1
|
Lodhi AF, Zhang Y, Adil M, Deng Y. Design and application of a novel culturing chip (cChip) for culturing the uncultured aquatic microorganisms. Arch Microbiol 2023; 205:285. [PMID: 37442830 DOI: 10.1007/s00203-023-03613-w] [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: 10/11/2022] [Revised: 05/18/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023]
Abstract
Culturing uncultured microorganisms is an important aspect of microbiology. Once cultured, these microorganisms can be a source of useful antibiotics, enzymes etc. In this study, we have designed a novel culturing chip (cChip) to facilitate the growth of uncultured aquatic bacterial community by concentrating the samples. cChip was optimized for microbial growth using known bacteria in the laboratory as a pre-experiment. Then microorganisms from a freshwater lake were concentrated and inoculated, before putting the inoculated cChip in a simulated lake environment and further sub-culturing on laboratory media. High-throughput sequencing and traditional culturing were also performed for comparison. These three methods were able to detect 265 genera of microorganisms in the sample, of which 78.87% were detected by high-throughput sequencing, 30.94% by cChip, while only 6.42% were obtained by traditional culture. Moreover, all microorganisms obtained by traditional culture were also cultured using the cChip. A total of 45 new strains were isolated from the cChip, and their 16S rRNA gene sequences were 91.35% to 98.7% similar to their closest relatives according to NCBI GenBank database. We conclude that the design and simple operation of cChip can improve the culture efficiency of traditional culture by almost 5 times. To the best of our knowledge, this is the first report comparing a novel culturing method with high-throughput sequencing data and traditional culturing of the same samples.
Collapse
Affiliation(s)
- Adil Farooq Lodhi
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceutical, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
- Department of Microbiology, Faculty of Biological and Health Sciences, Hazara University, Mansehra, Pakistan
| | - Ying Zhang
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceutical, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Maria Adil
- Department of Microbiology, Faculty of Biological and Health Sciences, Hazara University, Mansehra, Pakistan
| | - Yulin Deng
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceutical, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China.
| |
Collapse
|
2
|
Yang L, Han D, Jin D, Zhang J, Shan Y, Wan M, Hu Y, Jiao W. Soil physiochemical properties and bacterial community changes under long-term polycyclic aromatic hydrocarbon stress in situ steel plant soils. CHEMOSPHERE 2023; 334:138926. [PMID: 37182712 DOI: 10.1016/j.chemosphere.2023.138926] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/28/2023] [Accepted: 05/11/2023] [Indexed: 05/16/2023]
Abstract
In situ soils were collected at two depths in Jinan and Hangzhou steel plants, which both have a long history of operation and polycyclic aromatic hydrocarbons (PAHs) contamination. The richness of 16 S rRNA gene and bacterial community of the soil were determined by real-time PCR and high-throughput sequencing. Soil physicochemical properties, PAHs contamination characteristics, and their interrelationships were also analyzed. In general, the PAHs contamination decreased with increasing soil depths. The physicochemical properties and PAH concentration of soil had synergistic impacts on the composition of the bacterial community. The long-term higher PAHs stress in Hangzhou contaminated soil (982 mg kg-1) increased the bacterial abundance and diversity, while that of Jinan contaminated soil (63 mg kg-1) decreased bacterial abundance and diversity. The pH value, sand content of the soil were positively correlated (P < 0.05) with the bacterial diversity including Simpson, Shannon, Observed_species and Chao1 indexes., and the other soil properties exhibited negative correlations with different strengths. The abundances of Curvibacter, Pseudomonas, Thiobacillus, Lysobacter, and Limnobacter were positively correlated with the PAHs concentration (P < 0.01). Additionally, the network structure of the PAHs-contaminated soils was more complex compared to that of uncontaminated soils, with stronger linkages and correlations between the different bacteria. These findings provide a theoretical basis for microbial remediation of PAHs-polluted soil.
Collapse
Affiliation(s)
- Liuqing Yang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Dongfei Han
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China
| | - Decai Jin
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Jingran Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Yongping Shan
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Mengxue Wan
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Yongfei Hu
- College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China
| | - Wentao Jiao
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
| |
Collapse
|
3
|
Microbial community structure and exploration of bioremediation enzymes: functional metagenomics insight into Arabian Sea sediments. Mol Genet Genomics 2023; 298:627-651. [PMID: 36933058 DOI: 10.1007/s00438-023-01995-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 01/28/2023] [Indexed: 03/19/2023]
Abstract
Deep-sea sediments provide important information on oceanic biogeochemical processes mediated by the microbiome and their functional roles which could be unravelled using genomic tools. The present study aimed to delineate microbial taxonomic and functional profiles from Arabian Sea sediment samples through whole metagenome sequencing using Nanopore technology. Arabian Sea is considered as a major microbial reservoir with significant bio-prospecting potential which needs to be explored extensively using recent advances in genomics. Assembly, co-assembly, and binning methods were used to predict Metagenome Assembled Genomes (MAGs) which were further characterized by their completeness and heterogeneity. Nanopore sequencing of Arabian Sea sediment samples generated around 1.73 tera basepairs of data. Proteobacteria (78.32%) was found to be the most dominant phylum followed by Bacteroidetes (9.55%) and Actinobacteria (2.14%) in the sediment metagenome. Further, 35 MAGs from assembled and 38 MAGs of co-assembled reads were generated from long-read sequence dataset with major representations from the genera Marinobacter, Kangiella, and Porticoccus. RemeDB analysis revealed a high representation of pollutant-degrading enzymes involved in hydrocarbon, plastic and dye degradation. Validation of enzymes with long nanopore reads using BlastX resulted in better characterization of complete gene signatures involved in hydrocarbon (6-monooxygenase and 4-hydroxyacetophenone monooxygenase) and dye degradation (Arylsulfatase). Enhancing the cultivability of deep-sea microbes predicted from the uncultured WGS approaches by I-tip method resulted in isolation of facultative extremophiles. This study presents a comprehensive insight into the taxonomic and functional profiles of Arabian Sea sediments, indicating a potential hotspot for bioprospection.
Collapse
|
4
|
Zhao Y, Wang J, Liu Y, Zheng P, Hu B. Microbial interaction promotes desulfurization efficiency under high pH condition. ENVIRONMENTAL RESEARCH 2021; 200:111423. [PMID: 34118244 DOI: 10.1016/j.envres.2021.111423] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/22/2021] [Accepted: 05/25/2021] [Indexed: 06/12/2023]
Abstract
The existence of H2S in biogas may cause equipment corrosion and considerable SO2 emission. Commonly used biotrickling filters may cause biogas dilution or generation of explosive mixtures. Compared with biotrickling filters, two-step process such as bioscrubber filters can overcome these shortages. However, its removal efficiency was still limited due to low microbial activity under high pH condition. Here, a bioreactor filter was carried out under pH 9.0. Removal efficiency higher than 99% was achieved under sulfide loading rate reaching 4.24 kg S m-3d-1. Results of network and high throughput sequencing showed that Thiobacillus acted as both dominant species (accounting for 75%) and unique kinless hub in this bioreactor. Other bacteria (accounting for 25%) contributed 75% to the network, which implied the intensive interaction between Thiobacillus and others. Sulfide removal ability and pH tolerance of pure bacteria and mixed culture were considered to verify how microbial interaction influenced them. Compared with pure bacteria, mixed culture had better performance under high pH condition, which confirmed that microbial interaction promoted desulfurization efficiency under high pH condition. These results showed that intensive microbial interaction might be the key to enhance sulfide removal efficiency under high pH condition.
Collapse
Affiliation(s)
- Yuxiang Zhao
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Jiaqi Wang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Yan Liu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Ping Zheng
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China; Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, China; Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, China.
| |
Collapse
|
5
|
Sefrji FO, Marasco R, Michoud G, Seferji KA, Merlino G, Daffonchio D. Kaustia mangrovi gen. nov., sp. nov. isolated from Red Sea mangrove sediments belongs to the recently proposed Parvibaculaceae family within the order Rhizobiales. Int J Syst Evol Microbiol 2021; 71:004806. [PMID: 33999795 PMCID: PMC8289202 DOI: 10.1099/ijsem.0.004806] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 04/09/2021] [Indexed: 12/17/2022] Open
Abstract
We isolated a novel strain, R1DC25T, described as Kaustia mangrovi gen. nov. sp. nov. from the sediments of a mangrove forest on the coast of the Red Sea in Saudi Arabia. This isolate is a moderately halophilic, aerobic/facultatively anaerobic Gram-stain-negative bacterium showing optimum growth at between 30 and 40 °C, at a pH of 8.5 and with 3-5 % NaCl. The genome of R1DC25T comprises a circular chromosome that is 4 630 536 bp in length, with a DNA G+C content of 67.3 mol%. Phylogenetic analyses based on the 16S rRNA gene sequence and whole-genome multilocus sequence analysis of 120 concatenated single-copy genes revealed that R1DC25T represents a distinct lineage within the family Parvibaculaceae in the order Rhizobiales within the class Alphaproteobacteria. R1DC25T showing 95.8, 95.3 and 94.5 % 16S rRNA gene sequence identity with Rhodoligotrophos appendicifer, Rhodoligotrophos jinshengii and Rhodoligotrophos defluvii, respectively. The predominant quinone was Q-10, and the polar lipids were phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, as well as several distinct aminolipids and lipids. The predominant cellular fatty acids were C19 : 0 cyclo ω8c, a combination of C18 : 1ω7c and/or C18 : 1ω6c and C16 : 0. On the basis of the differences in the phenotypic, physiological and biochemical characteristics from its known relatives and the results of our phylogenetic analyses, R1DC25T (=KCTC 72348T;=JCM 33619T;=NCCB 100699T) is proposed to represent a novel species in a novel genus, and we propose the name Kaustia mangrovi gen. nov., sp. nov. (Kaustia, subjective name derived from the abbreviation KAUST for King Abdullah University of Science and Technology; mangrovi, of a mangrove).
Collapse
Affiliation(s)
- Fatmah O. Sefrji
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Ramona Marasco
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Grégoire Michoud
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Kholoud A. Seferji
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Giuseppe Merlino
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Daniele Daffonchio
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| |
Collapse
|
6
|
Jung D, Liu B, He X, Owen JS, Liu L, Yuan Y, Zhang W, He S. Accessing previously uncultured marine microbial resources by a combination of alternative cultivation methods. Microb Biotechnol 2021; 14:1148-1158. [PMID: 33638935 PMCID: PMC8085940 DOI: 10.1111/1751-7915.13782] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 02/04/2021] [Accepted: 02/10/2021] [Indexed: 11/29/2022] Open
Abstract
Few microbes can grow under laboratory conditions, highlighting the fact that the majority of microbes in environment are still uncultured and untapped resources. This study used alternative cultivation methods, diffusion chambers (DC), dilution-to-extinction culture (DTE) and modified agar preparation step (PS media) to cultivate previously uncultured marine bacterial species. These methods were applied to samples from a coastal intertidal zone, and the results were compared with those from standard direct plating (SDP) cultivation. Among the strains isolated with DC, DTE and PS media methods, 28%, 48% and 33% were novel species, respectively, while the SDP method resulted in the isolation of only 9% of novel species. Most isolates were unique to the method used for their cultivation. This implies that each method is selective in its own way, which is different from SDP, thus able to access species that are difficult to obtain using conventional approaches. Comparing the diversity showed that 75 genera were recovered by the alternative methods, 2.7 times higher than that of the SDP cultivation, which constituted 45% of total diversity from culture-independent sequencing. We conclude that combining alternative cultivation methods represents a highly promising key for accessing 'microbial dark matter'.
Collapse
Affiliation(s)
- Dawoon Jung
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research CenterCollege of Food and Pharmaceutical SciencesNingbo UniversityNingboChina
| | - Biyin Liu
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research CenterCollege of Food and Pharmaceutical SciencesNingbo UniversityNingboChina
| | - Xiaoping He
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research CenterCollege of Food and Pharmaceutical SciencesNingbo UniversityNingboChina
| | - Jeffrey S. Owen
- Department of Environmental ScienceHankuk University of Foreign StudiesYonginKorea
| | - Liwei Liu
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research CenterCollege of Food and Pharmaceutical SciencesNingbo UniversityNingboChina
| | - Ye Yuan
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research CenterCollege of Food and Pharmaceutical SciencesNingbo UniversityNingboChina
| | - Weiyan Zhang
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research CenterCollege of Food and Pharmaceutical SciencesNingbo UniversityNingboChina
| | - Shan He
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research CenterCollege of Food and Pharmaceutical SciencesNingbo UniversityNingboChina
| |
Collapse
|
7
|
Relevance of FeoAB system in Rhodanobacter sp. B2A1Ga4 resistance to heavy metals, aluminium, gallium, and indium. Appl Microbiol Biotechnol 2021; 105:3301-3314. [PMID: 33791837 DOI: 10.1007/s00253-021-11254-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/19/2021] [Accepted: 03/21/2021] [Indexed: 10/21/2022]
Abstract
Aluminium (Al), gallium (Ga), and indium (In) are metals widely used in diverse applications in industry, which consequently result in a source of environmental contamination. In this study, strain Rhodanobacter sp. B2A1Ga4, highly resistant to Al, Ga, and In, was studied to reveal the main effects of these metals on the strain and the bacterial mechanisms linked to the ability to cope with them. An indium-sensitive mutant obtained by random transposon mutagenesis has the feoA gene interrupted. This gene together with the feoB gene is part of the feo operon which encodes a ferrous uptake system (FeoAB). The mutant strain exhibited higher oxidative stress supported by a high concentration of reactive oxygen species (ROS) and low levels of reduced glutathione (GSH) in the presence of metals. The iron supplementation of the growth medium reverted the growth inhibition of the mutant strain caused by Ga and In, significantly reduced the ROS amounts in mutant cells grown in all conditions, and increased its GSH/total glutathione ratio to values similar to those of the native strain. Moreover, the mutant strain when submitted to In increased the production of siderophores. The genome sequence analysis of strain B2A1Ga4 showed a large number of genes encoding putative proteins involved in iron uptake from the cell surface to the cytoplasm. Understanding the bacteria-metal interactions linked to resistance to high-tech metals is relevant to future application of microorganisms in bioremediation and/or biorecovery processes of these metals. KEY POINTS: • The disruption of FeoAB system compromises the bacterial resistance to Al, Ga, and In. • The iron acquisition in Rhodanobacter sp. B2A1Ga4 controls the oxidative stress. • Genome mining of strain B2A1Ga4 reveals several iron transport related genes.
Collapse
|
8
|
Morrison KD, Zavarin M, Kersting AB, Begg JD, Mason HE, Balboni E, Jiao Y. Influence of Uranium Concentration and pH on U-Phosphate Biomineralization by Caulobacter OR37. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:1626-1636. [PMID: 33471994 DOI: 10.1021/acs.est.0c05437] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Uranium contamination of soils and groundwater in the United States represents a significant health risk and will require multiple remediation approaches. Microbial phosphatase activity coupled to the addition of an organic P source has recently been studied as a remediation strategy that provides an extended release of inorganic P (Pi) into U-contaminated sites, resulting in the precipitation of meta-autunite minerals. Previous laboratory- and field-based biomineralization studies have investigated environments with relatively high U concentrations (>20 μM). However, most contaminated sites have much lower U concentrations (<2 μM). The Environmental Protection Agency (EPA) limit for U in drinking water is 0.126 μM. Reaching this regulatory limit becomes challenging as U concentrations approach autunite solubility. We studied the precipitation of U(VI)-phosphate minerals by an environmental isolate of Caulobacter sp. (strain OR37) from an Oak Ridge, Tennessee, U-contaminated site. Abiotic U(VI) solubility experiments reveal that U(VI)-phosphate minerals do not form in the presence of excess Pi (500 μM) when U(VI) concentrations are <1 μM and pH is <5. When OR37 cells are reacted under the same conditions with Pi or glycerol-2-phosphate, U(VI)-phosphate mineral formation was observed, along with the formation of intracellular polyphosphate granules. These results show that bacteria provide supersaturated microenvironments needed for U(VI)-phosphate mineralization while hydrolyzing organic P sources. This provides a pathway to lower U concentrations to below EPA limits for drinking water.
Collapse
|
9
|
Wu X, Spencer S, Gushgari-Doyle S, Yee MO, Voriskova J, Li Y, Alm EJ, Chakraborty R. Culturing of "Unculturable" Subsurface Microbes: Natural Organic Carbon Source Fuels the Growth of Diverse and Distinct Bacteria From Groundwater. Front Microbiol 2020; 11:610001. [PMID: 33391234 PMCID: PMC7773641 DOI: 10.3389/fmicb.2020.610001] [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: 09/24/2020] [Accepted: 11/19/2020] [Indexed: 11/23/2022] Open
Abstract
Recovery and cultivation of diverse environmentally-relevant microorganisms from the terrestrial subsurface remain a challenge despite recent advances in modern molecular technology. Here, we applied complex carbon (C) sources, i.e., sediment dissolved organic matter (DOM) and bacterial cell lysate, to enrich groundwater microbial communities for 30 days. As comparisons, we also included enrichments amended with simple C sources including glucose, acetate, benzoate, oleic acid, cellulose, and mixed vitamins. Our results demonstrate that complex C is far more effective in enriching diverse and distinct microorganisms from groundwater than simple C. Simple C enrichments yield significantly lower biodiversity, and are dominated by few phyla (e.g., Proteobacteria and Bacteroidetes), while microcosms enriched with complex C demonstrate significantly higher biodiversity including phyla that are poorly represented in published culture collections (e.g., Verrucomicrobia, Planctomycetes, and Armatimonadetes). Subsequent isolation from complex C enrichments yielded 228 bacterial isolates representing five phyla, 17 orders, and 56 distinct species, including candidate novel, rarely cultivated, and undescribed organisms. Results from this study will substantially advance cultivation and isolation strategies for recovering diverse and novel subsurface microorganisms. Obtaining axenic representatives of “once-unculturable” microorganisms will enhance our understanding of microbial physiology and function in different biogeochemical niches of terrestrial subsurface ecosystems.
Collapse
Affiliation(s)
- Xiaoqin Wu
- Department of Ecology, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Sarah Spencer
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Sara Gushgari-Doyle
- Department of Ecology, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Mon Oo Yee
- Department of Ecology, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Jana Voriskova
- Department of Ecology, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Yifan Li
- Department of Ecology, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Eric J Alm
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Romy Chakraborty
- Department of Ecology, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| |
Collapse
|
10
|
Wang Y, Wang H, Wang X, Xiao Y, Zhou Y, Su X, Cai J, Sun F. Resuscitation, isolation and immobilization of bacterial species for efficient textile wastewater treatment: A critical review and update. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 730:139034. [PMID: 32416505 DOI: 10.1016/j.scitotenv.2020.139034] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 04/23/2020] [Accepted: 04/25/2020] [Indexed: 06/11/2023]
Abstract
Given highly complex and recalcitrant nature of synthetic dyes, textile wastewater poses a serious challenge on surrounding environments. Until now, biological treatment of textile wastewater using efficient bacterial species is still considered as an environmentally friendly and cost-effective approach. The advances in resuscitating viable but non-culturable (VBNC) bacteria via signaling compounds such as resuscitation-promoting factors (Rpfs) and quorum sensing (QS) autoinducers, provide a vast majority of potent microbial resources for biological wastewater treatment. So far, textile wastewater treatment from resuscitating and isolating VBNC state bacteria has not been critically reviewed. Thus, this review aims to provide a comprehensive picture of resuscitation, isolation and application of bacterial species with this new strategy, while the recent advances in synthetic dye decolorization were also elaborated together with the mechanisms involved. Discussion was further extended to immobilization methods to tackle its application. We concluded that the resuscitation of VBNC bacteria via signaling compounds, together with biochar-based immobilization technologies, may lead to an appealing biological treatment of textile wastewater. However, further development and optimization of the integrated process are still required for their wide applications.
Collapse
Affiliation(s)
- Yuyang Wang
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua 321004, China
| | - Hangli Wang
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua 321004, China
| | - Xiaomin Wang
- Zhejiang Environmental Science Research Institute Co., Ltd., Hangzhou 310007, China
| | - Yeyuan Xiao
- Department of Civil and Environmental Engineering, Shantou University, Shantou 515063, China
| | - Yan Zhou
- Advanced Environmental Biotechnology Centre, Nanyang Environment and Water Research Institute, Nanyang Technological University, 637141, Singapore; School of Civil and Environmental Engineering, Nanyang Technological University, 639798, Singapore
| | - Xiaomei Su
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua 321004, China
| | - Jiafang Cai
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua 321004, China
| | - Faqian Sun
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua 321004, China.
| |
Collapse
|
11
|
Pathak A, Jaswal R, Xu X, White JR, Edwards B, Hunt J, Brooks S, Rathore RS, Agarwal M, Chauhan A. Characterization of Bacterial and Fungal Assemblages From Historically Contaminated Metalliferous Soils Using Metagenomics Coupled With Diffusion Chambers and Microbial Traps. Front Microbiol 2020; 11:1024. [PMID: 32655505 PMCID: PMC7325934 DOI: 10.3389/fmicb.2020.01024] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 04/27/2020] [Indexed: 01/05/2023] Open
Abstract
The majority of environmental microbiomes are not amenable to cultivation under standard laboratory growth conditions and hence remain uncharacterized. For environmental applications, such as bioremediation, it is necessary to isolate microbes performing the desired function, which may not necessarily be the fast growing or the copiotroph microbiota. Toward this end, cultivation and isolation of microbial strains using diffusion chambers (DC) and/or microbial traps (MT) have both been recently demonstrated to be effective strategies because microbial enrichment is facilitated by soil nutrients and not by synthetically defined media, thus simulating their native habitat. In this study, DC/MT chambers were established using soils collected from two US Department of Energy (DOE) sites with long-term history of heavy metal contamination, including mercury (Hg). To characterize the contamination levels and nutrient status, soils were first analyzed for total mercury (THg), methylmercury (MeHg), total carbon (TC), total nitrogen (TN), and total phosphorus (TP). Multivariate statistical analysis on these measurements facilitated binning of soils under high, medium and low levels of contamination. Bacterial and fungal microbiomes that developed within the DC and MT chambers were evaluated using comparative metagenomics, revealing Chthoniobacter, Burkholderia and Bradyrhizobium spp., as the predominant bacteria while Penicillium, Thielavia, and Trichoderma predominated among fungi. Many of these core microbiomes were also retrieved as axenic isolates. Furthermore, canonical correspondence analysis (CCA) of biogeochemical measurements, metal concentrations and bacterial communities revealed a positive correlation of Chthoniobacter/Bradyrhizobium spp., to THg whereas Burkholderia spp., correlated with MeHg. Penicillium spp., correlated with THg whereas Trichoderma spp., and Aspergillus spp., correlated with MeHg, from the MT approach. This is the first metagenomics-based assessment, isolation and characterization of soil-borne bacterial and fungal communities colonizing the diffusion chambers (DC) and microbial traps (MT) established with long-term metal contaminated soils. Overall, this study provides proof-of-concept for the successful application of DC/MT based assessment of mercury resistant (HgR) microbiomes in legacy metal-contaminated soils, having complex contamination issues. Overall, this study brings out the significance of microbial communities and their relevance in context to heavy metal cycling for better stewardship and restoration of such historically contaminated systems.
Collapse
Affiliation(s)
- Ashish Pathak
- School of the Environment, Florida A&M University, Tallahassee, FL, United States
| | - Rajneesh Jaswal
- School of the Environment, Florida A&M University, Tallahassee, FL, United States
| | - Xiaoyu Xu
- Savannah River Ecology Laboratory, University of Georgia, Aiken, SC, United States
| | - John R White
- Department of Oceanography and Coastal Sciences, Louisiana State University, Baton Rouge, LA, United States
| | - Bobby Edwards
- School of the Environment, Florida A&M University, Tallahassee, FL, United States
| | - Jaden Hunt
- School of the Environment, Florida A&M University, Tallahassee, FL, United States
| | - Scott Brooks
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Rajesh Singh Rathore
- School of the Environment, Florida A&M University, Tallahassee, FL, United States
| | - Meenakshi Agarwal
- School of the Environment, Florida A&M University, Tallahassee, FL, United States
| | - Ashvini Chauhan
- School of the Environment, Florida A&M University, Tallahassee, FL, United States
| |
Collapse
|
12
|
Complete Genome Sequences of Four Microbacterium Strains Isolated from Metal- and Radionuclide-Rich Soils. Microbiol Resour Announc 2019; 8:8/42/e00846-19. [PMID: 31624160 PMCID: PMC6797525 DOI: 10.1128/mra.00846-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Here, we present the genome sequences of four Microbacterium strains, which were isolated at different locations in Europe from metal- or radionuclide-rich soils. High-quality complete genome sequences were obtained with PacBio and Illumina data sets with an original two-step procedure.
Collapse
|
13
|
Metagenomic Evaluation of Bacterial and Fungal Assemblages Enriched within Diffusion Chambers and Microbial Traps Containing Uraniferous Soils. Microorganisms 2019; 7:microorganisms7090324. [PMID: 31489900 PMCID: PMC6780890 DOI: 10.3390/microorganisms7090324] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 08/27/2019] [Accepted: 09/02/2019] [Indexed: 01/06/2023] Open
Abstract
Despite significant technological advancements in the field of microbial ecology, cultivation and subsequent isolation of the vast majority of environmental microorganisms continues to pose challenges. Isolation of the environmental microbiomes is prerequisite to better understand a myriad of ecosystem services they provide, such as bioremediation of contaminants. Towards this end, in this culturomics study, we evaluated the colonization of soil bacterial and fungal communities within diffusion chambers (DC) and microbial traps (MT) established using uraniferous soils collected from a historically contaminated soil from Aiken, USA. Microbial assemblages were compared between the DC and MT relative to the native soils using amplicon based metagenomic and bioinformatic analysis. The overall rationale of this study is that DC and MT growth chambers provide the optimum conditions under which desired microbiota, identified in a previous study to serve as the “core” microbiomes, will proliferate, leading to their successful isolation. Specifically, the core microbiomes consisted of assemblages of bacteria (Burkholderia spp.) and fungi (Penicillium spp.), respectively. The findings from this study further supported previous data such that the abundance and diversity of the desired “core” microbiomes significantly increased as a function of enrichments over three consecutive generations of DC and MT, respectively. Metagenomic analysis of the DC/MT generations also revealed that enrichment and stable populations of the desired “core” bacterial and fungal microbiomes develop within the first 20 days of incubation and the practice of subsequent transfers for second and third generations, as is standard in previous studies, may be unnecessary. As a cost and time cutting measure, this study recommends running the DC/MT chambers for only a 20-day time period, as opposed to previous studies, which were run for months. In summation, it was concluded that, using the diffusion chamber-based enrichment techniques, growth of desired microbiota possessing environmentally relevant functions can be achieved in a much shorter time frame than has been previously shown.
Collapse
|
14
|
Metagenomics-Guided Survey, Isolation, and Characterization of Uranium Resistant Microbiota from the Savannah River Site, USA. Genes (Basel) 2019; 10:genes10050325. [PMID: 31035394 PMCID: PMC6562407 DOI: 10.3390/genes10050325] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 04/19/2019] [Accepted: 04/24/2019] [Indexed: 11/17/2022] Open
Abstract
Despite the recent advancements in culturomics, isolation of the majority of environmental microbiota performing critical ecosystem services, such as bioremediation of contaminants, remains elusive. Towards this end, we conducted a metagenomics-guided comparative assessment of soil microbial diversity and functions present in uraniferous soils relative to those that grew in diffusion chambers (DC) or microbial traps (MT), followed by isolation of uranium (U) resistant microbiota. Shotgun metagenomic analysis performed on the soils used to establish the DC/MT chambers revealed Proteobacterial phyla and Burkholderia genus to be the most abundant among bacteria. The chamber-associated growth conditions further increased their abundances relative to the soils. Ascomycota was the most abundant fungal phylum in the chambers relative to the soils, with Penicillium as the most dominant genus. Metagenomics-based taxonomic findings completely mirrored the taxonomic composition of the retrieved isolates such that the U-resistant bacteria and fungi mainly belonged to Burkholderia and Penicillium species, thus confirming that the chambers facilitated proliferation and subsequent isolation of specific microbiota with environmentally relevant functions. Furthermore, shotgun metagenomic analysis also revealed that the gene classes for carbohydrate metabolism, virulence, and respiration predominated with functions related to stress response, membrane transport, and metabolism of aromatic compounds were also identified, albeit at lower levels. Of major note was the successful isolation of a potentially novel Penicillium species using the MT approach, as evidenced by whole genome sequence analysis and comparative genomic analysis, thus enhancing our overall understanding on the uranium cycling microbiota within the tested uraniferous soils.
Collapse
|
15
|
Complete Genome Sequence for Asinibacterium sp. Strain OR53 and Draft Genome Sequence for Asinibacterium sp. Strain OR43, Two Bacteria Tolerant to Uranium. Microbiol Resour Announc 2019; 8:8/14/e01701-18. [PMID: 30948472 PMCID: PMC6449563 DOI: 10.1128/mra.01701-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Asinibacterium sp. strains OR43 and OR53 belong to the phylum Bacteroidetes and were isolated from subsurface sediments in Oak Ridge, TN. Both strains grow at elevated levels of heavy metals. Here, we present the closed genome sequence of Asinibacterium sp. strain OR53 and the draft genome sequence of Asinibacterium sp. strain OR43.
Collapse
|
16
|
Learman DR, Ahmad Z, Brookshier A, Henson MW, Hewitt V, Lis A, Morrison C, Robinson A, Todaro E, Wologo E, Wynne S, Alm EW, Kourtev PS. Comparative genomics of 16 Microbacterium spp. that tolerate multiple heavy metals and antibiotics. PeerJ 2019; 6:e6258. [PMID: 30671291 PMCID: PMC6336093 DOI: 10.7717/peerj.6258] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 12/06/2018] [Indexed: 11/20/2022] Open
Abstract
A total of 16 different strains of Microbacterium spp. were isolated from contaminated soil and enriched on the carcinogen, hexavalent chromium [Cr(VI)]. The majority of the isolates (11 of the 16) were able to tolerate concentrations (0.1 mM) of cobalt, cadmium, and nickel, in addition to Cr(VI) (0.5–20 mM). Interestingly, these bacteria were also able to tolerate three different antibiotics (ranges: ampicillin 0–16 μg ml−1, chloramphenicol 0–24 μg ml−1, and vancomycin 0–24 μg ml−1). To gain genetic insight into these tolerance pathways, the genomes of these isolates were assembled and annotated. The genomes of these isolates not only have some shared genes (core genome) but also have a large amount of variability. The genomes also contained an annotated Cr(VI) reductase (chrR) that could be related to Cr(VI) reduction. Further, various heavy metal tolerance (e.g., Co/Zn/Cd efflux system) and antibiotic resistance genes were identified, which provide insight into the isolates’ ability to tolerate metals and antibiotics. Overall, these isolates showed a wide range of tolerances to heavy metals and antibiotics and genetic diversity, which was likely required of this population to thrive in a contaminated environment.
Collapse
Affiliation(s)
- Deric R Learman
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
| | - Zahra Ahmad
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
| | - Allison Brookshier
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
| | - Michael W Henson
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
| | - Victoria Hewitt
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
| | - Amanda Lis
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
| | - Cody Morrison
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
| | - Autumn Robinson
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
| | - Emily Todaro
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
| | - Ethan Wologo
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
| | - Sydney Wynne
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
| | - Elizabeth W Alm
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
| | - Peter S Kourtev
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
| |
Collapse
|
17
|
Smith HJ, Zelaya AJ, De León KB, Chakraborty R, Elias DA, Hazen TC, Arkin AP, Cunningham AB, Fields MW. Impact of hydrologic boundaries on microbial planktonic and biofilm communities in shallow terrestrial subsurface environments. FEMS Microbiol Ecol 2018; 94:5107865. [PMID: 30265315 PMCID: PMC6192502 DOI: 10.1093/femsec/fiy191] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 09/26/2018] [Indexed: 12/12/2022] Open
Abstract
Subsurface environments contain a large proportion of planetary microbial biomass and harbor diverse communities responsible for mediating biogeochemical cycles important to groundwater used by human society for consumption, irrigation, agriculture and industry. Within the saturated zone, capillary fringe and vadose zones, microorganisms can reside in two distinct phases (planktonic or biofilm), and significant differences in community composition, structure and activity between free-living and attached communities are commonly accepted. However, largely due to sampling constraints and the challenges of working with solid substrata, the contribution of each phase to subsurface processes is largely unresolved. Here, we synthesize current information on the diversity and activity of shallow freshwater subsurface habitats, discuss the challenges associated with sampling planktonic and biofilm communities across spatial, temporal and geological gradients, and discuss how biofilms may be constrained within shallow terrestrial subsurface aquifers. We suggest that merging traditional activity measurements and sequencing/-omics technologies with hydrological parameters important to sediment biofilm assembly and stability will help delineate key system parameters. Ultimately, integration will enhance our understanding of shallow subsurface ecophysiology in terms of bulk-flow through porous media and distinguish the respective activities of sessile microbial communities from more transient planktonic communities to ecosystem service and maintenance.
Collapse
Affiliation(s)
- H J Smith
- Center for Biofilm Engineering, Montana State University, Bozeman, MT
- ENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, CA 94720
| | - A J Zelaya
- Center for Biofilm Engineering, Montana State University, Bozeman, MT
- Department of Microbiology & Immunology, Montana State University, Bozeman, MT
- ENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, CA 94720
| | - K B De León
- Department of Biochemistry, University of Missouri, Columbia, MO
- ENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, CA 94720
| | - R Chakraborty
- Climate and Ecosystems Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA
- ENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, CA 94720
| | - D A Elias
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN
- ENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, CA 94720
| | - T C Hazen
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN
- ENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, CA 94720
| | - A P Arkin
- Department of Bioengineering, Lawrence Berkeley National Laboratory, Berkeley, CA
- ENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, CA 94720
| | - A B Cunningham
- Center for Biofilm Engineering, Montana State University, Bozeman, MT
- Department of Civil Engineering, Montana State University, Montana State University, Bozeman, MT
| | - M W Fields
- Center for Biofilm Engineering, Montana State University, Bozeman, MT
- Department of Microbiology & Immunology, Montana State University, Bozeman, MT
- ENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, CA 94720
| |
Collapse
|
18
|
Kolhe N, Zinjarde S, Acharya C. Responses exhibited by various microbial groups relevant to uranium exposure. Biotechnol Adv 2018; 36:1828-1846. [PMID: 30017503 DOI: 10.1016/j.biotechadv.2018.07.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 07/08/2018] [Accepted: 07/09/2018] [Indexed: 11/28/2022]
Abstract
There is a strong interest in knowing how various microbial systems respond to the presence of uranium (U), largely in the context of bioremediation. There is no known biological role for uranium so far. Uranium is naturally present in rocks and minerals. The insoluble nature of the U(IV) minerals keeps uranium firmly bound in the earth's crust minimizing its bioavailability. However, anthropogenic nuclear reaction processes over the last few decades have resulted in introduction of uranium into the environment in soluble and toxic forms. Microbes adsorb, accumulate, reduce, oxidize, possibly respire, mineralize and precipitate uranium. This review focuses on the microbial responses to uranium exposure which allows the alteration of the forms and concentrations of uranium within the cell and in the local environment. Detailed information on the three major bioprocesses namely, biosorption, bioprecipitation and bioreduction exhibited by the microbes belonging to various groups and subgroups of bacteria, fungi and algae is provided in this review elucidating their intrinsic and engineered abilities for uranium removal. The survey also highlights the instances of the field trials undertaken for in situ uranium bioremediation. Advances in genomics and proteomics approaches providing the information on the regulatory and physiologically important determinants in the microbes in response to uranium challenge have been catalogued here. Recent developments in metagenomics and metaproteomics indicating the ecologically relevant traits required for the adaptation and survival of environmental microbes residing in uranium contaminated sites are also included. A comprehensive understanding of the microbial responses to uranium can facilitate the development of in situ U bioremediation strategies.
Collapse
Affiliation(s)
- Nilesh Kolhe
- Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Pune 411007, India; Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
| | - Smita Zinjarde
- Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Pune 411007, India; Department of Microbiology, Savitribai Phule Pune University, Pune 411007, India.
| | - Celin Acharya
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India; Homi Bhabha National Institute, Anushakti Nagar, Trombay, Mumbai 400094, India.
| |
Collapse
|
19
|
Antibiotic discovery: combining isolation chip (iChip) technology and co-culture technique. Appl Microbiol Biotechnol 2018; 102:7333-7341. [DOI: 10.1007/s00253-018-9193-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 05/18/2018] [Accepted: 06/20/2018] [Indexed: 10/28/2022]
|
20
|
Jung D, Seo EY, Owen JS, Aoi Y, Yong S, Lavrentyeva EV, Ahn TS. Application of the filter plate microbial trap (FPMT), for cultivating thermophilic bacteria from thermal springs in Barguzin area, eastern Baikal, Russia. Biosci Biotechnol Biochem 2018; 82:1624-1632. [PMID: 29882485 DOI: 10.1080/09168451.2018.1482194] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
Hot springs are regarded as treasury of valuable thermophiles. Like other bacteria, thermophiles are not easily cultivated using conventional culture methods. We used an advanced cultivation method, the filter plate microbial trap (FPMT), to isolate bacteria from thermal springs. In total, 184 isolates were obtained from five thermal springs using the FPMT and standard agar plate method, and their 16S rRNA gene sequences were analyzed. FPMT allowed us to obtain a culture collection that was larger, richer, and more novel than that obtained by standard cultivation. Seven novel species were obtained using the FPMT technique, whereas only one was isolated using a standard cultivation. We also found clear differences in the patterns of phylogenetic diversity and physiological properties between isolates from two cultivation methods. The results have encouraged us to apply the FPMT method in other extreme environments and offer further support for fostering the development of new cultivation methods.
Collapse
Affiliation(s)
- Dawoon Jung
- a Department of Environmental Science , Kangwon National University , Chuncheon , Republic of Korea
| | - Eun-Young Seo
- a Department of Environmental Science , Kangwon National University , Chuncheon , Republic of Korea
| | - Jeffrey S Owen
- b Department of Environmental Science , Hankuk University of Foreign Studies , Yongin , Republic of Korea
| | - Yoshiteru Aoi
- c Department of Molecular Biotechnology , Graduate School of Advanced Sciences of Matter, Hiroshima University , Higashi Hiroshima , Japan
| | - Seungcheon Yong
- d Department of Codes , Insilicogen Inc , Yongin , Republic of Korea
| | - Elena V Lavrentyeva
- e Department of Microbiology , Institute of General and Experimental Biology SB RAS , Ulan-Ude , Russia
| | - Tae Seok Ahn
- c Department of Molecular Biotechnology , Graduate School of Advanced Sciences of Matter, Hiroshima University , Higashi Hiroshima , Japan
| |
Collapse
|
21
|
Microbial diversity and activity of an aged soil contaminated by polycyclic aromatic hydrocarbons. Bioprocess Biosyst Eng 2018; 41:871-883. [PMID: 29546466 DOI: 10.1007/s00449-018-1921-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Accepted: 03/08/2018] [Indexed: 01/27/2023]
Abstract
In-depth understanding of indigenous microbial assemblages resulted from aged contamination by polycyclic aromatic hydrocarbons (PAHs) is of vital importance in successful in situ bioremediation treatments. Soil samples of three boreholes were collected at 12 different vertical depths. Overall, the dominating three-ring PAHs (76.2%) were closely related to distribution patterns of soil dehydrogenase activity, microbial cell numbers, and Shannon biodiversity index (H') of indigenous microorganisms. High-molecular-weight PAHs tend to yield more diverse communities. Results from 16S rRNA analysis indicated that possible functional groups of PAH degradation include three species in Bacillus cereus group, Bacillus sp. SA Ant14, Nocardioides sp., and Ralstonia pickettii. Principal component analysis indicates significant positive correlations between the content of high-molecular-weight PAHs and the distribution of Bacillus weihenstephanensis KBAB4 and Nocardioides sp. The species B. cereus 03BB102, Bacillus thuringiensis, B. weihenstephanensis KBAB4, and Nocardioides sp. were recognized as main PAH degraders and thus recommended to be utilized in further bioremediation applications. The vertical distribution characteristics of PAHs in soil profiles (1-12 m) and the internal relationship between the transport mechanisms of PAHs and the response of soil biological properties help further understand the microbial diversity and activity in an aged site.
Collapse
|
22
|
Abstract
Contamination from anthropogenic activities has significantly impacted Earth’s biosphere. However, knowledge about how environmental contamination affects the biodiversity of groundwater microbiomes and ecosystem functioning remains very limited. Here, we used a comprehensive functional gene array to analyze groundwater microbiomes from 69 wells at the Oak Ridge Field Research Center (Oak Ridge, TN), representing a wide pH range and uranium, nitrate, and other contaminants. We hypothesized that the functional diversity of groundwater microbiomes would decrease as environmental contamination (e.g., uranium or nitrate) increased or at low or high pH, while some specific populations capable of utilizing or resistant to those contaminants would increase, and thus, such key microbial functional genes and/or populations could be used to predict groundwater contamination and ecosystem functioning. Our results indicated that functional richness/diversity decreased as uranium (but not nitrate) increased in groundwater. In addition, about 5.9% of specific key functional populations targeted by a comprehensive functional gene array (GeoChip 5) increased significantly (P < 0.05) as uranium or nitrate increased, and their changes could be used to successfully predict uranium and nitrate contamination and ecosystem functioning. This study indicates great potential for using microbial functional genes to predict environmental contamination and ecosystem functioning. Disentangling the relationships between biodiversity and ecosystem functioning is an important but poorly understood topic in ecology. Predicting ecosystem functioning on the basis of biodiversity is even more difficult, particularly with microbial biomarkers. As an exploratory effort, this study used key microbial functional genes as biomarkers to provide predictive understanding of environmental contamination and ecosystem functioning. The results indicated that the overall functional gene richness/diversity decreased as uranium increased in groundwater, while specific key microbial guilds increased significantly as uranium or nitrate increased. These key microbial functional genes could be used to successfully predict environmental contamination and ecosystem functioning. This study represents a significant advance in using functional gene markers to predict the spatial distribution of environmental contaminants and ecosystem functioning toward predictive microbial ecology, which is an ultimate goal of microbial ecology.
Collapse
|
23
|
Shin D, Lee Y, Park J, Moon HS, Hyun SP. Soil microbial community responses to acid exposure and neutralization treatment. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2017; 204:383-393. [PMID: 28910736 DOI: 10.1016/j.jenvman.2017.09.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 08/02/2017] [Accepted: 09/05/2017] [Indexed: 06/07/2023]
Abstract
Changes in microbial community induced by acid shock were studied in the context of potential release of acids to the environment due to chemical accidents. The responses of microbial communities in three different soils to the exposure to sulfuric or hydrofluoric acid and to the subsequent neutralization treatment were investigated as functions of acid concentration and exposure time by using 16S-rRNA gene based pyrosequencing and DGGE (Denaturing Gradient Gel Electrophoresis). Measurements of soil pH and dissolved ion concentrations revealed that the added acids were neutralized to different degrees, depending on the mineral composition and soil texture. Hydrofluoric acid was more effectively neutralized by the soils, compared with sulfuric acid at the same normality. Gram-negative ß-Proteobacteria were shown to be the most acid-sensitive bacterial strains, while spore-forming Gram-positive Bacilli were the most acid-tolerant. The results of this study suggest that the Gram-positive to Gram-negative bacterial ratio may serve as an effective bio-indicator in assessing the impact of the acid shock on the microbial community. Neutralization treatments helped recover the ratio closer to their original values. The findings of this study show that microbial community changes as well as geochemical changes such as pH and dissolved ion concentrations need to be considered in estimating the impact of an acid spill, in selecting an optimal remediation strategy, and in deciding when to end remedial actions at the acid spill impacted site.
Collapse
Affiliation(s)
- Doyun Shin
- Resource Recovery Research Center, Mineral Resources Research Division, Korea Institute of Geoscience and Mineral Resources (KIGAM), Daejeon, 34132, Republic of Korea; Department of Resource Recycling, Korea University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Yunho Lee
- Groundwater & Ecohydrology Research Center, Geologic Environment Division, Korea Institute of Geoscience and Mineral Resources (KIGAM), Daejeon, 34132, Republic of Korea; Department of Geology, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Jeonghyun Park
- Resource Recovery Research Center, Mineral Resources Research Division, Korea Institute of Geoscience and Mineral Resources (KIGAM), Daejeon, 34132, Republic of Korea
| | - Hee Sun Moon
- Groundwater & Ecohydrology Research Center, Geologic Environment Division, Korea Institute of Geoscience and Mineral Resources (KIGAM), Daejeon, 34132, Republic of Korea; Department of Mineral & Groundwater Resources, Korea University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Sung Pil Hyun
- Department of Mineral & Groundwater Resources, Korea University of Science and Technology, Daejeon, 34113, Republic of Korea; Center for HLW Geological Disposal, Climate Change Mitigation and Sustainability Division, Korea Institute of Geoscience and Mineral Resources (KIGAM), Daejeon, 34132, Republic of Korea.
| |
Collapse
|
24
|
Berdy B, Spoering AL, Ling LL, Epstein SS. In situ cultivation of previously uncultivable microorganisms using the ichip. Nat Protoc 2017. [PMID: 29532802 DOI: 10.1038/nprot.2017.074] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Most microbial species remain uncultivated, and modifying artificial nutrient media brings only an incremental increase in cultivability. We reasoned that an alternative way to cultivate species with unknown requirements is to use naturally occurring combinations of growth factors. To achieve this, we moved cultivation into the microbes' natural habitat by placing cells taken from varying environmental samples into diffusion chambers, which are then returned to nature for incubation. By miniaturizing the chambers and placing only one to several cells into each chamber, we can grow and isolate microorganisms in axenic culture in one step. We call this cultivation platform the 'isolation chip', or 'ichip'. This platform has been shown to increase microbial recovery from 5- to 300-fold, depending on the study. Furthermore, it provides access to a unique set of microbes that are inaccessible by standard cultivation. Here we provide a simple protocol for building and applying ichips for environmental cultivation of soil bacteria as an example; the protocol consists of (i) preparing the ichip; (ii) collecting an environmental sample; (iii) serially diluting cells and loading them into the ichip; (iv) returning the ichip to the environment for incubation; (v) retrieving the ichip and harvesting grown material; and (vi) domestication of the ichip-derived colonies for growth in the laboratory. The ichip's full assembly and deployment is a relatively simple procedure that, with experience, takes ∼2-3 h. After in situ incubation, retrieval of the ichip and processing of its contents will take ∼1-4 h, depending on which specific procedures are used.
Collapse
Affiliation(s)
- Brittany Berdy
- Department of Biology, Northeastern University, Boston, Massachusetts, USA
| | - Amy L Spoering
- NovoBiotic Pharmaceuticals, Cambridge, Massachusetts, USA
| | - Losee L Ling
- NovoBiotic Pharmaceuticals, Cambridge, Massachusetts, USA
| | - Slava S Epstein
- Department of Biology, Northeastern University, Boston, Massachusetts, USA.,NovoBiotic Pharmaceuticals, Cambridge, Massachusetts, USA.,LiDakSum Marine Biopharmaceutical Research Center, Ningbo University, Ningbo, China
| |
Collapse
|
25
|
Pudasaini S, Wilson J, Ji M, van Dorst J, Snape I, Palmer AS, Burns BP, Ferrari BC. Microbial Diversity of Browning Peninsula, Eastern Antarctica Revealed Using Molecular and Cultivation Methods. Front Microbiol 2017; 8:591. [PMID: 28439263 PMCID: PMC5383709 DOI: 10.3389/fmicb.2017.00591] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 03/22/2017] [Indexed: 01/07/2023] Open
Abstract
Browning Peninsula is an ice-free polar desert situated in the Windmill Islands, Eastern Antarctica. The entire site is described as a barren landscape, comprised of frost boils with soils dominated by microbial life. In this study, we explored the microbial diversity and edaphic drivers of community structure across this site using traditional cultivation methods, a novel approach the soil substrate membrane system (SSMS), and culture-independent 454-tag pyrosequencing. The measured soil environmental and microphysical factors of chlorine, phosphate, aspect and elevation were found to be significant drivers of the bacterial community, while none of the soil parameters analyzed were significantly correlated to the fungal community. Overall, Browning Peninsula soil harbored a distinctive microbial community in comparison to other Antarctic soils comprised of a unique bacterial diversity and extremely limited fungal diversity. Tag pyrosequencing data revealed the bacterial community to be dominated by Actinobacteria (36%), followed by Chloroflexi (18%), Cyanobacteria (14%), and Proteobacteria (10%). For fungi, Ascomycota (97%) dominated the soil microbiome, followed by Basidiomycota. As expected the diversity recovered from culture-based techniques was lower than that detected using tag sequencing. However, in the SSMS enrichments, that mimic the natural conditions for cultivating oligophilic “k-selected” bacteria, a larger proportion of rare bacterial taxa (15%), such as Blastococcus, Devosia, Herbaspirillum, Propionibacterium and Methylocella and fungal (11%) taxa, such as Nigrospora, Exophiala, Hortaea, and Penidiella were recovered at the genus level. At phylum level, a comparison of OTU's showed that the SSMS shared 21% of Acidobacteria, 11% of Actinobacteria and 10% of Proteobacteria OTU's with soil. For fungi, the shared OTUs was 4% (Basidiomycota) and <0.5% (Ascomycota). This was the first known attempt to culture microfungi using the SSMS which resulted in an increase in diversity from 14 to 57 microfungi OTUs compared to standard cultivation. Furthermore, the SSMS offers the opportunity to retrieve a greater diversity of bacterial and fungal taxa for future exploitation.
Collapse
Affiliation(s)
- Sarita Pudasaini
- School of Biotechnology and Biomolecular Sciences, University of New South WalesKensington, NSW, Australia
| | - John Wilson
- School of Biotechnology and Biomolecular Sciences, University of New South WalesKensington, NSW, Australia
| | - Mukan Ji
- School of Biotechnology and Biomolecular Sciences, University of New South WalesKensington, NSW, Australia
| | - Josie van Dorst
- School of Biotechnology and Biomolecular Sciences, University of New South WalesKensington, NSW, Australia
| | - Ian Snape
- Australian Antarctic Division, Department of Sustainability, Environment, Water, Population and CommunitiesKingston, TAS, Australia
| | - Anne S Palmer
- Australian Antarctic Division, Department of Sustainability, Environment, Water, Population and CommunitiesKingston, TAS, Australia
| | - Brendan P Burns
- School of Biotechnology and Biomolecular Sciences, University of New South WalesKensington, NSW, Australia
| | - Belinda C Ferrari
- School of Biotechnology and Biomolecular Sciences, University of New South WalesKensington, NSW, Australia
| |
Collapse
|
26
|
Park DM, Overton KW, Liou MJ, Jiao Y. Identification of a U/Zn/Cu responsive global regulatory two-component system in Caulobacter crescentus. Mol Microbiol 2017; 104:46-64. [PMID: 28035693 DOI: 10.1111/mmi.13615] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/23/2016] [Indexed: 01/18/2023]
Abstract
Despite the well-known toxicity of uranium (U) to bacteria, little is known about how cells sense and respond to U. The recent finding of a U-specific stress response in Caulobacter crescentus has provided a foundation for studying the mechanisms of U- perception in bacteria. To gain insight into this process, we used a forward genetic screen to identify the regulatory components governing expression of the urcA promoter (PurcA ) that is strongly induced by U. This approach unearthed a previously uncharacterized two-component system, named UzcRS, which is responsible for U-dependent activation of PurcA . UzcRS is also highly responsive to zinc and copper, revealing a broader specificity than previously thought. Using ChIP-seq, we found that UzcR binds extensively throughout the genome in a metal-dependent manner and recognizes a noncanonical DNA-binding site. Coupling the genome-wide occupancy data with RNA-seq analysis revealed that UzcR is a global regulator of transcription, predominately activating genes encoding proteins that are localized to the cell envelope; these include metallopeptidases, multidrug-resistant efflux (MDR) pumps, TonB-dependent receptors and many proteins of unknown function. Collectively, our data suggest that UzcRS couples the perception of U, Zn and Cu with a novel extracytoplasmic stress response.
Collapse
Affiliation(s)
- Dan M Park
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - K Wesley Overton
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Megan J Liou
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Yongqin Jiao
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| |
Collapse
|
27
|
Jung D, Aoi Y, Epstein SS. In Situ Cultivation Allows for Recovery of Bacterial Types Competitive in Their Natural Environment. Microbes Environ 2016; 31:456-459. [PMID: 27682804 PMCID: PMC5158119 DOI: 10.1264/jsme2.me16079] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Standard cultivation fails to grow most microorganisms, whereas in situ cultivation allows for the isolation of comparatively diverse and novel microorganisms. Information on similarities and differences in the physiological properties of isolates obtained from in situ cultivation and standard cultivation is limited. Therefore, we used the arctic sediment samples and compared two culture collections obtained using standard and novel cultivation techniques. Even though there was no temperature selection at the isolation step, isolates from each method showed different reactions to temperature. The results of the present study suggest that isolates from in situ cultivation are more competitive in their natural environment.
Collapse
Affiliation(s)
- Dawoon Jung
- Institute for Sustainable Sciences and development, Hiroshima University
| | | | | |
Collapse
|
28
|
Abstract
BACKGROUND The majority of environmental bacteria and around a third of oral bacteria remain uncultivated. Furthermore, several bacterial phyla have no cultivable members and are recognised only by detection of their DNA by molecular methods. Possible explanations for the resistance of certain bacteria to cultivation in purity in vitro include: unmet fastidious growth requirements; inhibition by environmental conditions or chemical factors produced by neighbouring bacteria in mixed cultures; or conversely, dependence on interactions with other bacteria in the natural environment, without which they cannot survive in isolation. Auxotrophic bacteria, with small genomes lacking in the necessary genetic material to encode for essential nutrients, frequently rely on close symbiotic relationships with other bacteria for survival, and may therefore be recalcitrant to cultivation in purity. HIGHLIGHT Since in-vitro culture is essential for the comprehensive characterisation of bacteria, particularly with regard to virulence and antimicrobial resistance, the cultivation of uncultivated organisms has been a primary focus of several research laboratories. Many targeted and open-ended strategies have been devised and successfully used. Examples include: the targeted detection of specific bacteria in mixed plate cultures using colony hybridisation; growth in simulated natural environments or in co-culture with 'helper' strains; and modified media preparation techniques or development of customised media eg. supplementation of media with potential growth-stimulatory factors such as siderophores. CONCLUSION Despite significant advances in recent years in methodologies for the cultivation of previously uncultivated bacteria, a substantial proportion remain to be cultured and efforts to devise high-throughput strategies should be a high priority.
Collapse
Affiliation(s)
- Sonia R Vartoukian
- Barts and The London School of Medicine and Dentistry, Queen Mary University of London, UK
| |
Collapse
|
29
|
Abstract
Unraveling the drivers controlling the response and adaptation of biological communities to environmental change, especially anthropogenic activities, is a central but poorly understood issue in ecology and evolution. Comparative genomics studies suggest that lateral gene transfer (LGT) is a major force driving microbial genome evolution, but its role in the evolution of microbial communities remains elusive. To delineate the importance of LGT in mediating the response of a groundwater microbial community to heavy metal contamination, representative Rhodanobacter reference genomes were sequenced and compared to shotgun metagenome sequences. 16S rRNA gene-based amplicon sequence analysis indicated that Rhodanobacter populations were highly abundant in contaminated wells with low pHs and high levels of nitrate and heavy metals but remained rare in the uncontaminated wells. Sequence comparisons revealed that multiple geochemically important genes, including genes encoding Fe2+/Pb2+ permeases, most denitrification enzymes, and cytochrome c553, were native to Rhodanobacter and not subjected to LGT. In contrast, the Rhodanobacter pangenome contained a recombinational hot spot in which numerous metal resistance genes were subjected to LGT and/or duplication. In particular, Co2+/Zn2+/Cd2+ efflux and mercuric resistance operon genes appeared to be highly mobile within Rhodanobacter populations. Evidence of multiple duplications of a mercuric resistance operon common to most Rhodanobacter strains was also observed. Collectively, our analyses indicated the importance of LGT during the evolution of groundwater microbial communities in response to heavy metal contamination, and a conceptual model was developed to display such adaptive evolutionary processes for explaining the extreme dominance of Rhodanobacter populations in the contaminated groundwater microbiome. Lateral gene transfer (LGT), along with positive selection and gene duplication, are the three main mechanisms that drive adaptive evolution of microbial genomes and communities, but their relative importance is unclear. Some recent studies suggested that LGT is a major adaptive mechanism for microbial populations in response to changing environments, and hence, it could also be critical in shaping microbial community structure. However, direct evidence of LGT and its rates in extant natural microbial communities in response to changing environments is still lacking. Our results presented in this study provide explicit evidence that LGT played a crucial role in driving the evolution of a groundwater microbial community in response to extreme heavy metal contamination. It appears that acquisition of genes critical for survival, growth, and reproduction via LGT is the most rapid and effective way to enable microorganisms and associated microbial communities to quickly adapt to abrupt harsh environmental stresses.
Collapse
|
30
|
Vartoukian SR, Adamowska A, Lawlor M, Moazzez R, Dewhirst FE, Wade WG. In Vitro Cultivation of 'Unculturable' Oral Bacteria, Facilitated by Community Culture and Media Supplementation with Siderophores. PLoS One 2016; 11:e0146926. [PMID: 26764907 PMCID: PMC4713201 DOI: 10.1371/journal.pone.0146926] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 12/23/2015] [Indexed: 11/18/2022] Open
Abstract
Over a third of oral bacteria are as-yet-uncultivated in-vitro. Siderophores have been previously shown to enable in-vitro growth of previously uncultivated bacteria. The objective of this study was to cultivate novel oral bacteria in siderophore-supplemented culture media. Various compounds with siderophore activity, including pyoverdines-Fe-complex, desferricoprogen and salicylic acid, were found to stimulate the growth of difficult-to-culture strains Prevotella sp. HOT-376 and Fretibacterium fastidiosum. Furthermore, pyrosequencing analysis demonstrated increased proportions of the as-yet-uncultivated phylotypes Dialister sp. HOT-119 and Megasphaera sp. HOT-123 on mixed culture plates supplemented with siderophores. Therefore a culture model was developed, which incorporated 15 μg siderophore (pyoverdines-Fe-complex or desferricoprogen) or 150 μl neat subgingival-plaque suspension into a central well on agar plates that were inoculated with heavily-diluted subgingival-plaque samples from subjects with periodontitis. Colonies showing satellitism were passaged onto fresh plates in co-culture with selected helper strains. Five novel strains, representatives of three previously-uncultivated taxa (Anaerolineae bacterium HOT-439, the first oral taxon from the Chloroflexi phylum to have been cultivated; Bacteroidetes bacterium HOT-365; and Peptostreptococcaceae bacterium HOT-091) were successfully isolated. All novel isolates required helper strains for growth, implying dependence on a biofilm lifestyle. Their characterisation will further our understanding of the human oral microbiome.
Collapse
Affiliation(s)
- Sonia R. Vartoukian
- Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Aleksandra Adamowska
- Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Megan Lawlor
- Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Rebecca Moazzez
- King’s College London Dental Institute, London, United Kingdom
| | - Floyd E. Dewhirst
- The Forsyth Institute, Cambridge, United States of America
- Harvard School of Dental Medicine, Boston, United States of America
| | - William G. Wade
- Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
- * E-mail:
| |
Collapse
|
31
|
Ni C, Horton DJ, Rui J, Henson MW, Jiang Y, Huang X, Learman DR. High concentrations of bioavailable heavy metals impact freshwater sediment microbial communities. ANN MICROBIOL 2015. [DOI: 10.1007/s13213-015-1189-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
|
32
|
Brzoska RM, Bollmann A. The long-term effect of uranium and pH on the community composition of an artificial consortium. FEMS Microbiol Ecol 2015; 92:fiv158. [DOI: 10.1093/femsec/fiv158] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2015] [Indexed: 11/12/2022] Open
|
33
|
Steinert G, Taylor MW, Schupp PJ. Diversity of Actinobacteria Associated with the Marine Ascidian Eudistoma toealensis. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2015; 17:377-385. [PMID: 25678260 DOI: 10.1007/s10126-015-9622-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 01/20/2015] [Indexed: 06/04/2023]
Abstract
Ascidians have yielded a wide variety of bioactive natural products. The colonial ascidian Eudistoma toealensis from Micronesia has been identified as the source of a series of staurosporine derivatives, though the exact origin of these derivatives is still unknown. To identify known staurosporine-producing microbes associated with E. toealensis, we analyzed with 16S rRNA gene tag pyrosequencing the overall bacterial community and focused on potential symbiotic bacteria already known from other ascidians or other marine hosts, such as sponges. The described microbiota was one of very high diversity, comprising 43 phyla: two from archaea, 34 described bacterial phyla, and seven candidate bacterial phyla. Many bacteria, which are renowned community members of other ascidians and marine holobionts, such as sponges and corals, were also part of the E. toealensis microbial community. Furthermore, two known producers of indolocarbazoles, Salinispora and Verrucosispora, were found with high abundance exclusively in the ascidian tissue, suggesting that microbial symbionts and not the organism itself may be the true producers of the staurosporines in E. toealensis.
Collapse
Affiliation(s)
- Georg Steinert
- Institute for the Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany,
| | | | | |
Collapse
|
34
|
Aylan KM, Daniele BDS, Rodrigo NM, Lucia HST, Eliana GDML, Lucia MCA. Bacterial community in two subtropical fishponds in So Paulo, Brazil. ACTA ACUST UNITED AC 2015. [DOI: 10.5897/ajmr2014.7249] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
|
35
|
Steinert G, Whitfield S, Taylor MW, Thoms C, Schupp PJ. Application of diffusion growth chambers for the cultivation of marine sponge-associated bacteria. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2014; 16:594-603. [PMID: 24838766 DOI: 10.1007/s10126-014-9575-y] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 04/30/2014] [Indexed: 06/03/2023]
Abstract
Marine sponges contain dense and diverse microbial communities, which are renowned as a source of bioactive metabolites. The biological activities of sponge-microbe natural products span a broad spectrum, from antibacterial and antifungal to antitumor and antiviral applications. However, the potential of sponge-derived compounds has not been fully realized, due largely to the acknowledged "supply issue." Most bacteria from environmental samples have resisted cultivation on artificial growth media, and cultivation of sponge-associated bacteria has been a major focus in the search for novel marine natural products. One approach to isolate so-called "uncultivable" microorganisms from different environments is the diffusion growth chamber method. Here, we describe the first application of diffusion growth chambers for the isolation of cultivable and previously uncultivated bacteria from sponges. The study was conducted by implanting diffusion growth chambers in the tissue of Rhabdastrella globostellata reef sponges. In total, 255 16S rRNA gene sequences were obtained, with phylogenetic analyses revealing their affiliations with the Alpha- and Gammaproteobacteria, Bacteroidetes, Actinobacteria, and Firmicutes. Fifteen sequences represented previously uncultivated bacteria belonging to the Bacteroidetes and Proteobacteria (Alpha and Gamma classes). Our results indicate that the diffusion growth chamber approach can be successfully applied in a natural, living marine environment such as sponges.
Collapse
Affiliation(s)
- Georg Steinert
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | | | | | | | | |
Collapse
|
36
|
Milshteyn A, Schneider JS, Brady SF. Mining the metabiome: identifying novel natural products from microbial communities. CHEMISTRY & BIOLOGY 2014; 21:1211-23. [PMID: 25237864 PMCID: PMC4171686 DOI: 10.1016/j.chembiol.2014.08.006] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 08/06/2014] [Accepted: 08/08/2014] [Indexed: 12/21/2022]
Abstract
Microbial-derived natural products provide the foundation for most of the chemotherapeutic arsenal available to contemporary medicine. In the face of a dwindling pipeline of new lead structures identified by traditional culturing techniques and an increasing need for new therapeutics, surveys of microbial biosynthetic diversity across environmental metabiomes have revealed enormous reservoirs of as yet untapped natural products chemistry. In this review, we touch on the historical context of microbial natural product discovery and discuss innovations and technological advances that are facilitating culture-dependent and culture-independent access to new chemistry from environmental microbiomes with the goal of reinvigorating the small molecule therapeutics discovery pipeline. We highlight the successful strategies that have emerged and some of the challenges that must be overcome to enable the development of high-throughput methods for natural product discovery from complex microbial communities.
Collapse
Affiliation(s)
- Aleksandr Milshteyn
- Laboratory of Genetically Encoded Small Molecules, Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Jessica S Schneider
- Laboratory of Genetically Encoded Small Molecules, Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, Rockefeller University, 1230 York Avenue, New York, NY 10065, USA; Howard Hughes Medical Institute, Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
| |
Collapse
|
37
|
Kaci A, Petit F, Lesueur P, Boust D, Vrel A, Berthe T. Distinct diversity of the czcA gene in two sedimentary horizons from a contaminated estuarine core. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2014; 21:10787-10802. [PMID: 24894751 DOI: 10.1007/s11356-014-3029-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 05/08/2014] [Indexed: 06/03/2023]
Abstract
In estuarine ecosystems, trace metals are mainly associated with fine grain sediments which settle on mudflats. Over time, the layers of sediments accumulate and are then transformed by diagenetic processes, recording the history of the estuary's chemical contamination. In such a specific environment, we investigated to what extent a chronic exposure to contaminants could affect metal-resistant sedimentary bacteria in subsurface sediments. The occurrence and diversity of cadmium resistance genes (cadA, czcA) was investigated in 5- and 33-year-old sediments from a highly contaminated estuary (Seine France). Primers were designed to detect a 252-bp fragment of the czcA gene, specifically targeting a transmembrane helice domain (TMH IV) involved in the proton substrate antiport of this efflux pump. Although the cadA gene was not detected, the highest diversity of the sequence of the czcA gene was observed in the 5-year-old sediment. According to the percentage of identity at the amino acid level, the closest CzcA relatives were identified among Proteobacteria (α, β, γ, and δ), Verrucomicrobia, Nitrospirae, and Bacteroidetes. The most abundant sequences were affiliated with Stenotrophomonas. In contrast, in the 33-year-old sediment, CzcA sequences were mainly related to Rhodanobacter thiooxydans and Stenotrophomonas, suggesting a shaping of the metal-resistant microbial communities over time by both diagenetic processes and trace metal contamination.
Collapse
Affiliation(s)
- Assia Kaci
- CNRS, UMR 6143 M2C, Universités de Rouen-Caen, Normandie Université, 76821, Mont-Saint-Aignan, Cedex, France
| | | | | | | | | | | |
Collapse
|
38
|
Modulation of medium pH by Caulobacter crescentus facilitates recovery from uranium-induced growth arrest. Appl Environ Microbiol 2014; 80:5680-8. [PMID: 25002429 DOI: 10.1128/aem.01294-14] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The oxidized form of uranium [U(VI)] predominates in oxic environments and poses a major threat to ecosystems. Due to its ability to mineralize U(VI), the oligotroph Caulobacter crescentus is an attractive candidate for U(VI) bioremediation. However, the physiological basis for U(VI) tolerance is unclear. Here we demonstrated that U(VI) caused a temporary growth arrest in C. crescentus and three other bacterial species, although the duration of growth arrest was significantly shorter for C. crescentus. During the majority of the growth arrest period, cell morphology was unaltered and DNA replication initiation was inhibited. However, during the transition from growth arrest to exponential phase, cells with shorter stalks were observed, suggesting a decoupling between stalk development and the cell cycle. Upon recovery from growth arrest, C. crescentus proliferated with a growth rate comparable to that of a control without U(VI), although a fraction of these cells appeared filamentous with multiple replication start sites. Normal cell morphology was restored by the end of exponential phase. Cells did not accumulate U(VI) resistance mutations during the prolonged growth arrest, but rather, a reduction in U(VI) toxicity occurred concomitantly with an increase in medium pH. Together, these data suggest that C. crescentus recovers from U(VI)-induced growth arrest by reducing U(VI) toxicity through pH modulation. Our finding represents a unique U(VI) detoxification strategy and provides insight into how microbes cope with U(VI) under nongrowing conditions, a metabolic state that is prevalent in natural environments.
Collapse
|
39
|
Li H, Pan G. Enhanced and continued degradation of microcystins using microorganisms obtained through natural media. J Microbiol Methods 2013; 96:73-80. [PMID: 24246232 DOI: 10.1016/j.mimet.2013.11.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Revised: 11/05/2013] [Accepted: 11/05/2013] [Indexed: 10/26/2022]
Abstract
Microorganisms isolated through artificial media are often unsustainable in biodegrading microcystins (MCs) in natural water. Here we studied alternative approaches to isolate MCs-degrading bacteria using natural media. In comparison to two species (MS-1 and MS-2) isolated from artificial media and the failure of bacterial colonies formation using water extracts of sediment (10%, w/v), five colony species (WC-1 to WC-5) appeared using concentrated water extracts of sediment that is 10-fold enhancement of nutrient level. In the simulated biodegradation test in Lake Taihu water with continuous supply of MCs, a lag phase of 6days was required for MS-1 and M-2 to degrade 13% and 15% of the added MC-RR and MC-LR, respectively, whereas the lag phase was only 3days with approximately 44% and 31% removal of the added MC-RR and MC-LR by WC-1 to WC-5. During the continuous supply experiment, degradation of MCs by MS-1 and MS-2 stopped after 3days, while degradation of MCs by WC-1 to WC-5 lasted continuously throughout the 18day test period with 2 to 6-fold enhancement of removal rate. 16S rRNA gene sequences and phylogenetic analysis indicated the potential to amplify species of MCs-degrading bacteria when natural media were used. The results suggested that the increased adaptability of bacteria obtained through concentrated natural media was responsible for the enhanced and continued biodegradation under simulated natural water conditions.
Collapse
Affiliation(s)
- Hong Li
- Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing 100085, People's Republic of China
| | - Gang Pan
- Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing 100085, People's Republic of China.
| |
Collapse
|
40
|
Epstein SS. The phenomenon of microbial uncultivability. Curr Opin Microbiol 2013; 16:636-42. [DOI: 10.1016/j.mib.2013.08.003] [Citation(s) in RCA: 154] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 08/13/2013] [Accepted: 08/13/2013] [Indexed: 11/15/2022]
|
41
|
Draft Genome Sequence for Ralstonia sp. Strain OR214, a Bacterium with Potential for Bioremediation. GENOME ANNOUNCEMENTS 2013; 1:1/3/e00321-13. [PMID: 23792748 PMCID: PMC3675513 DOI: 10.1128/genomea.00321-13] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Ralstonia sp. strain OR214 belongs to the class Betaproteobacteria and was isolated from subsurface sediments in Oak Ridge, TN. A member of this genus has been described as a potential bioremediation agent. Strain OR214 is tolerant to various heavy metals, such as uranium, nickel, cobalt, and cadmium. We present its draft genome sequence here.
Collapse
|
42
|
Draft Genome Sequence for Caulobacter sp. Strain OR37, a Bacterium Tolerant to Heavy Metals. GENOME ANNOUNCEMENTS 2013; 1:1/3/e00322-13. [PMID: 23792749 PMCID: PMC3675514 DOI: 10.1128/genomea.00322-13] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Caulobacter sp. strain OR37 belongs to the class Alphaproteobacteria and was isolated from subsurface sediments in Oak Ridge, TN. Strain OR37 is noteworthy due to its tolerance to high concentrations of heavy metals, such as uranium, nickel, cobalt, and cadmium, and we present its draft genome sequence here.
Collapse
|
43
|
Draft genome sequence for Microbacterium laevaniformans strain OR221, a bacterium tolerant to metals, nitrate, and low pH. J Bacteriol 2012; 194:3279-80. [PMID: 22628508 DOI: 10.1128/jb.00474-12] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microbacterium laevaniformans strain OR221 was isolated from subsurface sediments obtained from the Field Research Center (FRC) in Oak Ridge, TN. It was characterized as a bacterium tolerant to heavy metals, such as uranium, nickel, cobalt, and cadmium, as well as nitrate and low pH. We present its draft genome sequence.
Collapse
|
44
|
Abstract
The bacteria that can be grown in the laboratory are only a small fraction of the total diversity that exists in nature. At all levels of bacterial phylogeny, uncultured clades that do not grow on standard media are playing critical roles in cycling carbon, nitrogen, and other elements, synthesizing novel natural products, and impacting the surrounding organisms and environment. While molecular techniques, such as metagenomic sequencing, can provide some information independent of our ability to culture these organisms, it is essentially impossible to learn new gene and pathway functions from pure sequence data. A true understanding of the physiology of these bacteria and their roles in ecology, host health, and natural product production requires their cultivation in the laboratory. Recent advances in growing these species include coculture with other bacteria, recreating the environment in the laboratory, and combining these approaches with microcultivation technology to increase throughput and access rare species. These studies are unraveling the molecular mechanisms of unculturability and are identifying growth factors that promote the growth of previously unculturable organisms. This minireview summarizes the recent discoveries in this area and discusses the potential future of the field.
Collapse
|
45
|
Denitrifying bacteria from the genus Rhodanobacter dominate bacterial communities in the highly contaminated subsurface of a nuclear legacy waste site. Appl Environ Microbiol 2011; 78:1039-47. [PMID: 22179233 DOI: 10.1128/aem.06435-11] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The effect of long-term mixed-waste contamination, particularly uranium and nitrate, on the microbial community in the terrestrial subsurface was investigated at the field scale at the Oak Ridge Integrated Field Research Challenge (ORIFRC) site in Oak Ridge, TN. The abundance, community composition, and distribution of groundwater microorganisms were examined across the site during two seasonal sampling events. At representative locations, subsurface sediment was also examined from two boreholes, one sampled from the most heavily contaminated area of the site and another from an area with low contamination. A suite of DNA- and RNA-based molecular tools were employed for community characterization, including quantitative PCR of rRNA and nitrite reductase genes, community composition fingerprinting analysis, and high-throughput pyrotag sequencing of rRNA genes. The results demonstrate that pH is a major driver of the subsurface microbial community structure and that denitrifying bacteria from the genus Rhodanobacter (class Gammaproteobacteria) dominate at low pH. The relative abundance of bacteria from this genus was positively correlated with lower-pH conditions, and these bacteria were abundant and active in the most highly contaminated areas. Other factors, such as the concentration of nitrogen species, oxygen level, and sampling season, did not appear to strongly influence the distribution of Rhodanobacter bacteria. The results indicate that these organisms are acid-tolerant denitrifiers, well suited to the acidic, nitrate-rich subsurface conditions, and pH is confirmed as a dominant driver of bacterial community structure in this contaminated subsurface environment.
Collapse
|
46
|
New approaches for isolation of previously uncultivated oral bacteria. Appl Environ Microbiol 2011; 78:194-203. [PMID: 22057871 DOI: 10.1128/aem.06813-11] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
A significant number of microorganisms from the human oral cavity remain uncultivated. This is a major impediment to the study of human health since some of the uncultivated species may be involved in a variety of systemic diseases. We used a range of innovations previously developed to cultivate microorganisms from the human oral cavity, focusing on anaerobic species. These innovations include (i) in vivo cultivation to specifically enrich for species actively growing in the oral cavity (the "minitrap" method), (ii) single-cell long-term cultivation to minimize the effect of fast-growing microorganisms, and (iii) modifications of conventional enrichment techniques, using media that did not contain sugar, including glucose. To enable cultivation of obligate anaerobes, we maintained strict anaerobic conditions in most of our cultivation experiments. We report that, on a per cell basis, the most successful recovery was achieved using minitrap enrichment (11%), followed by single-cell cultivation (3%) and conventional plating (1%). Taxonomically, the richest collection was obtained using the single-cell cultivation method, followed by minitrap and conventional enrichment, comprising representatives of 13, 9, and 4 genera, respectively. Interestingly, no single species was isolated by all three methods, indicating method complementarity. An important result is the isolation and maintenance in pure culture of 10 strains previously only known by their molecular signatures, as well as representatives of what are likely to be three new microbial genera. We conclude that the ensemble of new methods we introduced will likely help close the gap between cultivated and uncultivated species from the human oral cavity.
Collapse
|
47
|
|