1
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Mei R, Liu WT. Meta-Omics-Supervised Characterization of Respiration Activities Associated with Microbial Immigrants in Anaerobic Sludge Digesters. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:6689-6698. [PMID: 35510767 DOI: 10.1021/acs.est.2c01029] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Immigration has been recently recognized as an important ecological process that affects the microbial community structure in diverse ecosystems. However, the fate of microbial immigrants in the new environment and their involvement in the local biochemical network remain unclear. In this study, we performed meta-omics-supervised characterization of immigrants' activities in anaerobic sludge digesters. Metagenomic analyses revealed that immigrants from the feed sludge accounted for the majority of populations capable of anaerobic respiration in a digester. Electron acceptors that were predicted to be respired, including nitrate, nitrite, sulfate, and elemental sulfur, were added to digester sludge in batch tests. Consumption of up to 91% of the added electron acceptors was observed within the experiment period. 16S rRNA sequencing detected populations that were stimulated by the electron acceptors, largely overlapping with respiration-capable immigrants identified by metagenomic analysis. Metatranscriptomic analysis of the batch tests provided additional evidence for upregulated expression of respiration genes and concomitant suppressed expression of methanogenesis. Anaerobic respiration activity was further evaluated in full-scale digesters in nine wastewater treatment plants. Although nitrate and sulfate respiration were ubiquitous, the expression level of respiration genes was generally 2-3 orders of magnitude lower than the expression of methanogenesis in most digesters, suggesting marginal ecological roles by immigrants in full-scale digester ecosystems.
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Affiliation(s)
- Ran Mei
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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2
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Kim J, Mei R, Wilson FP, Yuan H, Bocher BTW, Liu WT. Ecogenomics-Based Mass Balance Model Reveals the Effects of Fermentation Conditions on Microbial Activity. Front Microbiol 2020; 11:595036. [PMID: 33343535 PMCID: PMC7738435 DOI: 10.3389/fmicb.2020.595036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 11/16/2020] [Indexed: 01/04/2023] Open
Abstract
Fermentation of waste activated sludge (WAS) is an alternative approach to reduce solid wastes while providing valuable soluble products, such as volatile fatty acids and alcohols. This study systematically identified optimal fermentation conditions and key microbial populations by conducting two sets of experiments under different combinations of biochemical and physical parameters. Based on fermentation product concentrations, methane production, and solid removal, fermentation performance was enhanced under the combined treatments of inoculum heat shock (>60°C), pH 5, 55°C, and short solid retention time (<10 days). An ecogenomics-based mass balance (EGMB) approach was used to determine the net growth rates of individual microbial populations, and classified them into four microbial groups: known syntrophs, known methanogens, fermenters, and WAS-associated populations. Their growth rates were observed to be affected by the treatment conditions. The growth rates of syntrophs and fermenters, such as Syntrophomonas and Parabacteroides increased with a decrease in SRT. In contrast, treatment conditions, such as inoculum heat shock and high incubation temperature inhibited the growth of WAS-associated populations, such as Terrimonas and Bryobacter. There were also populations insensitive to the treatment conditions, such as those related to Microbacter and Rikenellaceae. Overall, the EGMB approach clearly revealed the ecological roles of important microbial guilds in the WAS fermentation system, and guided the selection of optimal conditions for WAS fermentation in future pilot-scale operation.
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Affiliation(s)
- Jinha Kim
- Department of Civil and Environmental Engineering, University of Illinois, Urbana-Champaign, Urbana, IL, United States
| | - Ran Mei
- Department of Civil and Environmental Engineering, University of Illinois, Urbana-Champaign, Urbana, IL, United States
| | - Fernanda P Wilson
- Department of Civil and Environmental Engineering, University of Illinois, Urbana-Champaign, Urbana, IL, United States
| | - Heyang Yuan
- Department of Civil and Environmental Engineering, University of Illinois, Urbana-Champaign, Urbana, IL, United States
| | - Benjamin T W Bocher
- British Petroleum America, Petrochemicals Technology, Naperville, IL, United States
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois, Urbana-Champaign, Urbana, IL, United States
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3
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Mei R, Nobu MK, Narihiro T, Liu WT. Metagenomic and Metatranscriptomic Analyses Revealed Uncultured Bacteroidales Populations as the Dominant Proteolytic Amino Acid Degraders in Anaerobic Digesters. Front Microbiol 2020; 11:593006. [PMID: 33193263 PMCID: PMC7661554 DOI: 10.3389/fmicb.2020.593006] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Accepted: 10/13/2020] [Indexed: 01/22/2023] Open
Abstract
Current understanding of amino acid (AA) degraders in anaerobic digesters is mainly based on cultured species, whereas microorganisms that play important roles in a complex microbial community remain poorly characterized. This study investigated short-term enrichments degrading single AAs using metagenomics and metatranscriptomics. Metagenomic analysis revealed that populations related to cultured AA degraders had an abundance <2.5% of the sequences. In contrast, metagenomic-assembled bins related to uncultured Bacteroidales collectively accounted for >35% of the sequences. Phylogenetic analyses suggested that these Bacteroidales populations represented a yet-to-be characterized family lineage, i.e., Bacteroidetes vadinHA17. The bins possessed the genetic capacity related to protein degradation, including surface adhesion (3–7 genes), secreted peptidase (52–77 genes), and polypeptide-specific transporters (2–5 genes). Furthermore, metatranscriptomics revealed that these Bacteroidales populations expressed the complete metabolic pathways for degrading 16 to 17 types of AAs in enrichments fed with respective substrates. These characteristics were distinct from cultured AA degraders including Acidaminobacter and Peptoclostridium, suggesting the uncultured Bacteroidales were the major protein-hydrolyzing and AA-degrading populations. These uncultured Bacteroidales were further found to be dominant and active in full-scale anaerobic digesters, indicating their important ecological roles in the native habitats. “Candidatus Aminobacteroidaceae” was proposed to represent the previously uncharted family Bacteroidetes vadinHA17.
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Affiliation(s)
- Ran Mei
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Masaru K Nobu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, United States.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Takashi Narihiro
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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4
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Subramani R, Sipkema D. Marine Rare Actinomycetes: A Promising Source of Structurally Diverse and Unique Novel Natural Products. Mar Drugs 2019; 17:E249. [PMID: 31035452 PMCID: PMC6562664 DOI: 10.3390/md17050249] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 04/18/2019] [Accepted: 04/23/2019] [Indexed: 12/18/2022] Open
Abstract
Rare actinomycetes are prolific in the marine environment; however, knowledge about their diversity, distribution and biochemistry is limited. Marine rare actinomycetes represent a rather untapped source of chemically diverse secondary metabolites and novel bioactive compounds. In this review, we aim to summarize the present knowledge on the isolation, diversity, distribution and natural product discovery of marine rare actinomycetes reported from mid-2013 to 2017. A total of 97 new species, representing 9 novel genera and belonging to 27 families of marine rare actinomycetes have been reported, with the highest numbers of novel isolates from the families Pseudonocardiaceae, Demequinaceae, Micromonosporaceae and Nocardioidaceae. Additionally, this study reviewed 167 new bioactive compounds produced by 58 different rare actinomycete species representing 24 genera. Most of the compounds produced by the marine rare actinomycetes present antibacterial, antifungal, antiparasitic, anticancer or antimalarial activities. The highest numbers of natural products were derived from the genera Nocardiopsis, Micromonospora, Salinispora and Pseudonocardia. Members of the genus Micromonospora were revealed to be the richest source of chemically diverse and unique bioactive natural products.
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Affiliation(s)
- Ramesh Subramani
- School of Biological and Chemical Sciences, Faculty of Science, Technology & Environment, The University of the South Pacific, Laucala Campus, Private Mail Bag, Suva, Republic of Fiji.
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.
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5
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Vuillemin A, Ariztegui D, Horn F, Kallmeyer J, Orsi WD. Microbial community composition along a 50 000-year lacustrine sediment sequence. FEMS Microbiol Ecol 2019; 94:4880442. [PMID: 29471361 PMCID: PMC5905624 DOI: 10.1093/femsec/fiy029] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 02/19/2018] [Indexed: 02/01/2023] Open
Abstract
For decades, microbial community composition in subseafloor sediments has been the focus of extensive studies. In deep lacustrine sediments, however, the taxonomic composition of microbial communities remains undercharacterized. Greater knowledge on microbial diversity in lacustrine sediments would improve our understanding of how environmental factors, and resulting selective pressures, shape subsurface biospheres in marine and freshwater sediments. Using high-throughput sequencing of 16S rRNA genes across high-resolution climate intervals covering the last 50 000 years in Laguna Potrok Aike, Argentina, we identified changes in microbial populations in response to both past environmental conditions and geochemical changes of the sediment during burial. Microbial communities in Holocene sediments were most diverse, reflecting a layering of taxa linked to electron acceptors availability. In deeper intervals, the data show that salinity, organic matter and the depositional conditions over the Last Glacial-interglacial cycle were all selective pressures in the deep lacustrine assemblage resulting in a genetically distinct biosphere from the surface dominated primarily by Bathyarchaeota and Atribacteria groups. However, similar to marine sediments, some dominant taxa in the shallow subsurface persisted into the subsurface as minor fraction of the community. The subsequent establishment of a deep subsurface community likely results from a combination of paleoenvironmental factors that have shaped the pool of available substrates, together with substrate depletion and/or reworking of organic matter with depth.
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Affiliation(s)
- Aurèle Vuillemin
- Department of Earth & Environmental Science, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333 Munich, Germany.,Section of Earth & Environmental Sciences, University of Geneva, rue des Maraichers 13, 1205 Geneva, Switzerland.,GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3: Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany
| | - Daniel Ariztegui
- Section of Earth & Environmental Sciences, University of Geneva, rue des Maraichers 13, 1205 Geneva, Switzerland
| | - Fabian Horn
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3: Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany
| | - Jens Kallmeyer
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3: Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany
| | - William D Orsi
- Department of Earth & Environmental Science, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333 Munich, Germany.,Geobio-Center, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333 Munich, Germany
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6
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Tripathi VC, Satish S, Horam S, Raj S, lal A, Arockiaraj J, Pasupuleti M, Dikshit DK. Natural products from polar organisms: Structural diversity, bioactivities and potential pharmaceutical applications. POLAR SCIENCE 2018; 18:147-166. [DOI: 10.1016/j.polar.2018.04.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/16/2023]
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7
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Lasudee K, Tokuyama S, Lumyong S, Pathom-Aree W. Actinobacteria Associated With Arbuscular Mycorrhizal Funneliformis mosseae Spores, Taxonomic Characterization and Their Beneficial Traits to Plants: Evidence Obtained From Mung Bean ( Vigna radiata) and Thai Jasmine Rice ( Oryza sativa). Front Microbiol 2018; 9:1247. [PMID: 29942292 PMCID: PMC6004784 DOI: 10.3389/fmicb.2018.01247] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 05/23/2018] [Indexed: 01/01/2023] Open
Abstract
In this study, we report on the isolation of actinobacteria obtained from spores of Funneliformis mosseae and provide evidence for their potential in agricultural uses as plant growth promoters in vitro and in vivo. Actinobacteria were isolated from spores of F. mosseae using the dilution plate technique and media designed for the selective isolation of members of specific actinobacterial taxa. Six strains namely 48, S1, S3, S4, S4-1 and SP, were isolated and identified based on16S rRNA gene sequences. Phylogenetic analysis showed that isolate SP belonged to the genus Pseudonocardia with P. nantongensis KLBMP 1282T as its closest neighbor. The remaining isolates belonged to the genus Streptomyces. Two isolates, 48 and S3 were most closely related to S. thermocarboxydus DSM 44293T. Isolates S4 and S4-1 shared the highest 16S RNA gene similarity with S. pilosus NBRC 127772T. Isolate S1 showed its closest relationship with the type strain of S. spinoverrucosus NBRC14228T. The ability of these isolates to produce indole-3-acetic acid (IAA), siderophores and the ability to solubilize phosphate in vitro were examined. All isolates produced siderophores, four isolates produced IAA and two isolates solubilized inorganic phosphate at varying levels. S. thermocarboxydus isolate S3 showed the highest IAA production with high activities of phosphate solubilization and siderophore production. The inoculation of mung beans (Vigna radiata) with this strain resulted in a significant increase in fresh weight, root length and total length as an effect of IAA production. In an experiment with rice (Oryza sativa), S. thermocarboxydus isolate S3 promoted the growth of rice plants grown in low nutritional soil under induced drought stress. This report supports the view that the inoculation of rice with plant growth promoting actinobacteria mitigates some adverse effects of low nutrient and drought stress on rice.
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Affiliation(s)
- Krisana Lasudee
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Shinji Tokuyama
- Department of Applied Biological Chemistry, Faculty of Agriculture, Shizuoka University, Shizuoka, Japan
| | - Saisamorn Lumyong
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Wasu Pathom-Aree
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand.,Center of Excellence in Bioresources for Agriculture, Industry and Medicine, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
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8
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Carrazco-Palafox J, Rivera-Chavira BE, Ramírez-Baca N, Manzanares-Papayanopoulos LI, Nevárez-Moorillón GV. Improved method for qualitative screening of lipolytic bacterial strains. MethodsX 2018; 5:68-74. [PMID: 30622910 PMCID: PMC6318097 DOI: 10.1016/j.mex.2018.01.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 01/18/2018] [Indexed: 11/19/2022] Open
Abstract
Esterases and lipases are lipolytic enzymes that catalyse the hydrolysis of triacylglycerols, Determination of lipolysis on agar plates is a simple approach to determine lipase or esterase action, but visual evaluation of lipolysis is frequently difficult in practice. Therefore, the aim of this work was to improve the efficiency of lipolysis visualization in tributyrin agar (mTBA) by adding calcium and/or magnesium ions in the screening of lipolytic microbial strains. Lipolytic activity was evaluated in mTBA using the well diffusion technique, where a clear zone around the inoculated wells indicated lipid hydrolysis. Results suggest that the addition of 2.5 mM calcium and 5.0 mM magnesium was the best combination of ion addition to TBA. Lipolytic activity increased the clearing zone up to 38% more than without the addition of ions and the clear zone was clearly observed. The mTBA plate was used with culture collection microbial strains, as well as with a collection of soil microorganisms, to identify lipase producers. The addition of calcium and magnesium ions can provide an easier screening procedure for selection of lipolytic bacterial strains. •A modified tributyrin agar for screening of lipolytic bacteria was prepared by adding calcium and magnesium ions.•The modified TBA agar was tested with control bacterial strains, and, based on the results, 2.5 mM Ca and 5.0 mM Mg ions were added in the mTBA.•mTBA was validated with environmental bacterial strains for screening of lipolytic activity.
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Affiliation(s)
- Jair Carrazco-Palafox
- Facultad de Medicina y Ciencias Biomédicas, Universidad Autónoma de Chihuahua, Circuito No. 1, Campus Universitario II Chihuahua, Chihuahua 31125, Mexico
- Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitario s/n, Campus Universitario II, Chihuahua, Chihuahua 31125, Mexico
| | - Blanca E. Rivera-Chavira
- Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitario s/n, Campus Universitario II, Chihuahua, Chihuahua 31125, Mexico
| | - Norma Ramírez-Baca
- Secretaría de Comunicaciones y Obras Públicas, Gobierno del Estado de Chihuahua, Beethoven 4000, Fraccionamiento la Herradura, Chihuahua, Chihuahua 31206, Mexico
| | - Luisa I. Manzanares-Papayanopoulos
- Capítulo Mexicano del Consejo Empresarial Mundial para el Desarrollo Sostenible, Comisión de Estudios del Sector Privado para el Desarrollo Sustentable, Lancaster 15, Col. Juárez, Mexico City, D.F. 06600, Mexico
| | - Guadalupe V. Nevárez-Moorillón
- Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitario s/n, Campus Universitario II, Chihuahua, Chihuahua 31125, Mexico
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9
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Nobu MK, Narihiro T, Liu M, Kuroda K, Mei R, Liu WT. Thermodynamically diverse syntrophic aromatic compound catabolism. Environ Microbiol 2017; 19:4576-4586. [PMID: 28892300 DOI: 10.1111/1462-2920.13922] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Accepted: 08/19/2017] [Indexed: 11/28/2022]
Abstract
Specialized organotrophic Bacteria 'syntrophs' and methanogenic Archaea 'methanogens' form a unique metabolic interaction to accomplish cooperative mineralization of organic compounds to CH4 and CO2 . Due to challenges in cultivation of syntrophs, mechanisms for how their organotrophic catabolism circumvents thermodynamic restrictions remain unclear. In this study, we investigate two communities hosting diverse syntrophic aromatic compound metabolizers (Syntrophus, Syntrophorhabdus, Pelotomaculum and an uncultivated Syntrophorhabdacaeae member) to uncover their catabolic diversity and flexibility. Although syntrophs have been generally presumed to metabolize aromatic compounds to acetate, CO2 , H2 and formate, combined metagenomics and metatranscriptomics show that uncultured syntrophs utilize unconventional alternative metabolic pathways in situ producing butyrate, cyclohexanecarboxylate and benzoate as catabolic byproducts. In addition, we also find parallel utilization of diverse H2 and formate generating pathways to facilitate interactions with partner methanogens. Based on thermodynamic calculations, these pathways may enable syntrophs to combat thermodynamic restrictions. In addition, when fed with specific substrates (i.e., benzoate, terephthalate or trimellitate), each syntroph population expresses different pathways, suggesting ecological diversification among syntrophs. These findings suggest we may be drastically underestimating the biochemical capabilities, strategies and diversity of syntrophic bacteria thriving at the thermodynamic limit.
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Affiliation(s)
- Masaru Konishi Nobu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 205 North Mathews Ave, Urbana, IL 61801, USA
| | - Takashi Narihiro
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 205 North Mathews Ave, Urbana, IL 61801, USA.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki 305-8566, Japan
| | - Miaomiao Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 205 North Mathews Ave, Urbana, IL 61801, USA
| | - Kyohei Kuroda
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 205 North Mathews Ave, Urbana, IL 61801, USA
| | - Ran Mei
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 205 North Mathews Ave, Urbana, IL 61801, USA
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 205 North Mathews Ave, Urbana, IL 61801, USA
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10
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Affiliation(s)
- Takashi Narihiro
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
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11
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Okamoto T, Aino K, Narihiro T, Matsuyama H, Yumoto I. Analysis of microbiota involved in the aged natural fermentation of indigo. World J Microbiol Biotechnol 2017; 33:70. [DOI: 10.1007/s11274-017-2238-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 03/03/2017] [Indexed: 10/20/2022]
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12
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Abe T, Ushiki N, Fujitani H, Tsuneda S. A rapid collection of yet unknown ammonia oxidizers in pure culture from activated sludge. WATER RESEARCH 2017; 108:169-178. [PMID: 27836171 DOI: 10.1016/j.watres.2016.10.070] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 10/25/2016] [Accepted: 10/27/2016] [Indexed: 06/06/2023]
Abstract
Nitrification is an important reaction in the biological nitrogen removal process in wastewater treatment plants (WWTPs). As ammonia-oxidizing microbes are slow-growing and sensitive to environmental factors such as free ammonia, pure strains are hard to obtain, preventing our understanding of their physiological characteristics. To conquer this hurdle, we report a high-throughput isolation technique based on scattering signatures, which exploits the tendency of many ammonia-oxidizing bacteria (AOB) to form microcolonies in activated sludge. The AOB microcolonies were directly sorted from the activated sludge without long incubation and enrichment bias, and were sequentially inoculated into 96-well microtiter plates containing growth medium. Phylogenetic analysis of the pure strains isolated in this study revealed a deeply branching and unrecognized lineage and diversity within the genus Nitrosomonas, beyond our expectation.
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Affiliation(s)
- Takuma Abe
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Norisuke Ushiki
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Hirotsugu Fujitani
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Satoshi Tsuneda
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.
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13
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Aoi Y, Kaneko Y, Tsuneda S. pH-gradient ion-exchange microbial cell chromatography as a simple method for microbial separation. J Biosci Bioeng 2016; 123:431-436. [PMID: 27923729 DOI: 10.1016/j.jbiosc.2016.10.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 10/05/2016] [Accepted: 10/29/2016] [Indexed: 11/19/2022]
Abstract
Selective separation of specific microbial types from a heterogeneous microbial population, such as an environmental microbial community, is an important process for microbial research and biotechnological industries. In the present study, pH-gradient ion-exchange microbial cell chromatography (PIE-MCC) was developed as a new method for microbial separation. The proposed method enables target microorganisms to be separated from a microbial community based on differences in microbial surface characteristics, because these characteristics, such as the ζ (zeta)-potential, vary among microbial cells. PIE-MCC was conducted by controlling the adhesion and detachment of microbial cells to and from the carrier surface by manipulating the pH of the running buffer. As a proof of concept, microbial cell separation via PIE-MCC was demonstrated using pure-cultured strains, model mixtures of two different pure-cultured strains, and an environmental sample targeting uncultivated microorganisms; i.e., each pure-cultured strain showed unique chromatograms; specific single species were separated from the model mixture; and a specific, uncultivated target was separated from the environmental sample. The ζ-potential of several tested strains suggested that not only electrostatic interactions, but also other factors affected microbial adhesion to the carrier surface. The newly developed method has several potential advantages compared with other techniques, not only in terms of its microbial separation capability, but also in terms of its simplicity and ability to be scaled up. Thus, the method has the potential to be widely used for a variety of purposes in the microbiology and biotechnology fields.
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Affiliation(s)
- Yoshiteru Aoi
- Institute for Sustainable Sciences and Developments, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8527, Japan.
| | - Yuji Kaneko
- Department of Life Science and Medical Bio-Science, Waseda University, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Satoshi Tsuneda
- Department of Life Science and Medical Bio-Science, Waseda University, Shinjuku-ku, Tokyo 162-8480, Japan
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14
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Mochimaru H, Tamaki H, Katayama T, Imachi H, Sakata S, Kamagata Y. Methanomicrobium antiquum sp. nov., a hydrogenotrophic methanogen isolated from deep sedimentary aquifers in a natural gas field. Int J Syst Evol Microbiol 2016; 66:4873-4877. [PMID: 27553654 DOI: 10.1099/ijsem.0.001444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
A mesophilic, hydrogenotrophic methanogen, designated strain MobHT, was isolated from sediments derived from deep sedimentary, natural-gas-bearing aquifers in Japan. Strain MobHT utilized H2/CO2 or formate, but not ethanol, 1-propanol, 2-propanol, 2-butanol or cyclopentanol, for growth and methane production. In addition, acetate and tungsten were required for growth. Yeast extract stimulated the growth, but was not required. The cells were weakly motile with multiple flagella, presented as a curved-rod-shaped (0.8×2.0 µm) and occurred singly or in pairs. Strain MobHT grew at 15-40 °C (optimum 35 °C) and at pH 5.9-7.9 (optimum pH 7.0-7.5). The sodium chloride range for growth was 0-5.8 % (optimum 2 %). The G+C content of the genomic DNA was 37.6 mol%. In the phylogenetic tree based on the 16S rRNA gene sequences, strain MobHT clustered together with Methanomicrobium mobile (95.4 % in sequence similarity), and formed a distinct clade from Methanolacinia petrolearia SEBR 4847T (95.6 %) and Methanolacinia paynteri G-2000T (95.4 %). The two species of the genus Methanolacinia utilized 2-propanol, whereas strain MobHT and Methanomicrobium mobile, the sole species of the genus Methanomicrobium, do not. Based on phenotypic and phylogenetic features, we propose a novel species for the isolate with the name, Methanomicrobiumantiquum sp. nov. The type strain is MobHT (=DSM 21220T=NBRC 104160T).
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Affiliation(s)
- Hanako Mochimaru
- Institute for Geo-Resources and Environment, Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8567, Japan
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan
| | - Taiki Katayama
- Institute for Geo-Resources and Environment, Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8567, Japan
| | - Hiroyuki Imachi
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
| | - Susumu Sakata
- Institute for Geo-Resources and Environment, Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8567, Japan
| | - Yoichi Kamagata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan
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