1
|
Bolhuis H, Grego M. Cryopreservation and recovery of a complex hypersaline microbial mat community. Cryobiology 2024; 114:104859. [PMID: 38336089 DOI: 10.1016/j.cryobiol.2024.104859] [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: 11/07/2023] [Revised: 01/15/2024] [Accepted: 02/04/2024] [Indexed: 02/12/2024]
Abstract
Cryopreservation of microorganisms is an essential tool in industrial- and food applications where conservation of microbial activity and critical beneficial traits need to be guaranteed to provide a consistent product or production process. This often refers to simple, single species or low diversity assemblages in liquid cultures that can easily be revived and regrown to perform the desired process. Cryopreservation is also of essence for scientific experimentation where many environmental samples are taken in remote sampling sites and at high costs. Biobanking, or the long term preservation and potential revival of complex, structured samples come with an additional challenge related to maintaining the structure upon revival. Here we look at cryopreserving and reviving a complex photosynthesis driven microbial mat from a hypersaline ecosystem. Amplicon sequencing of the 16S and 18S ribosomal RNA gene was used to determine the community composition of bacteria and eukaryotes respectively. The tests included the use of different cryopreservative agents and different times of cryopreservation at -150 °C. Upon revival, the cryopreservatives cannot be separated from the preserved samples without disturbing the community structure, while carryover of these compounds may influence reconstitution of the communities. Indeed, although both glycerol and Me2SO are good cryopreservatives of microbial assemblages, carryover of these compounds had a profound negative effect on the reestablishment of a functional microbial mat. Best cryopreservation and reconstitution results were obtained in the absence of a cryopreservative agent or when methanol was used.
Collapse
Affiliation(s)
- Henk Bolhuis
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ), Den Hoorn, the Netherlands.
| | - Michele Grego
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ), Den Hoorn, the Netherlands.
| |
Collapse
|
2
|
Zhao SY, Hughes GL, Coon KL. A cryopreservation method to recover laboratory- and field-derived bacterial communities from mosquito larval habitats. PLoS Negl Trop Dis 2023; 17:e0011234. [PMID: 37018374 PMCID: PMC10109488 DOI: 10.1371/journal.pntd.0011234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 04/17/2023] [Accepted: 03/10/2023] [Indexed: 04/06/2023] Open
Abstract
Mosquitoes develop in a wide range of aquatic habitats containing highly diverse and variable bacterial communities that shape both larval and adult traits, including the capacity of adult females of some mosquito species to transmit disease-causing organisms to humans. However, while most mosquito studies control for host genotype and environmental conditions, the impact of microbiota variation on phenotypic outcomes of mosquitoes is often unaccounted for. The inability to conduct reproducible intra- and inter-laboratory studies of mosquito-microbiota interactions has also greatly limited our ability to identify microbial targets for mosquito-borne disease control. Here, we developed an approach to isolate and cryopreserve bacterial communities derived from lab and field-based larval rearing environments of the yellow fever mosquito Aedes aegypti-a primary vector of dengue, Zika, and chikungunya viruses. We then validated the use of our approach to generate experimental microcosms colonized by standardized lab- and field-derived bacterial communities. Our results overall reveal minimal effects of cryopreservation on the recovery of both lab- and field-derived bacteria when directly compared with isolation from non-cryopreserved fresh material. Our results also reveal improved reproducibility of bacterial communities in replicate microcosms generated using cryopreserved stocks over fresh material. Communities in replicate microcosms further captured the majority of total bacterial diversity present in both lab- and field-based larval environments, although the relative richness of recovered taxa as compared to non-recovered taxa was substantially lower in microcosms containing field-derived bacteria. Altogether, these results provide a critical next step toward the standardization of mosquito studies to include larval rearing environments colonized by defined microbial communities. They also lay the foundation for long-term studies of mosquito-microbe interactions and the identification and manipulation of taxa with potential to reduce mosquito vectorial capacity.
Collapse
Affiliation(s)
- Serena Y. Zhao
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Grant L. Hughes
- Departments of Vector Biology and Tropical Disease Biology, Centre for Neglected Topical Disease, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Kerri L. Coon
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| |
Collapse
|
3
|
Isenring J, Bircher L, Geirnaert A, Lacroix C. In vitro human gut microbiota fermentation models: opportunities, challenges, and pitfalls. MICROBIOME RESEARCH REPORTS 2023; 2:2. [PMID: 38045607 PMCID: PMC10688811 DOI: 10.20517/mrr.2022.15] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/12/2022] [Accepted: 01/09/2023] [Indexed: 12/05/2023]
Abstract
The human gut microbiota (HGM) plays a pivotal role in health and disease. Consequently, nutritional and medical research focusing on HGM modulation strategies as a means of improving host health is steadily increasing. In vitro HGM fermentation models offer a valid complement to human and animal studies when it comes to the mechanistic exploration of novel modulation approaches and their direct effects on HGM composition and activity, while excluding interfering host effects. However, in vitro cultivation of HGM can be challenging due to its high oxygen sensitivity and the difficulties of accurately modeling the physio-chemical complexity of the gut environment. Despite the increased use of in vitro HGM models, there is no consensus about appropriate model selection and operation, sometimes leading to major deficiencies in study design and result interpretation. In this review paper, we aim to analyze crucial aspects of the application, setup and operation, data validation and result interpretation of in vitro HGM models. When carefully designed and implemented, in vitro HGM modeling is a powerful strategy for isolating and investigating biotic and abiotic factors in the HGM, as well as evaluating their effects in a controlled environment akin to the gut. Furthermore, complementary approaches combining different in vitro and in vivo models can strengthen the design and interpretation of human studies.
Collapse
Affiliation(s)
| | | | | | - Christophe Lacroix
- Department of Health Sciences and Technology, ETH Zurich, Zürich 8092, Switzerland
| |
Collapse
|
4
|
Coker J, Zhalnina K, Marotz C, Thiruppathy D, Tjuanta M, D’Elia G, Hailu R, Mahosky T, Rowan M, Northen TR, Zengler K. A Reproducible and Tunable Synthetic Soil Microbial Community Provides New Insights into Microbial Ecology. mSystems 2022; 7:e0095122. [PMID: 36472419 PMCID: PMC9765266 DOI: 10.1128/msystems.00951-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 10/26/2022] [Indexed: 12/12/2022] Open
Abstract
Microbial soil communities form commensal relationships with plants to promote the growth of both parties. The optimization of plant-microbe interactions to advance sustainable agriculture is an important field in agricultural research. However, investigation in this field is hindered by a lack of model microbial community systems and efficient approaches for building these communities. Two key challenges in developing standardized model communities are maintaining community diversity over time and storing/resuscitating these communities after cryopreservation, especially considering the different growth rates of organisms. Here, a model synthetic community (SynCom) of 16 soil microorganisms commonly found in the rhizosphere of diverse plant species, isolated from soil surrounding a single switchgrass plant, has been developed and optimized for in vitro experiments. The model soil community grows reproducibly between replicates and experiments, with a high community α-diversity being achieved through growth in low-nutrient media and through the adjustment of the starting composition ratios for the growth of individual organisms. The community can additionally be cryopreserved with glycerol, allowing for easy replication and dissemination of this in vitro system. Furthermore, the SynCom also grows reproducibly in fabricated ecosystem devices (EcoFABs), demonstrating the application of this community to an existing in vitro plant-microbe system. EcoFABs allow reproducible research in model plant systems, offering the precise control of environmental conditions and the easy measurement of plant microbe metrics. Our results demonstrate the generation of a stable and diverse microbial SynCom for the rhizosphere that can be used with EcoFAB devices and can be shared between research groups for maximum reproducibility. IMPORTANCE Microbes associate with plants in distinct soil communities to the benefit of both the soil microbes and the plants. Interactions between plants and these microbes can improve plant growth and health and are therefore a field of study in sustainable agricultural research. In this study, a model community of 16 soil bacteria has been developed to further the reproducible study of plant-soil microbe interactions. The preservation of the microbial community has been optimized for dissemination to other research settings. Overall, this work will advance soil microbe research through the optimization of a robust, reproducible model community.
Collapse
Affiliation(s)
- Joanna Coker
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
| | - Kateryna Zhalnina
- Environmental Genomics and Systems Biology Division, Berkeley Lab, Berkeley, California, USA
| | - Clarisse Marotz
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
| | - Deepan Thiruppathy
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Megan Tjuanta
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Gavin D’Elia
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Rodas Hailu
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Talon Mahosky
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Meagan Rowan
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Trent R. Northen
- Environmental Genomics and Systems Biology Division, Berkeley Lab, Berkeley, California, USA
- The DOE Joint Genome Institute, Berkeley Lab, Berkeley, California, USA
| | - Karsten Zengler
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, California, USA
| |
Collapse
|
5
|
Cuellar-Gempeler C, terHorst CP, Mason OU, Miller T. Predator dispersal influences predator distribution but not prey diversity in pitcher plant microbial metacommunities. Ecology 2022; 104:e3912. [PMID: 36335567 DOI: 10.1002/ecy.3912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 09/16/2022] [Accepted: 09/20/2022] [Indexed: 11/08/2022]
Abstract
The spatial distribution of predators can affect both the distribution and diversity of their prey. Therefore, differences in predator dispersal ability that affect their spatial distribution, could also affect prey communities. Here, we use the microbial communities within pitcher plant leaves as a model system to test the relationship between predator (protozoa) dispersal ability and distribution, and its consequences for prey (bacteria) diversity and composition. We hypothesized that limited predator dispersal results in clustered distributions and heterogeneous patches for prey species, whereas wide predator dispersal and distribution could homogenize prey metacommunities. We analyzed the distribution of two prominent bacterivore protozoans from a 2-year survey of an intact field of Sarracenia purpurea pitcher plants, and found a clustered distribution of Tetrahymena and homogeneous distribution of Poterioochromonas. We manipulated the sources of protozoan colonists and recorded protozoan recruitment and bacterial diversity in target leaves in a field experiment. We found the large ciliate, Tetrahymena, was dispersal limited and occupied few leaves, whereas the small flagellate Poterioochromonas was widely dispersed. However, the bacterial communities these protozoans feed on was unaffected by clustering of Tetrahymena, but likely influenced by Poterioochromonas and other bacterivores dispersing in the field. We propose that bacterial communities in this system are structured by a combination of well dispersed bacterivores, bacterial dispersal, and bottom-up mechanisms. Clustered predators could become strong drivers of prey communities if they were specialists or keystone predators, or if they exerted a dominant influence on other predators in top-down controlled systems. Linking dispersal ability within trophic levels and its consequences for trophic dynamics can lead to a more robust perspective on trophic metacommunities.
Collapse
Affiliation(s)
- Catalina Cuellar-Gempeler
- Department of Biological Sciences, California State Polytechnic University, Humboldt, California, USA
| | - Casey P terHorst
- Department of Biology, California State University, Northridge, California, USA
| | - Olivia U Mason
- Department of Earth, Ocean, and Atmospheric Science, Florida State University, Tallahassee, Florida, USA
| | - Thomas Miller
- Department of Biological Science, Florida State University, Tallahassee, Florida, USA
| |
Collapse
|
6
|
Zhang Q, Lin JG, Kong Z, Zhang Y. A critical review of exogenous additives for improving the anammox process. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 833:155074. [PMID: 35398420 DOI: 10.1016/j.scitotenv.2022.155074] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 03/22/2022] [Accepted: 04/02/2022] [Indexed: 06/14/2023]
Abstract
Anammox achieves chemoautotrophic nitrogen removal under anaerobic and anoxic conditions and is a low-carbon wastewater biological nitrogen removal process with broad application potential. However, the physiological limitations of AnAOB often cause problems in engineering applications, such as a long start-up time, unstable operation, easily inhibited reactions, and difficulty in long-term strain preservation. Exogenous additives have been considered an alternative strategy to address these issues by retaining microbes, shortening the doubling time of AnAOB and improving functional enzyme activity. This paper reviews the role of carriers, biochar, intermediates, metal ions, reaction substrates, redox buffers, cryoprotectants and organics in optimizing anammox. The pathways and mechanisms of exogenous additives, which are explored to solve problems, are systematically summarized and analyzed in this article according to operational performance, functional enzyme activity, and microbial abundance to provide helpful information for the engineering application of anammox.
Collapse
Affiliation(s)
- Qi Zhang
- College of the Environment & Ecology, Xiamen University, South Xiang'an Road, Xiang'an District, Xiamen, Fujian 361102, China
| | - Jih-Gaw Lin
- College of the Environment & Ecology, Xiamen University, South Xiang'an Road, Xiang'an District, Xiamen, Fujian 361102, China; Institute of Environmental Engineering, National Chiao Tung University, 1001 University Road, Hsinchu 30010, Taiwan
| | - Zhe Kong
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Yanlong Zhang
- College of the Environment & Ecology, Xiamen University, South Xiang'an Road, Xiang'an District, Xiamen, Fujian 361102, China.
| |
Collapse
|
7
|
Liu C, Lei J, Zhang M, Wu F, Ren M, Yang J, Wu Q, Shi X. Optimization of Preservation Methods Provides Insights into Photosynthetic Picoeukaryotes in Lakes. Microbiol Spectr 2022; 10:e0255721. [PMID: 35546573 PMCID: PMC9241741 DOI: 10.1128/spectrum.02557-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 04/18/2022] [Indexed: 11/28/2022] Open
Abstract
As the key contributor to plankton biomass and nutrient cycling in aquatic ecosystems, photosynthetic picoeukaryotes (PPEs) have been recently investigated in freshwater ecosystems. However, the limited access to remote areas creates challenges for PPE sample preservation before sorting and counting by flow cytometry (FCM) in the laboratory. Here, we explored the effects of different preservation methods on the PPE community by combining FCM sorting and high-throughput sequencing. Our results showed that dimethyl sulfoxide (DMSO) cryoprotection could destroy the fluorescence and cell structure of the PPEs, making the subsequent FCM analysis and sorting difficult. Aldehyde fixation maintained the PPE fluorescence, and the fixed samples were of sufficient quality for abundance analysis and sorting by FCM. However, the sequencing results showed that, after preservation by aldehydes, the proportion of PPEs dramatically decreased to approximately 10%, in comparison to 90% in the fresh samples, and the sequences of Ascomycota significantly increased. In contrast, preservation with Pluronic F68 (F68) not only could maintain the PPE abundance close to the initial value but also could keep the PPE community similar to that in the fresh samples over a storage time of 6 months. Thus, F68 cryopreservation is a suitable preservation method for PPE communities from freshwater lakes. IMPORTANCE PPEs contribute significantly to primary productivity in freshwater ecosystems. The combination of FCM sorting and high-throughput sequencing has been shown to be a powerful approach and can largely improve our view of the PPE diversity. However, the water samples could not be counted and sorted immediately after sampling from many lakes due to the inaccessibility of FCM in the field. Thus, the comparison of different preservation methods that allow subsequent analysis of the community structure by high-throughput sequencing is an urgent need. Our results indicated that F68 cryopreservation could maintain the PPE abundance close to the initial value and keep the community similar to that in the fresh samples over a storage time of 6 months.
Collapse
Affiliation(s)
- Changqing Liu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jin Lei
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Min Zhang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Fan Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mingdong Ren
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jinsheng Yang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qinglong Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Xiaoli Shi
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environmental Protection, Huaiyin Normal University, Huaiyin, China
| |
Collapse
|
8
|
Biclot A, Huys GRB, Bacigalupe R, D’hoe K, Vandeputte D, Falony G, Tito RY, Raes J. Effect of cryopreservation medium conditions on growth and isolation of gut anaerobes from human faecal samples. MICROBIOME 2022; 10:80. [PMID: 35644616 PMCID: PMC9150342 DOI: 10.1186/s40168-022-01267-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 04/03/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Novel strategies for anaerobic bacterial isolations from human faecal samples and various initiatives to generate culture collections of gut-derived bacteria have instigated considerable interest for the development of novel microbiota-based treatments. Early in the process of building a culture collection, optimal faecal sample preservation is essential to safeguard the viability of the broadest taxonomic diversity range possible. In contrast to the much more established faecal storage conditions for meta-omics applications, the impact of stool sample preservation conditions on bacterial growth recovery and isolation remains largely unexplored. In this study, aliquoted faecal samples from eleven healthy human volunteers selected based on a range of physicochemical and microbiological gradients were cryopreserved at - 80 °C either without the addition of any medium (dry condition) or in different Cary-Blair medium conditions with or without a cryoprotectant, i.e. 20% (v/v) glycerol or 5% (v/v) DMSO. Faecal aliquots were subjected to bulk 16S rRNA gene sequencing as well as dilution plating on modified Gifu Anaerobic Medium after preservation for culturable fraction profiling and generation of bacterial culture collections. RESULTS Analyses of compositional variation showed that cryopreservation medium conditions affected quantitative recovery but not the overall community composition of cultured fractions. Post-preservation sample dilution and richness of the uncultured source samples were the major drivers of the cultured fraction richness at genus level. However, preservation conditions differentially affected recovery of specific genera. Presence-absence analysis indicated that twenty-two of the 45 most abundant common genera (>0.01% abundance, dilution 10-4) were recovered in cultured fractions from all preservation conditions, while nine genera were only detected in fractions from a single preservation condition. Overall, the highest number of common genera (i.e. 35/45) in cultured fractions were recovered from sample aliquots preserved without medium and in the presence of Cary-Blair medium containing 5% (v/v) DMSO. Also, in the culture collection generated from the cultured fractions, these two preservation conditions yielded the highest species richness (72 and 66, respectively). CONCLUSION Our results demonstrate that preservation methods partly determine richness and taxonomic diversity of gut anaerobes recovered from faecal samples. Complementing the current standard practice of cryopreserving stool samples in dry conditions with other preservation conditions, such as Cary-Blair medium with DMSO, could increase the species diversity of gut-associated culture collections. Video abstract.
Collapse
Affiliation(s)
- Anaïs Biclot
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Geert R. B. Huys
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Rodrigo Bacigalupe
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Kevin D’hoe
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Doris Vandeputte
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
- Present address: Meinig School of Biomedical Engineering, Cornell, USA
| | - Gwen Falony
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Raul Y. Tito
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Jeroen Raes
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| |
Collapse
|
9
|
Miller TE, Pastore A, Cuellar-Gempeler C, Canter E, Mason OU. Effects of community richness and competitive asymmetry on protozoa evolution in Sarracenia purpurea leaves. Am Nat 2022; 200:691-703. [DOI: 10.1086/721010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
10
|
Li Y, Xiang T, Liang H, Wang P, Gao D. Achieving rapid mainstream deammonification through inoculating long-term refrigerated sidestream sludge in plug-flow fixed-bed biofilm reactor. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:151415. [PMID: 34742959 DOI: 10.1016/j.scitotenv.2021.151415] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/29/2021] [Accepted: 10/30/2021] [Indexed: 06/13/2023]
Abstract
The start-up of a stable mainstream deammonification requires sufficient anaerobic ammonia-oxidizing bacteria (AnAOB). This study used a plug-flow fixed-bed reactor (PFBR) to verify the feasibility of establishing the mainstream deammonification system by inoculating the sidestream sludge after long-term refrigeration. A rapid resuscitation of the mainstream deammonification system was accomplished by controlling the front-end aeration rate of the PFBR. Results showed that the system was rapidly resuscitated in 44 days eventually with the nitrogen removal rate and nitrogen removal efficiency of 0.1 kg N·(m3·d)-1 and 79.1%, respectively. Also, the efficient performance was secured by the proportionate approaching equilibrium of AnAOB and ammonia-oxidizing bacteria (AOB) activity of 2.35 ± 0.40 and 2.60 ± 0.29 mg N·(g VSS·h)-1, respectively. In addition, Pearson correlation analysis revealed that AnAOB abundance (detected Candidatus Kuenenia) negatively correlated with the AOB (mainly Nitrosomonas)/AnAOB abundance ratio, while correlated positively with the residual ammonium concentration of a region. Furthermore, long-term refrigeration probably reduced the cross-feed relationship between AnAOB and other symbiotic organisms (Armatimonadetes and Chloroflexi) to maintain the basic metabolism. Meanwhile, extracellular polymeric substances produced by other genera (order Xanthomonadales and Pseudomonadales) decreased the mass transfer, protecting AnAOB from unfavorable conditions, thereby facilitating high AnAOB abundance during refrigeration. Thus, this study provides a promising perspective towards the practical applications of mainstream process.
Collapse
Affiliation(s)
- Yuqi Li
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, Heilongjiang, China
| | - Tao Xiang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, Heilongjiang, China
| | - Hong Liang
- School of Environment and Energy Engineering, Beijing University of Civil Engineering and Architecture, Beijing 100044, China
| | - Peng Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, Heilongjiang, China
| | - Dawen Gao
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, Heilongjiang, China; School of Environment and Energy Engineering, Beijing University of Civil Engineering and Architecture, Beijing 100044, China.
| |
Collapse
|
11
|
BIOME-Preserve: A novel storage and transport medium for preserving anaerobic microbiota samples for culture recovery. PLoS One 2022; 17:e0261820. [PMID: 35061732 PMCID: PMC8782539 DOI: 10.1371/journal.pone.0261820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 12/10/2021] [Indexed: 11/20/2022] Open
Abstract
Sequencing-based protocols for studying the human microbiome have unearthed a wealth of information about the relationship between the microbiome and human health. But these microbes cannot be leveraged as therapeutic targets without culture-based studies to phenotype species of interest and to establish culture collections for use in animal models. Traditional sample collection protocols are focused on preserving nucleic acids and metabolites and are largely inappropriate for preserving sensitive anaerobic bacteria for later culture recovery. Here we introduce a novel microbiome preservation kit (BIOME-Preserve) that facilitates recovery of anaerobic bacteria from human stool. Using a combination of culture recovery and shallow whole-genome shotgun sequencing, we characterized the anaerobes cultured from fresh human stool and from human stool held at room temperature in BIOME-Preserve for up to 120 hours. We recovered several species of interest to microbiome researchers, including Bifidobacterium spp., Bacteroides spp., Blautia spp., Eubacterium halii (now Anaerobutyricum hallii), Akkermansia muciniphila, and Faecalibacterium prausnitzii. We also demonstrated that freezing at -80°C did not adversely affect our ability to culture organisms from BIOME-Preserve, suggesting that it is appropriate both as a transport medium and as a medium for longer-term ultra-cold storage. Together, our results suggest BIOME-Preserve is practical for the collection, transport, and culture of anaerobic bacteria from human samples and can help enable researchers to better understand the link between the microbiome and human health and how to leverage that link through novel microbiome-based therapeutics.
Collapse
|
12
|
Growth Performance, Biochemical Composition and Nutrient Recovery Ability of Twelve Microalgae Consortia Isolated from Various Local Organic Wastes Grown on Nano-Filtered Pig Slurry. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27020422. [PMID: 35056737 PMCID: PMC8781922 DOI: 10.3390/molecules27020422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/07/2022] [Accepted: 01/08/2022] [Indexed: 11/17/2022]
Abstract
This paper demonstrated the growth ability of twelve algae-microbial consortia (AC) isolated from organic wastes when a pig slurry-derived wastewater (NFP) was used as growth substrate in autotrophic cultivation. Nutrient recovery, biochemical composition, fatty acid and amino acid profiles of algae consortia were evaluated and compared. Three algae-microbial consortia, i.e., a Chlorella-dominated consortium (AC_1), a Tetradesmus and Synechocystis co-dominated consortium (AC_10), and a Chlorella and Tetradesmus co-dominated consortium (AC_12) were found to have the best growth rates (µ of 0.55 ± 0.04, 0.52 ± 0.06, and 0.58 ± 0.03 d−1, respectively), which made them good candidates for further applications. The ACs showed high carbohydrates and lipid contents but low contents of both proteins and essential amino acids, probably because of the low N concentration of NFP. AC_1 and AC_12 showed optimal ω6:ω3 ratios of 3.1 and 3.6, which make them interesting from a nutritional point of view.
Collapse
|
13
|
Bhattacharjee A, Dubey S, Sharma S. Storage of soil microbiome for application in sustainable agriculture: prospects and challenges. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:3171-3183. [PMID: 34718953 DOI: 10.1007/s11356-021-17164-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 10/19/2021] [Indexed: 06/13/2023]
Abstract
Soil microbiome is a dynamic micro-ecosystem driving and fine-tuning several biological processes in the global macro-ecosystems. Its tremendous potential towards mediating sustainability in the ecosystem necessitates the urgent need to store it optimally and efficiently as "next-generation biologicals" for future applications via soil transplantation. The challenge, therefore, is to devise a strategy for the storage of soil microbiome such that its "functionality" is preserved for later application. This review discusses the current endeavours made towards storage of the soil microbiome. The methods for assessing the integrity of soil microbiome by targeting the structural diversity and functional potential of the preserved microbiomes have also been discussed. Further, the success stories related to the storage of fecal microbiome for application in transplants have also been highlighted. This is done primarily with the objective of learning lessons, and parallel application of the knowledge gained, in bringing about improvement in the research domain of soil microbiome storage. Subsequently, the limitations of current techniques of preservation have also been delineated. Further, the open questions in the area have been critically discussed. In conclusion, possible alternatives for storage, comprehensive analyses of the composition of the stored microbiome and their potential have been presented.
Collapse
Affiliation(s)
- Annapurna Bhattacharjee
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - Shubham Dubey
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - Shilpi Sharma
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India.
| |
Collapse
|
14
|
Swei A, Kwan JY. Response to Holmes - practical considerations for vector microbiome studies. Mol Ecol 2021; 30:2214-2219. [PMID: 33904214 DOI: 10.1111/mec.15922] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/12/2021] [Indexed: 01/04/2023]
Affiliation(s)
- Andrea Swei
- Department of Biology, San Francisco State University, San Francisco, CA, USA
| | - Jessica Y Kwan
- School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| |
Collapse
|
15
|
Benchmarking DNA isolation kits used in analyses of the urinary microbiome. Sci Rep 2021; 11:6186. [PMID: 33731788 PMCID: PMC7969918 DOI: 10.1038/s41598-021-85482-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 03/02/2021] [Indexed: 12/22/2022] Open
Abstract
The urinary microbiome has been increasingly characterized using next-generation sequencing. However, many of the technical methods have not yet been specifically optimized for urine. We sought to compare the performance of several DNA isolation kits used in urinary microbiome studies. A total of 11 voided urine samples and one buffer control were divided into 5 equal aliquots and processed in parallel using five commercial DNA isolation kits. DNA was quantified and the V4 segment of the 16S rRNA gene was sequenced. Data were processed to identify the microbial composition and to assess alpha and beta diversity of the samples. Tested DNA isolation kits result in significantly different DNA yields from urine samples. DNA extracted with the Qiagen Biostic Bacteremia and DNeasy Blood & Tissue kits showed the fewest technical issues in downstream analyses, with the DNeasy Blood & Tissue kit also demonstrating the highest DNA yield. Nevertheless, all five kits provided good quality DNA for high throughput sequencing with non-significant differences in the number of reads recovered, alpha, or beta diversity.
Collapse
|
16
|
Rain-Franco A, de Moraes GP, Beier S. Cryopreservation and Resuscitation of Natural Aquatic Prokaryotic Communities. Front Microbiol 2021; 11:597653. [PMID: 33584565 PMCID: PMC7877341 DOI: 10.3389/fmicb.2020.597653] [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: 08/21/2020] [Accepted: 12/30/2020] [Indexed: 11/25/2022] Open
Abstract
Experimental reproducibility in aquatic microbial ecology is critical to predict the dynamics of microbial communities. However, controlling the initial composition of naturally occurring microbial communities that will be used as the inoculum in experimental setups is challenging, because a proper method for the preservation of those communities is lacking. To provide a feasible method for preservation and resuscitation of natural aquatic prokaryote assemblages, we developed a cryopreservation procedure applied to natural aquatic prokaryotic communities. We studied the impact of inoculum size, processing time, and storage time on the success of resuscitation. We further assessed the effect of different growth media supplemented with dissolved organic matter (DOM) prepared from naturally occurring microorganisms on the recovery of the initially cryopreserved communities obtained from two sites that have contrasting trophic status and environmental heterogeneity. Our results demonstrated that the variability of the resuscitation process among replicates decreased with increasing inoculum size. The degree of similarity between initial and resuscitated communities was influenced by both the growth medium and origin of the community. We further demonstrated that depending on the inoculum source, 45-72% of the abundant species in the initially natural microbial communities could be detected as viable cells after cryopreservation. Processing time and long-term storage up to 12 months did not significantly influence the community composition after resuscitation. However, based on our results, we recommend keeping handling time to a minimum and ensure identical incubation conditions for repeated resuscitations from cryo-preserved aliquots at different time points. Given our results, we recommend cryopreservation as a promising tool to advance experimental research in the field of microbial ecology.
Collapse
Affiliation(s)
- Angel Rain-Franco
- UMR 7621 Laboratoire d’Océanographie Microbienne, Observatoire Océanologique de Banyuls-sur-Mer, Sorbonne Université, Banyuls-sur-Mer, France
| | - Guilherme Pavan de Moraes
- UMR 7621 Laboratoire d’Océanographie Microbienne, Observatoire Océanologique de Banyuls-sur-Mer, Sorbonne Université, Banyuls-sur-Mer, France
- Graduate Program in Ecology and Natural Resources (PPGERN), Laboratory of Phycology, Department of Botany, Universidade Federal de São Carlos, São Carlos, Brazil
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde, Rostock, Germany
| | - Sara Beier
- UMR 7621 Laboratoire d’Océanographie Microbienne, Observatoire Océanologique de Banyuls-sur-Mer, Sorbonne Université, Banyuls-sur-Mer, France
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde, Rostock, Germany
| |
Collapse
|
17
|
Exploring microbial consortia from various environments for plastic degradation. Methods Enzymol 2020; 648:47-69. [PMID: 33579417 DOI: 10.1016/bs.mie.2020.12.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Many complex natural and synthetic compounds are degraded by microbial assemblages rather than single strains, due to usually limited metabolic capacities of single organisms. It can therefore be assumed that plastics can be more efficiently degraded by microbial consortia, although this field has not been as widely explored as plastic degradation by individual strains. In this chapter, we present some of the current studies on this topic and methods to enrich and cultivate plastic-degrading microbial consortia from aquatic and terrestrial ecosystems, including substrate preparation and biodegradation assessment. We focus on both conventional and biodegradable plastics as potential growth substrates. Cultivation methods for both aerobic and anaerobic microorganisms are presented.
Collapse
|
18
|
Park M, Kim M, Park T, Lee CS. Effect of cryopreservation on the bacterial community structure of filamentous cyanobacteria, Trichormus variabilis (Nostocales, Cyanobacteria). Cryobiology 2020; 98:87-95. [PMID: 33309711 DOI: 10.1016/j.cryobiol.2020.12.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 11/07/2020] [Accepted: 12/05/2020] [Indexed: 12/26/2022]
Abstract
Cryopreservation is an efficient method used to preserve microorganisms for long periods of time, such as up to 30 years, without changes in genetic and physiological characteristics. As cyanobacteria and microalgae are usually maintained as both axenic and xenic cultures, knowledge of co-cultured bacteria and changes in their community structure is important for the successful maintenance of microbial culture collections. In this study, research on the changes in co-cultured bacterial community structure during cyanobacterial cryopreservation were investigated using three different experimental groups by next generation sequencing (NGS): 1) cultured Trichormus variabilis without cryopreservation (control group), 2) cultured T. variabilis after cryopreservation in 10% dimethyl sulfoxide (Me2SO) for 14 days (cryo-cell group), and 3) cultured T. variabilis after cryopreservation in 10% Me2SO for 14 days within alginate beads (cryo-bead group). The results showed that the abundance of Sphingomonas and Hydrogenophaga (belonging to phylum Proteobacteria) was significantly increased in the cryo-bead group (Sphingomonas, control: 0.25%, cryo-cell: 1.32%, cryo-bead: 41.70%; Hydrogenophaga, control: 5.47%, cryo-cell: 5.24%, cryo-bead: 12.32%). However, the abundance of the phylum Bacteroidetes was significantly decreased in the cryo-bead group compared to that in the other groups (control: 26.29%, cryo-cell: 38.84%, cryo-bead: 11.43%). Bacterial diversity was generally reduced after cryopreservation in the cryo-bead group, where the overgrowth of a few unique bacteria was observed in the co-cultured bacterial community. These results imply that changes in the co-cultured bacterial community during preservation should be considered as an important factor for the development of methods for cyanobacterial cryopreservation.
Collapse
Affiliation(s)
- Mirye Park
- Algae Research Team, Microbial Research Department, Nakdonggang National Institute of Biological Resources, Sangju, 37242, Republic of Korea
| | - Minseok Kim
- Department of Animal Science, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Tansol Park
- US Dairy Forage Research Center, USDA-ARS, Madison, WI, 53706, USA
| | - Chang Soo Lee
- Algae Research Team, Microbial Research Department, Nakdonggang National Institute of Biological Resources, Sangju, 37242, Republic of Korea.
| |
Collapse
|
19
|
Toe LC, Kerckhof FM, De Bodt J, Morel FB, Ouedraogo JB, Kolsteren P, Van de Wiele T. A prebiotic-enhanced lipid-based nutrient supplement (LNSp) increases Bifidobacterium relative abundance and enhances short-chain fatty acid production in simulated colonic microbiota from undernourished infants. FEMS Microbiol Ecol 2020; 96:5858895. [PMID: 32568403 DOI: 10.1093/femsec/fiaa105] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 06/16/2020] [Indexed: 12/11/2022] Open
Abstract
Undernutrition remains a public health problem in the developing world with an attributable under-five death proportion of 45%. Lower gut microbiota diversity and poor metabolic output are associated with undernutrition and new therapeutic paths may come from steering gut microbiota composition and functionality. Using a dynamic gut model, the Simulator of Human Intestinal Microbial Ecosystem (SHIME®), we investigated the effect of a lipid-based nutrient supplement enriched with prebiotics (LNSp), compared to LNS alone and control treatment, on the composition and metabolic functionality of fecal microbiota from three infants suffering from undernutrition. LNS elicited a significant increase in acetate and branched-chain fatty acid production, and a higher relative abundance of the genera Prevotella, Megasphaera, Acinetobacter, Acidaminococcus and Pseudomonas. In contrast, LNSp treatment resulted in a significant 9-fold increase in Bifidobacterium relative abundance and a decrease in that of potential pathogens and detrimental bacteria such as Enterobacteriaceae spp. and Bilophila sp. Moreover, the LNSp treatment resulted in a significantly higher production of acetate, butyrate and propionate, as compared to control and LNS. Our results suggest that provision of prebiotic-enhanced LNS to undernourished children could be a possible strategy to steer the microbiota toward a more beneficial composition and metabolic activity. Further in vivo investigations are needed to assess these effects and their repercussion on nutritional status.
Collapse
Affiliation(s)
- Laeticia Celine Toe
- Department of Food Technology, Safety and Health, Ghent University, Coupure links 653, 9000 Ghent, Belgium.,Center for Microbial Ecology and Technology, Ghent University, Coupure links 653, 9000 Ghent, Belgium.,Institut de Recherche en Sciences de la Santé, Avenue de la Liberté 399, Bobo-Dioulasso, Burkina Faso
| | | | - Jana De Bodt
- Center for Microbial Ecology and Technology, Ghent University, Coupure links 653, 9000 Ghent, Belgium
| | - Fanny B Morel
- Nutriset SAS, Hameau du Bois Ricard, CS 80035, 76770 Malaunay, France
| | - Jean-Bosco Ouedraogo
- Institut de Recherche en Sciences de la Santé, Avenue de la Liberté 399, Bobo-Dioulasso, Burkina Faso
| | - Patrick Kolsteren
- Department of Food Technology, Safety and Health, Ghent University, Coupure links 653, 9000 Ghent, Belgium
| | - Tom Van de Wiele
- Center for Microbial Ecology and Technology, Ghent University, Coupure links 653, 9000 Ghent, Belgium
| |
Collapse
|
20
|
Prevalence of ESBL, AmpC and Carbapenemase-Producing Enterobacterales Isolated from Raw Vegetables Retailed in Romania. Foods 2020; 9:foods9121726. [PMID: 33255315 PMCID: PMC7760756 DOI: 10.3390/foods9121726] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 11/19/2020] [Accepted: 11/20/2020] [Indexed: 02/06/2023] Open
Abstract
(1) Background: As β-lactamase-producing Enterobacterales are no longer exclusively associated with the health care system, investigating the potential risk they pose to the integrity of the environment and food safety has become of utmost importance. This study aimed to determine the prevalence of extended-spectrum β-lactamase (ESBL), AmpC, and carbapenemase-producing Enterobacterales isolates from retailed raw vegetables and to determine if household washing is an effective method of lowering bacterial load; (2) Methods: Seasonal vegetables (n = 165) were acquired from supermarkets (n = 2) and farmer markets (n = 2) in Romania. Following sample processing and isolation, identification of Enterobacterales was performed by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF). Polymerase chain reaction (PCR) multiplex was used to ascertain the presence of the main ESBL, AmpC, and Carbapenemase genes. Phenotypic antibiotic resistance profiles of isolates were determined by extended antibiograms. Enterobacteriaceae colony-forming units (CFU) counts were compared between vegetable types; (3) Results: Beta-lactamase producing bacteria were observed on 7.9% of vegetables, with 5.5% displaying ESBL/AmpC phenotype and 2.4% identified as Carbapenemase producers. The most frequently detected β-lactamase genes were blaSHV (n = 4), followed by blaCTX-M and blaTEM (each with n = 3). Phenotypic antibiotic resistance analysis showed that 46% of isolates were multiple drug resistant, with aminoglycosides (38.5%) the most prevalent non-β-lactam resistance, followed by first-generation quinolones (38.5%). (4) Conclusions: The present study has described for the first time the presence of β-lactamase producing Enterobacterales in fresh produce retailed in Romania.
Collapse
|
21
|
Zalomova LV, Reshetnikov DA, Ugraitskaya SV, Mezhevikina LM, Zagainova AV, Makarov VV, Yudin SM, Fesenko (Jr.) EE. The Efficiency of the Preservation of Human Gut Microbiota in Liquid Nitrogen Depending on the Composition of the Cryoprotective Medium. Biophysics (Nagoya-shi) 2020. [DOI: 10.1134/s000635092005022x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|
22
|
Ryan MJ, Schloter M, Berg G, Kostic T, Kinkel LL, Eversole K, Macklin JA, Schelkle B, Kazou M, Sarand I, Singh BK, Fischer D, Maguin E, Ferrocino I, Lima N, McClure RS, Charles TC, de Souza RSC, Kiran GS, Krug HL, Taffner J, Roume H, Selvin J, Smith D, Rybakova D, Sessitsch A. Development of Microbiome Biobanks - Challenges and Opportunities. Trends Microbiol 2020; 29:89-92. [PMID: 32800611 DOI: 10.1016/j.tim.2020.06.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/20/2020] [Accepted: 06/25/2020] [Indexed: 12/16/2022]
Abstract
The microbiome research field is rapidly evolving, but the required biobanking infrastructure is currently fragmented and not prepared for the biobanking of microbiomes. The rapid advancement of technologies requires an urgent assessment of how biobanks can underpin research by preserving microbiome samples and their functional potential.
Collapse
Affiliation(s)
| | - M Schloter
- Helmholtz Zentrum München, National Research Center for Environmental Health, Research Unit for Comparative Microbiome Analysis, Oberschleissheim, Germany
| | - G Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - T Kostic
- AIT Austrian Institute of Technology, Center for Health and Bioresources, Bioresources Unit, Tulln, Austria
| | - L L Kinkel
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, USA
| | - K Eversole
- International Alliance for Phytobiomes Research, Lee's Summit, MO, USA; Eversole Associates, Bethesda, MD, USA
| | - J A Macklin
- Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - B Schelkle
- European Food Information Council, Brussels, Belgium
| | - M Kazou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
| | - I Sarand
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - B K Singh
- Global Centre for Land Based Innovation, Hawkesbury Institute for the Environment, Western Sydney University, Penrith, Australia
| | - D Fischer
- Helmholtz Zentrum München, National Research Center for Environmental Health, Research Unit for Comparative Microbiome Analysis, Oberschleissheim, Germany
| | - E Maguin
- INRAE, MICALIS Institute, Metagenopolis, Jouy-en-Josas, France
| | - I Ferrocino
- Department of Agricultural, Forest and Food Science, University of Turin, Grugliasco, Italy
| | - N Lima
- Biological Engineering Centre, University of Minho, Braga, Portugal
| | - R S McClure
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - T C Charles
- Waterloo Centre for Microbial Research, University of Waterloo, Waterloo, ON, Canada
| | - R S C de Souza
- Genomics for Climate Change Research Center, Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | - G S Kiran
- Department of Food Science and Technology, Pondicherry University, Puducherry, India
| | - H L Krug
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - J Taffner
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - H Roume
- INRAE, MICALIS Institute, Metagenopolis, Jouy-en-Josas, France
| | - J Selvin
- Department of Microbiology, Pondicherry University, Puducherry, India
| | | | - D Rybakova
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - A Sessitsch
- AIT Austrian Institute of Technology, Center for Health and Bioresources, Bioresources Unit, Tulln, Austria
| |
Collapse
|
23
|
A Recent Overview of Microbes and Microbiome Preservation. Indian J Microbiol 2020; 60:297-309. [PMID: 32655197 DOI: 10.1007/s12088-020-00880-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 05/06/2020] [Indexed: 12/17/2022] Open
Abstract
Microbes are mediators in almost all ecosystem processes and act as a pivotal game changer in various ecological activities, globally. Therefore, understanding of microbial community structure and related functions in different environmental and micro-environmental niches is not only critical, but also a matter of greatest importance. Due to our inability to cultivate and preserve all sorts of microorganisms, we are losing some ecologically and industrially relevant components of microbial community, due to extinction caused by environmental and climatic variations with time. Intact sample and microbiome preservation are crucial for future cultivation as well as to study the effects of ecological and climatic variations on community functionality and shift with time, using OMICS. Although, methods for pure culture preservation are almost optimized, the techniques of microbiome preservation still remain as an unsolved challenge for microbiologists due to technical and physiological constraints. Present article discusses, recent approaches of microbial preservation with special reference to intact sample, mixed culture and microbiome preservation. It also incorporates recent practices used to achieve the highest viability and metabolic activities in long-term preserved microbiome.
Collapse
|
24
|
Grimalt-Alemany A, Łężyk M, Asimakopoulos K, Skiadas IV, Gavala HN. Cryopreservation and fast recovery of enriched syngas-converting microbial communities. WATER RESEARCH 2020; 177:115747. [PMID: 32283432 DOI: 10.1016/j.watres.2020.115747] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 03/17/2020] [Accepted: 03/20/2020] [Indexed: 06/11/2023]
Abstract
Over the last decades, the use of mixed microbial communities has attracted increasing scientific attention due to their potential biotechnological applications in several emerging technological platforms such as the carboxylate, bioplastic, syngas and bio-electrochemical synthesis platforms. However, this increasing interest has not been accompanied by a parallel development of suitable cryopreservation techniques for microbial communities. While cryopreservation methods for the long-term storage of axenic cultures are well established, their effectiveness in preserving the microbial diversity and functionality of microbial communities has rarely been studied. In this study, the effect of the addition of different cryopreservation agents on the long-term storage of microbial communities at -80 °C was studied using a stable enrichment culture converting syngas into acetate and ethanol. The cryopreservation agents considered in the study were glycerol, dimethylsulfoxide, polyvinylpyrrolidone, Tween 80 and yeast extract, as well as with no addition of cryopreservation agent. Their effectiveness was evaluated based on the microbial activity recovery and the maintenance of the microbial diversity and community structure upon revival of the microbial community. The results showed that the commonly used glycerol and no addition of cryopreservation agent were the least recommendable methods for the long-term frozen storage of microbial communities, while Tween 80 and polyvinylpyrrolidone were overall the most effective. Among the cryoprotectants studied, polyvinylpyrrolidone and especially Tween 80 were the only ones assuring reproducible results in terms of microbial activity recovery and microbial community structure preservation.
Collapse
Affiliation(s)
- Antonio Grimalt-Alemany
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Søltofts Plads 229, 2800 Kgs, Lyngby, Denmark
| | - Mateusz Łężyk
- Institute of Environmental Engineering and Building Installations, Faculty of Environmental Engineering and Energy, Poznan University of Technology, Berdychowo 4, 60-965, Poznań, Poland
| | - Konstantinos Asimakopoulos
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Søltofts Plads 229, 2800 Kgs, Lyngby, Denmark
| | - Ioannis V Skiadas
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Søltofts Plads 229, 2800 Kgs, Lyngby, Denmark
| | - Hariklia N Gavala
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Søltofts Plads 229, 2800 Kgs, Lyngby, Denmark.
| |
Collapse
|
25
|
Manzoor SS, Doedens A, Burns MB. The promise and challenge of cancer microbiome research. Genome Biol 2020; 21:131. [PMID: 32487228 PMCID: PMC7265652 DOI: 10.1186/s13059-020-02037-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 05/07/2020] [Indexed: 02/06/2023] Open
Abstract
Many microbial agents have been implicated as contributors to cancer genesis and development, and the search to identify and characterize new cancer-related organisms is ongoing. Modern developments in methodologies, especially culture-independent approaches, have accelerated and driven this research. Recent work has shed light on the multifaceted role that the community of organisms in and on the human body plays in cancer onset, development, detection, treatment, and outcome. Much remains to be discovered, however, as methodological variation and functional testing of statistical correlations need to be addressed for the field to advance.
Collapse
Affiliation(s)
| | - Annemiek Doedens
- Department of Biology, Loyola University Chicago, Chicago, IL, 60660, USA
| | - Michael B Burns
- Department of Biology, Loyola University Chicago, Chicago, IL, 60660, USA.
| |
Collapse
|
26
|
Ilgrande C, Mastroleo F, Christiaens MER, Lindeboom REF, Prat D, Van Hoey O, Ambrozova I, Coninx I, Heylen W, Pommerening-Roser A, Spieck E, Boon N, Vlaeminck SE, Leys N, Clauwaert P. Reactivation of Microbial Strains and Synthetic Communities After a Spaceflight to the International Space Station: Corroborating the Feasibility of Essential Conversions in the MELiSSA Loop. ASTROBIOLOGY 2019; 19:1167-1176. [PMID: 31161957 DOI: 10.1089/ast.2018.1973] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
To sustain human deep space exploration or extra-terrestrial settlements where no resupply from the Earth or other planets is possible, technologies for in situ food production, water, air, and waste recovery need to be developed. The Micro-Ecological Life Support System Alternative (MELiSSA) is such a Regenerative Life Support System (RLSS) and it builds on several bacterial bioprocesses. However, alterations in gravity, temperature, and radiation associated with the space environment can affect survival and functionality of the microorganisms. In this study, representative strains of different carbon and nitrogen metabolisms with application in the MELiSSA were selected for launch and Low Earth Orbit (LEO) exposure. An edible photoautotrophic strain (Arthrospira sp. PCC 8005), a photoheterotrophic strain (Rhodospirillum rubrum S1H), a ureolytic heterotrophic strain (Cupriavidus pinatubonensis 1245), and combinations of C. pinatubonensis 1245 and autotrophic ammonia and nitrite oxidizing strains (Nitrosomonas europaea ATCC19718, Nitrosomonas ureae Nm10, and Nitrobacter winogradskyi Nb255) were sent to the International Space Station (ISS) for 7 days. There, the samples were exposed to 2.8 mGy, a dose 140 times higher than on the Earth, and a temperature of 22°C ± 1°C. On return to the Earth, the cultures were reactivated and their growth and activity were compared with terrestrial controls stored under refrigerated (5°C ± 2°C) or room temperature (22°C ± 1°C and 21°C ± 0°C) conditions. Overall, no difference was observed between terrestrial and ISS samples. Most cultures presented lower cell viability after the test, regardless of the type of exposure, indicating a harsher effect of the storage and sample preparation than the spaceflight itself. Postmission analysis revealed the successful survival and proliferation of all cultures except for Arthrospira, which suffered from the premission depressurization test. These observations validate the possibility of launching, storing, and reactivating bacteria with essential functionalities for microbial bioprocesses in RLSS.
Collapse
Affiliation(s)
- Chiara Ilgrande
- Center for Microbial Ecology and Technology (CMET), Ghent University, Gent, Belgium
| | - Felice Mastroleo
- Unit of Microbiology, Belgian Nuclear Research Centre (SCK•CEN), Mol, Belgium
| | | | - Ralph E F Lindeboom
- Center for Microbial Ecology and Technology (CMET), Ghent University, Gent, Belgium
- Section Sanitary Engineering, Department of Water Management, Faculty of Civil Engineering and Geosciences, Delft University of Technology, Delft, the Netherlands
| | - Delphine Prat
- Center for Microbial Ecology and Technology (CMET), Ghent University, Gent, Belgium
| | - Olivier Van Hoey
- Unit of Research in Dosimetric Applications, Belgian Nuclear Research Centre (SCK•CEN), Mol, Belgium
| | - Iva Ambrozova
- Department of Radiation Dosimetry, Nuclear Physics Institute of the Academy of Sciences of the Czech Republic, Praha, Czech Republic
| | - Ilse Coninx
- Unit of Microbiology, Belgian Nuclear Research Centre (SCK•CEN), Mol, Belgium
| | - Wietse Heylen
- Unit of Microbiology, Belgian Nuclear Research Centre (SCK•CEN), Mol, Belgium
| | | | - Eva Spieck
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), Ghent University, Gent, Belgium
| | - Siegfried E Vlaeminck
- Center for Microbial Ecology and Technology (CMET), Ghent University, Gent, Belgium
- Research Group of Sustainable Energy, Air and Water Technology, Department of Bioscience Engineering, University of Antwerp, Antwerpen, Belgium
| | - Natalie Leys
- Unit of Microbiology, Belgian Nuclear Research Centre (SCK•CEN), Mol, Belgium
| | - Peter Clauwaert
- Center for Microbial Ecology and Technology (CMET), Ghent University, Gent, Belgium
| |
Collapse
|
27
|
Ryan MJ, McCluskey K, Verkleij G, Robert V, Smith D. Fungal biological resources to support international development: challenges and opportunities. World J Microbiol Biotechnol 2019; 35:139. [PMID: 31451943 PMCID: PMC6710219 DOI: 10.1007/s11274-019-2709-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 08/04/2019] [Indexed: 11/03/2022]
Abstract
Exploitation of microbes, especially fungi, has the potential to help humankind meet the UN's sustainable development goals, help feed the worlds growing population and improve bioeconomies of poorer nations. The majority of the world's fungal genetic resources are held in collections in developed countries, primarily within the USA, Europe and Japan. Very little capacity exists in low to middle income countries, which are often rich in biodiversity but lack resources to be able to conserve and exploit their own microbial resources. In this paper we review the current challenges facing culture collections and the challenges of integrating new approaches, the worth of collaborative networks, and the importance of technology, taxonomy and data handling. We address the need to underpin research and development in developing countries through the need to build 'in country' infrastructure to address these challenges, whilst tackling the global challenges to meet the requirements of the research community through the impacts of legislation and the Nagoya protocol on access to biological resources.
Collapse
Affiliation(s)
- M J Ryan
- CABI, Bakeham Lane, Egham, TW20 9TY, Surrey, UK.
| | | | - G Verkleij
- Westerdijk Fungal Biodiversity Institute, P.O. Box 85167, 3508 AD, Utrecht, The Netherlands
| | - V Robert
- Westerdijk Fungal Biodiversity Institute, P.O. Box 85167, 3508 AD, Utrecht, The Netherlands
| | - D Smith
- CABI, Bakeham Lane, Egham, TW20 9TY, Surrey, UK
| |
Collapse
|
28
|
Smirnova DV, Zalomova LV, Zagainova AV, Makarov VV, Mezhevikina LM, Fesenko EE, Yudin SM. Cryopreservation of the human gut microbiota: Current state and perspectives. Int J Med Microbiol 2019; 309:259-269. [PMID: 31204202 DOI: 10.1016/j.ijmm.2019.06.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 05/21/2019] [Accepted: 06/02/2019] [Indexed: 02/06/2023] Open
Abstract
The human intestinal microbiota is a complex ecosystem that consists of thousands of bacterial species that are responsible for human health and disease. The intestinal microbiota is a natural resource for production of therapeutic and preventive medicals, such as probiotics and fecal transplants. Modern lifestyles have resulted in the extinction of evolutionally selected microbial populations upon exposure to environmental factors. Therefore, it is very important to preserve the human gut microbiota to have the opportunity for timely restoration with minimal safety risks. Cryopreservation techniques that are suitable for the preservation of viable, mixed microbial communities and a biobanking approach are currently under development in different countries. However, the number of studies in this area is very limited. The variety of morphological and physiological characteristics of microbes in the microbiota, the different cryopreservation goals, and the criteria for the evaluation of cryopreservation effectiveness are the main challenges in the creation of a universal and standardized cryopreservation protocol. In this review, we summarized the current progress of the main cryopreservation techniques for gut microbiota communities and the methods for the assessment of the effectiveness of these techniques in the context of practical application.
Collapse
Affiliation(s)
- Daria V Smirnova
- Center for Strategic Planning and Management of Medical and Biological Health Risks, Moscow, 119121, Russian Federation.
| | - Ljubov V Zalomova
- Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russian Federation
| | - Angelika V Zagainova
- Center for Strategic Planning and Management of Medical and Biological Health Risks, Moscow, 119121, Russian Federation
| | - Valentin V Makarov
- Center for Strategic Planning and Management of Medical and Biological Health Risks, Moscow, 119121, Russian Federation
| | - Ludmila M Mezhevikina
- Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russian Federation
| | - Eugeny E Fesenko
- Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russian Federation
| | - Sergey M Yudin
- Center for Strategic Planning and Management of Medical and Biological Health Risks, Moscow, 119121, Russian Federation
| |
Collapse
|
29
|
Lambrechts S, Willems A, Tahon G. Uncovering the Uncultivated Majority in Antarctic Soils: Toward a Synergistic Approach. Front Microbiol 2019; 10:242. [PMID: 30828325 PMCID: PMC6385771 DOI: 10.3389/fmicb.2019.00242] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 01/29/2019] [Indexed: 01/22/2023] Open
Abstract
Although Antarctica was once believed to be a sterile environment, it is now clear that the microbial communities inhabiting the Antarctic continent are surprisingly diverse. Until the beginning of the new millennium, little was known about the most abundant inhabitants of the continent: prokaryotes. From then on, however, the rising use of deep sequencing techniques has led to a better understanding of the Antarctic prokaryote diversity and provided insights in the composition of prokaryotic communities in different Antarctic environments. Although these cultivation-independent approaches can produce millions of sequences, linking these data to organisms is hindered by several problems. The largest difficulty is the lack of biological information on large parts of the microbial tree of life, arising from the fact that most microbial diversity on Earth has never been characterized in laboratory cultures. These unknown prokaryotes, also known as microbial dark matter, have been dominantly detected in all major environments on our planet. Laboratory cultures provide access to the complete genome and the means to experimentally verify genomic predictions and metabolic functions and to provide evidence of horizontal gene transfer. Without such well-documented reference data, microbial dark matter will remain a major blind spot in deep sequencing studies. Here, we review our current understanding of prokaryotic communities in Antarctic ice-free soils based on cultivation-dependent and cultivation-independent approaches. We discuss advantages and disadvantages of both approaches and how these strategies may be combined synergistically to strengthen each other and allow a more profound understanding of prokaryotic life on the frozen continent.
Collapse
Affiliation(s)
- Sam Lambrechts
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | | | - Guillaume Tahon
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| |
Collapse
|
30
|
Lee KM, Adams M, Klassen JL. Evaluation of DESS as a storage medium for microbial community analysis. PeerJ 2019; 7:e6414. [PMID: 30740279 PMCID: PMC6368006 DOI: 10.7717/peerj.6414] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 12/24/2018] [Indexed: 12/14/2022] Open
Abstract
Microbial ecology research requires sampling strategies that accurately represent the microbial community under study. These communities must typically be transported from the collection location to the laboratory and then stored until they can be processed. However, there is a lack of consensus on how best to preserve microbial communities during transport and storage. Here, we evaluated dimethyl sulfoxide, ethylenediamine tetraacetic acid, saturated salt (DESS) solution as a broadly applicable preservative for microbial ecology experiments. We stored fungus gardens grown by the ant Trachymyrmex septentrionalis in DESS, 15% glycerol, and phosphate buffered saline (PBS) to test their impact on the fungus garden microbial community. Variation in microbial community structure due to differences in preservative type was minimal when compared to variation between ant colonies. Additionally, DESS preserved the structure of a defined mock community more faithfully than either 15% glycerol or PBS. DESS is inexpensive, easy to transport, and effective in preserving microbial community structure. We therefore conclude that DESS is a valuable preservative for use in microbial ecology research.
Collapse
Affiliation(s)
- Kevin M Lee
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Madison Adams
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Jonathan L Klassen
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| |
Collapse
|
31
|
Stiles WAV, Styles D, Chapman SP, Esteves S, Bywater A, Melville L, Silkina A, Lupatsch I, Fuentes Grünewald C, Lovitt R, Chaloner T, Bull A, Morris C, Llewellyn CA. Using microalgae in the circular economy to valorise anaerobic digestate: challenges and opportunities. BIORESOURCE TECHNOLOGY 2018; 267:732-742. [PMID: 30076074 DOI: 10.1016/j.biortech.2018.07.100] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 07/18/2018] [Accepted: 07/19/2018] [Indexed: 06/08/2023]
Abstract
Managing organic waste streams is a major challenge for the agricultural industry. Anaerobic digestion (AD) of organicwastes is a preferred option in the waste management hierarchy, as this processcangenerate renewableenergy, reduce emissions from wastestorage, andproduce fertiliser material.However, Nitrate Vulnerable Zone legislation and seasonal restrictions can limit the use of digestate on agricultural land. In this paper we demonstrate the potential of cultivating microalgae on digestate as a feedstock, either directlyafter dilution, or indirectlyfromeffluent remaining after biofertiliser extraction. Resultant microalgal biomass can then be used to produce livestock feed, biofuel or for higher value bio-products. The approach could mitigate for possible regional excesses, and substitute conventional high-impactproducts with bio-resources, enhancing sustainability withinacircular economy. Recycling nutrients from digestate with algal technology is at an early stage. We present and discuss challenges and opportunities associated with developing this new technology.
Collapse
Affiliation(s)
- William A V Stiles
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Gogerddan Campus, Aberystwyth, UK.
| | - David Styles
- School of Environment, Natural Resources & Geography, Bangor University, Bangor, UK
| | - Stephen P Chapman
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Gogerddan Campus, Aberystwyth, UK
| | - Sandra Esteves
- Wales Centre of Excellence for Anaerobic Digestion, Sustainable Environment Research Centre, Faculty of Computing, Engineering and Science, University of South Wales, Pontypridd, UK
| | - Angela Bywater
- University of Southampton, University Road, Southampton, UK
| | - Lynsey Melville
- Centre for Low Carbon Research, Faculty of Computing, Engineering and the Built Environment, Birmingham City University, City Centre Campus, Millennium Point, Birmingham, UK
| | - Alla Silkina
- Department of Biosciences, Swansea University, Singleton Park, Swansea, UK
| | - Ingrid Lupatsch
- AB Agri Ltd, 64 Innovation Way, Peterborough Business Park, Lynchwood, Peterborough, UK
| | | | - Robert Lovitt
- Department of Biosciences, Swansea University, Singleton Park, Swansea, UK
| | | | - Andy Bull
- Severn Wye Energy Agency, Unit 15, Highnam Business Centre, Highnam, Gloucester, UK
| | - Chris Morris
- Fre-energy Ltd, Lodge Farm, Commonwood, Holt, Wrexham, UK
| | - Carole A Llewellyn
- Department of Biosciences, Swansea University, Singleton Park, Swansea, UK
| |
Collapse
|
32
|
Lindeboom REF, Ilgrande C, Carvajal-Arroyo JM, Coninx I, Van Hoey O, Roume H, Morozova J, Udert KM, Sas B, Paille C, Lasseur C, Ilyin V, Clauwaert P, Leys N, Vlaeminck SE. Nitrogen cycle microorganisms can be reactivated after Space exposure. Sci Rep 2018; 8:13783. [PMID: 30214003 PMCID: PMC6137101 DOI: 10.1038/s41598-018-32055-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 08/28/2018] [Indexed: 11/09/2022] Open
Abstract
Long-term human Space missions depend on regenerative life support systems (RLSS) to produce food, water and oxygen from waste and metabolic products. Microbial biotechnology is efficient for nitrogen conversion, with nitrate or nitrogen gas as desirable products. A prerequisite to bioreactor operation in Space is the feasibility to reactivate cells exposed to microgravity and radiation. In this study, microorganisms capable of essential nitrogen cycle conversions were sent on a 44-days FOTON-M4 flight to Low Earth Orbit (LEO) and exposed to 10-3-10-4 g (gravitational constant) and 687 ± 170 µGy (Gray) d-1 (20 ± 4 °C), about the double of the radiation prevailing in the International Space Station (ISS). After return to Earth, axenic cultures, defined and reactor communities of ureolytic bacteria, ammonia oxidizing archaea and bacteria, nitrite oxidizing bacteria, denitrifiers and anammox bacteria could all be reactivated. Space exposure generally yielded similar or even higher nitrogen conversion rates as terrestrial preservation at a similar temperature, while terrestrial storage at 4 °C mostly resulted in the highest rates. Refrigerated Space exposure is proposed as a strategy to maximize the reactivation potential. For the first time, the combined potential of ureolysis, nitritation, nitratation, denitrification (nitrate reducing activity) and anammox is demonstrated as key enabler for resource recovery in human Space exploration.
Collapse
Affiliation(s)
- Ralph E F Lindeboom
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Gent, Belgium.,Section Sanitary Engineering, Department of Water Management, Faculty of Civil Engineering and Geosciences, Delft University of Technology, Stevinweg 1, 2628CN, Delft, The Netherlands
| | - Chiara Ilgrande
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Gent, Belgium
| | - José M Carvajal-Arroyo
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Gent, Belgium
| | - Ilse Coninx
- Unit of Microbiology, Belgian Nuclear Research Centre (SCK•CEN), Boeretang 200, 2400, Mol, Belgium
| | - Olivier Van Hoey
- Unit of Research in Dosimetric Applications, Belgian Nuclear Research Centre (SCK•CEN), Boeretang 200, 2400, Mol, Belgium
| | - Hugo Roume
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Gent, Belgium.,MetaGenoPolis, INRA, Université Paris-Saclay Domaine de Vilvert, Bat. 325 78352, Jouy-en-Josas, France
| | - Julia Morozova
- Institute of Biomedical Problems (IMBP), State Research Center of The Russian Federation, Khoroshevskoye Shosse, 76a, 123007, Moscow, Russia
| | - Kai M Udert
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600, Dübendorf, Switzerland.,ETH Zürich, Institute of Environmental Engineering, 8093, Zürich, Switzerland
| | - Benedikt Sas
- Laboratory of Food Microbiology and Food Preservation, Ghent University, Coupure links 653, 9000, Gent, Belgium
| | | | | | - Vyacheslav Ilyin
- Institute of Biomedical Problems (IMBP), State Research Center of The Russian Federation, Khoroshevskoye Shosse, 76a, 123007, Moscow, Russia
| | - Peter Clauwaert
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Gent, Belgium
| | - Natalie Leys
- Unit of Microbiology, Belgian Nuclear Research Centre (SCK•CEN), Boeretang 200, 2400, Mol, Belgium
| | - Siegfried E Vlaeminck
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Gent, Belgium. .,Research of Sustainable Energy, Air and Water Technology, Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerpen, Belgium.
| |
Collapse
|
33
|
Sánchez-Sanhueza G, Bello-Toledo H, González-Rocha G, Gonçalves AT, Valenzuela V, Gallardo-Escárate C. Metagenomic study of bacterial microbiota in persistent endodontic infections using Next-generation sequencing. Int Endod J 2018; 51:1336-1348. [PMID: 29786880 DOI: 10.1111/iej.12953] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 05/13/2018] [Indexed: 12/16/2022]
Abstract
AIM To determine the bacterial microbiota in root canals associated with persistent apical periodontitis and their relationship with the clinical characteristics of patients using next-generation sequencing (NGS). METHODOLOGY Bacterial samples from root canals associated with teeth having persistent apical periodontitis were taken from 24 patients undergoing root canal retreatment. Bacterial DNA was extracted, and V3-V4 variable regions of the 16S rRNA gene were amplified. The amplification was deep sequenced by Illumina technology to establish the metagenetic relationships among the bacterial species identified. The composition and diversity of microbial communities in the root canal and their relationships with clinical features were analysed. Parametric and nonparametric tests were used to analyse differences between patient characteristics and microbial data. RESULTS A total of 86 different operational taxonomic units (OTUs) were identified and Good's nonparametric coverage estimator method indicated that 99.9 ± 0.00001% diversity was recovered per sample. The largest number of bacteria belonged to the phylum Proteobacteria. According to the medical history from the American Society of Anesthesiologists (ASA) Classification System, ASA II-III had higher richness estimates and distinct phylogenetic relationships compared to ASA I individuals (P < 0.05). Periapical index (PAI) score 5 was associated with increased microbiota diversity in comparison to PAI score 4, and this index was reduced in symptomatic patients. CONCLUSIONS Based on the findings of this study, it is possible to suggest a close relationship between several clinical features and greater microbiota diversity with persistent endodontic infections. This work provides a better understanding on how microbial communities interact with their host and vice versa.
Collapse
Affiliation(s)
- G Sánchez-Sanhueza
- Discipline of Endodontics, Faculty of Dentistry, Department of Restorative Dentistry, University of Concepción, Concepción, Chile
| | - H Bello-Toledo
- Research Laboratory on Antibacterial Agents, Faculty of Biological Sciences, Department of Microbiology, University of Concepción, Concepción, Chile
| | - G González-Rocha
- Research Laboratory on Antibacterial Agents, Faculty of Biological Sciences, Department of Microbiology, University of Concepción, Concepción, Chile
| | - A T Gonçalves
- Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, University of Concepción, Concepción, Chile
| | - V Valenzuela
- Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, University of Concepción, Concepción, Chile
| | - C Gallardo-Escárate
- Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, University of Concepción, Concepción, Chile
| |
Collapse
|
34
|
Abstract
Continuous cultures in chemostats have proven their value in microbiology, microbial ecology, systems biology and bioprocess engineering, among others. In these systems, microbial growth and ecosystem performance can be quantified under stable and defined environmental conditions. This is essential when linking microbial diversity to ecosystem function. Here, a new system to test this link in anaerobic, methanogenic microbial communities is introduced. Rigorously replicated experiments or a suitable experimental design typically require operating several chemostats in parallel. However, this is labor intensive, especially when measuring biogas production. Commercial solutions for multiplying reactors performing continuous anaerobic digestion exist but are expensive and use comparably large reactor volumes, requiring the preparation of substantial amounts of media. Here, a flexible system of Lab-scale Automated and Multiplexed Anaerobic Chemostat system (LAMACs) with a working volume of 200 mL is introduced. Sterile feeding, biomass wasting and pressure monitoring are automated. One module containing six reactors fits the typical dimensions of a lab bench. Thanks to automation, time required for reactor operation and maintenance are reduced compared to traditional lab-scale systems. Several modules can be used together, and so far the parallel operation of 30 reactors was demonstrated. The chemostats are autoclavable. Parameters like reactor volume, flow rates and operating temperature can be freely set. The robustness of the system was tested in a two-month long experiment in which three inocula in four replicates, i.e., twelve continuous digesters were monitored. Statistically significant differences in the biogas production between inocula were observed. In anaerobic digestion, biogas production and consequently pressure development in a closed environment is a proxy for ecosystem performance. The precision of the pressure measurement is thus crucial. The measured maximum and minimum rates of gas production could be determined at the same precision. The LAMACs is a tool that enables us to put in practice the often-demanded need for replication and rigorous testing in microbial ecology as well as bioprocess engineering.
Collapse
|
35
|
Harnessing the Power of PCR Molecular Fingerprinting Methods and Next Generation Sequencing for Understanding Structure and Function in Microbial Communities. Methods Mol Biol 2018; 1620:225-248. [PMID: 28540712 DOI: 10.1007/978-1-4939-7060-5_16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Abstract
Polymerase chain reaction (PCR) is central to methods in molecular ecology. Here, we describe PCR-dependent approaches useful for investigating microbial diversity and its function in various natural, human-associated, and built environment ecosystems. Protocols routinely used for DNA extraction, purification, cloning, and sequencing are included along with various resources for the statistical analysis following gel electrophoresis-based methods (DGGE) and sequencing. We also provide insights into eukaryotic microbiome analysis, sample preservation techniques, PCR troubleshooting, DNA quantification methods, and commonly used ordination techniques.
Collapse
|
36
|
Canter EJ, Cuellar-Gempeler C, Pastore AI, Miller TE, Mason OU. Predator identity more than predator richness structures aquatic microbial assemblages in Sarracenia purpurea
leaves. Ecology 2018; 99:652-660. [DOI: 10.1002/ecy.2128] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 11/19/2017] [Accepted: 12/07/2017] [Indexed: 11/07/2022]
Affiliation(s)
- Erin J. Canter
- Department of Earth, Ocean and Atmospheric Science; Florida State University; Tallahassee Florida USA
| | | | - Abigail I. Pastore
- Department of Biological Science; Florida State University; Tallahassee Florida USA
| | - Thomas E. Miller
- Department of Biological Science; Florida State University; Tallahassee Florida USA
| | - Olivia U. Mason
- Department of Earth, Ocean and Atmospheric Science; Florida State University; Tallahassee Florida USA
| |
Collapse
|
37
|
Bircher L, Schwab C, Geirnaert A, Lacroix C. Cryopreservation of artificial gut microbiota produced with in vitro fermentation technology. Microb Biotechnol 2017; 11:163-175. [PMID: 28980453 PMCID: PMC5743790 DOI: 10.1111/1751-7915.12844] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 06/29/2017] [Accepted: 07/28/2017] [Indexed: 12/13/2022] Open
Abstract
Interest in faecal microbiota transplantation (FMT) has increased as therapy for intestinal diseases, but safety issues limit its widespread use. Intestinal fermentation technology (IFT) can produce controlled, diverse and metabolically active ‘artificial’ colonic microbiota as potential alternative to common FMT. However, suitable processing technology to store this artificial microbiota is lacking. In this study, we evaluated the impact of the two cryoprotectives, glycerol (15% v/v) and inulin (5% w/v) alone and in combination, in preserving short‐chain fatty acid formation and recovery of major butyrate‐producing bacteria in three artificial microbiota during cryopreservation for 3 months at −80°C. After 24 h anaerobic fermentation of the preserved microbiota, butyrate and propionate production were maintained when glycerol was used as cryoprotectant, while acetate and butyrate were formed more rapidly with glycerol in combination with inulin. Glycerol supported cryopreservation of the Roseburia spp./Eubacterium rectale group, while inulin improved the recovery of Faecalibacterium prausnitzii. Eubacterium hallii growth was affected minimally by cryopreservation. Our data indicate that butyrate producers, which are key organisms for gut health, can be well preserved with glycerol and inulin during frozen storage. This is of high importance if artificially produced colonic microbiota is considered for therapeutic purposes.
Collapse
Affiliation(s)
- Lea Bircher
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zürich, Schmelzbergstrasse 7, 8092, Zürich, Switzerland
| | - Clarissa Schwab
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zürich, Schmelzbergstrasse 7, 8092, Zürich, Switzerland
| | - Annelies Geirnaert
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zürich, Schmelzbergstrasse 7, 8092, Zürich, Switzerland
| | - Christophe Lacroix
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zürich, Schmelzbergstrasse 7, 8092, Zürich, Switzerland
| |
Collapse
|
38
|
Ridley CJA, Day JG, Smith AG. Cryopreservation studies of an artificial co-culture between the cobalamin-requiring green alga Lobomonas rostrata and the bacterium Mesorhizobium loti. JOURNAL OF APPLIED PHYCOLOGY 2017; 30:995-1003. [PMID: 29755204 PMCID: PMC5928187 DOI: 10.1007/s10811-017-1270-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 09/04/2017] [Accepted: 09/04/2017] [Indexed: 06/08/2023]
Abstract
Algal-bacterial co-cultures, rather than cultures of algae alone, are regarded as having the potential to enhance productivity and stability in industrial algal cultivation. As with other inocula in biotechnology, to avoid loss of production strains, it is important to develop preservation methods for the long-term storage of these cultures, and one of the most commonly used approaches is cryopreservation. However, whilst there are many reports of cryopreserved xenic algal cultures, little work has been reported on the intentional preservation of both algae and beneficial bacteria in xenic cultures. Instead, studies have focused on the development of methods to conserve the algal strain(s) present, or to avoid overgrowth of bacteria in xenic isolates during the post-thaw recovery phase. Here, we have established a co-cryopreservation method for the long-term storage of both partners in a unialgal-bacterial co-culture. This is an artificial model mutualism between the alga Lobomonas rostrata and the bacterium Mesorhizobium loti, which provides vitamin B12 (cobalamin) to the alga in return for photosynthate. Using a Planer Kryo 360 controlled-rate cooler, post-thaw viability (PTV) values of 72% were obtained for the co-culture, compared to 91% for the axenic alga. The cultures were successfully revived after 6 months storage in liquid nitrogen, and continued to exhibit mutualism. Furthermore, the alga could be cryopreserved with non-symbiotic bacteria, without bacterial overgrowth occurring. It was also possible to use less controllable passive freezer chambers to cryopreserve the co-cultures, although the PTV was lower. Finally, we demonstrated that an optimised cryopreservation method may be used to prevent the overgrowth potential of non-symbiotic, adventitious bacteria in both axenic and co-cultures of L. rostrata after thawing.
Collapse
Affiliation(s)
| | - John G. Day
- Scottish Association for Marine Science, Scottish Marine Institute, Oban, PA37 1QA UK
| | - Alison G. Smith
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA UK
| |
Collapse
|
39
|
Vandeputte D, Tito RY, Vanleeuwen R, Falony G, Raes J. Practical considerations for large-scale gut microbiome studies. FEMS Microbiol Rev 2017; 41:S154-S167. [PMID: 28830090 PMCID: PMC7207147 DOI: 10.1093/femsre/fux027] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 06/19/2017] [Indexed: 12/14/2022] Open
Abstract
First insights on the human gut microbiome have been gained from medium-sized, cross-sectional studies. However, given the modest portion of explained variance of currently identified covariates and the small effect size of gut microbiota modulation strategies, upscaling seems essential for further discovery and characterisation of the multiple influencing factors and their relative contribution. In order to guide future research projects and standardisation efforts, we here review currently applied collection and preservation methods for gut microbiome research. We discuss aspects such as sample quality, applicable omics techniques, user experience and time and cost efficiency. In addition, we evaluate the protocols of a large-scale microbiome cohort initiative, the Flemish Gut Flora Project, to give an idea of perspectives, and pitfalls of large-scale faecal sampling studies. Although cryopreservation can be regarded as the gold standard, freezing protocols generally require more resources due to cold chain management. However, here we show that much can be gained from an optimised transport chain and sample aliquoting before freezing. Other protocols can be useful as long as they preserve the microbial signature of a sample such that relevant conclusions can be drawn regarding the research question, and the obtained data are stable and reproducible over time.
Collapse
Affiliation(s)
- Doris Vandeputte
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Herestraat 49, B-3000 Leuven, Belgium
- VIB, Center for Microbiology, Herestraat 49, B-3000 Leuven, Belgium
- Microbiology Unit, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Raul Y. Tito
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Herestraat 49, B-3000 Leuven, Belgium
- VIB, Center for Microbiology, Herestraat 49, B-3000 Leuven, Belgium
- Microbiology Unit, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Rianne Vanleeuwen
- Universiteit Antwerpen, Productontwikkeling, Ambtmanstraat 1, B-2000 Antwerpen, Belgium
| | - Gwen Falony
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Herestraat 49, B-3000 Leuven, Belgium
- VIB, Center for Microbiology, Herestraat 49, B-3000 Leuven, Belgium
| | - Jeroen Raes
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Herestraat 49, B-3000 Leuven, Belgium
- VIB, Center for Microbiology, Herestraat 49, B-3000 Leuven, Belgium
| |
Collapse
|
40
|
Siniscalchi LAB, Leite LR, Oliveira G, Chernicharo CAL, de Araújo JC. Illumina sequencing-based analysis of a microbial community enriched under anaerobic methane oxidation condition coupled to denitrification revealed coexistence of aerobic and anaerobic methanotrophs. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:16751-16764. [PMID: 28567677 DOI: 10.1007/s11356-017-9197-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 05/02/2017] [Indexed: 06/07/2023]
Abstract
Methane is produced in anaerobic environments, such as reactors used to treat wastewaters, and can be consumed by methanotrophs. The composition and structure of a microbial community enriched from anaerobic sewage sludge under methane-oxidation condition coupled to denitrification were investigated. Denaturing gradient gel electrophoresis (DGGE) analysis retrieved sequences of Methylocaldum and Chloroflexi. Deep sequencing analysis revealed a complex community that changed over time and was affected by methane concentration. Methylocaldum (8.2%), Methylosinus (2.3%), Methylomonas (0.02%), Methylacidiphilales (0.45%), Nitrospirales (0.18%), and Methanosarcinales (0.3%) were detected. Despite denitrifying conditions provided, Nitrospirales and Methanosarcinales, known to perform anaerobic methane oxidation coupled to denitrification (DAMO) process, were in very low abundance. Results demonstrated that aerobic and anaerobic methanotrophs coexisted in the reactor together with heterotrophic microorganisms, suggesting that a diverse microbial community was important to sustain methanotrophic activity. The methanogenic sludge was a good inoculum to enrich methanotrophs, and cultivation conditions play a selective role in determining community composition.
Collapse
Affiliation(s)
- Luciene Alves Batista Siniscalchi
- Department of Sanitary and Environmental Engineering, Federal University of Minas Gerais, Antonio Carlos Avenue, 6627, Belo Horizonte, Minas Gerais State, 31270-901, Brazil
- Department of Engineering, Federal University of Lavras, Dr. Sylvio Menicucci Avenue, 1001, Lavras, Minas Gerais State, 37200-000, Brazil
| | - Laura Rabelo Leite
- Department of Engineering, Federal University of Lavras, Dr. Sylvio Menicucci Avenue, 1001, Lavras, Minas Gerais State, 37200-000, Brazil
| | - Guilherme Oliveira
- Genomics and Computational Biology Group, René Rachou Research Center, Oswaldo Cruz Foundation, Augusto de Lima Avenue 1715, Belo Horizonte, Minas Gerais State, 30.190-002, Brazil
- Instituto Vale de Tecnologia, Rua Boaventura da Silva, 955, Belém, Pará, 66055-090, Brazil
| | - Carlos Augusto Lemos Chernicharo
- Department of Sanitary and Environmental Engineering, Federal University of Minas Gerais, Antonio Carlos Avenue, 6627, Belo Horizonte, Minas Gerais State, 31270-901, Brazil
| | - Juliana Calabria de Araújo
- Department of Sanitary and Environmental Engineering, Federal University of Minas Gerais, Antonio Carlos Avenue, 6627, Belo Horizonte, Minas Gerais State, 31270-901, Brazil.
| |
Collapse
|
41
|
Kim D, Hofstaedter CE, Zhao C, Mattei L, Tanes C, Clarke E, Lauder A, Sherrill-Mix S, Chehoud C, Kelsen J, Conrad M, Collman RG, Baldassano R, Bushman FD, Bittinger K. Optimizing methods and dodging pitfalls in microbiome research. MICROBIOME 2017; 5:52. [PMID: 28476139 PMCID: PMC5420141 DOI: 10.1186/s40168-017-0267-5] [Citation(s) in RCA: 325] [Impact Index Per Article: 46.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Accepted: 04/21/2017] [Indexed: 05/09/2023]
Abstract
Research on the human microbiome has yielded numerous insights into health and disease, but also has resulted in a wealth of experimental artifacts. Here, we present suggestions for optimizing experimental design and avoiding known pitfalls, organized in the typical order in which studies are carried out. We first review best practices in experimental design and introduce common confounders such as age, diet, antibiotic use, pet ownership, longitudinal instability, and microbial sharing during cohousing in animal studies. Typically, samples will need to be stored, so we provide data on best practices for several sample types. We then discuss design and analysis of positive and negative controls, which should always be run with experimental samples. We introduce a convenient set of non-biological DNA sequences that can be useful as positive controls for high-volume analysis. Careful analysis of negative and positive controls is particularly important in studies of samples with low microbial biomass, where contamination can comprise most or all of a sample. Lastly, we summarize approaches to enhancing experimental robustness by careful control of multiple comparisons and to comparing discovery and validation cohorts. We hope the experimental tactics summarized here will help researchers in this exciting field advance their studies efficiently while avoiding errors.
Collapse
Affiliation(s)
- Dorothy Kim
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 USA
| | - Casey E. Hofstaedter
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 USA
| | - Chunyu Zhao
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 USA
| | - Lisa Mattei
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 USA
| | - Ceylan Tanes
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 USA
| | - Erik Clarke
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 USA
| | - Abigail Lauder
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 USA
| | - Scott Sherrill-Mix
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 USA
| | - Christel Chehoud
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 USA
| | - Judith Kelsen
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 USA
| | - Máire Conrad
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 USA
| | - Ronald G. Collman
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104 USA
| | - Robert Baldassano
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 USA
| | - Frederic D. Bushman
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 USA
| |
Collapse
|
42
|
Gaci N, Chaudhary PP, Tottey W, Alric M, Brugère JF. Functional amplification and preservation of human gut microbiota. MICROBIAL ECOLOGY IN HEALTH AND DISEASE 2017; 28:1308070. [PMID: 28572754 PMCID: PMC5443092 DOI: 10.1080/16512235.2017.1308070] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 03/15/2017] [Indexed: 12/13/2022]
Abstract
Background: The availability of fresh stool samples is a prerequisite in most gut microbiota functional studies. Objective: Strategies for amplification and long-term gut microbiota preservation from fecal samples would favor sample sharing, help comparisons and reproducibility over time and between laboratories, and improve the safety and ethical issues surrounding fecal microbiota transplantations. Design: Taking advantage of in vitro gut-simulating systems, we amplified the microbial repertoire of a fresh fecal sample and assessed the viability and resuscitation of microbes after preservation with some common intracellular and extracellular acting cryoprotective agents (CPAs), alone and in different combinations. Preservation efficiencies were determined after 3 and 6 months and compared with the fresh initial microbiota diversity and metabolic activity, using the chemostat-based Environmental Control System for Intestinal Microbiota (ECSIM) in vitro model of the gut environment. Microbial populations were tested for fermentation gas, short-chain fatty acids, and composition of amplified and resuscitated microbiota, encompassing methanogenic archaea. Results: Amplification of the microbial repertoire from a fresh fecal sample was achieved with high fidelity. Dimethylsulfoxide, alone or mixed with other CPAs, showed the best efficiency for functional preservation, and the duration of preservation had little effect. Conclusions: The amplification and resuscitation of fecal microbiota can be performed using specialized in vitro gut models. Correct amplification of the initial microbes should ease the sharing of clinical samples and improve the safety of fecal microbiota transplantation. Abbreviations: CDI, Clostridium difficile infection; CPA, cryoprotective agent; D, DMSO, dimethylsulfoxide; FMT, fecal microbiota transplantation; G, glycerol; IBD, inflammatory bowel disease; P, PEG-4000, polyethylene glycol 4000 g.mol−1; SCFA, short-chain fatty acid; SNR, signal-to-noise ratio
Collapse
Affiliation(s)
- Nadia Gaci
- EA-4678 CIDAM, Clermont Université, Université d'Auvergne, Clermont-Ferrand, France
| | | | - William Tottey
- EA-4678 CIDAM, Clermont Université, Université d'Auvergne, Clermont-Ferrand, France
| | - Monique Alric
- EA-4678 CIDAM, Clermont Université, Université d'Auvergne, Clermont-Ferrand, France
| | | |
Collapse
|
43
|
Silkina A, Nelson GD, Bayliss CE, Pooley CL, Day JG. Bioremediation efficacy-comparison of nutrient removal from an anaerobic digest waste-based medium by an algal consortium before and after cryopreservation. JOURNAL OF APPLIED PHYCOLOGY 2017; 29:1331-1341. [PMID: 28572708 PMCID: PMC5429893 DOI: 10.1007/s10811-017-1066-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 01/17/2017] [Accepted: 01/18/2017] [Indexed: 06/07/2023]
Abstract
An algal consortium was isolated from an integrated steelmaking site at TATA Steel Strip Products Ltd. in Port Talbot, UK, and its bioremediation capacity tested. Excellent "bioremediation" was observed when the mixed culture was "applied" to diluted effluent from an enhanced anaerobic digestion plant at Dŵr Cymru Welsh Water at Port Talbot, UK. After 5 days of cultivation in a 600-L photobioreactor, 99% of the total nitrogen (initial level, 4500 μmol L-1) and total phosphorus (initial level, 690.4 μmol L-1) were removed from the waste stream. The consortium was deposited in the Culture Collection of Algae and Protozoa (CCAP), an international depository authority for microalgal patents, as CCAP 293/1. This material has been successfully cryopreserved using a two-step cryopreservation protocol with dimethyl sulphoxide (5% v/v) used as a cryoprotectant. On recovery of samples after 3 months storage at -196 °C, the specific bioremediation activity of the revived consortium was tested. The capacity of the revived culture to bioremediate effluent was not significantly different (p < 0.05) from a non-cryopreserved control, with 99% of total nitrogen and phosphorus remediated by day 4. Although non-axenic algal cultures have previously been cryopreserved, this is the first report of the successful cryopreservation of mixed algal consortium, with validation of its ability to bioremediate after thawing comparing non-cryopreserved cultures with a revived post-thaw algal consortium. The study also highlights the need to ensure the long-term security and the requirement to validate the functionality of conserved inocula with biotechnological/bioremediation potential.
Collapse
Affiliation(s)
- Alla Silkina
- Centre for Sustainable Aquatic Research (CSAR), Swansea University, Swansea, SA2 8PP UK
| | - Graham D. Nelson
- Centre for Sustainable Aquatic Research (CSAR), Swansea University, Swansea, SA2 8PP UK
| | - Catherine E. Bayliss
- Centre for Sustainable Aquatic Research (CSAR), Swansea University, Swansea, SA2 8PP UK
| | - Craig L. Pooley
- Centre for Sustainable Aquatic Research (CSAR), Swansea University, Swansea, SA2 8PP UK
| | - John G. Day
- The Culture Collection for Algae and Protozoa, Scottish Association for Marine Science, Scottish Marine Institute, Oban, PA37 1QA UK
| |
Collapse
|
44
|
Aguirre M, Venema K. Challenges in simulating the human gut for understanding the role of the microbiota in obesity. Benef Microbes 2016; 8:31-53. [PMID: 27903093 DOI: 10.3920/bm2016.0113] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
There is an elevated incidence of cases of obesity worldwide. Therefore, the development of strategies to tackle this condition is of vital importance. This review focuses on the necessity of optimising in vitro systems to model human colonic fermentation in obese subjects. This may allow to increase the resolution and the physiological relevance of the information obtained from this type of studies when evaluating the potential role that the human gut microbiota plays in obesity. In light of the parameters that are currently used for the in vitro simulation of the human gut (which are mostly based on information derived from healthy subjects) and the possible difference with an obese condition, we propose to revise and improve specific standard operating procedures.
Collapse
Affiliation(s)
- M Aguirre
- 1 Top Institute of Food and Nutrition, P.O. Box 557, 6700 AA Wageningen, the Netherlands.,2 Department of Human Biology, Faculty of Health, Medicine and Life Sciences, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, P.O. Box 616, 6200 MD Maastricht, the Netherlands.,3 The Netherlands Organization for Applied Scientific Research (TNO), P.O. Box 360, 3700 AJ Zeist, the Netherlands
| | - K Venema
- 1 Top Institute of Food and Nutrition, P.O. Box 557, 6700 AA Wageningen, the Netherlands.,2 Department of Human Biology, Faculty of Health, Medicine and Life Sciences, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, P.O. Box 616, 6200 MD Maastricht, the Netherlands.,4 Beneficial Microbes Consultancy, Johan Karschstraat 3, 6709 TN Wageningen, the Netherlands
| |
Collapse
|
45
|
Van Herreweghen F, Van den Abbeele P, De Mulder T, De Weirdt R, Geirnaert A, Hernandez-Sanabria E, Vilchez-Vargas R, Jauregui R, Pieper DH, Belzer C, De Vos WM, Van de Wiele T. In vitro colonisation of the distal colon by Akkermansia muciniphila is largely mucin and pH dependent. Benef Microbes 2016; 8:81-96. [PMID: 27824274 DOI: 10.3920/bm2016.0013] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Host mucin is the main constituent of the mucus layer that covers the gut epithelium of the host, and an important source of glycans for the bacteria colonising the intestine. Akkermansia muciniphila is a mucin-degrading bacterium, abundant in the human gut, that is able to produce acetate and propionate during this degradation process. A. muciniphila has been correlated with human health in previous studies, but a mechanistic explanation is lacking. In this study, the main site of colonisation was characterised alongside additional conditions, such as differences in colon pH, prebiotic supplementation and variable mucin supply. To overcome the limitations of in vivo studies concerning variations in mucin availability and difficult access to proximal regions of the colon, a dynamic in vitro gut model (SHIME) was used. In this model, A. muciniphila was found to colonise the distal colon compartment more abundantly than the proximal colon ((±8 log copies/ml compared to ±4 log copies/ml) and the preference for the distal compartment was found to be pH-dependent. The addition of mucin caused a specific increase of A. muciniphila (±4.5 log increase over two days), far exceeding the response of other bacteria present, together with an increase in propionate. These findings suggest that colonisation and mucin degradation by A. muciniphila is dependent on pH and the concentration of mucin. Our results revealed the preference of A. muciniphila for the distal colon environment due to its higher pH and uncovered the quick and stable response of A. muciniphila to mucin supplementation.
Collapse
Affiliation(s)
- F Van Herreweghen
- 1 Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - P Van den Abbeele
- 1 Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium.,4 ProDigest BVBA, Technologiepark 3, 9052 Zwijnaarde (Ghent), Belgium
| | - T De Mulder
- 1 Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - R De Weirdt
- 1 Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - A Geirnaert
- 1 Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - E Hernandez-Sanabria
- 1 Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - R Vilchez-Vargas
- 1 Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - R Jauregui
- 3 Microbial Interactions and Processes Research Group, Department of Medical Microbiology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - D H Pieper
- 3 Microbial Interactions and Processes Research Group, Department of Medical Microbiology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - C Belzer
- 2 Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands
| | - W M De Vos
- 2 Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands
| | - T Van de Wiele
- 1 Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| |
Collapse
|
46
|
Roume H, Arends JBA, Ameril CP, Patil SA, Rabaey K. Enhanced Product Recovery from Glycerol Fermentation into 3-Carbon Compounds in a Bioelectrochemical System Combined with In Situ Extraction. Front Bioeng Biotechnol 2016; 4:73. [PMID: 27725929 PMCID: PMC5035740 DOI: 10.3389/fbioe.2016.00073] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 09/06/2016] [Indexed: 11/20/2022] Open
Abstract
Given the large amount of crude glycerol formed as a by-product in the biodiesel industries and the concomitant decrease in its overall market price, there is a need to add extra value to this biorefinery side stream. Upgrading can be achieved by new biotechnologies dealing with recovery and conversion of glycerol present in wastewaters into value-added products, aiming at a zero-waste policy and developing an economically viable process. In microbial bioelectrochemical systems (BESs), the mixed microbial community growing on the cathode can convert glycerol reductively to 1,3-propanediol (1,3-PDO). However, the product yield is rather limited in BESs compared with classic fermentation processes, and the synthesis of side-products, resulting from oxidation of glycerol, such as organic acids, represents a major burden for recovery of 1,3-PDO. Here, we show that the use of an enriched mixed-microbial community of glycerol degraders and in situ extraction of organic acids positively impacts 1,3-PDO yield and allows additional recovery of propionate from glycerol. We report the highest production yield achieved (0.72 mol1,3-PDO mol−1glycerol) in electricity-driven 1,3-PDO biosynthesis from raw glycerol, which is very close to the 1,3-PDO yield reported thus far for a mixed-microbial culture-based glycerol fermentation process. We also present a combined approach for 1,3-PDO production and propionate extraction in a single three chamber reactor system, which leads to recovery of additional 3-carbon compounds in BESs. This opens up further opportunities for an economical upgrading of biodiesel refinery side or waste streams.
Collapse
Affiliation(s)
- Hugo Roume
- Faculty of Bioscience Engineering, Center for Microbial Ecology and Technology (CMET), Ghent University , Gent , Belgium
| | - Jan B A Arends
- Faculty of Bioscience Engineering, Center for Microbial Ecology and Technology (CMET), Ghent University , Gent , Belgium
| | - Camar P Ameril
- Faculty of Bioscience Engineering, Center for Microbial Ecology and Technology (CMET), Ghent University , Gent , Belgium
| | - Sunil A Patil
- Faculty of Bioscience Engineering, Center for Microbial Ecology and Technology (CMET), Ghent University , Gent , Belgium
| | - Korneel Rabaey
- Faculty of Bioscience Engineering, Center for Microbial Ecology and Technology (CMET), Ghent University , Gent , Belgium
| |
Collapse
|
47
|
Ho A, Angel R, Veraart AJ, Daebeler A, Jia Z, Kim SY, Kerckhof FM, Boon N, Bodelier PLE. Biotic Interactions in Microbial Communities as Modulators of Biogeochemical Processes: Methanotrophy as a Model System. Front Microbiol 2016; 7:1285. [PMID: 27602021 PMCID: PMC4993757 DOI: 10.3389/fmicb.2016.01285] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 08/04/2016] [Indexed: 11/13/2022] Open
Abstract
Microbial interaction is an integral component of microbial ecology studies, yet the role, extent, and relevance of microbial interaction in community functioning remains unclear, particularly in the context of global biogeochemical cycles. While many studies have shed light on the physico-chemical cues affecting specific processes, (micro)biotic controls and interactions potentially steering microbial communities leading to altered functioning are less known. Yet, recent accumulating evidence suggests that the concerted actions of a community can be significantly different from the combined effects of individual microorganisms, giving rise to emergent properties. Here, we exemplify the importance of microbial interaction for ecosystem processes by analysis of a reasonably well-understood microbial guild, namely, aerobic methane-oxidizing bacteria (MOB). We reviewed the literature which provided compelling evidence for the relevance of microbial interaction in modulating methane oxidation. Support for microbial associations within methane-fed communities is sought by a re-analysis of literature data derived from stable isotope probing studies of various complex environmental settings. Putative positive interactions between active MOB and other microbes were assessed by a correlation network-based analysis with datasets covering diverse environments where closely interacting members of a consortium can potentially alter the methane oxidation activity. Although, methanotrophy is used as a model system, the fundamentals of our postulations may be applicable to other microbial guilds mediating other biogeochemical processes.
Collapse
Affiliation(s)
- Adrian Ho
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands
| | - Roey Angel
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry meets Microbiology, University of Vienna Vienna, Austria
| | - Annelies J Veraart
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands
| | - Anne Daebeler
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry meets Microbiology, University of Vienna Vienna, Austria
| | - Zhongjun Jia
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences Nanjing, China
| | - Sang Yoon Kim
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands
| | - Frederiek-Maarten Kerckhof
- Center for Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University Ghent, Belgium
| | - Nico Boon
- Center for Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University Ghent, Belgium
| | - Paul L E Bodelier
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands
| |
Collapse
|
48
|
Grunert O, Hernandez-Sanabria E, Vilchez-Vargas R, Jauregui R, Pieper DH, Perneel M, Van Labeke MC, Reheul D, Boon N. Mineral and organic growing media have distinct community structure, stability and functionality in soilless culture systems. Sci Rep 2016; 6:18837. [PMID: 26728128 PMCID: PMC4700413 DOI: 10.1038/srep18837] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 11/25/2015] [Indexed: 11/11/2022] Open
Abstract
The choice of soilless growing medium for plant nutrition, growth and support is crucial for improving the eco-sustainability of the production in horticultural systems. As our current understanding of the functional microbial communities inhabiting this ecosystem is still limited, we examined the microbial community development of the two most important growing media (organic and mineral) used in open soilless horticultural systems. We aimed to identify factors that influence community composition over time, and to compare the distribution of individual taxa across growing media, and their potential functionality. High throughput sequencing analysis revealed a distinctive and stable microbial community in the organic growing medium. Humidity, pH, nitrate-N, ammonium-N and conductivity were uncovered as the main factors associated with the resident bacterial communities. Ammonium-N was correlated with Rhizobiaceae abundance, while potential competitive interactions among both Methylophilaceae and Actinobacteridae with Rhizobiaceae were suggested. Our results revealed that soilless growing media are unique niches for diverse bacterial communities with temporal functional stability, which may possibly impact the resistance to external forces. These differences in communities can be used to develop strategies to move towards a sustainable horticulture with increased productivity and quality.
Collapse
Affiliation(s)
- Oliver Grunert
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, B-9000 Gent, Belgium
- Peltracom NV, Skaldenstraat 7a, B-9042 Ghent-Desteldonk, Belgium
| | - Emma Hernandez-Sanabria
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, B-9000 Gent, Belgium
| | - Ramiro Vilchez-Vargas
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, B-9000 Gent, Belgium
| | - Ruy Jauregui
- Microbial Interactions and Processes Research Group, Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Inhoffenstraße 7, D-38124, Braunschweig, Germany
| | - Dietmar H. Pieper
- Microbial Interactions and Processes Research Group, Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Inhoffenstraße 7, D-38124, Braunschweig, Germany
| | - Maaike Perneel
- Peltracom NV, Skaldenstraat 7a, B-9042 Ghent-Desteldonk, Belgium
| | | | - Dirk Reheul
- Department of Plant Production, Ghent University, Coupure Links 653, B-9000 Gent, Belgium
| | - Nico Boon
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, B-9000 Gent, Belgium
| |
Collapse
|
49
|
Yu C, Reddy AP, Simmons CW, Simmons BA, Singer SW, VanderGheynst JS. Preservation of microbial communities enriched on lignocellulose under thermophilic and high-solid conditions. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:206. [PMID: 26633993 PMCID: PMC4667496 DOI: 10.1186/s13068-015-0392-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Accepted: 11/17/2015] [Indexed: 06/05/2023]
Abstract
BACKGROUND Microbial communities enriched from diverse environments have shown considerable promise for the targeted discovery of microorganisms and enzymes for bioconversion of lignocellulose to liquid fuels. While preservation of microbial communities is important for commercialization and research, few studies have examined storage conditions ideal for preservation. The goal of this study was to evaluate the impact of preservation method on composition of microbial communities enriched on switchgrass before and after storage. The enrichments were completed in a high-solid and aerobic environment at 55 °C. Community composition was examined for each enrichment to determine when a stable community was achieved. Preservation methods included cryopreservation with the cryoprotective agents DMSO and glycerol, and cryopreservation without cryoprotective agents. Revived communities were examined for their ability to decompose switchgrass under high-solid and thermophilic conditions. RESULTS High-throughput 16S rRNA gene sequencing of DNA extracted from enrichment samples showed that the majority of the shift in composition of the switchgrass-degrading community occurred during the initial three 2-week enrichments. Shifts in community structure upon storage occurred in all cryopreserved samples. Storage in liquid nitrogen in the absence of cryoprotectant resulted in variable preservation of dominant microorganisms in enriched samples. Cryopreservation with either DMSO or glycerol provided consistent and equivalent preservation of dominant organisms. CONCLUSIONS A stable switchgrass-degrading microbial community was achieved after three 2-week enrichments. Dominant microorganisms were preserved equally well with DMSO and glycerol. DMSO-preserved communities required more incubation time upon revival to achieve pre-storage activity levels during high-solid thermophilic cultivation on switchgrass. Despite shifts in the community with storage, the samples were active upon revival under thermophilic and high-solid conditions. The results suggest that the presence of microorganisms may be more important than their relative abundance in retaining an active microbial community.
Collapse
Affiliation(s)
- Chaowei Yu
- />Department of Biological and Agricultural Engineering, University of California, One Shields Ave, Davis, CA 95616 USA
| | - Amitha P. Reddy
- />Department of Biological and Agricultural Engineering, University of California, One Shields Ave, Davis, CA 95616 USA
- />Joint BioEnergy Institute, Emeryville, CA 94608 USA
| | - Christopher W. Simmons
- />Joint BioEnergy Institute, Emeryville, CA 94608 USA
- />Department of Food Science and Technology, University of California, Davis, CA 95616 USA
| | - Blake A. Simmons
- />Joint BioEnergy Institute, Emeryville, CA 94608 USA
- />Biological and Materials Science Center, Sandia National Laboratories, Livermore, CA 94551 USA
| | - Steven W. Singer
- />Joint BioEnergy Institute, Emeryville, CA 94608 USA
- />Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Jean S. VanderGheynst
- />Department of Biological and Agricultural Engineering, University of California, One Shields Ave, Davis, CA 95616 USA
- />Joint BioEnergy Institute, Emeryville, CA 94608 USA
| |
Collapse
|
50
|
Kadri Z, Spitaels F, Cnockaert M, Praet J, El Farricha O, Swings J, Vandamme P. Enterococcus bulliens sp. nov., a novel lactic acid bacterium isolated from camel milk. Antonie van Leeuwenhoek 2015; 108:1257-65. [DOI: 10.1007/s10482-015-0579-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 08/31/2015] [Indexed: 01/02/2023]
|