources and quality. Partial nitritation-anaerobic ammonium oxidation (PN/A) processes emerged as a valid, but unexplored, solution. In this study, the performance of a PN/A pilot-scale (9 m3) sequencing batch reactor treating digital textile printing wastewater (10-40 m3 d-1) was monitored by computing nitrogen (N) removal rate and efficiencies. Moreover, the structure of the bacterial community was assessed by next generation sequencing and quantitative polymerase chain reaction (qPCR) analyses of several genes, which are involved in the N cycle. Although anaerobic ammonium oxidation activity was inhibited and denitrification occurred, N removal rate increased from 16 to 61 mg N g VSS-1 d-1 reaching satisfactory removal efficiency (up to 70%). Ammonium (18-70 mg L-1) and nitrite (16-82 mg L-1) were detected in the effluent demonstrating an unbalance between the aerobic and anaerobic ammonia oxidation activity, while constant organic N was attributed to recalcitrant azo dyes. Ratio between nitrification and anammox genes remained stable reflecting a constant ammonia oxidation activity. A prevalence of ammonium oxidizing bacteria and denitrifiers suggested the presence of alternative pathways. PN/A resulted a promising cost-effective alternative for textile wastewater N treatment as shown by the technical-economic assessment. However, operational conditions and design need further tailoring to promote the activity of the anammox bacteria.
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Affiliation(s)
- Elisa Clagnan
- Free University of Bolzano, Faculty of Science and Technology, Piazza Università 1, 39100 Bolzano, Italy
| | - Lorenzo Brusetti
- Free University of Bolzano, Faculty of Science and Technology, Piazza Università 1, 39100 Bolzano, Italy
| | - Silvia Pioli
- Free University of Bolzano, Faculty of Science and Technology, Piazza Università 1, 39100 Bolzano, Italy
| | - Simone Visigalli
- Politecnico di Milano, Department of Civil and Environmental Engineering (DICA), Piazza L. da Vinci 32, 20133 Milano, Italy
| | - Andrea Turolla
- Politecnico di Milano, Department of Civil and Environmental Engineering (DICA), Piazza L. da Vinci 32, 20133 Milano, Italy
| | - Mingsheng Jia
- Politecnico di Milano, Department of Civil and Environmental Engineering (DICA), Piazza L. da Vinci 32, 20133 Milano, Italy
| | - Martina Bargna
- Lariana Depur Spa, Via Laghetto 1, 22073 Fino Mornasco, Italy
| | - Elena Ficara
- Politecnico di Milano, Department of Civil and Environmental Engineering (DICA), Piazza L. da Vinci 32, 20133 Milano, Italy
| | - Giovanni Bergna
- Lariana Depur Spa, Via Laghetto 1, 22073 Fino Mornasco, Italy
| | - Roberto Canziani
- Politecnico di Milano, Department of Civil and Environmental Engineering (DICA), Piazza L. da Vinci 32, 20133 Milano, Italy
| | - Micol Bellucci
- Politecnico di Milano, Department of Civil and Environmental Engineering (DICA), Piazza L. da Vinci 32, 20133 Milano, Italy
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23
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Ezzedine JA, Desdevises Y, Jacquet S. Bdellovibrio and like organisms: current understanding and knowledge gaps of the smallest cellular hunters of the microbial world. Crit Rev Microbiol 2021; 48:428-449. [PMID: 34595998 DOI: 10.1080/1040841x.2021.1979464] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Almost sixty years ago, Bdellovibrio and like organisms (BALOs) were discovered as the first obligate bacterial predators of other bacteria known to science. Since then, they were shown to be diverse and ubiquitous in the environment, and to bear astonishing ecological, physiological, and metabolic capabilities. The last decade has seen important strides made in understanding the mechanistic basis of their life cycle, the dynamics of their interactions with prey, along with significant developments towards their use in medicine, agriculture, and industry. This review details these achievements, identify current understanding and knowledge gaps to encourage and guide future BALO research.
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Affiliation(s)
- Jade A Ezzedine
- Université Savoie Mont-Blanc, INRAE, CARRTEL, Thonon-les-Bains, France.,Laboratoire de Physiologie Cellulaire et Végétale, CNRS, CEA, INRAE, IRIG, Université Grenoble Alpes, Grenoble, France
| | - Yves Desdevises
- CNRS, Biologie Intégrative des Organismes Marins, Observatoire Océanologique, Sorbonne Université, Banyuls-sur-Mer, France
| | - Stéphan Jacquet
- Université Savoie Mont-Blanc, INRAE, CARRTEL, Thonon-les-Bains, France
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24
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Cohen Y, Pasternak Z, Müller S, Hübschmann T, Schattenberg F, Sivakala KK, Abed-Rabbo A, Chatzinotas A, Jurkevitch E. Community and single cell analyses reveal complex predatory interactions between bacteria in high diversity systems. Nat Commun 2021; 12:5481. [PMID: 34531395 PMCID: PMC8446003 DOI: 10.1038/s41467-021-25824-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 08/25/2021] [Indexed: 02/08/2023] Open
Abstract
A fundamental question in community ecology is the role of predator-prey interactions in food-web stability and species coexistence. Although microbial microcosms offer powerful systems to investigate it, interrogating the environment is much more arduous. Here, we show in a 1-year survey that the obligate predators Bdellovibrio and like organisms (BALOs) can regulate prey populations, possibly in a density-dependent manner, in the naturally complex, species-rich environments of wastewater treatment plants. Abundant as well as rarer prey populations are affected, leading to an oscillating predatory landscape shifting at various temporal scales in which the total population remains stable. Shifts, along with differential prey range, explain co-existence of the numerous predators through niche partitioning. We validate these sequence-based findings using single-cell sorting combined with fluorescent hybridization and community sequencing. Our approach should be applicable for deciphering community interactions in other systems.
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Affiliation(s)
- Yossi Cohen
- Department of Plant Pathology and Microbiology, Institute of Environmental Sciences, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 76100, Israel
| | - Zohar Pasternak
- Department of Plant Pathology and Microbiology, Institute of Environmental Sciences, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 76100, Israel
- Division of Identification and Forensic Science, Israel Police, National Headquarters, Jerusalem, Israel
| | - Susann Müller
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318, Leipzig, Germany
| | - Thomas Hübschmann
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318, Leipzig, Germany
| | - Florian Schattenberg
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318, Leipzig, Germany
| | - Kunjukrishnan Kamalakshi Sivakala
- Department of Plant Pathology and Microbiology, Institute of Environmental Sciences, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 76100, Israel
| | | | - Antonis Chatzinotas
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318, Leipzig, Germany
- Institute of Biology, Leipzig University, Talstrasse 33, 04103, Leipzig, Germany
- Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany
| | - Edouard Jurkevitch
- Department of Plant Pathology and Microbiology, Institute of Environmental Sciences, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 76100, Israel.
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25
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Sathyamoorthy R, Huppert A, Kadouri DE, Jurkevitch E. Effects of the prey landscape on the fitness of the bacterial predators Bdellovibrio and like organisms. FEMS Microbiol Ecol 2021; 97:6178867. [PMID: 33739375 DOI: 10.1093/femsec/fiab047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 03/17/2021] [Indexed: 11/12/2022] Open
Abstract
Bdellovibrio and like organisms (BALOs) are obligate predatory bacteria commonly encountered in the environment. In dual predator-prey cultures, prey accessibility ensures optimal feeding and replication and rapid BALO population growth. However, the environmental prey landscape is complex, as it also incorporates non-prey cells and other particles. These may act as decoys, generating unproductive encounters which in turn may affect both predator and prey population dynamics. In this study, we hypothesized that increasing decoy:prey ratios would bring about increasing costs on the predator's reproductive fitness. We also tested the hypothesis that different BALOs and decoys would have different effects. To this end, we constructed prey landscapes including periplasmic or epibiotic predators including two types of decoy under a large range of initial decoy:prey ratio, and mixed cultures containing multiple predators and prey. We show that as decoy:prey ratios increase, the maximal predator population sizes is reduced and the time to reach it significantly increases. We found that BALOs spent less time handling non-prey (including superinfection-immune invaded prey) than prey cells, and did not differentiate between efficient and less efficient prey. This may explain why in multiple predator and prey cultures, less preferred prey appear to act as decoy.
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Affiliation(s)
- Rajesh Sathyamoorthy
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 76100, Israel
| | - Amit Huppert
- Bio-statistical Unit, The Gertner Institute for Epidemiology and Health Policy Research, Chaim Sheba Medical Center, Tel Hashomer, Israel
| | - Daniel E Kadouri
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ, USA
| | - Edouard Jurkevitch
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 76100, Israel
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26
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Qian H, Hou C, Liao H, Wang L, Han S, Peng S, Chen W, Huang Q, Luo X. The species evenness of "prey" bacteria correlated with Bdellovibrio-and-like-organisms (BALOs) in the microbial network supports the biomass of BALOs in a paddy soil. FEMS Microbiol Ecol 2021; 96:5911575. [PMID: 32975583 DOI: 10.1093/femsec/fiaa195] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 09/23/2020] [Indexed: 11/14/2022] Open
Abstract
To seek how soil biotic and abiotic factors which might shape the Bdellovibrio-and-like-organisms community, we sampled paddy soils under different fertilization treatments including fertilization without nitrogen (Control), the nitrogen use treatment (N) and the nitrogen overuse one (HNK) at three rice growing stages. The abundances of BALOs were impacted by the rice-growing stages but not the fertilization treatments. The abundances of Bdellovibrionaceae-like were positively associated with soil moisture, which showed a negative relationship with Bacteriovoracaceae-like bacteria. High-throughput sequencing analysis of the whole bacterial community revealed that the α-diversity of BALOs was not correlated with any soil properties data. Network analysis detected eight families directly linked to BALOs, namely, Pseudomonadaceae, Peptostreptococcaceae, Flavobacteriaceae, Sediment-4, Verrucomicrobiaceae, OM27, Solirubrobacteraceae and Roseiflexaceae. The richness and composition of OTUs in the eight families were correlated with different soil properties, while the evenness of them had a positive effect on the predicted BALO biomass. These results highlighted that the bottom-up control of BALOs in paddy soil at least partially relied on the changes of soil water content and the diversity of bacteria directly linked to BALOs in the microbial network.
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Affiliation(s)
- Hang Qian
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.,Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Chunli Hou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.,Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Hao Liao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.,Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Li Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.,Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Shun Han
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.,College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Shaobing Peng
- Crop Physiology and Production Center (CPPC), College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Wenli Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.,College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiaoyun Huang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.,Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Xuesong Luo
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.,Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
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27
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Chan SH, Ismail MH, Tan CH, Rice SA, McDougald D. Microbial predation accelerates granulation and modulates microbial community composition. BMC Microbiol 2021; 21:91. [PMID: 33773594 PMCID: PMC8004422 DOI: 10.1186/s12866-021-02156-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 03/08/2021] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Bacterial communities are responsible for biological nutrient removal and flocculation in engineered systems such as activated floccular sludge. Predators such as bacteriophage and protozoa exert significant predation pressure and cause bacterial mortality within these communities. However, the roles of bacteriophage and protozoan predation in impacting granulation process remain limited. Recent studies hypothesised that protozoa, particularly sessile ciliates, could have an important role in granulation as these ciliates were often observed in high abundance on surfaces of granules. Bacteriophages were hypothesized to contribute to granular stability through bacteriophage-mediated extracellular DNA release by lysing bacterial cells. This current study investigated the bacteriophage and protozoan communities throughout the granulation process. In addition, the importance of protozoan predation during granulation was also determined through chemical killing of protozoa in the floccular sludge. RESULTS Four independent bioreactors seeded with activated floccular sludge were operated for aerobic granulation for 11 weeks. Changes in the phage, protozoa and bacterial communities were characterized throughout the granulation process. The filamentous phage, Inoviridae, increased in abundance at the initiation phase of granulation. However, the abundance shifted towards lytic phages during the maturation phase. In contrast, the abundance and diversity of protozoa decreased initially, possibly due to the reduction in settling time and subsequent washout. Upon the formation of granules, ciliated protozoa from the class Oligohymenophorea were the dominant group of protozoa based on metacommunity analysis. These protozoa had a strong, positive-correlation with the initial formation of compact aggregates prior to granule development. Furthermore, chemical inhibition of these ciliates in the floccular sludge delayed the initiation of granule formation. Analysis of the bacterial communities in the thiram treated sludge demonstrated that the recovery of 'Candidatus Accumulibacter' was positively correlated with the formation of compact aggregates and granules. CONCLUSION Predation by bacteriophage and protozoa were positively correlated with the formation of aerobic granules. Increases in Inoviridae abundance suggested that filamentous phages may promote the structural formation of granules. Initiation of granules formation was delayed due to an absence of protozoa after chemical treatment. The presence of 'Candidatus Accumulibacter' was necessary for the formation of granules in the absence of protozoa.
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Affiliation(s)
- Siew Herng Chan
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
- Interdisciplinary Graduate School, Nanyang Technological University, Singapore, Singapore
| | - Muhammad Hafiz Ismail
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Chuan Hao Tan
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
- School of Materials Science and Engineering, Nanyang Technological University, Singapore, Singapore
| | - Scott A Rice
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
- The iThree Institute, University of Technology Sydney, Sydney, Australia.
| | - Diane McDougald
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
- The iThree Institute, University of Technology Sydney, Sydney, Australia.
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28
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Abstract
Freshwater iron mats are dynamic geochemical environments with broad ecological diversity, primarily formed by the iron-oxidizing bacteria. The community features functional groups involved in biogeochemical cycles for iron, sulfur, carbon, and nitrogen. Despite this complexity, iron mat communities provide an excellent model system for exploring microbial ecological interactions and ecological theories in situ Syntrophies and competition between the functional groups in iron mats, how they connect cycles, and the maintenance of these communities by taxons outside bacteria (the eukaryota, archaea, and viruses) have been largely unstudied. Here, we review what is currently known about freshwater iron mat communities, the taxa that reside there, and the interactions between these organisms, and we propose ways in which future studies may uncover exciting new discoveries. For example, the archaea in these mats may play a greater role than previously thought as they are diverse and widespread in iron mats based on 16S rRNA genes and include methanogenic taxa. Studies with a holistic view of the iron mat community members focusing on their diverse interactions will expand our understanding of community functions, such as those involved in pollution removal. To begin addressing questions regarding the fundamental interactions and to identify the conditions in which they occur, more laboratory culturing techniques and coculture studies, more network and keystone species analyses, and the expansion of studies to more freshwater iron mat systems are necessary. Increasingly accessible bioinformatic, geochemical, and culturing tools now open avenues to address the questions that we pose herein.
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Affiliation(s)
- Chequita N Brooks
- Department of Biology, East Carolina University, Greenville, North Carolina, USA
| | - Erin K Field
- Department of Biology, East Carolina University, Greenville, North Carolina, USA
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29
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Sathyamoorthy R, Kushmaro Y, Rotem O, Matan O, Kadouri DE, Huppert A, Jurkevitch E. To hunt or to rest: prey depletion induces a novel starvation survival strategy in bacterial predators. ISME JOURNAL 2020; 15:109-123. [PMID: 32884113 DOI: 10.1038/s41396-020-00764-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 08/12/2020] [Accepted: 08/25/2020] [Indexed: 02/06/2023]
Abstract
The small size of bacterial cells necessitates rapid adaption to sudden environmental changes. In Bdellovibrio bacteriovorus, an obligate predator of bacteria common in oligotrophic environments, the non-replicative, highly motile attack phase (AP) cell must invade a prey to ensure replication. AP cells swim fast and respire at high rates, rapidly consuming their own contents. How the predator survives in the absence of prey is unknown. We show that starvation for prey significantly alters swimming patterns and causes exponential decay in prey-searching cells over hours, until population-wide swim-arrest. Swim-arrest is accompanied by changes in energy metabolism, enabling rapid swim-reactivation upon introduction of prey or nutrients, and a sweeping change in gene expression and gene regulation that largely differs from those of the paradigmatic stationary phase. Swim-arrest is costly as it imposes a fitness penalty in the form of delayed growth. We track the control of the swim arrest-reactivation process to cyclic-di-GMP (CdG) effectors, including two motility brakes. CRISPRi transcriptional inactivation, and in situ localization of the brakes to the cell pole, demonstrated their essential role for effective survival under prey-induced starvation. Thus, obligate predators evolved a unique CdG-controlled survival strategy, enabling them to sustain their uncommon lifestyle under fluctuating prey supply.
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Affiliation(s)
- Rajesh Sathyamoorthy
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, 76100, Rehovot, Israel
| | - Yuval Kushmaro
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, 76100, Rehovot, Israel
| | - Or Rotem
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, 76100, Rehovot, Israel.,Seed-x., Magshimim, Israel
| | - Ofra Matan
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, 76100, Rehovot, Israel
| | - Daniel E Kadouri
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ, USA
| | - Amit Huppert
- Bio-statistical Unit, The Gertner Institute for Epidemiology and Health Policy Research, Chaim Sheba Medical Center, Tel Hashomer, Israel
| | - Edouard Jurkevitch
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, 76100, Rehovot, Israel.
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30
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Albright MBN, Thompson J, Kroeger ME, Johansen R, Ulrich DEM, Gallegos-Graves LV, Munsky B, Dunbar J. Differences in substrate use linked to divergent carbon flow during litter decomposition. FEMS Microbiol Ecol 2020; 96:5867763. [DOI: 10.1093/femsec/fiaa135] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 07/02/2020] [Indexed: 12/20/2022] Open
Abstract
ABSTRACT
Discovering widespread microbial processes that create variation in soil carbon (C) cycling within ecosystems may improve soil C modeling. Toward this end, we screened 206 soil communities decomposing plant litter in a common garden microcosm environment and examined features linked to divergent patterns of C flow. C flow was measured as carbon dioxide (CO2) and dissolved organic carbon (DOC) from 44-days of litter decomposition. Two large groups of microbial communities representing ‘high’ and ‘low’ DOC phenotypes from original soil and 44-day microcosm samples were down-selected for fungal and bacterial profiling. Metatranscriptomes were also sequenced from a smaller subset of communities in each group. The two groups exhibited differences in average rate of CO2 production, demonstrating that the divergent patterns of C flow arose from innate functional constraints on C metabolism, not a time-dependent artefact. To infer functional constraints, we identified features – traits at the organism, pathway or gene level – linked to the high and low DOC phenotypes using RNA-Seq approaches and machine learning approaches. Substrate use differed across the high and low DOC phenotypes. Additional features suggested that divergent patterns of C flow may be driven in part by differences in organism interactions that affect DOC abundance directly or indirectly by controlling community structure.
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Affiliation(s)
- Michaeline B N Albright
- Biosciences Division, Los Alamos National Laboratory, Mailstop M888, Los Alamos, NM 87545, USA
| | - Jaron Thompson
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO 80523, USA
| | - Marie E Kroeger
- Biosciences Division, Los Alamos National Laboratory, Mailstop M888, Los Alamos, NM 87545, USA
| | - Renee Johansen
- Biosciences Division, Los Alamos National Laboratory, Mailstop M888, Los Alamos, NM 87545, USA
| | - Danielle E M Ulrich
- Biosciences Division, Los Alamos National Laboratory, Mailstop M888, Los Alamos, NM 87545, USA
| | | | - Brian Munsky
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO 80523, USA
- School of Biomedical Engineering, Colorado State University, Fort Collins, CO 80523, USA
| | - John Dunbar
- Biosciences Division, Los Alamos National Laboratory, Mailstop M888, Los Alamos, NM 87545, USA
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31
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Zhang S, Li B, Yu Z, Meng F. Aggregate size-dependence of bacterial community separation in a full-scale membrane bioreactor plant. FEMS Microbiol Ecol 2020; 96:5818762. [PMID: 32275301 DOI: 10.1093/femsec/fiaa060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 04/02/2020] [Indexed: 11/13/2022] Open
Abstract
The size of bacterial aggregates can determine both nutrient removal and sludge/water separation in activated sludge processes. In this study, the bacterial community structures and network associations of different sized aggregates obtained from a full-scale membrane bioreactor plant over a one-year period were investigated. Our results showed that biodiversity of larger sized aggregates was significantly higher than that of smaller ones and that the bacterial compositions of different sized aggregates differed significantly from each other. Bacteria related to nutrient removal (e.g. denitrification, hydrolysis and fermentation) were found to be significantly more abundant in larger aggregates than smaller ones. Network analysis revealed significant difference in species-species interactions, topological roles of individual OTU and keystone populations among different sized aggregates. Moreover, the occurrence of keystone OTUs affiliated with denitrifiers (Thermomonas) in networks of large and medium aggregates may suggest that denitrification influences bacterial interactions in large and medium aggregates. Overall, our results indicate the aggregates size-dependence of bacterial community separation in activated sludge. The current findings not only can provide guidance for process design and operation optimization, but also highlight the necessity for paying more attentions to the aggregate-based community, metabolic function and gene expression of activated sludge in future studies.
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Affiliation(s)
- Shaoqing Zhang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China.,Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology (Sun Yat-sen University), Guangzhou 510275, PR China
| | - Bing Li
- Division of Energy and Environment, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, PR China
| | - Zhong Yu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China.,Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology (Sun Yat-sen University), Guangzhou 510275, PR China
| | - Fangang Meng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China.,Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology (Sun Yat-sen University), Guangzhou 510275, PR China
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32
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Bratanis E, Andersson T, Lood R, Bukowska-Faniband E. Biotechnological Potential of Bdellovibrio and Like Organisms and Their Secreted Enzymes. Front Microbiol 2020; 11:662. [PMID: 32351487 PMCID: PMC7174725 DOI: 10.3389/fmicb.2020.00662] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 03/23/2020] [Indexed: 02/01/2023] Open
Abstract
Bdellovibrio and like organisms (BALOs) are obligate predatory bacteria that selectively prey on a broad range of Gram-negative bacteria, including multidrug-resistant human pathogens. Due to their unique lifestyle, they have been long recognized as a potential therapeutic and biocontrol agent. Research on BALOs has rapidly grown over the recent decade, resulting in many publications concerning molecular details of bacterial predation as well as applications thereof in medicine and biotechnology. This review summarizes the current knowledge on biotechnological potential of obligate predatory bacteria and their secreted enzymes.
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Affiliation(s)
- Eleni Bratanis
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Tilde Andersson
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Rolf Lood
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Ewa Bukowska-Faniband
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden
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Separating and Characterizing Functional Nitrogen Degraders via Magnetic Nanoparticle-Mediated Isolation. J CHEM-NY 2020. [DOI: 10.1155/2020/1841364] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Magnetic nanoparticle-mediated isolation (MMI) is a new method for isolating active functional microbes from complex microorganisms without substrate labeling. In this study, the composition and properties of magnetic nanoparticles (MNPs) were characterized by a number of techniques, indicating that MNPs have characteristics such as microinterfaces and can be efficiently fixed on the surface of microbial cells. It also introduced the MMI technology in activated sludge after stable long-term treatment. With further addition of promotor carbon sources, the enrichment of the functional nitrogen degraders in MMI was significantly higher than in samples without MNPs, showing the advantages of MMI in identifying the active degraders. Redundancy analysis (RDA) also showed that the functional nitrogen degraders such as Comamonadaceae_unclassified and Thiobacillus absolutely dominated in situ ammonia degradation, and the change in dominant genera had the same trend as the degradation rate of ammonia nitrogen. In the magnetically functionalized system, the separated functional nitrogen degraders significantly improved ammonia nitrogen degradation efficiency, making it basically stable at more than 80%, up to 91.6%. These results prove that the complex flora created after the addition of MNPs is more adaptable to newly introduced pollutants, and MMI is a powerful tool for studying pollutant-degrading microorganisms under in situ conditions.
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Macey MC, Pratscher J, Crombie AT, Murrell JC. Impact of plants on the diversity and activity of methylotrophs in soil. MICROBIOME 2020; 8:31. [PMID: 32156318 PMCID: PMC7065363 DOI: 10.1186/s40168-020-00801-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 02/10/2020] [Indexed: 05/16/2023]
Abstract
BACKGROUND Methanol is the second most abundant volatile organic compound in the atmosphere, with the majority produced as a metabolic by-product during plant growth. There is a large disparity between the estimated amount of methanol produced by plants and the amount which escapes to the atmosphere. This may be due to utilisation of methanol by plant-associated methanol-consuming bacteria (methylotrophs). The use of molecular probes has previously been effective in characterising the diversity of methylotrophs within the environment. Here, we developed and applied molecular probes in combination with stable isotope probing to identify the diversity, abundance and activity of methylotrophs in bulk and in plant-associated soils. RESULTS Application of probes for methanol dehydrogenase genes (mxaF, xoxF, mdh2) in bulk and plant-associated soils revealed high levels of diversity of methylotrophic bacteria within the bulk soil, including Hyphomicrobium, Methylobacterium and members of the Comamonadaceae. The community of methylotrophic bacteria captured by this sequencing approach changed following plant growth. This shift in methylotrophic diversity was corroborated by identification of the active methylotrophs present in the soils by DNA stable isotope probing using 13C-labelled methanol. Sequencing of the 16S rRNA genes and construction of metagenomes from the 13C-labelled DNA revealed members of the Methylophilaceae as highly abundant and active in all soils examined. There was greater diversity of active members of the Methylophilaceae and Comamonadaceae and of the genus Methylobacterium in plant-associated soils compared to the bulk soil. Incubating growing pea plants in a 13CO2 atmosphere revealed that several genera of methylotrophs, as well as heterotrophic genera within the Actinomycetales, assimilated plant exudates in the pea rhizosphere. CONCLUSION In this study, we show that plant growth has a major impact on both the diversity and the activity of methanol-utilising methylotrophs in the soil environment, and thus, the study contributes significantly to efforts to balance the terrestrial methanol and carbon cycle. Video abstract.
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Affiliation(s)
- Michael C. Macey
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ UK
- AstrobiologyOU, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, Buckinghamshire MK7 6AA UK
| | - Jennifer Pratscher
- The Lyell Centre, School of Energy, Geoscience, Infrastructure and Society, Heriot-Watt University, Research Avenue South, Edinburgh, EH14 4AP UK
| | - Andrew T. Crombie
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ UK
| | - J. Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ UK
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Williams LE, Cullen N, DeGiorgis JA, Martinez KJ, Mellone J, Oser M, Wang J, Zhang Y. Variation in genome content and predatory phenotypes between Bdellovibrio sp. NC01 isolated from soil and B. bacteriovorus type strain HD100. MICROBIOLOGY (READING, ENGLAND) 2019; 165:1315-1330. [PMID: 31592759 PMCID: PMC7137782 DOI: 10.1099/mic.0.000861] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 09/20/2019] [Indexed: 12/23/2022]
Abstract
Defining phenotypic and associated genotypic variation among Bdellovibrio may further our understanding of how this genus attacks and kills different Gram-negative bacteria. We isolated Bdellovibrio sp. NC01 from soil. Analysis of 16S rRNA gene sequences and average amino acid identity showed that NC01 belongs to a different species than the type species bacteriovorus. By clustering amino acid sequences from completely sequenced Bdellovibrio and comparing the resulting orthologue groups to a previously published analysis, we defined a 'core genome' of 778 protein-coding genes and identified four protein-coding genes that appeared to be missing only in NC01. To determine how horizontal gene transfer (HGT) may have impacted NC01 genome evolution, we performed genome-wide comparisons of Bdellovibrio nucleotide sequences, which indicated that eight NC01 genomic regions were likely acquired by HGT. To investigate how genome variation may impact predation, we compared protein-coding gene content between NC01 and the B. bacteriovorus type strain HD100, focusing on genes implicated as important in successful killing of prey. Of these, NC01 is missing ten genes that may play roles in lytic activity during predation. Compared to HD100, NC01 kills fewer tested prey strains and kills Escherichia coli ML35 less efficiently. NC01 causes a smaller log reduction in ML35, after which the prey population recovers and the NC01 population decreases. In addition, NC01 forms turbid plaques on lawns of E. coli ML35, in contrast to clear plaques formed by HD100. Linking phenotypic variation in interactions between Bdellovibrio and Gram-negative bacteria with underlying Bdellovibrio genome variation is valuable for understanding the ecological significance of predatory bacteria and evaluating their effectiveness in clinical applications.
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Affiliation(s)
| | - Nicole Cullen
- Department of Biology, Providence College, Providence, RI, USA
| | - Joseph A. DeGiorgis
- Department of Biology, Providence College, Providence, RI, USA
- Cellular Dynamics Program, Marine Biological Laboratory, Woods Hole, MA, USA
| | | | - Justina Mellone
- Department of Biology, Providence College, Providence, RI, USA
| | - Molly Oser
- Department of Biology, Providence College, Providence, RI, USA
| | - Jing Wang
- Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, Kingston, RI, USA
| | - Ying Zhang
- Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, Kingston, RI, USA
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36
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Cinà P, Bacci G, Arancio W, Gallo G, Fani R, Puglia AM, Di Trapani D, Mannina G. Assessment and characterization of the bacterial community structure in advanced activated sludge systems. BIORESOURCE TECHNOLOGY 2019; 282:254-261. [PMID: 30870691 DOI: 10.1016/j.biortech.2019.03.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 03/02/2019] [Accepted: 03/04/2019] [Indexed: 06/09/2023]
Abstract
The present study is aimed to assess and characterize the structure of bacterial community in advanced activated sludge systems. In particular, activated sludge samples were collected from an Integrated Fixed-film Activated Sludge - Membrane Bioreactor pilot plant under a University of Cape Town configuration with in-series anaerobic (Noair)/anoxic (Anox)/aerobic (Oxy) reactors - and further analyzed. The achieved results - based on Next Generation Sequencing (NGS) of 16S rDNA amplicons - revealed that the bacterial biofilm (bf) communities on plastic carriers of Oxy and Anox reactors had a greater diversity compared to suspended (sp) bacterial flocs of Oxy, Anox and Noair. Indeed, the Shannon diversity indices of both biofilm communities were higher than those of suspended growth samples (Oxy-bf = 4.1 and Anox-bf = 4.2 vs. Oxy-sp = 3.4, Anox-sp = 3.5 and Noair-sp = 3.4). The most striking differences have been reported in Rhodobacteraceae being more abundant in biofilm specimens than in suspended biomass samples. The vast majority of the identified bacteria differs from those obtained by culture dependent method, thus suggesting that NGS-based method is really suitable to analyze the bacterial community composition, even in advanced systems for wastewater treatment.
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Affiliation(s)
- Paolo Cinà
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche, Università di Palermo, Viale delle Scienze, Ed. 16, 90100 Palermo, Italy
| | - Giovanni Bacci
- Dipartimento di Biologia, Università di Firenze, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy
| | - Walter Arancio
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche, Università di Palermo, Viale delle Scienze, Ed. 16, 90100 Palermo, Italy
| | - Giuseppe Gallo
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche, Università di Palermo, Viale delle Scienze, Ed. 16, 90100 Palermo, Italy
| | - Renato Fani
- Dipartimento di Biologia, Università di Firenze, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy
| | - Anna Maria Puglia
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche, Università di Palermo, Viale delle Scienze, Ed. 16, 90100 Palermo, Italy
| | - Daniele Di Trapani
- Dipartimento di Ingegneria, Università di Palermo, Viale delle Scienze, Ed. 8, 90100 Palermo, Italy
| | - Giorgio Mannina
- Dipartimento di Ingegneria, Università di Palermo, Viale delle Scienze, Ed. 8, 90100 Palermo, Italy.
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Worrich A, Musat N, Harms H. Associational effects in the microbial neighborhood. ISME JOURNAL 2019; 13:2143-2149. [PMID: 31114015 DOI: 10.1038/s41396-019-0444-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 05/08/2019] [Accepted: 05/08/2019] [Indexed: 11/09/2022]
Abstract
Even though "perfect" metagenomes or metatranscriptomes are close at hand, the implicit assumption of spatial homogeneity in the "omic" approaches makes it difficult if not impossible to relate those data to ecological processes occurring in natural and man-made ecosystems. In fact, the distribution of microbes in their habitats is far from being uniform and random. Microbial communities show a high degree of spatial organization that stems from environmental gradients and local interactions. These interactions can be very complex and may involve multiple species. Several studies highlighted the importance of indirect interactions for community stability, but the absence of a theoretical framework for microbial ecology restricts the possibilities to strike a balance between the investigation of simple communities with purely pairwise interactions and the attempts to understand interaction patterns in whole communities based on meta-omics studies. Here we suggest adapting the concept of Associational Effects (AE) from plant ecology, to better understand the link between ecological interactions, spatial arrangement, and stability in microbial communities. By bringing together a conceptual framework developed for plants and observations made for microbes, this perspective article fosters synthesis of related disciplines to yield novel insights into the advancing field of spatial microbial ecology. To promote the integration into microbial ecology, we (i) outline the theoretical background of AE, (ii) collect underlying mechanisms by literature synthesis, (iii) propose a three-point roadmap for the investigation of AE in microbial communities, and (iv) discuss its implications for microbial ecology research.
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Affiliation(s)
- Anja Worrich
- Department of Environmental Microbiology, UFZ - Helmholtz Centre for Environmental Research, Permoserstrasse 15, 04318, Leipzig, Germany.
| | - Niculina Musat
- Department of Isotope Biogeochemistry, UFZ - Helmholtz Centre for Environmental Research, Permoserstrasse 15, 04318, Leipzig, Germany
| | - Hauke Harms
- Department of Environmental Microbiology, UFZ - Helmholtz Centre for Environmental Research, Permoserstrasse 15, 04318, Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany
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Kpan TF, Ernst R, Kouassi PK, Rödel M. Prevalence of endoparasitic mites on four West African leaf‐litter frogs depends on habitat humidity. Biotropica 2019. [DOI: 10.1111/btp.12649] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Tokouaho Flora Kpan
- Museum für Naturkunde – Leibniz Institute for Evolution and Biodiversity Science Berlin Germany
- Centre Suisse de Recherche Scientifique Abidjan Côte d´Ivoire
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research – BBIB Berlin Germany
| | - Raffael Ernst
- Museum of ZoologySenckenberg Natural History Collections Dresden Dresden Germany
| | - Philippe K. Kouassi
- U.F.R BiosciencesLaboratory of ZoologyUniversity Félix Houphoüet‐Boigny of Cocody Abidjan Côte d´Ivoire
| | - Mark‐Oliver Rödel
- Museum für Naturkunde – Leibniz Institute for Evolution and Biodiversity Science Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research – BBIB Berlin Germany
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Miura T, Sánchez R, Castañeda LE, Godoy K, Barbosa O. Shared and unique features of bacterial communities in native forest and vineyard phyllosphere. Ecol Evol 2019; 9:3295-3305. [PMID: 30962893 PMCID: PMC6434556 DOI: 10.1002/ece3.4949] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Accepted: 12/31/2018] [Indexed: 01/06/2023] Open
Abstract
Phyllosphere bacteria have received little attention despite their important roles in shaping plant performance traits. In this study, we characterize the bacterial communities on leaves of native trees inhabiting sclerophyllous forests in central Chile, one of the world's biodiversity hotspots. Additionally, we provide profiles of bacterial communities on grape leaves and berries of organic and conventional vineyards. Results of 16S rRNA gene amplicon sequence analysis showed that 45% of OTUs were shared across forest leaves, grape leaves, and grape berries. Conventional management had higher number of OTUs shared with forest leaves than organic management. In addition, grape leaves subjected to conventional management had higher alpha diversity than those with organic management, while no significant effect of agricultural management was observed in grape berries. Indicator analysis showed that Bdellovibrio, Beijerinckia, and Spirosoma were typical for forest leaves, whereas Enhydrobacter, Delftia, Proteiniclasticum, Arsenicicoccus, and Alkaliphilus were typical for the vineyard phyllosphere. Regarding agricultural managements, Beijerinckia, Sedimentibacter, Nesterenkonia, Gluconobacter, Conexibacter, and Anaeromyxobacter were typical for conventional grape leaves, whereas no genus-level indicator was found for organic vineyard leaves. These results provide new insights of the diversity patterns of the phyllosphere microbiome in native and cultivated lands and suggest that both of these microbiomes are connected and integrated systems.
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Affiliation(s)
- Toshiko Miura
- Instituto de Ecología & Biodiversidad (IEB‐Chile)SantiagoChile
- Research Institute of Environment, Agriculture and FisheriesOsakaJapan
| | - Roland Sánchez
- Instituto de Ecología & Biodiversidad (IEB‐Chile)SantiagoChile
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de CienciasUniversidad Austral de ChileValdiviaChile
| | - Luis E. Castañeda
- Programa de Genética Humana, Instituto de Ciencias Biomédicas, Facultad de MedicinaUniversidad de ChileSantiagoChile
| | - Karina Godoy
- Instituto de Ecología & Biodiversidad (IEB‐Chile)SantiagoChile
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de CienciasUniversidad Austral de ChileValdiviaChile
| | - Olga Barbosa
- Instituto de Ecología & Biodiversidad (IEB‐Chile)SantiagoChile
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de CienciasUniversidad Austral de ChileValdiviaChile
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