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Shen Q, Chen Y, Zhao Y, Zhu Y, Xu C, Chang M, Gao Y, Ji F. Operational strategy for solid phase denitrification to achieve carbon balance between organic release and denitrification consumption. BIORESOURCE TECHNOLOGY 2025; 422:132239. [PMID: 39961518 DOI: 10.1016/j.biortech.2025.132239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2024] [Revised: 01/22/2025] [Accepted: 02/14/2025] [Indexed: 02/21/2025]
Abstract
This study developed a pilot-scale vertical-baffled solid-phase denitrification reactor (VbSPDR) incorporating polycaprolactone (PCL) and ceramsite as fillers to balance organic carbon release and denitrification consumption. The Box-Behnken design was employed to assess the effects of hydraulic retention time (HRT), temperature, and influent nitrate concentration on nitrate removal efficiency and COD accumulation. Optimal conditions yielded a 95 % nitrate removal rate at 33 °C, an HRT of 1.22 h, and an influent nitrate concentration of 19 mg/L. Conversely, effluent COD concentration was minimized and dropped 2.5 mg/L at 13 °C, an HRT of 0.39 h, and an influent nitrate concentration of 19 mg/L. The PCL layer enriched hydrolysis-acidification and heterotrophic denitrifying bacteria by unclassified_f__Comamonadaceae and Acidovorax, while heterotrophic genera Phreatobacter thrived in ceramsite layer, enhancing the metabolism of COD over-released from PCL. These findings indicate that inorganic fillers can effectively enhance nitrate removal and controll effluent COD under varied operational parameters.
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Affiliation(s)
- Qiushi Shen
- YANGTZE Eco-Environment Engineering Research Center, China Three Gorges Corporation, Wuhan 430012, PR China; National Engineering Research Center for Ecological Environment of Yangtze River Economic Belt, Wuhan 430012, PR China
| | - Yasong Chen
- YANGTZE Eco-Environment Engineering Research Center, China Three Gorges Corporation, Wuhan 430012, PR China; National Engineering Research Center for Ecological Environment of Yangtze River Economic Belt, Wuhan 430012, PR China
| | - Yunpeng Zhao
- YANGTZE Eco-Environment Engineering Research Center, China Three Gorges Corporation, Wuhan 430012, PR China; National Engineering Research Center for Ecological Environment of Yangtze River Economic Belt, Wuhan 430012, PR China
| | - Yating Zhu
- YANGTZE Eco-Environment Engineering Research Center, China Three Gorges Corporation, Wuhan 430012, PR China; National Engineering Research Center for Ecological Environment of Yangtze River Economic Belt, Wuhan 430012, PR China
| | - Chaowei Xu
- YANGTZE Eco-Environment Engineering Research Center, China Three Gorges Corporation, Wuhan 430012, PR China; National Engineering Research Center for Ecological Environment of Yangtze River Economic Belt, Wuhan 430012, PR China
| | - Manqi Chang
- YANGTZE Eco-Environment Engineering Research Center, China Three Gorges Corporation, Wuhan 430012, PR China; National Engineering Research Center for Ecological Environment of Yangtze River Economic Belt, Wuhan 430012, PR China
| | - Yanjin Gao
- YANGTZE Eco-Environment Engineering Research Center, China Three Gorges Corporation, Wuhan 430012, PR China; National Engineering Research Center for Ecological Environment of Yangtze River Economic Belt, Wuhan 430012, PR China
| | - Fangying Ji
- Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, PR China.
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Purcell M, DuPont J, Somenahally A, McLawrence JF, Case CL, Gowda P, King N, Rouquette MJ, Yu RQ. Long-Term Grazing and Nitrogen Management Impacted Methane Emission Potential and Soil Microbial Community in Grazing Pastures. ENVIRONMENT & HEALTH (WASHINGTON, D.C.) 2025; 3:68-78. [PMID: 39839247 PMCID: PMC11744396 DOI: 10.1021/envhealth.4c00138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2024] [Revised: 09/11/2024] [Accepted: 09/12/2024] [Indexed: 01/23/2025]
Abstract
Achieving sustainable development in livestock agriculture by balancing livestock production, reduction of greenhouse gas (GHG) emissions, and effective utilization of nitrogen nutrient has indeed been challenging. This study investigated the long-term effects of continuous cattle grazing, stocking rates, and fertilization regimens on methane (CH4) emissions, soil microbial communities, and soil organic carbon (SOC) stocks in Bermudagrass pastures in East Texas, USA. Pastures were subjected to high or low stocking rates for over 50 years, with further subdivision based on fertilization: nitrogen-based fertilizer application or no fertilizer but with the growth of annual clover. Seasonal soil cores (0-60 cm) were collected, and laboratory microcosm incubation studies revealed unexpectedly high in vitro CH4 emissions in surface soils, particularly in the top 0-5 cm soil layer, reaching up to 300 nmol of CH4 mL-1. Higher CH4 emissions and methanogen abundance, along with lower SOC stocks, were observed in pastures subjected to high stocking rates compared to those with low stocking rates and in clover pastures compared to those with N-fertilized ryegrass. On the contrary, in low-stocked, N-fertilized annual ryegrass pastures, methanogen abundance was lowest, CH4 emissions were negligible, and SOC stocks were highest. Furthermore, animal excreta deposition significantly contributed to increased CH4 emissions. Prokaryotic and potential methanotrophic taxa, as compared to fungi, exhibited greater responsiveness to N-fertilization than to cattle stocking treatments with higher levels of methanotrophs observed in pastures subjected to high stocking rates and clover growth. This study suggests that strategic management practices such as optimal grazing and nitrogen management could effectively mitigate CH4 emissions in grazing lands.
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Affiliation(s)
- Maura Purcell
- Department
of Biology, University of Texas at Tyler, Tyler, Texas 75799, United States
| | - Jesse DuPont
- Grazinglands
Research Laboratory, USDA-ARS, El Reno, Oklahoma 73036, United States
| | - Anil Somenahally
- Texas
A&M AgriLife Research Center, Overton, Texas 75684, United States
| | | | - Cara L. Case
- Texas
A&M AgriLife Research Center, Overton, Texas 75684, United States
| | - Prasanna Gowda
- Grazinglands
Research Laboratory, USDA-ARS, El Reno, Oklahoma 73036, United States
| | - Nevada King
- Department
of Biology, University of Texas at Tyler, Tyler, Texas 75799, United States
| | | | - Ri-Qing Yu
- Department
of Biology, University of Texas at Tyler, Tyler, Texas 75799, United States
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3
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Aranda A, Primo-Catalunya D, Pijuan M, Balcázar JL. Draft genome sequence of Methyloversatilis sp. strain NSM2, isolated from a wastewater treatment plant. Microbiol Resour Announc 2024; 13:e0095224. [PMID: 39436067 PMCID: PMC11556028 DOI: 10.1128/mra.00952-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2024] [Accepted: 10/08/2024] [Indexed: 10/23/2024] Open
Abstract
Here, we report the draft genome sequence of Methyloversatilis sp. NSM2, isolated from a wastewater treatment plant. This strain was enriched using methane as the sole carbon source. The 4.5-Mb genome, with a GC content of 66.5%, provides valuable insights into the strain's ecological role and metabolic capabilities.
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Affiliation(s)
- Alicia Aranda
- Catalan Institute for Water Research (ICRA-CERCA), Girona, Spain
| | | | - Maite Pijuan
- Catalan Institute for Water Research (ICRA-CERCA), Girona, Spain
| | - José L. Balcázar
- Catalan Institute for Water Research (ICRA-CERCA), Girona, Spain
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4
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Beals DG, Munn JJ, Puri AW. Methane-oxidizing bacterial community dynamics in sub-alpine forest soil. Microbiol Spectr 2024; 12:e0083424. [PMID: 39287454 PMCID: PMC11537040 DOI: 10.1128/spectrum.00834-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 08/23/2024] [Indexed: 09/19/2024] Open
Abstract
Microbial activities in sub-alpine forest soil influence global cycling of the potent greenhouse gas methane. Understanding the dynamics of methane-oxidizing bacterial communities, particularly the roles of potentially active versus total microbial populations, is necessary for reducing uncertainty in global methane budget estimates. However, our understanding of the factors influencing methane cycling in forest soils is limited by our lack of knowledge about the biology of the microbes involved and how these communities are shaped by their environment. Here, we compared the composition and potential activity of microbial communities using 16S rRNA gene amplicon sequencing of total genomic DNA (gDNA) and potentially active complementary DNA (cDNA) from shallow soil in Red Butte Canyon (Salt Lake City, Utah, USA). We compared riparian and upland soils at two time points in the growing season and found distinct differences in both the community composition of the gDNA and cDNA libraries and the potential drivers of these community structures. Aerobic methane-oxidizing bacteria (methanotrophs) were detected in all samples, with cDNA libraries containing a higher average relative abundance and diversity of methanotrophs compared to gDNA libraries. Methane flux at the sample sites did not significantly correlate to the relative abundance (gDNA) or potential activity (cDNA) of methanotrophs. In the cDNA libraries, there were significant positive correlations between the abundance of Methylococcaceae family methanotrophs and several non-methanotrophic methylotrophs previously found to be associated with methane-oxidizing bacterial communities. These findings suggest a complex relationship between methane-cycling bacterial communities and methane flux and highlight the need for further in situ studies to understand the environmental and ecological influences of these microbial consortia. IMPORTANCE Methane-oxidizing bacteria are found in diverse soil and sediment environments and play an important role in mitigating flux of this potent greenhouse gas into the atmosphere. However, it is unclear how these bacteria and their associated communities are structured in the environment and how their activity ultimately influences methane flux. In this work, we examine the composition and structure of methane-oxidizing bacterial communities in sub-alpine forest soil and find soil- and time-specific differences between the stable and potentially active populations. We also find that the potentially active populations of certain methanotrophs and non-methanotrophs are positively correlated. This work provides a step toward refining our understanding of microbially mediated biogeochemical cycles.
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Affiliation(s)
- Delaney G. Beals
- Department of Chemistry and the Henry Eyring Center for Cell and Genome Science, University of Utah, Salt Lake City, Utah, USA
| | - J. Jackson Munn
- Department of Chemistry and the Henry Eyring Center for Cell and Genome Science, University of Utah, Salt Lake City, Utah, USA
| | - Aaron W. Puri
- Department of Chemistry and the Henry Eyring Center for Cell and Genome Science, University of Utah, Salt Lake City, Utah, USA
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Li X, Li Z, Zhu J, Wu Z, Dai R, Wang Z. Anaerobic biodegradation enables zero liquid discharge of two-stage nanofiltration system for microelectronic wastewater treatment. JOURNAL OF HAZARDOUS MATERIALS 2024; 475:134924. [PMID: 38880045 DOI: 10.1016/j.jhazmat.2024.134924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 06/06/2024] [Accepted: 06/13/2024] [Indexed: 06/18/2024]
Abstract
Nanofiltration (NF) is a promising technology in the treatment of microelectronic wastewater. However, the treatment of concentrate derived from NF system remains a substantial technical challenge, impeding the achievement of the zero liquid discharge (ZLD) goal in microelectronic wastewater industries. Herein, a ZLD system, coupling a two-stage NF technology with anaerobic biotechnology was proposed for the treatment of tetramethylammonium hydroxide (TMAH)-contained microelectronic wastewater. The two-stage NF system exhibited favorable efficacy in the removal of conductivity (96 %), total organic carbon (TOC, 90 %), and TMAH (96 %) from microelectronic wastewater. The membrane fouling of this system was dominated by organic fouling, with the second stage NF membrane experiencing a more serious fouling compared to the first stage membrane. The anaerobic biotechnology achieved a near-complete removal of TMAH and an 80 % reduction in TOC for the first stage NF concentrate. Methyloversatilis was the key genus involved in the anaerobic treatment of the microelectronic wastewater concentrate. Specific genes, including dmd-tmd, mtbA, mttB and mttC were identified as significant players in mediating the dehydrogenase and methyl transfer pathways during the process of TMAH biodegradation. This study highlights the potential of anaerobic biodegradation to achieve ZLD in the treatment of TMAH-contained microelectronic wastewater by NF system.
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Affiliation(s)
- Xianfeng Li
- State Key Laboratory of Pollution Control and Resource Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji Advanced Membrane Technology Center, School of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Zhouyan Li
- State Key Laboratory of Pollution Control and Resource Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji Advanced Membrane Technology Center, School of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Junhao Zhu
- Green Technology Bank, Shanghai 200082, China
| | - Zhichao Wu
- State Key Laboratory of Pollution Control and Resource Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji Advanced Membrane Technology Center, School of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Ruobin Dai
- State Key Laboratory of Pollution Control and Resource Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji Advanced Membrane Technology Center, School of Environmental Science and Engineering, Tongji University, Shanghai 200092, China.
| | - Zhiwei Wang
- State Key Laboratory of Pollution Control and Resource Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji Advanced Membrane Technology Center, School of Environmental Science and Engineering, Tongji University, Shanghai 200092, China.
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Samanta B, Sharma S, Budhwar R. Metagenome Analysis of Speleothem Microbiome from Subterranean Cave Reveals Insight into Community Structure, Metabolic Potential, and BGCs Diversity. Curr Microbiol 2023; 80:317. [PMID: 37561193 DOI: 10.1007/s00284-023-03431-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 07/26/2023] [Indexed: 08/11/2023]
Abstract
The Borra caves, the second largest subterranean karst cave ecosystem in the Indian sub-continent, are located at the Ananthagiri hills of Araku Valley in the Alluri district of Andhra Pradesh, India. The present investigation applied a shotgun metagenomic approach to gain insights into the microbial community structure, metabolic potential, and biosynthetic gene cluster (BGC) diversity of the microbes colonizing the surface of the speleothems from the aphotic zone of Borra caves. The taxonomic analysis of the metagenome data illustrated that the speleothem-colonizing core microbial community was dominated mainly by Alpha-, Beta-, and Gamma-Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes. The key energy metabolic pathways analysis provides strong evidence of chemolithoautotrophic and chemoheterotrophic modes of nutrition in the speleothem-colonizing microbial community. Metagenome data suggests that sulfur reducers and sulfur-disproportionating microbes might play a vital role in energy generation in this ecosystem. Our metagenome data also suggest that the dissimilatory nitrifiers and nitrifying denitrifiers might play an essential role in conserving nitrogen pools in the ecosystem. Furthermore, metagenome-wide BGCs mining retrieved 451 putative BGCs; NRPS was the most abundant (24%). Phylogenetic analysis of the C domain of NRPS showed that sequences were distributed across all six function categories of the known C domain, including several novel subclades. For example, a novel subclade had been recovered within the LCL domain clade as a sister subclade of immunosuppressant cyclosporin encoding C domain sequences. Our result suggested that subterranean cave microbiomes might be a potential reservoir of novel microbial metabolites.
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Affiliation(s)
- Brajogopal Samanta
- Department of Microbiology and FST, GITAM School of Science, GITAM (Deemed to Be University), Rushikonda, Visakhapatnam, Andhra Pradesh, 530045, India.
| | - Shivasmi Sharma
- Bionivid Technology Private Limited, Bengaluru, Karnataka, 560043, India
| | - Roli Budhwar
- Bionivid Technology Private Limited, Bengaluru, Karnataka, 560043, India
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Castillo J, Alom J, Gomez-Arias A, Cebekhulu S, Matu A, Cason E, Valverde A. Bacterial communities shift and influence in an acid mine drainage treatment using barium carbonate disperse alkaline substrate system. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 885:163526. [PMID: 37116802 DOI: 10.1016/j.scitotenv.2023.163526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 04/09/2023] [Accepted: 04/11/2023] [Indexed: 05/12/2023]
Abstract
Chemical passive treatment systems used to remediate acid mine drainage has been evaluated based mainly on the reactivity of the chemical alkaline reagents, overlooking the activity of the microorganisms that proliferate in these artificial ecosystems. In this study, the bacterial communities of a unique passive treatment system known as BDAS (Barium carbonate Dispersed Alkaline Substrate) were investigated using 16S rRNA gene metagenomic sequencing combined with hydrochemical characterization of the AMD and phenotypic characterization of biogenic precipitates. According to the hydrochemical characterization, the water quality improved as the water progressed through the system, with a drastic increase in the pH (up to alkaline conditions) and total organic carbon, as well as the removal of main contaminants such as Ca2+, SO42-, Fe3+, Al3+, and Mn2+. These environmental changes resulted in an increase in bacterial diversity (richness) after the inlet and in the shift of the bacterial communities from chemoautotrophs (e.g., Ferrovum and Acidiphilum) to chemoheterotrophs (e.g., Brevundimonas and Geobacter). Some of these taxa harbour potential to immobilize metals, aiding in the treatment of the water. One of the mechanisms involved in the immobilization of metals is microbially induced calcium carbonate precipitation, which seems to occur spontaneously in BDAS. The production of biofilm was also observed in most parts of the system, except in the inlet, helping with the removal of metals. However, in the long run, the build-up of biofilm and precipitation of metals could clog (i.e., biofouling) the pores of the matrix, reducing the treatment efficiency. Potential human pathogens (e.g. Legionella) were also detected in BDAS indicating the need for a treatment step at the end of the system to remove pathogenic microorganisms. These findings present a new perspective of the bacterial communities and their effects (both positively and negatively) in a chemical passive treatment system.
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Affiliation(s)
- J Castillo
- Department of Microbiology and Biochemistry, University of the Free State, Bloemfontein, South Africa.
| | - J Alom
- Department of Microbiology and Biochemistry, University of the Free State, Bloemfontein, South Africa
| | - A Gomez-Arias
- Department of Chemistry, University of the Free State, Bloemfontein, South Africa
| | - S Cebekhulu
- Centre for Environmental Management, University of the Free State, Bloemfontein, South Africa
| | - A Matu
- Department of Microbiology and Biochemistry, University of the Free State, Bloemfontein, South Africa
| | - E Cason
- Department of Animal Sciences, University of the Free State, Bloemfontein, South Africa
| | - A Valverde
- Instituto de Recursos Naturales y Agrobiología de Salamanca (IRNASA-CSIC), Consejo Superior de Investigaciones Científicas, Salamanca, Spain
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Pápai M, Benedek T, Táncsics A, Bornemann TLV, Plewka J, Probst AJ, Hussein D, Maróti G, Menashe O, Kriszt B. Selective enrichment, identification, and isolation of diclofenac, ibuprofen, and carbamazepine degrading bacteria from a groundwater biofilm. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:44518-44535. [PMID: 36690856 PMCID: PMC10076411 DOI: 10.1007/s11356-022-24975-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
Diclofenac, ibuprofen, and carbamazepine are three of the most widely detected and most concerning pharmaceutical residues in aquatic ecosystems. The aim of this study was to identify bacteria that may be involved in their degradation from a bacterial biofilm. Selective enrichment cultures in mineral salt solution containing pharmaceutical compounds as sole source of carbon and energy were set up, and population dynamics were monitored using shotgun metagenome sequencing. Bacterial genomes were reconstructed using genome-resolved metagenomics. Thirty bacterial isolates were obtained, identified at species level, and tested regarding pharmaceutical biodegradation at an initial concentration of 1.5 mg l-1. The results indicated that most probably diclofenac biodegrading cultures consisted of members of genera Ferrovibrio, Hydrocarboniphaga, Zavarzinia, and Sphingopyxis, while in ibuprofen biodegradation Nocardioides and Starkeya, and in carbamazepine biodegradation Nocardioides, Pseudonocardia, and Sphingopyxis might be involved. During the enrichments, compared to the initial state the percentage relative abundance of these genera increased up to three orders of magnitude. Except Starkeya, the genomes of these bacteria were reconstructed and annotated. Metabolic analyses of the annotated genomes indicated that these bacteria harbored genes associated with pharmaceutical biodegradation. Stenotrophomonas humi DIC_5 and Rhizobium daejeonense IBU_18 isolates eliminated diclofenac and ibuprofen during the tests in the presence of either glucose (3 g l-1) or in R2A broth. Higher than 90% concentration reduction was observed in the case of both compounds.
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Affiliation(s)
- Márton Pápai
- Department of Molecular Ecology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Páter K. U. 1, 2100, Gödöllő, Hungary
| | - Tibor Benedek
- Department of Molecular Ecology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Páter K. U. 1, 2100, Gödöllő, Hungary.
| | - András Táncsics
- Department of Molecular Ecology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Páter K. U. 1, 2100, Gödöllő, Hungary
| | - Till L V Bornemann
- Group for Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Essen, Universitäts Str. 5, 45141, Essen, Germany
| | - Julia Plewka
- Group for Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Essen, Universitäts Str. 5, 45141, Essen, Germany
| | - Alexander J Probst
- Group for Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Essen, Universitäts Str. 5, 45141, Essen, Germany
| | - Daood Hussein
- Institute of Horticultural Sciences, Laboratories of Food Analysis, Hungarian University of Agriculture and Life Sciences, Páter K. U. 1, 2100, Gödöllő, Hungary
| | - Gergely Maróti
- Institute of Plant Biology, Biological Research Center, Temesvári Krt. 62., Szeged, Hungary
- Seqomics Biotechnology Ltd, Vállalkozók 7, 6782, Mórahalom, Hungary
| | - Ofir Menashe
- Water Industry Engineering Department, The Engineering Faculty, Kinneret Academic College On the Sea of Galilee, D.N. Emek Ha, 15132, Yarden, Israel
- BioCastle Water Technologies Ltd, Tzemah, Israel
| | - Balázs Kriszt
- Department of Environmental Safety, Hungarian University of Agriculture and Life Sciences, Institute of Aquaculture and Environmental Safety, Páter K. U. 1, 2100, Gödöllő, Hungary
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Uzun M, Koziaeva V, Dziuba M, Alekseeva L, Krutkina M, Sukhacheva M, Baslerov R, Grouzdev D. Recovery and genome reconstruction of novel magnetotactic Elusimicrobiota from bog soil. THE ISME JOURNAL 2023; 17:204-214. [PMID: 36302955 PMCID: PMC9859788 DOI: 10.1038/s41396-022-01339-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 10/12/2022] [Accepted: 10/17/2022] [Indexed: 01/22/2023]
Abstract
Studying the minor part of the uncultivated microbial majority ("rare biosphere") is difficult even with modern culture-independent techniques. The enormity of microbial diversity creates particular challenges for investigating low-abundance microbial populations in soils. Strategies for selective sample enrichment to reduce community complexity can aid in studying the rare biosphere. Magnetotactic bacteria, apart from being a minor part of the microbial community, are also found in poorly studied bacterial phyla and certainly belong to a rare biosphere. The presence of intracellular magnetic crystals within magnetotactic bacteria allows for their significant enrichment using magnetic separation techniques for studies using a metagenomic approach. This work investigated the microbial diversity of a black bog soil and its magnetically enriched fraction. The poorly studied phylum representatives in the magnetic fraction were enriched compared to the original soil community. Two new magnetotactic species, Candidatus Liberimonas magnetica DUR002 and Candidatus Obscuribacterium magneticum DUR003, belonging to different classes of the relatively little-studied phylum Elusimicrobiota, were proposed. Their genomes contain clusters of magnetosome genes that differ from the previously described ones by the absence of genes encoding magnetochrome-containing proteins and the presence of unique Elusimicrobiota-specific genes, termed mae. The predicted obligately fermentative metabolism in DUR002 and lack of flagellar motility in the magnetotactic Elusimicrobiota broadens our understanding of the lifestyles of magnetotactic bacteria and raises new questions about the evolutionary advantages of magnetotaxis. The findings presented here increase our understanding of magnetotactic bacteria, soil microbial communities, and the rare biosphere.
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Affiliation(s)
- Maria Uzun
- Skryabin Institute of Bioengineering Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Veronika Koziaeva
- Skryabin Institute of Bioengineering Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Marina Dziuba
- Skryabin Institute of Bioengineering Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
- Department of Microbiology, University of Bayreuth, Bayreuth, Germany
| | - Lolita Alekseeva
- Skryabin Institute of Bioengineering Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | | | - Marina Sukhacheva
- Skryabin Institute of Bioengineering Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Roman Baslerov
- Skryabin Institute of Bioengineering Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Denis Grouzdev
- SciBear OU, Tallinn, Estonia.
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, USA.
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Nosek D, Mikołajczyk T, Cydzik-Kwiatkowska A. Anode Modification with Fe 2O 3 Affects the Anode Microbiome and Improves Energy Generation in Microbial Fuel Cells Powered by Wastewater. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:2580. [PMID: 36767954 PMCID: PMC9916399 DOI: 10.3390/ijerph20032580] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/24/2023] [Accepted: 01/28/2023] [Indexed: 06/18/2023]
Abstract
This study investigated how anode electrode modification with iron affects the microbiome and electricity generation of microbial fuel cells (MFCs) fed with municipal wastewater. Doses of 0.0 (control), 0.05, 0.1, 0.2, and 0.4 g Fe2O3 per the total anode electrode area were tested. Fe2O3 doses from 0.05 to 0.2 g improved electricity generation; with a dose of 0.10 g Fe2O3, the cell power was highest (1.39 mW/m2), and the internal resistance was lowest (184.9 Ω). Although acetate was the main source of organics in the municipal wastewater, propionic and valeric acids predominated in the outflows from all MFCs. In addition, Fe-modification stimulated the growth of the extracellular polymer producers Zoogloea sp. and Acidovorax sp., which favored biofilm formation. Electrogenic Geobacter sp. had the highest percent abundance in the anode of the control MFC, which generated the least electricity. However, with 0.05 and 0.10 g Fe2O3 doses, Pseudomonas sp., Oscillochloris sp., and Rhizobium sp. predominated in the anode microbiomes, and with 0.2 and 0.4 g doses, the electrogens Dechloromonas sp. and Desulfobacter sp. predominated. This is the first study to holistically examine how different amounts of Fe on the anode affect electricity generation, the microbiome, and metabolic products in the outflow of MFCs fed with synthetic municipal wastewater.
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Affiliation(s)
- Dawid Nosek
- Department of Environmental Biotechnology, University of Warmia and Mazury in Olsztyn, Słoneczna 45 G, 10-709 Olsztyn, Poland
| | - Tomasz Mikołajczyk
- Department of Chemistry, University of Warmia and Mazury in Olsztyn, plac Łódzki 4, 10-721 Olsztyn, Poland
| | - Agnieszka Cydzik-Kwiatkowska
- Department of Environmental Biotechnology, University of Warmia and Mazury in Olsztyn, Słoneczna 45 G, 10-709 Olsztyn, Poland
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11
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Perrone MR, Romano S, De Maria G, Tundo P, Bruno AR, Tagliaferro L, Maffia M, Fragola M. Simultaneous monitoring of SARS-CoV-2 and bacterial profiles from the air of hospital environments with COVID-19-affected patients. AEROBIOLOGIA 2022; 38:391-412. [PMID: 36097443 PMCID: PMC9453715 DOI: 10.1007/s10453-022-09754-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 08/01/2022] [Indexed: 06/15/2023]
Abstract
UNLABELLED The SARS-CoV-2 presence and the bacterial community profile in air samples collected at the Intensive Care Unit (ICU) of the Operational Unit of Infectious Diseases of Santa Caterina Novella Hospital in Galatina (Lecce, Italy) have been evaluated in this study. Air samplings were performed in different rooms of the ICU ward with and without COVID-19 patients. No sample was found positive to SARS-CoV-2, according to Allplex 2019-nCoV Assay. The airborne bacterial community profiles determined by the 16S rRNA gene metabarcoding approach up to the species level were characterized by richness and biodiversity indices, Spearman correlation coefficients, and Principal Coordinate Analysis. Pathogenic and non-pathogenic bacterial species, also detected in outdoor air samples, were found in all collected indoor samples. Staphylococcus pettenkoferi, Corynebacterium tuberculostearicum, and others coagulase-negative staphylococci, detected at high relative abundances in all the patients' rooms, were the most abundant pathogenic species. The highest mean relative abundance of S. pettenkoferi and C. tuberculostearicum suggested that they were likely the main pathogens of COVID-19 patients at the ICU ward of this study. The identification of nosocomial pathogens representing potential patients' risks in ICU COVID-19 rooms and the still controversial airborne transmission of the SARS-CoV-2 are the main contributions of this study. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s10453-022-09754-7.
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Affiliation(s)
- Maria Rita Perrone
- Department of Mathematics and Physics, University of Salento, 73100 Lecce, Italy
| | - Salvatore Romano
- Department of Mathematics and Physics, University of Salento, 73100 Lecce, Italy
| | - Giuseppe De Maria
- Presidio Ospedaliero Santa Caterina Novella, Azienda Sanitaria Locale Lecce, 73013 Galatina, Lecce, Italy
| | - Paolo Tundo
- Presidio Ospedaliero Santa Caterina Novella, Azienda Sanitaria Locale Lecce, 73013 Galatina, Lecce, Italy
| | - Anna Rita Bruno
- Presidio Ospedaliero Santa Caterina Novella, Azienda Sanitaria Locale Lecce, 73013 Galatina, Lecce, Italy
| | - Luigi Tagliaferro
- Presidio Ospedaliero Santa Caterina Novella, Azienda Sanitaria Locale Lecce, 73013 Galatina, Lecce, Italy
| | - Michele Maffia
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy
| | - Mattia Fragola
- Department of Mathematics and Physics, University of Salento, 73100 Lecce, Italy
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12
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Kojima H, Watanabe M, Miyata N, Fukui M. Sulfuricystis multivorans gen. nov., sp. nov. and Sulfuricystis thermophila sp. nov., facultatively autotropic sulfur-oxidizing bacteria isolated from a hot spring, and emended description of the genus Rugosibacter. Arch Microbiol 2022; 204:595. [PMID: 36053377 DOI: 10.1007/s00203-022-03186-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 06/29/2022] [Accepted: 08/09/2022] [Indexed: 11/30/2022]
Abstract
Strains J5BT and M52T are facultatively autotrophic sulfur-oxidizing bacteria isolated from a microbial mat from a hot spring. They were isolated and partially characterized in previous studies, as facultative anaerobes which use nitrate as electron acceptor. In this study, additional characterizations were made to determine their taxonomic status. In both strains, major cellular fatty acids were C16:1 (C16:1ω7c and/or C16:1ω6c) and C16:0. Their chemolithoautotrophic growth was supported by thiosulfate and elemental sulfur. They used some organic acids as growth substrates. Their 16S rRNA gene sequences indicated the highest sequence identities to species in the family Sterolibacteriaceae, but the identities were 95% or lower. Phylogenetic analysis indicated that these strains do not belong to any existing genera. Values of average nucleotide identity and digital DNA-DNA hybridization between strains J5BT and M52T were 87.93% and 34.3%, respectively. On the basis of phenotypic and genomic characteristics, Sulfuricystis multivorans gen. nov. sp. nov., and Sulfuricystis thermophila sp. nov. are proposed, with type strains of J5BT and M52T, respectively. An emended description of the genus Rugosibacter is also proposed, for its reclassification to the family Sterolibacteriaceae.
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Affiliation(s)
- Hisaya Kojima
- The Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo, 060-0819, Japan. .,Department of Biological Environment, Faculty of Bioresource Sciences, Akita Prefectural University, Shimo-Shinjyo Nakano, Akita, 010-0195, Japan.
| | - Miho Watanabe
- Department of Biological Environment, Faculty of Bioresource Sciences, Akita Prefectural University, Shimo-Shinjyo Nakano, Akita, 010-0195, Japan
| | - Naoyuki Miyata
- Department of Biological Environment, Faculty of Bioresource Sciences, Akita Prefectural University, Shimo-Shinjyo Nakano, Akita, 010-0195, Japan
| | - Manabu Fukui
- The Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo, 060-0819, Japan
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13
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Xu R, Tao W, Lin H, Huang D, Su P, Gao P, Sun X, Yang Z, Sun W. Effects of Perfluorooctanoic Acid (PFOA) and Perfluorooctane Sulfonic Acid (PFOS) on Soil Microbial Community. MICROBIAL ECOLOGY 2022; 83:929-941. [PMID: 34283261 DOI: 10.1007/s00248-021-01808-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 06/22/2021] [Indexed: 06/13/2023]
Abstract
The extensive application of perfluoroalkyl and polyfluoroalkyl substances (PFASs) causes their frequent detection in various environments. In this work, two typical PFASs, perfluorooctanoic acid (PFOA) and perfluorooctanesulfonic acid (PFOS), are selected to investigate their effects on soil microorganisms. Microbial community structure and microbe-microbe relationships were investigated by high-throughput sequencing and co-occurrence network analysis. Under 90 days of exposure, the alpha-diversity of soil microbial communities was increased with the PFOS treatment, followed by the PFOA treatment. The exposure of PFASs substantially changed the compositions of soil microbial communities, leading to the enrichment of more PFASs-tolerant bacteria, such as Proteobacteria, Burkholderiales, and Rhodocyclales. Comparative co-occurrence networks were constructed to investigate the microbe-microbe interactions under different PFASs treatments. The majority of nodes in the PFOA and PFOS networks were associated with the genus Azospirillum and Hydrogenophaga, respectively. The LEfSe analysis further identified a set of biomarkers in the soil microbial communities, such as Azospirillum, Methyloversatilis, Hydrogenophaga, Pseudoxanthomonas, and Fusibacter. The relative abundances of these biomarkers were also changed by different PFASs treatments. Functional gene prediction suggested that the microbial metabolism processes, such as nucleotide transport and metabolism, cell motility, carbohydrate transport and metabolism, energy production and conversion, and secondary metabolites biosynthesis transport and catabolism, might be inhibited under PFAS exposure, which may further affect soil ecological services.
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Affiliation(s)
- Rui Xu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Wan Tao
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Hanzhi Lin
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Duanyi Huang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, People's Republic of China
| | - Pingzhou Su
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Pin Gao
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Xiaoxu Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Zhaohui Yang
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, People's Republic of China
| | - Weimin Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China.
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China.
- School of Environment, Henan Normal University, Xinxiang, China.
- Key Laboratory of Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, 808 Tianyuan Road, Guangzhou, Guangdong, China.
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14
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Sharma R, Kumari R, Pant D, Malaviya P. Bioelectricity generation from human urine and simultaneous nutrient recovery: Role of Microbial Fuel Cells. CHEMOSPHERE 2022; 292:133437. [PMID: 34973250 DOI: 10.1016/j.chemosphere.2021.133437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 12/20/2021] [Accepted: 12/23/2021] [Indexed: 06/14/2023]
Abstract
Urine is a 'valuable waste' that can be exploited to generate bioelectricity and recover key nutrients for producing NPK-rich biofertilizers. In recent times, improved and innovative waste management technologies have emerged to manage the rapidly increasing environmental pollution and to accomplish the goal of sustainable development. Microbial fuel cells (MFCs) have attracted the attention of environmentalists worldwide to treat human urine and produce power through bioelectrochemical reactions in presence of electroactive bacteria growing on the anode. The bacteria break down the complex organic matter present in urine into simpler compounds and release the electrons which flow through an external circuit generating current at the cathode. Many other useful products are harvested at the end of the process. So, in this review, an attempt has been made to synthesize the information on MFCs fuelled with urine to generate bioelectricity and recover value-added resources (nutrients), and their modifications to enhance productivity. Moreover, configuration and mode of system operation, and factors enhancing the performance of MFCs have been also presented.
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Affiliation(s)
- Rozi Sharma
- Department of Environmental Sciences, University of Jammu, Jammu, Jammu and Kashmir, India
| | - Rekha Kumari
- Department of Environmental Sciences, University of Jammu, Jammu, Jammu and Kashmir, India
| | - Deepak Pant
- Separation & Conversion Technology, Flemish Institute for Technological Research (VITO), Boeretang 200, Mol, 2400, Belgium
| | - Piyush Malaviya
- Department of Environmental Sciences, University of Jammu, Jammu, Jammu and Kashmir, India.
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15
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Microbial Depolymerization of Epoxy Resins: A Novel Approach to a Complex Challenge. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12010466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The objective of this project is evaluating the potential of microbes (fungi and bacteria) for the depolymerization of epoxy, aiming at the development of a circular management of natural resources for epoxy in a long-term prospective. For depolymerization, epoxy samples were incubated for 1, 3, 6 and 9 months in soil microcosms inoculated with Ganoderma adspersum. Contact angle data revealed a reduction in the hydrophobicity induced by the fungus. Environmental scanning electron microscopy on epoxy samples incubated for more than 3 years in microbiological water revealed abundant microbiota. This comprised microbes of different sizes and shapes. The fungi Trichoderma harzianum and Aspergillus calidoustus, as well as the bacteria Variovorax sp. and Methyloversatilis discipulorum, were isolated from this environment. Altogether, these results suggest that microbes are able to colonize epoxy surfaces and, most probably, also partially depolymerize them. This could open promising opportunities for the study of new metabolisms potentially able depolymerize epoxy materials.
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16
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Exploiting Aerobic Carboxydotrophic Bacteria for Industrial Biotechnology. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2021; 180:1-32. [PMID: 34894287 DOI: 10.1007/10_2021_178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Aerobic carboxydotrophic bacteria are a group of microorganisms which possess the unique trait to oxidize carbon monoxide (CO) as sole energy source with molecular oxygen (O2) to produce carbon dioxide (CO2) which subsequently is used for biomass formation via the Calvin-Benson-Bassham cycle. Moreover, most carboxydotrophs are also able to oxidize hydrogen (H2) with hydrogenases to drive the reduction of carbon dioxide in the absence of CO. As several abundant industrial off-gases contain significant amounts of CO, CO2, H2 as well as O2, these bacteria come into focus for industrial application to produce chemicals and fuels from such gases in gas fermentation approaches. Since the group of carboxydotrophic bacteria is rather unknown and not very well investigated, we will provide an overview about their lifestyle and the underlying metabolic characteristics, introduce promising members for industrial application, and give an overview of available genetic engineering tools. We will point to limitations and discuss challenges, which have to be overcome to apply metabolic engineering approaches and to utilize aerobic carboxydotrophs in the industrial environment.
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17
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Ramanaiah S, Cordas CM, Matias SC, Reddy M, Leitão JH, Fonseca LP. Bioelectricity generation using long-term operated biocathode: RFLP based microbial diversity analysis. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2021; 32:e00693. [PMID: 34917493 PMCID: PMC8666517 DOI: 10.1016/j.btre.2021.e00693] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/17/2021] [Accepted: 12/03/2021] [Indexed: 10/25/2022]
Abstract
In the present work, power generation and substrate removal efficiencies of long-term operated microbial fuel cells, containing abiotic cathodes and biocathodes, were evaluated for 220 days. Among the two microbial fuel cell (MFC) types, the one containing biocathode showed higher power density (54 mW/m2), current density (122 mA/m2) coulombic efficiency (33%), and substrate removal efficiency (94%) than the abiotic cathode containing MFC. Voltammetric analysis also witnessed higher and sustainable electron discharge for the MFC with biocathode, when compared with the abiotic cathode MFC. Over the tested period, both MFC have shown a cell voltage drop, after 150 and 165, days, for the MFC with biocathode and abiotic cathodes, respectively. Polymerase chain reaction (PCR) based restriction fragment length polymorphism (RFLP) analysis identified 281 clones. Bacteria belonging to Acinetobacter, Acidovorax, Pseudomonas and Burkholderia were observed in the abiotic cathode MFC. Bacteria belonging to Geobacter, Cupriavidus and Acidobacteria were observed in the biocathode MFC. Almost similar types of archaea (Methanosarcinales, Methanolinea, Nitrososphaera and Methanomicrobiales) were observed in both MFCs.
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Affiliation(s)
- S.V. Ramanaiah
- iBB – Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Avenida Rovisco Pais, Lisboa, 1049-001 Portugal
- Food and Biotechnology Research Lab, South Ural State University (National Research University), 76, Lenin prospekt, Chelyabinsk, 454080, Russian Federation
| | - Cristina M. Cordas
- LAQV- REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, 2829-516, Portugal
| | - Sara C. Matias
- iBB – Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Avenida Rovisco Pais, Lisboa, 1049-001 Portugal
| | - M.Venkateswar Reddy
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute,110 8th Street, Troy, NY 12180, USA
| | - Jorge Humberto Leitão
- Department of Bioengineering, iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Avenida Rovisco Pais, Lisboa, 1049-001 Portugal
| | - Luis P. Fonseca
- iBB – Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Avenida Rovisco Pais, Lisboa, 1049-001 Portugal
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18
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Yu X, Yu K, Liao Z, Chen B, Deng C, Yu J, Yao Q, Qin Z, Liang J. Seasonal fluctuations in symbiotic bacteria and their role in environmental adaptation of the scleractinian coral Acropora pruinosa in high-latitude coral reef area of the South China Sea. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 792:148438. [PMID: 34153755 DOI: 10.1016/j.scitotenv.2021.148438] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 06/09/2021] [Accepted: 06/09/2021] [Indexed: 06/13/2023]
Abstract
Coral-associated bacterial communities are paramount for coral ecosystems and holobiont health. However, the role of symbiotic bacteria in the adaptation of high-latitude corals to seasonal fluctuations remains underexplored. Therefore, we used 16S rRNA-based high-throughput sequencing to analyze the symbiotic bacterial diversity, composition, and core bacterial community in high-latitude coral and explored the seasonal fluctuation characteristics of symbiotic bacterial communities. We found that bacterial richness and α-diversity changed significantly across different seasons. Additionally, the community structure recombined seasonally, with different dominant bacterial phyla and genera in different seasons. However, the symbiotic bacterial community structures of Acropora pruinosa in winter and spring were similar. Proteobacteria were the dominant bacteria in spring, autumn, and winter. In summer, the dominant bacterial taxa were Bacteroidota and Proteobacteria. Ralstonia was the dominant bacterial genus in spring and winter, whereas in autumn, BD1-7_clade was dominant. Linear discriminant analysis effect size identified 20 abundant genera between the different groups. Core microbiome analysis revealed that 12 core bacterial operational taxonomic units were associated with A. pruinosa in all seasons, seven of which varied with the seasons, changing between dominant and rare. Distance-based redundancy and variation partitioning analyses revealed that sea surface temperature was the major contributor of variation in the microbial community structure. We hypothesized that the high diversity and abundance of symbiotic bacteria and the increase in Prosthecochloris abundance in coral in summer can help A. pruinosa maintain its physiological functions, ameliorating the negative physiological effects of the decrease in Symbiodiniaceae density under high-temperature stress. Thus, the rapid reorganization of the symbiotic bacterial community structure and core microflora in different seasons may allow the corals to adapt to large seasonal environmental fluctuations. In conclusion, seasonal variation of bacteria plays an important role in coral adaptation to large environmental fluctuations.
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Affiliation(s)
- Xiaopeng Yu
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Kefu Yu
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), China.
| | - Zhiheng Liao
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Biao Chen
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Chuanqi Deng
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Jiaoyang Yu
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Qiucui Yao
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Zhenjun Qin
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Jiayuan Liang
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
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19
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Ospina-Betancourth C, Acharya K, Allen B, Head IM, Sanabria J, Curtis TP. Valorization of pulp and paper industry wastewater using sludge enriched with nitrogen-fixing bacteria. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2021; 93:1734-1747. [PMID: 33765365 DOI: 10.1002/wer.1561] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 02/22/2021] [Accepted: 03/18/2021] [Indexed: 06/12/2023]
Abstract
Nitrogen-fixing bacteria (NFB) can reduce nitrogen at ambient pressure and temperature. In this study, we treated effluent from a paper mill in sequencing batch reactors (SBRs) and monitored the abundance and activity of NFB with a view to producing a sludge that could work as a biofertilizer. Four reactors were inoculated with activated sludge enriched with NFB and fed with a high C/N waste (100:0.5) from a paper mill. Though the reactors were able to reduce the organic load of the wastewater by up to 89%, they did not have any nitrogen-fixing activity and showed a decrease in the putative number of NFB (quantified with qPCR). The most abundant species in the reactors treating high C/N paper mill wastewater was identified by Illumina MiSeq 16S rRNA gene amplicon sequencing as Methyloversatilis sp. (relative abundance of 4.4%). Nitrogen fixation was observed when the C/N ratio was increased by adding sucrose. We suspect that real-world biological nitrogen fixation (BNF) will only occur where there is a C/N ratio ≤100:0.07. Consequently, operators should actively avoid adding or allowing nitrogen in the waste streams if they wish to valorize their sludge and reduce running costs. PRACTITIONER POINTS: Efficient biological wastewater treatment of low nitrogen paper mill effluent was achieved without nutrient supplementation. The sludge was still capable of fixing nitrogen although this process was not observed in the wastewater treatment system. This high C/N wastewater treatment technology could be used with effluents from cassava flour, olive oil, wine and dairy industries.
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Affiliation(s)
| | - Kishor Acharya
- School of Engineering, Newcastle University, Newcastle upon Tyne, UK
| | - Ben Allen
- School of Engineering, Newcastle University, Newcastle upon Tyne, UK
| | - Ian M Head
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Janeth Sanabria
- Environmental Microbiology and Biotechnology Laboratory, Engineering School of Environmental & Natural Resources, Engineering Faculty, Universidad del Valle, Cali, Colombia
| | - Thomas P Curtis
- School of Engineering, Newcastle University, Newcastle upon Tyne, UK
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20
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Luo YH, Long X, Wang B, Zhou C, Tang Y, Krajmalnik-Brown R, Rittmann BE. A Synergistic Platform for Continuous Co-removal of 1,1,1-Trichloroethane, Trichloroethene, and 1,4-Dioxane via Catalytic Dechlorination Followed by Biodegradation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:6363-6372. [PMID: 33881824 DOI: 10.1021/acs.est.1c00542] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Groundwater co-contaminated with 1,4-dioxane, 1,1,1-trichloroethane (TCA), and trichloroethene (TCE) is among the most urgent environmental concerns of the U.S. Department of Defense (DoD), U.S. Environmental Protection Agency (EPA), and industries related to chlorinated solvents. Inspired by the pressing need to remove all three contaminants at many sites, we tested a synergistic platform: catalytic reduction of 1,1,1-TCA and TCE to ethane in a H2-based membrane palladium-film reactor (H2-MPfR), followed by aerobic biodegradation of ethane and 1,4-dioxane in an O2-based membrane biofilm reactor (O2-MBfR). During 130 days of continuous operation, 1,1,1-TCA and TCE were 95-98% reductively dechlorinated to ethane in the H2-MPfR, and ethane served as the endogenous primary electron donor for promoting 98.5% aerobic biodegradation of 1,4-dioxane in the O2-MBfR. In addition, the small concentrations of the chlorinated intermediate from the H2-MPfR, dichloroethane (DCA) and monochloroethane (MCA), were fully biodegraded through aerobic biodegradation in the O2-MBfR. The biofilms in the O2-MBfR were enriched in phylotypes closely related to the genera Pseudonocardia known to biodegrade 1,4-dioxane.
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Affiliation(s)
- Yi-Hao Luo
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona 85287 United States
| | - Xiangxing Long
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona 85287 United States
- Nanosystems Engineering Research Center for Nanotechnology-Enabled Water Treatment, Arizona State University, Tempe, Arizona 85008, United States
| | - Boya Wang
- Department of Civil and Environmental Engineering, FAMU-FSU College of Engineering, Florida State University, Tallahassee, Florida 32310, United States
| | - Chen Zhou
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona 85287 United States
| | - Youneng Tang
- Department of Civil and Environmental Engineering, FAMU-FSU College of Engineering, Florida State University, Tallahassee, Florida 32310, United States
| | - Rosa Krajmalnik-Brown
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona 85287 United States
| | - Bruce E Rittmann
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona 85287 United States
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21
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Ma RC, Chu YX, Wang J, Wang C, Leigh MB, Chen Y, He R. Stable-isotopic and metagenomic analyses reveal metabolic and microbial link of aerobic methane oxidation coupled to denitrification at different O 2 levels. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 764:142901. [PMID: 33757249 DOI: 10.1016/j.scitotenv.2020.142901] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 10/02/2020] [Accepted: 10/03/2020] [Indexed: 06/12/2023]
Abstract
Aerobic methane (CH4) oxidation coupled to denitrification (AME-D) can not only mitigate CH4 emission into the atmosphere, but also potentially alleviate nitrogen pollution in surface waters and engineered ecosystems, and it has attracted substantial research interest. O2 concentration plays a key role in AME-D, yet little is understood about how it impacts microbial interactions. Here, we applied isotopically labeled K15NO3 and 13CH4 and metagenomic analyses to investigate the metabolic and microbial link of AME-D at different O2 levels. Among the four experimental O2 levels of 21%,10%, 5% and 2.5% and a CH4 concentration of 8% (i.e., the O2/CH4 ratios of 2.62, 1.26, 0.63 and 0.31), the highest NO3--N removal occurred in the AME-D system incubated at the O2 concentration of 10%. Methanol and acetate may serve as the trophic linkage between aerobic methanotrophs and denitrifers in the AME-D systems. Methylotrophs including Methylophilus, Methylovorus, Methyloversatilis and Methylotenera were abundant under the O2-sufficient condition with the O2 concentration of 21%, while denitrifiers such as Azoarcus, Thauera and Thiobacillus dominated in the O2-limited environment with the O2 concentration of 10%. The competition of denitrifiers and methylotrophs in the AME-D system for CH4-derived carbon, such as methanol and acetate, might be influenced by chemotactic responses. More methane-derived carbon flowed into methylotrophs under the O2-sufficient condition, while more methane-derived carbon was used for denitrification in the O2-limited environment. These findings can aid in evaluating the distribution and contribution of AME-D and in developing strategies for mitigating CH4 emission and nitrogen pollution in natural and engineered ecosystems.
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Affiliation(s)
- Ruo-Chan Ma
- Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China; Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, China
| | - Yi-Xuan Chu
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, China
| | - Jing Wang
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, China
| | - Cheng Wang
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, China
| | - Mary Beth Leigh
- Institute of Arctic Biology, University of Alaska Fairbanks, AK 99775, USA
| | - Yin Chen
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Ruo He
- Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China; Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, China.
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22
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Vieira S, Huber KJ, Neumann-Schaal M, Geppert A, Luckner M, Wanner G, Overmann J. Usitatibacter rugosus gen. nov., sp. nov. and Usitatibacter palustris sp. nov., novel members of Usitatibacteraceae fam. nov. within the order Nitrosomonadales isolated from soil. Int J Syst Evol Microbiol 2021; 71. [PMID: 33433313 DOI: 10.1099/ijsem.0.004631] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Members of the metabolically diverse order Nitrosomonadales inhabit a wide range of environments. Two strains affiliated with this order were isolated from soils in Germany and characterized by a polyphasic approach. Cells of strains 0125_3T and Swamp67T are Gram-negative rods, non-motile, non-spore-forming, non-capsulated and divide by binary fission. They tested catalase-negative, but positive for cytochrome c-oxidase. Both strains form small white colonies on agar plates and grow aerobically and chemoorganotrophically on SSE/HD 1 : 10 medium, preferably utilizing organic acids and proteinaceous substrates. Strains 0125_3T and Swamp67T are mesophilic and grow optimally without NaCl addition at slightly alkaline conditions. Major fatty acids are C16 : 1 ω7c, C16 : 0 and C14 : 0. The major polar lipids are diphosphatidylglycerol, phosphatidylethanolamine and phosphatidyglycerol. The predominant respiratory quinone is Q-8. The G+C content for 0125_3T and Swamp67T was 67 and 66.1 %, respectively. The 16S rRNA gene analysis indicated that the closest relatives (<91 % sequence similarity) of strain 0125_3T were Nitrosospira multiformis ATCC 25196T, Methyloversatilis universalis FAM5T and Denitratisoma oestradiolicum AcBE2-1T, while Nitrosospira multiformis ATCC 25196T, Nitrosospira tenuis Nv1T and Nitrosospira lacus APG3T were closest to strain Swamp67T. The two novel strains shared 97.4 % 16S rRNA gene sequence similarity with one another and show low average nucleotide identity of their genomes (83.8 %). Based on the phenotypic, chemotaxonomic, genomic and phylogenetic analysis, we propose the two novel species Usitatibacter rugosus sp. nov (type strain 0125_3T=DSM 104443T=LMG 29998T=CECT 9241T) and Usitatibacter palustris sp. nov. (type strain Swamp67T=DSM 104440T=LMG 29997T=CECT 9242T) of the novel genus Usitatibacter gen. nov., within the novel family Usitatibacteraceae fam. nov.
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Affiliation(s)
- Selma Vieira
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Katharina J Huber
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Meina Neumann-Schaal
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Alicia Geppert
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Manja Luckner
- Department of Biology I, Biozentrum Ludwig Maximilian University of Munich, Großhaderner Str. 2-4, 82152, Planegg-Martinsried, Germany
| | - Gerhard Wanner
- Department of Biology I, Biozentrum Ludwig Maximilian University of Munich, Großhaderner Str. 2-4, 82152, Planegg-Martinsried, Germany
| | - Jörg Overmann
- Braunschweig University of Technology, Spielmanstraße 7, 38106 Braunschweig, Germany.,Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
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23
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Methane utilizing plant growth-promoting microbial diversity analysis of flooded paddy ecosystem of India. World J Microbiol Biotechnol 2021; 37:56. [PMID: 33619649 DOI: 10.1007/s11274-021-03018-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 02/01/2021] [Indexed: 01/10/2023]
Abstract
Methane utilizing bacteria (MUB) are known to inhabit the flooded paddy ecosystem where they play an important role in regulating net methane (CH4) emission. We hypothesize that efficient MUB having plant growth-promoting (PGP) attributes can be used for developing novel bio-inoculant for flooded paddy ecosystem which might not only reduce methane emission but also assist in improving the plant growth parameters. Hence, soil and plant samples were collected from the phyllosphere, rhizosphere, and non-rhizosphere of five rice-growing regions of India at the tillering stage and investigated for efficient methane-oxidizing and PGP bacteria. Based on the monooxygenase activity and percent methane utilization on NMS medium with methane as the sole C source, 123 isolates were identified and grouped phylogenetically into 13 bacteria and 2 yeast genera. Among different regions, a significantly higher number of isolates were obtained from lowland flooded paddy ecosystems of Aduthurai (33.33%) followed by Ernakulum (20.33%) and Brahmaputra valley (19.51%) as compared to upland irrigated regions of Gaya (17.07%) and Varanasi (8.94%). Among sub-samples, a significantly higher number of isolates were found inhabiting the phyllosphere (58.54%) followed by non-rhizosphere (25.20%) and rhizosphere (15.45%). Significantly higher utilization of methane and PGP attributes were observed in 30 isolates belonging to genera Hyphomicrobium, Burkholderia, Methylobacterium, Paenibacillus, Pseudomonas, Rahnella, and Meyerozyma. M. oryzae MNL7 showed significantly better growth with 74.33% of CH4 utilization at the rate of 302.9 ± 5.58 and exhibited half-maximal growth rate, Ks of 1.92 ± 0.092 mg CH4 L-1. Besides the ability to utilize CH4, P. polymyxa MaAL70 possessed PGP attributes such as solubilization of P, K, and Zn, fixation of atmospheric N and production of indole acetic acid (IAA). Both these promising isolates can be explored in the future for developing novel biofertilizers for flooded paddies.
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24
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Wei H, Li X, Tang L, Yao H, Ren Z, Wang C, Mu C, Shi C, Wang H. 16S rRNA gene sequencing reveals the relationship between gut microbiota and ovarian development in the swimming crab Portunus trituberculatus. CHEMOSPHERE 2020; 254:126891. [PMID: 32957291 DOI: 10.1016/j.chemosphere.2020.126891] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 04/22/2020] [Accepted: 04/23/2020] [Indexed: 06/11/2023]
Abstract
Gut microbiota executes many beneficial functions. In this study, the relationship between gut microbiota and ovarian development in the swimming crab P. trituberculatus was explored for the first time. A total of 28 phyla and 422 genera were identified across all samples. However, 105 differential operational taxonomic units, and four differential phyla (Gemmatimonadetes, Actinobacteria, Firmicutes, Marinimicrobia_(SAR406_clade)) were identified. At the genus level, 42 differential genera were identified and 144 bacterial indicators were identified. A key finding was that the relative abundance of 139 indicator bacteria detected in the anisomycin-2 mg/kg group (AK group) was higher than that of blank group (BK group), control group (CK group), SP600125-15 mg/kg group (SK group). In addition, the relative abundance of three indicator bacteria (OTU_236, OTU_1395, OTU_552) detected in the SK group was higher than that of the BK, CK and AK groups. It was also found that the relative abundance of 20 differential genera (Methyloversatilis, Coprococcus_1, Erysipelotrichaceae_UCG_003, Rikenella, Corynebacterium, Ruminiclostridium, Fusicatenibacter, [Eubacterium]_ruminantium_group, Rikenellaceae_RC9_gut_group, Bifidobacterium, Lachnospiraceae_NK4A136_group, Ruminococcaceae_UCG_014, Christensenellaceae_R_7_group, uncultured_Bacteroidales_bacterium, Coprococcus_2, Desulfovibrio, Aggregatibacter, Ambiguous_taxa, Alloprevotella and Ruminococcaceae_NK4A214_group) in the SK, BK, CK, and AK group samples were increasing. These differential genera may reveal the relationship between gut microbial communities and ovarian development in P. trituberculatus after injection with the JNK pathway inhibitor SP600125 or the activator anisomycin. In summary, this study provides a new understanding into the relationship between gut microbiota and ovarian development in response to stimulation with inhibitor or activator.
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Affiliation(s)
- Hongling Wei
- School of Marine Science, Ningbo University, Ningbo, 315211, Zhejiang, China.
| | - Xing Li
- School of Marine Science, Ningbo University, Ningbo, 315211, Zhejiang, China.
| | - Lei Tang
- School of Marine Science, Ningbo University, Ningbo, 315211, Zhejiang, China.
| | - Hongzhi Yao
- School of Marine Science, Ningbo University, Ningbo, 315211, Zhejiang, China.
| | - Zhiming Ren
- School of Marine Science, Ningbo University, Ningbo, 315211, Zhejiang, China.
| | - Chunlin Wang
- School of Marine Science, Ningbo University, Ningbo, 315211, Zhejiang, China; Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, 315211, Zhejiang, China.
| | - Changkao Mu
- School of Marine Science, Ningbo University, Ningbo, 315211, Zhejiang, China; Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, 315211, Zhejiang, China.
| | - Ce Shi
- School of Marine Science, Ningbo University, Ningbo, 315211, Zhejiang, China; Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, 315211, Zhejiang, China.
| | - Huan Wang
- School of Marine Science, Ningbo University, Ningbo, 315211, Zhejiang, China; Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, 315211, Zhejiang, China.
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25
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Andrade MVF, Delforno TP, Sakamoto IK, Silva EL, Varesche MBA. Dynamics and response of microbial diversity to nutritional conditions in denitrifying bioreactor for linear alkylbenzene sulfonate removal. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2020; 263:110387. [PMID: 32174528 DOI: 10.1016/j.jenvman.2020.110387] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 02/28/2020] [Accepted: 03/02/2020] [Indexed: 06/10/2023]
Abstract
The aim of this study was to evaluate the microbial structure and phylogenetic diversity under the influence of nutritional conditions and hydraulic retention time (HRT) in fluidized bed reactors (FBR), operated in short HRT (8 h - FBR8; 12 h - FBR12) for linear alkylbenzene sulfonate (LAS) removal from laundry wastewater. After each phase, biofilm samples from FBR8 and FBR12 were submitted to microbial sequencing by Mi-Seq Illumina®. Higher LAS removal rates were observed after 313 days, achieving 99 ± 3% in FBR12 (22.5 ± 5.9 mg LAS/L affluent) and 93 ± 12% in FBR8 (20.6 ± 4.4 mg LAS/L affluent). Different modifications involving genera of bacteria were observed throughout the reactors operation. The identified microorganisms were, mostly, related to LAS degradation and nitrogen conversion such as Dechloromonas, Flavobacterium, Pseudomonas, and Zoogloea.
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Affiliation(s)
| | - Tiago Palladino Delforno
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), Campinas University - UNICAMP, Campinas, 13081-970, SP, Brazil
| | - Isabel Kimiko Sakamoto
- Department of Hydraulics and Sanitation, School of Engineering of São Carlos, University of São Paulo, Trabalhador São-carlense, 13566-590, São Carlos, SP, Brazil
| | - Edson Luiz Silva
- Department of Chemical Engineering, Federal University of São Carlos, Rod. Washington Luiz, Km 235, SP 310, 13565-905, São Carlos, SP, Brazil
| | - Maria Bernadete Amâncio Varesche
- Department of Hydraulics and Sanitation, School of Engineering of São Carlos, University of São Paulo, Trabalhador São-carlense, 13566-590, São Carlos, SP, Brazil
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26
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Liu X, Huang M, Bao S, Tang W, Fang T. Nitrate removal from low carbon-to-nitrogen ratio wastewater by combining iron-based chemical reduction and autotrophic denitrification. BIORESOURCE TECHNOLOGY 2020; 301:122731. [PMID: 31927457 DOI: 10.1016/j.biortech.2019.122731] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 12/28/2019] [Accepted: 12/31/2019] [Indexed: 06/10/2023]
Abstract
Nitrate removal from low carbon-to-nitrogen ratio (C/N) wastewater has always been a knotty problem due to the deficiency of organics. Here, a novel iron-based chemical reduction and autotrophic denitrification (ICAD) system was developed. ICAD system could maintain average nitrate removal efficiency of 97.2% for 131 days with feeding 20.3 mg NO3--N/L at hydraulic retention time (HRT) of 24 h. The optimal operational conditions was further explored, and results demonstrated that average nitrate removal efficiency of 85.5% and 98.4% could be achieved at HRT of 12 h and 24 h (influent 20.3 mg NO3--N/L), while average nitrate removal efficiency could reach 96.3% at optimal HRT of 12 h (influent 10.3 mg NO3--N/L). Hydrogenophaga, which can carry out hydrogenotrophic denitrification, showed a positive correlation with nitrate removal efficiency of the ICAD system. Low cost and simple operation make the ICAD system suitable for large-scale application.
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Affiliation(s)
- Xiawei Liu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Manqi Huang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shaopan Bao
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Wei Tang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Tao Fang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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27
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Macey MC, Pratscher J, Crombie AT, Murrell JC. Impact of plants on the diversity and activity of methylotrophs in soil. MICROBIOME 2020; 8:31. [PMID: 32156318 PMCID: PMC7065363 DOI: 10.1186/s40168-020-00801-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 02/10/2020] [Indexed: 05/16/2023]
Abstract
BACKGROUND Methanol is the second most abundant volatile organic compound in the atmosphere, with the majority produced as a metabolic by-product during plant growth. There is a large disparity between the estimated amount of methanol produced by plants and the amount which escapes to the atmosphere. This may be due to utilisation of methanol by plant-associated methanol-consuming bacteria (methylotrophs). The use of molecular probes has previously been effective in characterising the diversity of methylotrophs within the environment. Here, we developed and applied molecular probes in combination with stable isotope probing to identify the diversity, abundance and activity of methylotrophs in bulk and in plant-associated soils. RESULTS Application of probes for methanol dehydrogenase genes (mxaF, xoxF, mdh2) in bulk and plant-associated soils revealed high levels of diversity of methylotrophic bacteria within the bulk soil, including Hyphomicrobium, Methylobacterium and members of the Comamonadaceae. The community of methylotrophic bacteria captured by this sequencing approach changed following plant growth. This shift in methylotrophic diversity was corroborated by identification of the active methylotrophs present in the soils by DNA stable isotope probing using 13C-labelled methanol. Sequencing of the 16S rRNA genes and construction of metagenomes from the 13C-labelled DNA revealed members of the Methylophilaceae as highly abundant and active in all soils examined. There was greater diversity of active members of the Methylophilaceae and Comamonadaceae and of the genus Methylobacterium in plant-associated soils compared to the bulk soil. Incubating growing pea plants in a 13CO2 atmosphere revealed that several genera of methylotrophs, as well as heterotrophic genera within the Actinomycetales, assimilated plant exudates in the pea rhizosphere. CONCLUSION In this study, we show that plant growth has a major impact on both the diversity and the activity of methanol-utilising methylotrophs in the soil environment, and thus, the study contributes significantly to efforts to balance the terrestrial methanol and carbon cycle. Video abstract.
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Affiliation(s)
- Michael C. Macey
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ UK
- AstrobiologyOU, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, Buckinghamshire MK7 6AA UK
| | - Jennifer Pratscher
- The Lyell Centre, School of Energy, Geoscience, Infrastructure and Society, Heriot-Watt University, Research Avenue South, Edinburgh, EH14 4AP UK
| | - Andrew T. Crombie
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ UK
| | - J. Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ UK
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28
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Early Last Interglacial ocean warming drove substantial ice mass loss from Antarctica. Proc Natl Acad Sci U S A 2020; 117:3996-4006. [PMID: 32047039 PMCID: PMC7049167 DOI: 10.1073/pnas.1902469117] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The future response of the Antarctic ice sheet to rising temperatures remains highly uncertain. A useful period for assessing the sensitivity of Antarctica to warming is the Last Interglacial (LIG) (129 to 116 ky), which experienced warmer polar temperatures and higher global mean sea level (GMSL) (+6 to 9 m) relative to present day. LIG sea level cannot be fully explained by Greenland Ice Sheet melt (∼2 m), ocean thermal expansion, and melting mountain glaciers (∼1 m), suggesting substantial Antarctic mass loss was initiated by warming of Southern Ocean waters, resulting from a weakening Atlantic meridional overturning circulation in response to North Atlantic surface freshening. Here, we report a blue-ice record of ice sheet and environmental change from the Weddell Sea Embayment at the periphery of the marine-based West Antarctic Ice Sheet (WAIS), which is underlain by major methane hydrate reserves. Constrained by a widespread volcanic horizon and supported by ancient microbial DNA analyses, we provide evidence for substantial mass loss across the Weddell Sea Embayment during the LIG, most likely driven by ocean warming and associated with destabilization of subglacial hydrates. Ice sheet modeling supports this interpretation and suggests that millennial-scale warming of the Southern Ocean could have triggered a multimeter rise in global sea levels. Our data indicate that Antarctica is highly vulnerable to projected increases in ocean temperatures and may drive ice-climate feedbacks that further amplify warming.
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29
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Ogawa A, Takakura K, Hirai N, Kanematsu H, Kuroda D, Kougo T, Sano K, Terada S. Biofilm Formation Plays a Crucial Rule in the Initial Step of Carbon Steel Corrosion in Air and Water Environments. MATERIALS (BASEL, SWITZERLAND) 2020; 13:E923. [PMID: 32092999 PMCID: PMC7079648 DOI: 10.3390/ma13040923] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 02/13/2020] [Accepted: 02/14/2020] [Indexed: 12/15/2022]
Abstract
In this study, we examined the relationship between the effect of a zinc coating on protecting carbon steel against biofilm formation in both air and water environments. SS400 carbon steel coupons were covered with a zinc thermal spray coating or copper thermal spray coating. Coated coupons were exposed to either air or water conditions. Following exposure, the surface conditions of each coupon were observed using optical microscopy, and quantitatively analyzed using an x-ray fluorescence analyzer. Debris on the surface of the coupons was used for biofilm analysis including crystal violet staining for quantification, Raman spectroscopic analysis for qualification, and microbiome analysis. The results showed that the zinc thermal spray coating significantly inhibited iron corrosion as well as biofilm formation in both air and water environments. The copper thermal spray coating, however, accelerated iron corrosion in both air and water environments, but accelerated biofilm formation only in a water environment. microbially-influenced-corrosion-related bacteria were barely detected on any coupons, whereas biofilms were detected on all coupons. To summarize these results, electrochemical corrosion is dominant in an air environment and microbially influenced corrosion is strongly involved in water corrosion. Additionally, biofilm formation plays a crucial rule in carbon steel corrosion in both air and water, even though microbially-influenced-corrosion-related bacteria are barely involved in this corrosion.
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Affiliation(s)
- Akiko Ogawa
- Department of Chemistry and Biochemistry, National Institute of Technology (KOSEN), Suzuka College, Suzuka 510-0294, Japan; (K.T.); (N.H.)
| | - Keito Takakura
- Department of Chemistry and Biochemistry, National Institute of Technology (KOSEN), Suzuka College, Suzuka 510-0294, Japan; (K.T.); (N.H.)
| | - Nobumitsu Hirai
- Department of Chemistry and Biochemistry, National Institute of Technology (KOSEN), Suzuka College, Suzuka 510-0294, Japan; (K.T.); (N.H.)
| | - Hideyuki Kanematsu
- Department of Material Science and Engineering, National Institute of Technology (KOSEN), Suzuka College, Suzuka 510-0294, Japan; (H.K.); (D.K.); (T.K.)
| | - Daisuke Kuroda
- Department of Material Science and Engineering, National Institute of Technology (KOSEN), Suzuka College, Suzuka 510-0294, Japan; (H.K.); (D.K.); (T.K.)
| | - Takeshi Kougo
- Department of Material Science and Engineering, National Institute of Technology (KOSEN), Suzuka College, Suzuka 510-0294, Japan; (H.K.); (D.K.); (T.K.)
| | | | - Satoshi Terada
- Department of Materials Science and Biotechnology, University of Fukui, Fukui 910-8507, Japan;
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30
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Kuloyo O, Ruff SE, Cahill A, Connors L, Zorz JK, Hrabe de Angelis I, Nightingale M, Mayer B, Strous M. Methane oxidation and methylotroph population dynamics in groundwater mesocosms. Environ Microbiol 2020; 22:1222-1237. [PMID: 32017377 PMCID: PMC7187433 DOI: 10.1111/1462-2920.14929] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 01/25/2020] [Indexed: 01/21/2023]
Abstract
Extraction of natural gas from unconventional hydrocarbon reservoirs by hydraulic fracturing raises concerns about methane migration into groundwater. Microbial methane oxidation can be a significant methane sink. Here, we inoculated replicated, sand‐packed, continuous mesocosms with groundwater from a field methane release experiment. The mesocosms experienced thirty‐five weeks of dynamic methane, oxygen and nitrate concentrations. We determined concentrations and stable isotope signatures of methane, carbon dioxide and nitrate and monitored microbial community composition of suspended and attached biomass. Methane oxidation was strictly dependent on oxygen availability and led to enrichment of 13C in residual methane. Nitrate did not enhance methane oxidation under oxygen limitation. Methylotrophs persisted for weeks in the absence of methane, making them a powerful marker for active as well as past methane leaks. Thirty‐nine distinct populations of methylotrophic bacteria were observed. Methylotrophs mainly occurred attached to sediment particles. Abundances of methanotrophs and other methylotrophs were roughly similar across all samples, pointing at transfer of metabolites from the former to the latter. Two populations of Gracilibacteria (Candidate Phyla Radiation) displayed successive blooms, potentially triggered by a period of methane famine. This study will guide interpretation of future field studies and provides increased understanding of methylotroph ecophysiology.
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Affiliation(s)
- Olukayode Kuloyo
- Department of Geoscience, University of Calgary, Calgary, Alberta, Canada.,Shell International Exploration and Production Inc, Westhollow Technology Center, Houston, TX, USA
| | - S Emil Ruff
- Department of Geoscience, University of Calgary, Calgary, Alberta, Canada.,Ecosystems Center, Marine Biological Laboratory, Woods Hole, MA, USA
| | - Aaron Cahill
- The Lyell Centre, Heriot Watt University, Edinburgh, United Kingdom
| | - Liam Connors
- Biomedical Sciences Department, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Jackie K Zorz
- Department of Geoscience, University of Calgary, Calgary, Alberta, Canada
| | - Isabella Hrabe de Angelis
- Department of Geoscience, University of Calgary, Calgary, Alberta, Canada.,Multiphase Chemistry Department, Max Planck Institute for Chemistry, Mainz, Germany
| | | | - Bernhard Mayer
- Department of Geoscience, University of Calgary, Calgary, Alberta, Canada
| | - Marc Strous
- Department of Geoscience, University of Calgary, Calgary, Alberta, Canada
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Wang S, An Z, Wang ZW. Bioconversion of methane to chemicals and fuels by methane-oxidizing bacteria. ADVANCES IN BIOENERGY 2020. [DOI: 10.1016/bs.aibe.2020.04.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Xu J, Liu X, Huang J, Huang M, Wang T, Bao S, Tang W, Fang T. The contributions and mechanisms of iron-microbes-biochar in constructed wetlands for nitrate removal from low carbon/nitrogen ratio wastewater. RSC Adv 2020; 10:23212-23220. [PMID: 35520335 PMCID: PMC9054680 DOI: 10.1039/d0ra03609a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 06/11/2020] [Indexed: 11/21/2022] Open
Abstract
The removal efficiency of nitrate from low carbon/nitrogen ratio wastewater has been restricted by the lack of organics for several decades. Here, a system coupling chemical reduction, microbial denitrification and constructed wetlands (RDCWs) was developed to investigate the effect and possible mechanisms for nitrate degradation. The results showed that this coupling system could achieve a nitrate removal efficiency of 97.07 ± 1.76%, 85.91 ± 3.02% and 56.63 ± 2.88% at a hydraulic retention time of 24 h, 12 h and 6 h with feeding nitrate of 15 mg L−1, respectively. These removal efficiencies of nitrate were partly caused by microbes and biochar with a contribution rate of 31.08 ± 4.43% and 9.50 ± 3.30%. Besides, microbes were closely related to iron and biochar for the removal of nitrate. Simplicispira was able to utilize hydrogen produced by iron corrosion as an electron donor while nitrate accepted electrons to be reduced. Porous biochar could release dissolved organic matter, which provided a good living circumstance and carbon source for microbes. Therefore, the RDCW system is potential for large-scale application due to its low cost and simple operation. Schematic diagram of RDCWs system and proposed mechanisms for nitrate removal.![]()
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Affiliation(s)
- Jian Xu
- Institute of Hydrobiology
- Chinese Academy of Sciences
- Wuhan 430072
- China
- University of Chinese Academy of Sciences
| | - Xiawei Liu
- Institute of Hydrobiology
- Chinese Academy of Sciences
- Wuhan 430072
- China
- University of Chinese Academy of Sciences
| | - Jiaolong Huang
- Institute of Hydrobiology
- Chinese Academy of Sciences
- Wuhan 430072
- China
- University of Chinese Academy of Sciences
| | - Manqi Huang
- Institute of Hydrobiology
- Chinese Academy of Sciences
- Wuhan 430072
- China
- University of Chinese Academy of Sciences
| | - Tao Wang
- Institute of Hydrobiology
- Chinese Academy of Sciences
- Wuhan 430072
- China
- University of Chinese Academy of Sciences
| | - Shaopan Bao
- Institute of Hydrobiology
- Chinese Academy of Sciences
- Wuhan 430072
- China
| | - Wei Tang
- Institute of Hydrobiology
- Chinese Academy of Sciences
- Wuhan 430072
- China
| | - Tao Fang
- Institute of Hydrobiology
- Chinese Academy of Sciences
- Wuhan 430072
- China
- University of Chinese Academy of Sciences
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Pelomicrobium methylotrophicum gen. nov., sp. nov. a moderately thermophilic, facultatively anaerobic, lithoautotrophic and methylotrophic bacterium isolated from a terrestrial mud volcano. Extremophiles 2019; 24:177-185. [PMID: 31705207 DOI: 10.1007/s00792-019-01145-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 10/29/2019] [Indexed: 10/25/2022]
Abstract
A novel moderately thermophilic, bacterium, strain SM250T, was isolated from a terrestrial mud volcano, Taman peninsula, Krasnodar region, Russia. Cells of strain SM250T were Gram-negative non-spore forming motile straight rods. Growth was observed at temperatures 30-63 °C (optimum at 50 °C), pH 6.5-10.0 (optimum at pH 8.5) and NaCl concentrations 0-4.5% (w/v) (optimum at 1.0-1.5% (w/v)). The novel isolate grows by aerobic respiration or anaerobic respiration with nitrate as the terminal electron acceptor. Strain SM250T grows by the utilization of methanol, formate and a number of other organic compounds or lithoautotrophically with hydrogen, elemental sulfur or thiosulfate as electron donors. The total size of the genome of the novel isolate was 3,327,116 bp and a genomic DNA G + C content was 64.8 mol%. Analysis of the 16S rRNA gene sequences revealed that strain SM250T belongs to the class Hydrogenophilia within the phylum Proteobacteria, with less than 91% of 16S rRNA gene sequence similarity to any species with validly published name. We propose to assign strain SM250T to a new species of a novel genus Pelomicrobium methylotrophicum gen. nov., sp. nov. The type strain is SM250T (= KCTC 62861T = VKM B-3274T).
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Hirose S, Tank M, Hara E, Tamaki H, Mori K, Takaichi S, Haruta S, Hanada S. Aquabacterium pictum sp. nov., the first aerobic bacteriochlorophyll a-containing fresh water bacterium in the genus Aquabacterium of the class Betaproteobacteria. Int J Syst Evol Microbiol 2019; 70:596-603. [PMID: 31622237 DOI: 10.1099/ijsem.0.003798] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
A strictly aerobic, bacteriochlorophyll a-containing betaproteobacterium, designated strain W35T, was isolated from a biofilm sampled at Tama River in Japan. The non-motile and rod-shaped cells formed pink-beige pigmented colonies on agar plates containing organic compounds, and showed an in vivo absorption maximum at 871 nm in the near-infrared region, typical for the presence of bacteriochlorophyll a. The new bacterial strain is Gram-negative, and oxidase- and catalase-positive. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain W35T was closely related to species in the genus Aquabacterium. The closest phylogenetic relatives of strain W35T were Aquabacterium commune B8T (97.9 % sequence similarity), Aquabacterium citratiphilum B4T (97.2 %) and Aquabacterium limnoticum ABP-4T (97.0 %). The major cellular fatty acids were C16 : 1ω7c (50.4 %), C16 : 0 (22.7 %), summed feature 8 (C18 : 1ω7c/C18 : 1ω6c; 9.7 %), C18 : 3ω6c (5.5 %), C12 : 0 (5.3 %) and C10 : 0 3OH (2.7 %). The respiratory quinone was ubiquinone-8. Predominant polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The G+C content of the genomic DNA was 70.4 mol% (genome data) and 71.4 mol% (HPLC). The genome size of strain W35T is 6.1 Mbp and average nucleotide identity analysis indicated genome similarities of strain W35T and related Aquabacterium type strains to be 78-79 %. The results of polyphasic comparisons showed that strain W35T was clearly distinguishable from other members of the genus Aquabacterium. Therefore, we propose a new species in the genus Aquabacterium, namely, Aquabacterium pictum sp. nov. The type strain is W35T (=DSM 106757T=NBRC 111963T). The description of the genus Aquabacterium is also emended.
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Affiliation(s)
- Setsuko Hirose
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1, Minami-Osawa, Hachioji, Tokyo, 192-0397, Japan
| | - Marcus Tank
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1, Minami-Osawa, Hachioji, Tokyo, 192-0397, Japan
| | - Eri Hara
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1, Higashi, Tsukuba, Ibaraki, 305-8566, Japan
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1, Higashi, Tsukuba, Ibaraki, 305-8566, Japan
| | - Koji Mori
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8, Kazusakamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Shinichi Takaichi
- Department of Molecular Microbiology, Tokyo University of Agriculture, 1-1-1, Sakuragaoka, Setagaya-ku, Tokyo, 156-8502, Japan
| | - Shin Haruta
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1, Minami-Osawa, Hachioji, Tokyo, 192-0397, Japan
| | - Satoshi Hanada
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1, Minami-Osawa, Hachioji, Tokyo, 192-0397, Japan
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Zhang X, Zhao S, Gao J, Lei Y, Yuan Y, Jiang Y, Xu Z, He C. Microbial action and mechanisms for Cr(VI) removal performance by layered double hydroxide modified zeolite and quartz sand in constructed wetlands. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 246:636-646. [PMID: 31212217 DOI: 10.1016/j.jenvman.2019.06.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 05/30/2019] [Accepted: 06/05/2019] [Indexed: 06/09/2023]
Abstract
This study was conducted to evaluate the performance underlying the removal of hexavalent chromium Cr(VI) associated with Zn-layered double hydroxides (Zn-LDHs)-modified substrates utilized in simulated constructed wetlands (CWs) from a microbial perspective. To accomplish this, Zn-LDHs-modified substrates (zeolite and quartz sand (QS)) were synthesized at various Zn2+/Al3+ and Fe3+ molar ratios by co-precipitation under alkaline conditions. The experimental group was then compared with a control group to determine the microbial action responsible for Cr(VI) removal during the Cr(VI) removal experiments. The removal experiment revealed that the average Cr(VI) removal rates of the Zn-LDHs-modified substrates were superior to those of natural substrates. Subsequent evaluation of the microbial structure by Illumina high-throughput sequencing revealed that the relative abundance of Novosphingobium, Brevundimonas, Methylophilus, and Acidovorax related to Cr(VI) removal was relatively high in Zn-LDHs-modified substrates. Moreover, the extracellular polymeric substance (EPS) content was significantly influenced by the Zn-LDHs coating according to the relative microbial experiments. Similar trends were observed in enzyme activity. Taken together, these findings illustrated that the Zn-LDHs coating had a significant impact on microbial action, and the Cr(VI) removal efficiency of the Zn-LDHs-modified QS (zeolite) substrate was better than that of the natural substrate because of intracellular and extracellular removal mechanisms. Briefly, the microbial action of Zn-LDHs-modified QS played an important role in Cr(VI) removal, since the EPS content possessed the appropriate concentrations. Moreover, the microbial activity of ZnAl-LDHs-modified QS (zeolite) may have been higher than that of ZnFe-LDHs-modified QS (zeolite) because Al had a stronger promoting effect on Cr(VI) bio-removal than Fe. Therefore, the microbial Cr(VI) removal supported by ZnAl-LDHs-modified QS is a better choice for CWs.
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Affiliation(s)
- Xiangling Zhang
- School of Civil Engineering and Architecture, Wuhan University of Technology, Wuhan, 430070, China.
| | - Shuangjie Zhao
- School of Civil Engineering and Architecture, Wuhan University of Technology, Wuhan, 430070, China
| | - Jingtian Gao
- School of Civil Engineering and Architecture, Wuhan University of Technology, Wuhan, 430070, China; School of Energy and Environment, Inner Mongolia University of Science & Technology, Baotou, 014010, China
| | - Yu Lei
- School of Civil Engineering and Architecture, Wuhan University of Technology, Wuhan, 430070, China
| | - Ye Yuan
- School of Civil Engineering and Architecture, Wuhan University of Technology, Wuhan, 430070, China
| | - Yinghe Jiang
- School of Civil Engineering and Architecture, Wuhan University of Technology, Wuhan, 430070, China
| | - Zhouying Xu
- School of Civil Engineering and Architecture, Wuhan University of Technology, Wuhan, 430070, China
| | - Chunyan He
- School of Civil Engineering and Architecture, Wuhan University of Technology, Wuhan, 430070, China
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Kansal S, Catto-Smith AG, Boniface K, Thomas S, Cameron DJ, Oliver M, Alex G, Kirkwood CD, Wagner J. The Microbiome in Paediatric Crohn's Disease-A Longitudinal, Prospective,
Single-Centre Study. J Crohns Colitis 2019; 13:1044-1054. [PMID: 30927743 DOI: 10.1093/ecco-jcc/jjz016] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
BACKGROUND AND AIMS The gut mucosa is the principal site where Crohn's disease [CD] inflammation occurs. Limited information is available about the gut mucosal microbiome during CD relapse and remission. The aim of our study was to characterize specific changes in the gut microbiome during relapse and remission in a large single-centre paediatric CD cohort. METHODS We analysed the microbiome of 345 biopsies from 204 patients, including 88 CD first diagnosis [CDFD] patients, 38 relapse [CDRL] patients, 12 remission [CDRM] patients, and 66 controls. Species identification was conducted using oligotyping in combination with ARB/SILVA taxonomic annotation. RESULTS We observed 45 bacteria to differ between CDFD samples and controls with statistical significance, with Fusobacterium being the most implicated species in CDFD patients. We also identified gender-specific differences in CD. Five species showed a strong association with CDRL patients and 10 species with CDRM patients. Three taxa showed a positive co-occurrence across the two groups. Hespellia porcina [closest taxonomic neighbour to Clostridium oroticum] was the most strongly associated with CDRL samples. Interestingly, Fusobacterium was not part of the CDRL-associated taxa group. Faecalibacterium prausnitzii was equally present in CDFD and control samples. CONCLUSION This is the first study that has investigated the gut mucosal microbiome in a paediatric CD cohort with longitudinal sampling. Importantly, the microbiome of patients in CDRM did not return to a healthy control state. Neither did the microbiome of patients with CDRL return to the profile seen at CDFD.
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Affiliation(s)
- Shivani Kansal
- Department of Gastroenterology and Clinical Nutrition, The Royal Children's Hospital, Parkville, Victoria, Australia.,Enteric Virus group, Murdoch Children's Research Institute, Parkville, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
| | - Anthony G Catto-Smith
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia.,Department of Gastroenterology, Hepatology and Liver Transplant, Lady Cilento Children's Hospital, Brisbane, Queensland, Australia
| | - Karen Boniface
- Enteric Virus group, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Sarah Thomas
- Enteric Virus group, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Donald J Cameron
- Department of Gastroenterology and Clinical Nutrition, The Royal Children's Hospital, Parkville, Victoria, Australia
| | - Mark Oliver
- Department of Gastroenterology and Clinical Nutrition, The Royal Children's Hospital, Parkville, Victoria, Australia
| | - George Alex
- Department of Gastroenterology and Clinical Nutrition, The Royal Children's Hospital, Parkville, Victoria, Australia
| | - Carl D Kirkwood
- Enteric Virus group, Murdoch Children's Research Institute, Parkville, Victoria, Australia.,Enteric and Diarrheal Diseases, Global Health, Bill and Melinda Gates Foundation, Seattle, Washington, USA
| | - Josef Wagner
- Enteric Virus group, Murdoch Children's Research Institute, Parkville, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia.,Wellcome Sanger Institute, Cambridge, UK
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Tsao HF, Scheikl U, Herbold C, Indra A, Walochnik J, Horn M. The cooling tower water microbiota: Seasonal dynamics and co-occurrence of bacterial and protist phylotypes. WATER RESEARCH 2019; 159:464-479. [PMID: 31128471 PMCID: PMC6554697 DOI: 10.1016/j.watres.2019.04.028] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 04/04/2019] [Accepted: 04/13/2019] [Indexed: 05/30/2023]
Abstract
Cooling towers for heating, ventilation and air conditioning are ubiquitous in the built environment. Often located on rooftops, their semi-open water basins provide a suitable environment for microbial growth. They are recognized as a potential source of bacterial pathogens and have been associated with disease outbreaks such as Legionnaires' disease. While measures to minimize public health risks are in place, the general microbial and protist community structure and dynamics in these systems remain largely elusive. In this study, we analysed the microbiome of the bulk water from the basins of three cooling towers by 16S and 18S rRNA gene amplicon sequencing over the course of one year. Bacterial diversity in all three towers was broadly comparable to other freshwater systems, yet less diverse than natural environments; the most abundant taxa are also frequently found in freshwater or drinking water. While each cooling tower had a pronounced site-specific microbial community, taxa shared among all locations mainly included groups generally associated with biofilm formation. We also detected several groups related to known opportunistic pathogens, such as Legionella, Mycobacterium, and Pseudomonas species, albeit at generally low abundance. Although cooling towers represent a rather stable environment, microbial community composition was highly dynamic and subject to seasonal change. Protists are important members of the cooling tower water microbiome and known reservoirs for bacterial pathogens. Co-occurrence analysis of bacteria and protist taxa successfully captured known interactions between amoeba-associated bacteria and their hosts, and predicted a large number of additional relationships involving ciliates and other protists. Together, this study provides an unbiased and comprehensive overview of microbial diversity of cooling tower water basins, establishing a framework for investigating and assessing public health risks associated with these man-made freshwater environments.
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Affiliation(s)
- Han-Fei Tsao
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Ute Scheikl
- Institute of Specific Prophylaxis and Tropical Medicine, Medical University of Vienna, Vienna, Austria
| | - Craig Herbold
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Alexander Indra
- Department of Mycobacteriology and Clinical Molecular Biology, AGES, Vienna, Austria
| | - Julia Walochnik
- Institute of Specific Prophylaxis and Tropical Medicine, Medical University of Vienna, Vienna, Austria
| | - Matthias Horn
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
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Mei R, Kim J, Wilson FP, Bocher BTW, Liu WT. Coupling growth kinetics modeling with machine learning reveals microbial immigration impacts and identifies key environmental parameters in a biological wastewater treatment process. MICROBIOME 2019; 7:65. [PMID: 30995941 PMCID: PMC6471889 DOI: 10.1186/s40168-019-0682-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 04/08/2019] [Indexed: 05/11/2023]
Abstract
BACKGROUND Ubiquitous in natural and engineered ecosystems, microbial immigration is one of the mechanisms shaping community assemblage. However, quantifying immigration impact remains challenging especially at individual population level. The activities of immigrants in the receiving community are often inadequately considered, leading to potential bias in identifying the relationship between community composition and environmental parameters. RESULTS This study quantified microbial immigration from an upstream full-scale anaerobic reactor to downstream activated sludge reactors. A mass balance was applied to 16S rRNA gene amplicon sequencing data to calculate the net growth rates of individual populations in the activated sludge reactors. Among the 1178 observed operational taxonomic units (OTUs), 582 had a positive growth rate, including all the populations with abundance > 0.1%. These active populations collectively accounted for 99% of the total sequences in activated sludge. The remaining 596 OTUs with a growth rate ≤ 0 were classified as inactive populations. All the abundant populations in the upstream anaerobic reactor were inactive in the activated sludge process, indicating a negligible immigration impact. We used a supervised learning regressor to predict environmental parameters based on community composition and compared the prediction accuracy based on either the entire community or the active populations. Temperature was the most predictable parameter, and the prediction accuracy was improved when only active populations were used to train the regressor. CONCLUSIONS Calculating growth rate of individual microbial populations in the downstream system provides an effective approach to determine microbial activity and quantify immigration impact. For the studied biological process, a marginal immigration impact was observed, likely due to the significant differences in the growth environments between the upstream and downstream processes. Excluding inactive populations as a result of immigration further enhanced the prediction of key environmental parameters affecting process performance.
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Affiliation(s)
- Ran Mei
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 3207 Newmark Civil Engineering Laboratory, 205 North Mathews Ave, Urbana, IL 61801 USA
| | - Jinha Kim
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 3207 Newmark Civil Engineering Laboratory, 205 North Mathews Ave, Urbana, IL 61801 USA
| | - Fernanda P. Wilson
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 3207 Newmark Civil Engineering Laboratory, 205 North Mathews Ave, Urbana, IL 61801 USA
| | | | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 3207 Newmark Civil Engineering Laboratory, 205 North Mathews Ave, Urbana, IL 61801 USA
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Ding C, Enyi FO, Adrian L. Anaerobic Ammonium Oxidation (Anammox) with Planktonic Cells in a Redox-Stable Semicontinuous Stirred-Tank Reactor. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:5671-5681. [PMID: 29693390 DOI: 10.1021/acs.est.7b05979] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Anaerobic ammonium oxidizing (anammox) bacteria are routinely cultivated in mixed culture in biomass-retaining bioreactors or as planktonic cells in membrane bioreactors. Here, we demonstrate that anammox bacteria can also be cultivated as planktonic cells in a semicontinuous stirred-tank reactor (semi-CSTR) with a specific growth rate μ of 0.33 d-1 at 30 °C. Redox potential inside the reactor stabilized at around 10 mV (±15 mV; vs standard hydrogen electrode) without gas purging. Reactor headspace pressure was used as a sensitive and real-time indicator for nitrogen evolution and anammox activity. The reactor was dominated by an organism closely related to " Candidatus Kuenenia stuttgartiensis" (∼87% abundance) as shown by Illumina amplicon sequencing and fluorescence in situ hybridization. Epifluorescence microscopy demonstrated that all cells were in their planktonic form. Mass balance analysis revealed a nitrite/ammonium ratio of 1.270, a nitrate/ammonium ratio of 0.238, and a biomass yield of 1.97 g volatile suspended solids per mole of consumed ammonium. Batch experiments with the reactor effluent showed that anammox activities were sensitive to sulfide (IC50 = 5 μM) and chloramphenicol (IC50 = 19 mg L-1), much lower than reported for granular anammox biomass. This study shows that semi-CSTR is a powerful tool to study anammox bacteria.
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Affiliation(s)
- Chang Ding
- Helmholtz Centre for Environmental Research - UFZ , Isotope Biogeochemistry , Permoserstraße 15 , 04318 Leipzig , Germany
| | - Francis O Enyi
- Helmholtz Centre for Environmental Research - UFZ , Isotope Biogeochemistry , Permoserstraße 15 , 04318 Leipzig , Germany
| | - Lorenz Adrian
- Helmholtz Centre for Environmental Research - UFZ , Isotope Biogeochemistry , Permoserstraße 15 , 04318 Leipzig , Germany
- Chair of Geobiotechnology, Technische Universität Berlin , Ackerstraße 76 , 13355 Berlin , Germany
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Untapped bacterial diversity and metabolic potential within Unkeshwar hot springs, India. Arch Microbiol 2018; 200:753-770. [PMID: 29396619 DOI: 10.1007/s00203-018-1484-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 01/23/2018] [Accepted: 01/24/2018] [Indexed: 01/04/2023]
Abstract
Hot springs support diverse and interesting groups of microorganisms adapted to extreme conditions and gaining attention in biotechnological applications. However, due to limitations of cultivation methods, a majority of such extremophiles remain uncultivated and unexplored. The advent of multiple cultivation conditions and specialized culture media could possibly aid to access the unexplored microbial portion of hot springs. In the present study, different media and isolation strategies were applied to isolate hitherto unexplored bacterial taxa in the water samples collected from Unkeshwar hot springs, India. Molecular, phylogenetic and predictive functional characterization of the isolated bacterial population was done using 16S rRNA sequencing coupled with Tax4Fun tools. Furthermore, representative isolates were screened for important enzymes (cellulase, xylanase, amylase, and protease) and heavy metal tolerance (chromium, arsenic) properties. A total of 454 bacterial isolates obtained were mapped into 57 unique bacterial genera and 4 different bacterial phyla. Interestingly, 37 genera not previously isolated from Indian hot springs, were isolated for the first time in the present study. However, most of these genera (23 out of 37) were reported only in metagenomics studies from Indian and global hot springs. Furthermore, around 14 genera not previously cultivated and not detected in metagenomics studies of hot springs are documented here. The metabolic potential was ascertained by determining the abundance of specific genes using in silico based Tax4Fun tool, which identified around 315 metabolic pathways for metabolism of carbohydrates, synthesis of secondary metabolites and degradation of xenobiotic compounds. Bioprospection study revealed that 33 and 25 bacterial genera were positive for enzyme production and resistance to the heavy metals, respectively. The present study revealed the advantages of cultivation methods using a comprehensive multiple isolation approach for exploring untapped and unique bacterial diversity, and also utilities for various biotechnological and environmental applications.
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Gonzalez-Martinez A, Muñoz-Palazon B, Rodriguez-Sanchez A, Maza-Márquez P, Mikola A, Gonzalez-Lopez J, Vahala R. Start-up and operation of an aerobic granular sludge system under low working temperature inoculated with cold-adapted activated sludge from Finland. BIORESOURCE TECHNOLOGY 2017; 239:180-189. [PMID: 28521227 DOI: 10.1016/j.biortech.2017.05.037] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 05/04/2017] [Accepted: 05/07/2017] [Indexed: 06/07/2023]
Abstract
An aerobic granular sludge system has been started-up and operated at 7°C temperature using cold-adapted activated sludge as inoculum. The system could form granular biomass due to batch operation allowing for just 5-3min of biomass sedimentation. Scanning electron microscopy showed that fungi helped in the granular biomass formation in the early stages of the granule formation. The removal performance of the system was of 92-95% in BOD5, 75-80% in COD, 70-76% in total nitrogen and 50-60% in total phosphorous. The bacterial community structure from cold-adapted activated sludge changed during the operational time, leading to a final configuration dominated by Microbacteriaceae members Microbacterium and Leucobacter, which were strongly correlated to biomass settling velocity and bioreactor performance, as suggested by multivariate redundancy analyses. This experiment showed that aerobic granular sludge systems could be successfully started-up and operated, with high performance, under low operational temperatures when using cold-adapted biomass as inoculum.
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Affiliation(s)
| | - Barbara Muñoz-Palazon
- Institute of Water Research, University of Granada, C/Ramon y Cajal, 4, 18071 Granada, Spain
| | | | - Paula Maza-Márquez
- Institute of Water Research, University of Granada, C/Ramon y Cajal, 4, 18071 Granada, Spain
| | - Anna Mikola
- Department of Built Environment, University of Aalto, P.O. Box 15200, Aalto, FI-00076 Espoo, Finland
| | - Jesus Gonzalez-Lopez
- Institute of Water Research, University of Granada, C/Ramon y Cajal, 4, 18071 Granada, Spain
| | - Riku Vahala
- Department of Built Environment, University of Aalto, P.O. Box 15200, Aalto, FI-00076 Espoo, Finland
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Corteselli EM, Aitken MD, Singleton DR. Rugosibacter aromaticivorans gen. nov., sp. nov., a bacterium within the family Rhodocyclaceae, isolated from contaminated soil, capable of degrading aromatic compounds. Int J Syst Evol Microbiol 2017; 67:311-318. [PMID: 27902243 DOI: 10.1099/ijsem.0.001622] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A bacterial strain designated Ca6T was isolated from polycyclic aromatic hydrocarbon (PAH)-contaminated soil from the site of a former manufactured gas plant in Charlotte, NC, USA, and linked phylogenetically to the family Rhodocyclaceae of the class Betaproteobacteria. Its 16S rRNA gene sequence was highly similar to globally distributed environmental sequences, including those previously designated 'Pyrene Group 1' demonstrated to grow on the PAHs phenanthrene and pyrene by stable-isotope probing. The most closely related described relative was Sulfuritalea hydrogenivorans strain sk43HT (93.6 % 16S rRNA gene sequence identity). In addition to a limited number of organic acids, Ca6T was capable of growth on the monoaromatic compounds benzene and toluene, and the azaarene carbazole, as sole sources of carbon and energy. Growth on the PAHs phenanthrene and pyrene was also confirmed. Optimal growth was observed aerobically under mesophilic temperature, neutral pH and low salinity conditions. Major fatty acids present included summed feature 3 (C16 : 1ω7c or C16 : 1ω6c) and C16 : 0. The DNA G+C content of the single chromosome was 55.14 mol% as determined by complete genome sequencing. Due to its distinct genetic and physiological properties, strain Ca6T is proposed as a member of a novel genus and species within the family Rhodocyclaceae, for which the name Rugosibacter aromaticivorans gen. nov., sp. nov. is proposed. The type strain of the species is Ca6T (=ATCC TSD-59T=DSM 103039T).
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Affiliation(s)
- Elizabeth M Corteselli
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, NC 27599-7431, USA
| | - Michael D Aitken
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, NC 27599-7431, USA
| | - David R Singleton
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, NC 27599-7431, USA
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van der Kooij D, Bakker GL, Italiaander R, Veenendaal HR, Wullings BA. Biofilm Composition and Threshold Concentration for Growth of Legionella pneumophila on Surfaces Exposed to Flowing Warm Tap Water without Disinfectant. Appl Environ Microbiol 2017; 83:e02737-16. [PMID: 28062459 PMCID: PMC5311405 DOI: 10.1128/aem.02737-16] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Accepted: 12/13/2016] [Indexed: 02/07/2023] Open
Abstract
Legionella pneumophila in potable water installations poses a potential health risk, but quantitative information about its replication in biofilms in relation to water quality is scarce. Therefore, biofilm formation on the surfaces of glass and chlorinated polyvinyl chloride (CPVC) in contact with tap water at 34 to 39°C was investigated under controlled hydraulic conditions in a model system inoculated with biofilm-grown L. pneumophila The biofilm on glass (average steady-state concentration, 23 ± 9 pg ATP cm-2) exposed to treated aerobic groundwater (0.3 mg C liter-1; 1 μg assimilable organic carbon [AOC] liter-1) did not support growth of the organism, which also disappeared from the biofilm on CPVC (49 ± 9 pg ATP cm-2) after initial growth. L. pneumophila attained a level of 4.3 log CFU cm-2 in the biofilms on glass (1,055 ± 225 pg ATP cm-2) and CPVC (2,755 ± 460 pg ATP cm-2) exposed to treated anaerobic groundwater (7.9 mg C liter-1; 10 μg AOC liter-1). An elevated biofilm concentration and growth of L. pneumophila were also observed with tap water from the laboratory. The Betaproteobacteria Piscinibacter and Methyloversatilis and amoeba-resisting Alphaproteobacteria predominated in the clones and isolates retrieved from the biofilms. In the biofilms, the Legionella colony count correlated significantly with the total cell count (TCC), heterotrophic plate count, ATP concentration, and presence of Vermamoeba vermiformis This amoeba was rarely detected at biofilm concentrations of <100 pg ATP cm-2 A threshold concentration of approximately 50 pg ATP cm-2 (TCC = 1 × 106 to 2 × 106 cells cm-2) was derived for growth of L. pneumophila in biofilms.IMPORTANCELegionella pneumophila is the etiologic agent in more than 10,000 cases of Legionnaires' disease that are reported annually worldwide and in most of the drinking water-associated disease outbreaks reported in the United States. The organism proliferates in biofilms on surfaces exposed to warm water in engineered freshwater installations. An investigation with a test system supplied with different types of warm drinking water without disinfectant under controlled hydraulic conditions showed that treated aerobic groundwater (0.3 mg liter-1 of organic carbon) induced a low biofilm concentration that supported no or very limited growth of L. pneumophila Elevated biofilm concentrations and L. pneumophila colony counts were observed on surfaces exposed to two types of extensively treated groundwater, containing 1.8 and 7.9 mg C liter-1 and complying with the microbial water quality criteria during distribution. Control measures in warm tap water installations are therefore essential for preventing growth of L. pneumophila.
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Affiliation(s)
| | | | | | | | - Bart A Wullings
- KWR Watercycle Research Institute, Nieuwegein, the Netherlands
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Liu CT, Lin SY, Hameed A, Liu YC, Hsu YH, Wong WT, Tseng CH, Lur HS, Young CC. Oryzomicrobium terrae gen. nov., sp. nov., of the family Rhodocyclaceae isolated from paddy soil. Int J Syst Evol Microbiol 2017; 67:183-189. [DOI: 10.1099/ijsem.0.001565] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Chi-Te Liu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan, ROC
- Institute of Biotechnology, National Taiwan University, Taiwan, ROC
| | - Shih-Yao Lin
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Asif Hameed
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - You-Cheng Liu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Yi-Han Hsu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Wai-Tak Wong
- Department of Agronomy, National Taiwan University, Taipei, Taiwan, ROC
| | - Ching-Han Tseng
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan, ROC
| | - Huu-Sheng Lur
- Department of Agronomy, National Taiwan University, Taipei, Taiwan, ROC
| | - Chiu-Chung Young
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, ROC
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
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Graham EB, Crump AR, Resch CT, Fansler S, Arntzen E, Kennedy DW, Fredrickson JK, Stegen JC. Coupling Spatiotemporal Community Assembly Processes to Changes in Microbial Metabolism. Front Microbiol 2016; 7:1949. [PMID: 28123379 PMCID: PMC5226446 DOI: 10.3389/fmicb.2016.01949] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 11/21/2016] [Indexed: 11/13/2022] Open
Abstract
Community assembly processes generate shifts in species abundances that influence ecosystem cycling of carbon and nutrients, yet our understanding of assembly remains largely separate from ecosystem-level functioning. Here, we investigate relationships between assembly and changes in microbial metabolism across space and time in hyporheic microbial communities. We pair sampling of two habitat types (i.e., attached and planktonic) through seasonal and sub-hourly hydrologic fluctuation with null modeling and temporally explicit multivariate statistics. We demonstrate that multiple selective pressures-imposed by sediment and porewater physicochemistry-integrate to generate changes in microbial community composition at distinct timescales among habitat types. These changes in composition are reflective of contrasting associations of Betaproteobacteria and Thaumarchaeota with ecological selection and with seasonal changes in microbial metabolism. We present a conceptual model based on our results in which metabolism increases when oscillating selective pressures oppose temporally stable selective pressures. Our conceptual model is pertinent to both macrobial and microbial systems experiencing multiple selective pressures and presents an avenue for assimilating community assembly processes into predictions of ecosystem-level functioning.
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Affiliation(s)
- Emily B Graham
- Biological Sciences Division, Pacific Northwest National Laboratory Richland, WA, USA
| | - Alex R Crump
- Biological Sciences Division, Pacific Northwest National Laboratory Richland, WA, USA
| | - Charles T Resch
- Biological Sciences Division, Pacific Northwest National Laboratory Richland, WA, USA
| | - Sarah Fansler
- Biological Sciences Division, Pacific Northwest National Laboratory Richland, WA, USA
| | - Evan Arntzen
- Biological Sciences Division, Pacific Northwest National Laboratory Richland, WA, USA
| | - David W Kennedy
- Biological Sciences Division, Pacific Northwest National Laboratory Richland, WA, USA
| | - Jim K Fredrickson
- Biological Sciences Division, Pacific Northwest National Laboratory Richland, WA, USA
| | - James C Stegen
- Biological Sciences Division, Pacific Northwest National Laboratory Richland, WA, USA
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Chun J, Young Kang J, Cheol Jung Y, Yeop Jahng K. Niveibacterium umoris gen. nov., sp. nov., isolated from wetland freshwater. Int J Syst Evol Microbiol 2016; 66:997-1002. [DOI: 10.1099/ijsem.0.000826] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Jeesun Chun
- Department of Life Sciences, Chonbuk National University, Jeonju-si, 561-756, Republic of Korea
| | - Ji Young Kang
- Department of Life Sciences, Chonbuk National University, Jeonju-si, 561-756, Republic of Korea
- Applied Microbiology Research Center, Bio-Materials Research Institute, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup-si, 580-185, Republic of Korea
| | - Young Cheol Jung
- Department of Life Sciences, Chonbuk National University, Jeonju-si, 561-756, Republic of Korea
| | - Kwang Yeop Jahng
- Department of Life Sciences, Chonbuk National University, Jeonju-si, 561-756, Republic of Korea
- Institute for Molecular Biology and Genetics, Chonbuk National University, Jeonju-si, 561-756, Republic of Korea
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Fang L, Chen L, Liu Y, Tao W, Zhang Z, Liu H, Tang Y. Planktonic and sedimentary bacterial diversity of Lake Sayram in summer. Microbiologyopen 2015; 4:814-25. [PMID: 26242906 PMCID: PMC4618613 DOI: 10.1002/mbo3.281] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 06/23/2015] [Accepted: 07/06/2015] [Indexed: 12/21/2022] Open
Abstract
Lake Sayram is an ancient cold water lake locating at a mountain basin in Xinjiang, China. The lake water is brackish, alkaline, unpolluted, and abundant in SO4(2-) and Mg(2+). The lacustrine ecosystem of Lake Sayram has been intensely investigated. However, profiles of the microbial communities in the lake remain largely unknown. In this study, taxonomic compositions of the planktonic and sedimentary bacterial communities in Lake Sayram were investigated using 16S rRNA metagenomics. The lacustrine bacterial communities were generally structured by environmental conditions, including the hydrological and physicochemical parameters. Proteobacteria was the dominating phylum. In the lake water, the genera Acinetobacter and Ilumatobacter held an absolute predominance, implying their metabolic significance. In the bottom sediment, biogeochemically significant bacteria and thermophilic or acidothermophilic extremophiles were recovered. In contrast to the planktonic bacteria, an appreciable portion of the sedimentary bacteria could not be classified into any known taxonomic unit, indicating the largely unknown bacteriosphere hiding in the bottom sediment of Lake Sayram.
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Affiliation(s)
- Lei Fang
- School of Marine Science and Environmental Engineering, Dalian Ocean University, Dalian, 116023, China
| | - Lei Chen
- School of Marine Science and Environmental Engineering, Dalian Ocean University, Dalian, 116023, China.,School of Life Sciences, Liaoning Normal University, Dalian, 116029, China
| | - Yuan Liu
- School of Marine Science and Environmental Engineering, Dalian Ocean University, Dalian, 116023, China
| | - Wei Tao
- School of Marine Science and Environmental Engineering, Dalian Ocean University, Dalian, 116023, China
| | - Zhongzhe Zhang
- School of Marine Science and Environmental Engineering, Dalian Ocean University, Dalian, 116023, China
| | - Haiying Liu
- School of Marine Science and Environmental Engineering, Dalian Ocean University, Dalian, 116023, China
| | - Yong Tang
- School of Marine Science and Environmental Engineering, Dalian Ocean University, Dalian, 116023, China
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Smalley NE, Taipale S, De Marco P, Doronina NV, Kyrpides N, Shapiro N, Woyke T, Kalyuzhnaya MG. Functional and genomic diversity of methylotrophic Rhodocyclaceae: description of Methyloversatilis discipulorum sp. nov. Int J Syst Evol Microbiol 2015; 65:2227-2233. [PMID: 26231539 DOI: 10.1099/ijs.0.000190] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023] Open
Abstract
Three strains of methylotrophic Rhodocyclaceae (FAM1(T), RZ18-153 and RZ94) isolated from Lake Washington sediment samples were characterized. Based on phylogenetic analysis of 16S rRNA gene sequences the strains should be assigned to the genus Methyloversatilis. Similarly to other members of the family, the strains show broad metabolic capabilities and are able to utilize a number of organic acids, alcohols and aromatic compounds in addition to methanol and methylamine. The main fatty acids were 16:1ω7c (49-59%) and 16:0 (32-29%). Genomes of all isolates were sequenced, assembled and annotated in collaboration with the DOE Joint Genome Institute (JGI). Genome comparison revealed that the strains FAM1T, RZ18-153 and RZ94 are closely related to each other and almost equally distant from two previously described species of the genus Methyloversatilis, Methyloversatilis universalis and Methyloversatilis thermotolerans. Like other methylotrophic species of the genus Methyloversatilis, all three strains possess one-subunit PQQ-dependent ethanol/methanol dehydrogenase (Mdh-2), the N-methylglutamate pathway and the serine cycle (isocitrate lyase/malate synthase, Icl/ms(+) variant). Like M. universalis, strains FAM1(T), RZ18-153 and RZ94 have a quinohemoprotein amine dehydrogenase, a tungsten-containing formaldehyde ferredoxin oxidoreductase, phenol hydroxylase, and the complete Calvin cycle. Similarly to M. thermotolerans, the three strains possess two-subunit methanol dehydrogenase (MxaFI), monoamine oxidase (MAO) and nitrogenase. Based on the phenotypic and genomic data, the strains FAM1(T), RZ18-153 and RZ94 represent a novel species of the genus Methyloversatilis, for which the name Methyloversatilis discipulorum sp. nov. is proposed. The type strain is FAM1(T) ( = JCM 30542(T) = VKM = B-2888(T)).
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Affiliation(s)
- Nicole E Smalley
- Department of Microbiology, University of Washington, Seattle, WA, 98195, USA
| | - Sami Taipale
- Department of Biological and Environmental Science, University of Jyväskylä, PL 35 (YA), 40014 Jyväskylä, Finland
| | - Paolo De Marco
- IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Portugal
- CESPU, IINFACTS, Gandra PRD, Portugal
| | - Nina V Doronina
- Skryabin G.K. Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Prospect Nauki 5, Pushchino 142290, Moscow Region, Russia
| | - Nikos Kyrpides
- US DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Nicole Shapiro
- US DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Tanja Woyke
- US DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Marina G Kalyuzhnaya
- Department of Microbiology, University of Washington, Seattle, WA, 98195, USA
- Biology Department, San Diego State University, San Diego, CA, 92182-4614, USA
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Micó MM, González Ó, Bacardit J, Malfeito J, Sans C. High salinity effect on bioremediation of pretreated pesticide lixiviates from greenhouses. ENVIRONMENTAL TECHNOLOGY 2015; 36:3221-3231. [PMID: 26041507 DOI: 10.1080/09593330.2015.1057541] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 05/29/2015] [Indexed: 06/04/2023]
Abstract
Hydroponics culture greenhouses usually work in closed and semi-closed irrigation systems for nutrients and water-saving purposes. Photo-Fenton reaction has been revealed as an efficient way to depollute that kind of recycled effluents containing pesticides, even for high salinity concentrations. However, the inefficacy of organic matter chemical depletion imposes the use of a subsequent treatment. This work proposes the suitability of an integration of advanced oxidation process with a subsequent bioreactor to treat greenhouse lixiviates effluents at high or extremely high conductivity (salts concentration: up to 42 g L⁻¹). As a first step in this study, the performance of a series of sequencing batch reactors was monitored in order to check the biocompatibility of photo-Fenton pretreated effluents depending on their salinity content. In the second step, those same pretreated effluents were loaded to a biofiltration column filled with expanded clay. Finally, bacterial 16S rRNA gene sequencing was carried out to analyse microbial diversity of the biomass developed in the column. Results stated that the chemical-biological coupled system is effective for the treatment of water effluents containing pesticides. The integrated system is able to deplete more than 80% of the organic load, even under extremely high salinity.
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Affiliation(s)
- María M Micó
- a Departament d'Enginyeria Química , Universitat de Barcelona , Martí i Franquès 1, 6th floor; 08028 Barcelona , Spain
- b ACCIONA Agua , S.A.U. Avda. de les Garrigues, 22; Parque de Negocios Mas Blau II; 08820 El Prat de Llobregat, Barcelona , Spain
| | - Óscar González
- a Departament d'Enginyeria Química , Universitat de Barcelona , Martí i Franquès 1, 6th floor; 08028 Barcelona , Spain
| | - Jordi Bacardit
- b ACCIONA Agua , S.A.U. Avda. de les Garrigues, 22; Parque de Negocios Mas Blau II; 08820 El Prat de Llobregat, Barcelona , Spain
| | - Jorge Malfeito
- b ACCIONA Agua , S.A.U. Avda. de les Garrigues, 22; Parque de Negocios Mas Blau II; 08820 El Prat de Llobregat, Barcelona , Spain
| | - Carme Sans
- a Departament d'Enginyeria Química , Universitat de Barcelona , Martí i Franquès 1, 6th floor; 08028 Barcelona , Spain
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50
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Oosterkamp MJ, Boeren S, Atashgahi S, Plugge CM, Schaap PJ, Stams AJM. Proteomic analysis of nitrate-dependent acetone degradation by Alicycliphilus denitrificans strain BC. FEMS Microbiol Lett 2015; 362:fnv080. [PMID: 25977262 DOI: 10.1093/femsle/fnv080] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/05/2015] [Indexed: 11/13/2022] Open
Abstract
Alicycliphilus denitrificans strain BC grows anaerobically on acetone with nitrate as electron acceptor. Comparative proteomics of cultures of A. denitrificans strain BC grown on either acetone or acetate with nitrate was performed to study the enzymes involved in the acetone degradation pathway. In the proposed acetone degradation pathway, an acetone carboxylase converts acetone to acetoacetate, an AMP-dependent synthetase/ligase converts acetoacetate to acetoacetyl-CoA, and an acetyl-CoA acetyltransferase cleaves acetoacetyl-CoA to two acetyl-CoA. We also found a putative aldehyde dehydrogenase associated with acetone degradation. This enzyme functioned as a β-hydroxybutyrate dehydrogenase catalyzing the conversion of surplus acetoacetate to β-hydroxybutyrate that may be converted to the energy and carbon storage compound, poly-β-hydroxybutyrate. Accordingly, we confirmed the formation of poly-β-hydroxybutyrate in acetone-grown cells of strain BC. Our findings provide insight in nitrate-dependent acetone degradation that is activated by carboxylation of acetone. This will aid studies of similar pathways found in other microorganisms degrading acetone with nitrate or sulfate as electron acceptor.
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Affiliation(s)
- Margreet J Oosterkamp
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands
| | - Sjef Boeren
- Laboratory of Biochemistry, Wageningen University, Dreijenplein 3, 6703 HA Wageningen, the Netherlands
| | - Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands
| | - Caroline M Plugge
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands
| | - Peter J Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, the Netherlands
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands Centre of Biological Engineering, Campus de Gualtar, University of Minho, 4710-057, Braga, Portugal
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