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Singh A, Müller B, Schnürer A. Profiling temporal dynamics of acetogenic communities in anaerobic digesters using next-generation sequencing and T-RFLP. Sci Rep 2021; 11:13298. [PMID: 34168213 PMCID: PMC8225771 DOI: 10.1038/s41598-021-92658-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 06/14/2021] [Indexed: 02/06/2023] Open
Abstract
Acetogens play a key role in anaerobic degradation of organic material and in maintaining biogas process efficiency. Profiling this community and its temporal changes can help evaluate process stability and function, especially under disturbance/stress conditions, and avoid complete process failure. The formyltetrahydrofolate synthetase (FTHFS) gene can be used as a marker for acetogenic community profiling in diverse environments. In this study, we developed a new high-throughput FTHFS gene sequencing method for acetogenic community profiling and compared it with conventional terminal restriction fragment length polymorphism of the FTHFS gene, 16S rRNA gene-based profiling of the whole bacterial community, and indirect analysis via 16S rRNA profiling of the FTHFS gene-harbouring community. Analyses and method comparisons were made using samples from two laboratory-scale biogas processes, one operated under stable control and one exposed to controlled overloading disturbance. Comparative analysis revealed satisfactory detection of the bacterial community and its changes for all methods, but with some differences in resolution and taxonomic identification. FTHFS gene sequencing was found to be the most suitable and reliable method to study acetogenic communities. These results pave the way for community profiling in various biogas processes and in other environments where the dynamics of acetogenic bacteria have not been well studied.
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Affiliation(s)
- Abhijeet Singh
- grid.6341.00000 0000 8578 2742Anaerobic Microbiology and Biotechnology Group, Department of Molecular Sciences, Swedish University of Agricultural Sciences, Almas Allé 5, Box 7025, 750 07 Uppsala, Sweden
| | - Bettina Müller
- grid.6341.00000 0000 8578 2742Anaerobic Microbiology and Biotechnology Group, Department of Molecular Sciences, Swedish University of Agricultural Sciences, Almas Allé 5, Box 7025, 750 07 Uppsala, Sweden
| | - Anna Schnürer
- grid.6341.00000 0000 8578 2742Anaerobic Microbiology and Biotechnology Group, Department of Molecular Sciences, Swedish University of Agricultural Sciences, Almas Allé 5, Box 7025, 750 07 Uppsala, Sweden
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2
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Yu T, Ma H, Zhang H, Xiong M, Liu Y, Li F. Fabrication and characterization of purified esterase-embedded zeolitic imidazolate frameworks for the removal and remediation of herbicide pollution from soil. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 288:112450. [PMID: 33823448 DOI: 10.1016/j.jenvman.2021.112450] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 03/09/2021] [Accepted: 03/17/2021] [Indexed: 05/19/2023]
Abstract
The fragility and high cost of enzymes represent critical challenges limiting their practical application in the removal of pesticides. Herein, an aryloxyphenoxypropionate herbicide-hydrolyzing enzyme, QpeH, was purified via one-step affinity chromatography and embedded into two types of zeolitic imidazolate frameworks (ZIFs) through biomimetic mineralization. The catalytic activity towards the herbicide quizalofop-P-ethyl, the loading capacity and efficiency of the resulting two composites, QpeH@ZIF-10 with cruciate flower-like morphology and QpeH@ZIF-8 with rhombic dodecahedral morphology, were compared. Both composites had excellent stability and reusability after 10 reuse cycles, with QpeH@ZIF-10 having a better performance. More importantly, when applied for the removal of quizalofop-P-ethyl pollution in the watermelon field, QpeH@ZIF-10 (88%) showed a remarkably improved degradation efficiency compared to QpeH@ZIF-8 (84%) despite the latter having a greater loading capacity. Finally, the use of QpeH@ZIF composites was shown to recover the bacterial community in soil. This work provides a new insight into the low-cost synthesis of nanobiocatalysts combining simple purified enzymes and metal-organic frameworks (MOFs) for the remediation of pesticide-contaminated soils.
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Affiliation(s)
- Ting Yu
- College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China
| | - Hengyan Ma
- College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China
| | - Hui Zhang
- College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China.
| | - Minghua Xiong
- College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China
| | - Yuan Liu
- College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China
| | - Feng Li
- College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China.
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Zhou C, Wang J, Li R, Ye K. High-throughput sequencing analysis of the bacterial community for assessing the differences in extraction methods of bacteria separation from chilled pork. Lebensm Wiss Technol 2020. [DOI: 10.1016/j.lwt.2020.110213] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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4
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Young JM, Linacre A. Massively parallel sequencing is unlocking the potential of environmental trace evidence. Forensic Sci Int Genet 2020; 50:102393. [PMID: 33157385 DOI: 10.1016/j.fsigen.2020.102393] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/03/2020] [Accepted: 09/07/2020] [Indexed: 01/16/2023]
Abstract
Massively parallel sequencing (MPS) has revolutionised the field of genomics enabling substantial advances in human DNA profiling. Further, the advent of MPS now allows biological signatures to be obtained from complex DNA mixtures and trace amounts of low biomass samples. Environmental samples serve as ideal forms of contact trace evidence as detection at a scene can establish a link between a suspect, location and victim. Many studies have applied MPS technology to characterise the biodiversity within high biomass environmental samples (such as soil and water) to address questions related to ecology, conservation, climate change and human health. However, translation of these tools to forensic science remains in its infancy, due in part to the merging of traditional forensic ecology practices with unfamiliar DNA technologies and complex datasets. In addition, people and objects also carry low biomass environmental signals which have recently been shown to reflect a specific individual or location. The sensitivity, and reducing cost, of MPS is now unlocking the power of both high and low biomass environmental DNA (eDNA) samples as useful sources of genetic information in forensic science. This paper discusses the potential of eDNA to forensic science by reviewing the most explored applications that are leading the integration of this technology into the field. We introduce novel areas of forensic ecology that could also benefit from these tools with a focus on linking a suspect to a scene or establishing provenance of an unknown sample and discuss the current limitations and validation recommendations to achieve translation of eDNA into casework.
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Affiliation(s)
- J M Young
- College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia.
| | - A Linacre
- College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
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Fredriksson NJ, Hermansson M, Wilén BM. Long-term dynamics of the bacterial community in a Swedish full-scale wastewater treatment plant. ENVIRONMENTAL TECHNOLOGY 2019; 40:912-928. [PMID: 29187074 DOI: 10.1080/09593330.2017.1411396] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 09/07/2017] [Indexed: 06/07/2023]
Abstract
The operational efficiency of activated sludge wastewater treatment plants depends to a large extent on the microbial community structure of the activated sludge. The aims of this paper are to describe the composition of the bacterial community in a Swedish full-scale activated sludge wastewater treatment plant, to describe the dynamics of the community and to elucidate possible causes for bacterial community composition changes. The bacterial community composition in the activated sludge was described using 16S rRNA gene libraries and monitored for 15 months by a terminal restriction fragment (T-RF) length polymorphism (T-RFLP) analysis of the 16S rRNA gene. Despite variable environmental conditions, a large fraction of the observed T-RFs were present at all times, making up at least 50% in all samples, possibly representing a relatively stable core fraction of the bacterial community. However, the proportions of the different T-RFs in this fraction as well as the T-RFs in the more variable fraction showed a significant variation over time and temperature. The difference in community composition between summer and winter coincided with observed differences in floc structure. These observations suggest a relationship between floc properties and bacterial community composition, although additional experiments are required to determine causality.
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Affiliation(s)
- Nils Johan Fredriksson
- a Department of Architecture and Civil Engineering, Water Environment Technology , Chalmers University of Technology , Gothenburg , Sweden
| | - Malte Hermansson
- b Department of Chemistry and Molecular Biology, Microbiology , University of Gothenburg , Gothenburg , Sweden
| | - Britt-Marie Wilén
- a Department of Architecture and Civil Engineering, Water Environment Technology , Chalmers University of Technology , Gothenburg , Sweden
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Lindström S, Rowe O, Timonen S, Sundström L, Johansson H. Trends in bacterial and fungal communities in ant nests observed with Terminal-Restriction Fragment Length Polymorphism (T-RFLP) and Next Generation Sequencing (NGS) techniques-validity and compatibility in ecological studies. PeerJ 2018; 6:e5289. [PMID: 30042898 PMCID: PMC6055595 DOI: 10.7717/peerj.5289] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 07/01/2018] [Indexed: 11/30/2022] Open
Abstract
Microbes are ubiquitous and often occur in functionally and taxonomically complex communities. Unveiling these community dynamics is one of the main challenges of microbial research. Combining a robust, cost effective and widely used method such as Terminal Restriction Fragment Length Polymorphism (T-RFLP) with a Next Generation Sequencing (NGS) method (Illumina MiSeq), offers a solid alternative for comprehensive assessment of microbial communities. Here, these two methods were combined in a study of complex bacterial and fungal communities in the nest mounds of the ant Formica exsecta, with the aim to assess the degree to which these methods can be used to complement each other. The results show that these methodologies capture similar spatiotemporal variations, as well as corresponding functional and taxonomical detail, of the microbial communities in a challenging medium consisting of soil, decomposing plant litter and an insect inhabitant. Both methods are suitable for the analysis of complex environmental microbial communities, but when combined, they complement each other well and can provide even more robust results. T-RFLP can be trusted to show similar general community patterns as Illumina MiSeq and remains a good option if resources for NGS methods are lacking.
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Affiliation(s)
- Stafva Lindström
- Centre of Excellence in Biological Interactions, Department of Biosciences, University of Helsinki, Helsinki, Finland
- Tvärminne Zoological Station, University of Helsinki, Hanko, Finland
- Organismal and Evolutionary Biology, University of Helsinki, Helsinki, Finland
| | - Owen Rowe
- Umeå Marine Sciences Centre, Umeå University, Hörnefors, Sweden
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Sari Timonen
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Liselotte Sundström
- Centre of Excellence in Biological Interactions, Department of Biosciences, University of Helsinki, Helsinki, Finland
- Tvärminne Zoological Station, University of Helsinki, Hanko, Finland
- Organismal and Evolutionary Biology, University of Helsinki, Helsinki, Finland
| | - Helena Johansson
- Centre of Excellence in Biological Interactions, Department of Biosciences, University of Helsinki, Helsinki, Finland
- Tvärminne Zoological Station, University of Helsinki, Hanko, Finland
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Habtom H, Demanèche S, Dawson L, Azulay C, Matan O, Robe P, Gafny R, Simonet P, Jurkevitch E, Pasternak Z. Soil characterisation by bacterial community analysis for forensic applications: A quantitative comparison of environmental technologies. Forensic Sci Int Genet 2017; 26:21-29. [DOI: 10.1016/j.fsigen.2016.10.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Revised: 09/20/2016] [Accepted: 10/06/2016] [Indexed: 12/01/2022]
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Zimmermann J, Musyoki MK, Cadisch G, Rasche F. Biocontrol agent Fusarium oxysporum f.sp. strigae has no adverse effect on indigenous total fungal communities and specific AMF taxa in contrasting maize rhizospheres. FUNGAL ECOL 2016; 23:1-10. [PMID: 27721900 PMCID: PMC5045157 DOI: 10.1016/j.funeco.2016.05.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
We studied the effects of Fusarium oxysporum f.sp. strigae (Fos), a soil-borne biocontrol agent (BCA) against Striga hermonthica, on total fungal and arbuscular mycorrhizal fungal (AMF) taxa in rhizospheres of maize in both clayey and sandy soil. Effects of Fos-BCA ‘Foxy-2’ were evaluated against (1) S. hermonthica presence, and (2) organic fertilization with Tithonia diversifolia residues at 14, 28 and 42 d after ‘Foxy-2’ inoculation, via DNA-based quantitative PCR and TRFLP fingerprinting. In both soils, ‘Foxy-2’ occasionally promoted total fungal abundance, while the community composition was mainly altered by T. diversifolia and S. hermonthica. Notably, ‘Foxy-2’ stimulated AMF Gigaspora margarita abundance, while G. margarita was suppressed by S. hermonthica. Total fungal and AMF abundance were promoted by T. diversifolia residues. In conclusion, ‘Foxy-2’ resulted in no adverse effects on indigenous rhizosphere fungal communities substantiating its environmental safety as BCA against S. hermonthica. ‘Foxy-2’ promoted AMF Gigaspora margarita abundance. Total fungal abundance was only transiently stimulated by ‘Foxy-2’. Contrastingly, G. margarita abundance was suppressed by Striga hermonthica. ‘Foxy-2’ induced only a minor alteration of fungal community composition. ‘Foxy-2’ effects were generally superimposed by organic fertilization.
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Affiliation(s)
- Judith Zimmermann
- Institute of Agricultural Sciences in the Tropics (Hans-Ruthenberg-Institute), University of Hohenheim, Stuttgart, Germany
| | - Mary K Musyoki
- Institute of Agricultural Sciences in the Tropics (Hans-Ruthenberg-Institute), University of Hohenheim, Stuttgart, Germany
| | - Georg Cadisch
- Institute of Agricultural Sciences in the Tropics (Hans-Ruthenberg-Institute), University of Hohenheim, Stuttgart, Germany
| | - Frank Rasche
- Institute of Agricultural Sciences in the Tropics (Hans-Ruthenberg-Institute), University of Hohenheim, Stuttgart, Germany
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Zimmermann J, Musyoki MK, Cadisch G, Rasche F. Proliferation of the biocontrol agent Fusarium oxysporum f. sp. strigae and its impact on indigenous rhizosphere fungal communities in maize under different agro-ecologies. RHIZOSPHERE 2016; 1:17-25. [PMID: 27928553 PMCID: PMC5125437 DOI: 10.1016/j.rhisph.2016.06.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 06/13/2016] [Accepted: 06/16/2016] [Indexed: 06/06/2023]
Abstract
Our objectives were to (1) monitor the proliferation of the biocontrol agent (BCA) Fusarium oxysporum f. sp. strigae strain "Foxy-2", an effective soil-borne BCA against the parasitic weed Striga hermonthica, in the rhizosphere of maize under different agro-ecologies, and (2) investigate its impact on indigenous rhizosphere fungal community abundance and composition. Field experiments were conducted in Busia and Homa Bay districts in western Kenya during two cropping seasons to account for effects of soil type, climate, growth stage and seasonality. Maize seeds were coated with or without "Foxy-2" and soils were artificially infested with S. hermonthica seeds. One treatment with nitrogen rich organic residues (Tithonia diversifolia) was established to compensate hypothesized resource competition between "Foxy-2" and the indigenous fungal community. Rhizosphere soil samples collected at three growth stages (i.e., EC30, EC60, EC90) of maize were subjected to abundance measurement of "Foxy-2" and total indigenous fungi using quantitative polymerase chain reaction (qPCR) analysis. Terminal restriction fragment length polymorphism (TRFLP) analysis was used to assess potential alterations in the fungal community composition in response to "Foxy-2" presence. "Foxy-2" proliferated stronger in the soils with a sandy clay texture (Busia) than in those with a loamy sand texture (Homa Bay) and revealed slightly higher abundance in the second season. "Foxy-2" had, however, only a transient suppressive effect on total indigenous fungal abundance which ceased in the second season and was further markedly compensated after addition of T. diversifolia residues. Likewise, community structure of the indigenous fungal community was mainly altered by maize growth stages, but not by "Foxy-2". In conclusion, no adverse effects of "Foxy-2" inoculation on indigenous fungal rhizosphere communities were observed corroborating the safety of this BCA under the given agro-ecologies.
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Affiliation(s)
| | | | | | - Frank Rasche
- Institute of Agricultural Sciences in the Tropics (Hans-Ruthenberg-Institute), University of Hohenheim, Stuttgart, Germany
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Wang P, Li Y, Xiao H, Shi Y, Le GW, Sun J. Isolation of lactobacillus reuteri from Peyer's patches and their effects on sIgA production and gut microbiota diversity. Mol Nutr Food Res 2016; 60:2020-30. [PMID: 27030202 DOI: 10.1002/mnfr.201501065] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2015] [Revised: 02/27/2016] [Accepted: 03/16/2016] [Indexed: 01/04/2023]
Abstract
SCOPE We previously reported that specific Lactobacillus reuteri colonized within mouse Peyer's patches (PP) effectively prevented high fat diet induced obesity and low-grade chronic inflammation. We further investigated the role of PP Lactobacillus reuteri on sIgA production in rats in this study. METHODS AND RESULTS Lactobacilli were isolated from rat PP. All isolates were L. reuteri and belonged to three phenotypes according to amplified fragment length polymorphism analysis. Typical strains of two main clusters, PP1 and PP2, were used to treat control and vitamin A deficient (VAD) rats, respectively. The feeding of PP1 and PP2 affected sIgA and Lactobacillus diversity by strain-specific manner. Free sIgA was significantly increased by PP1 (p = 0.069) and PP2 (p < 0.05) in the control rats but not in the VAD rats. Only PP1 significantly changed PP Lactobacillus diversity in the control rats (p < 0.05). However, PP2 specifically changed ileal Lactobacillus diversity in both control and VAD rats. Fecal sIgA was correlated with PP Lactobacillus diversity (R(2) = 0.7958, p = 0.011). CONCLUSION Modulation of sIgA production by PP L. reuteri of rat is dependent on vitamin A and change of Lactobacillus diversity in PP.
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Affiliation(s)
- Panpan Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, PR China.,Food Nutrition and Functional Factors Research Center, School of Food Science and Technology, Jiangnan University, Wuxi, PR China
| | - Ya Li
- Food Nutrition and Functional Factors Research Center, School of Food Science and Technology, Jiangnan University, Wuxi, PR China
| | - Hang Xiao
- Department of Food Science, University of Massachusetts, Amherst, MA, USA
| | - Yonghui Shi
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, PR China.,Food Nutrition and Functional Factors Research Center, School of Food Science and Technology, Jiangnan University, Wuxi, PR China
| | - Guo-Wei Le
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, PR China.,Food Nutrition and Functional Factors Research Center, School of Food Science and Technology, Jiangnan University, Wuxi, PR China
| | - Jin Sun
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, PR China. .,Food Nutrition and Functional Factors Research Center, School of Food Science and Technology, Jiangnan University, Wuxi, PR China.
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