1
|
Wu JJ, Zhu S, Tang YF, Gu F, Liu JX, Sun HZ. Microbiota-host crosstalk in the newborn and adult rumen at single-cell resolution. BMC Biol 2022; 20:280. [PMID: 36514051 PMCID: PMC9749198 DOI: 10.1186/s12915-022-01490-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 12/01/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The rumen is the hallmark organ of ruminants, playing a vital role in their nutrition and providing products for humans. In newborn suckling ruminants milk bypasses the rumen, while in adults this first chamber of the forestomach has developed to become the principal site of microbial fermentation of plant fibers. With the advent of single-cell transcriptomics, it is now possible to study the underlying cell composition of rumen tissues and investigate how this relates the development of mutualistic symbiosis between the rumen and its epithelium-attached microbes. RESULTS We constructed a comprehensive cell landscape of the rumen epithelium, based on single-cell RNA sequencing of 49,689 high-quality single cells from newborn and adult rumen tissues. Our single-cell analysis identified six immune cell subtypes and seventeen non-immune cell subtypes of the rumen. On performing cross-species analysis of orthologous genes expressed in epithelial cells of cattle rumen and the human stomach and skin, we observed that the species difference overrides any cross-species cell-type similarity. Comparing adult with newborn cattle samples, we found fewer epithelial cell subtypes and more abundant immune cells, dominated by T helper type 17 cells in the rumen tissue of adult cattle. In newborns, there were more fibroblasts and myofibroblasts, an IGFBP3+ epithelial cell subtype not seen in adults, while dendritic cells were the most prevalent immune cell subtype. Metabolism-related functions and the oxidation-reduction process were significantly upregulated in adult rumen epithelial cells. Using 16S rDNA sequencing, fluorescence in situ hybridization, and absolute quantitative real-time PCR, we found that epithelial Desulfovibrio was significantly enriched in the adult cattle. Integrating the microbiome and metabolome analysis of rumen tissues revealed a high co-occurrence probability of Desulfovibrio with pyridoxal in the adult cattle compared with newborn ones while the scRNA-seq data indicated a stronger ability of pyroxidal binding in the adult rumen epithelial cell subtypes. These findings indicate that Desulfovibrio and pyridoxal likely play important roles in maintaining redox balance in the adult rumen. CONCLUSIONS Our integrated multi-omics analysis provides novel insights into rumen development and function and may facilitate the future precision improvement of rumen function and milk/meat production in cattle.
Collapse
Affiliation(s)
- Jia-Jin Wu
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
- Ministry of Education Innovation Team of Development and Function of Animal Digestive System, Zhejiang University, Hangzhou, 310058, China
- Ministry of Education Key laboratory of Molecular Animal Nutrition, Zhejiang University, Hangzhou, 310058, China
| | - Senlin Zhu
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
- Ministry of Education Innovation Team of Development and Function of Animal Digestive System, Zhejiang University, Hangzhou, 310058, China
- Ministry of Education Key laboratory of Molecular Animal Nutrition, Zhejiang University, Hangzhou, 310058, China
| | - Yi-Fan Tang
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
- Ministry of Education Innovation Team of Development and Function of Animal Digestive System, Zhejiang University, Hangzhou, 310058, China
- Ministry of Education Key laboratory of Molecular Animal Nutrition, Zhejiang University, Hangzhou, 310058, China
| | - Fengfei Gu
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
- Ministry of Education Innovation Team of Development and Function of Animal Digestive System, Zhejiang University, Hangzhou, 310058, China
- Ministry of Education Key laboratory of Molecular Animal Nutrition, Zhejiang University, Hangzhou, 310058, China
| | - Jian-Xin Liu
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
- Ministry of Education Innovation Team of Development and Function of Animal Digestive System, Zhejiang University, Hangzhou, 310058, China
- Ministry of Education Key laboratory of Molecular Animal Nutrition, Zhejiang University, Hangzhou, 310058, China
| | - Hui-Zeng Sun
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China.
- Ministry of Education Innovation Team of Development and Function of Animal Digestive System, Zhejiang University, Hangzhou, 310058, China.
- Ministry of Education Key laboratory of Molecular Animal Nutrition, Zhejiang University, Hangzhou, 310058, China.
| |
Collapse
|
2
|
Papadatou M, Knight M, Salta M. High-throughput method development for in-situ quantification of aquatic phototrophic biofilms. BIOFOULING 2022; 38:521-535. [PMID: 35791884 DOI: 10.1080/08927014.2022.2094259] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 06/13/2022] [Accepted: 06/21/2022] [Indexed: 06/15/2023]
Abstract
In the maritime field where biofouling has both economic and environmental impacts, in situ quantification methods of biofilm development are of outstanding importance. Indeed, it is challenging to temporally monitor biofilm formation due to the complexity of the marine ecosystem, common inaccessibility of sampling location and lack of standardized techniques. Here, an artificial polymeric surface was tested in situ and in vitro against natural phototrophic biofilms and monoculture biofilms using plate reader fluorescence. The suitability of the developed method was verified using fluorescence microscopy coupled with image analysis - a common quantification technique - demonstrating a strong correlation between the tested methods. The results indicated the efficiency of inherent chlorophyll fluorescence in quantifying undisturbed phototrophic biofilms in field and laboratory conditions using microplate reader. This work demonstrated that the suggested approach is promising for biofilm high-throughput testing, and therefore has the potential to be used in several research and industrial sectors for monitoring phototrophic biofilm development.
Collapse
Affiliation(s)
- Maria Papadatou
- School of Biological Sciences, University of Portsmouth, Portsmouth, UK
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Mollie Knight
- School of Biological Sciences, University of Portsmouth, Portsmouth, UK
| | - Maria Salta
- School of Biological Sciences, University of Portsmouth, Portsmouth, UK
- Department of MIC and Biofilm Research, Endures, Den Helder, The Netherlands
| |
Collapse
|
3
|
Alarcón-Vivero M, Moena NRT, Gonzalez F, Jopia-Contreras P, Aspé E, Briones HU, Fernandez KS. Anaerobic biofilm enriched with an ammonia tolerant methanogenic consortium to improve wastewater treatment in the fishing industry. Biotechnol Lett 2022; 44:239-251. [PMID: 35037233 DOI: 10.1007/s10529-021-03213-y] [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: 06/21/2021] [Accepted: 11/29/2021] [Indexed: 11/29/2022]
Abstract
The digestion efficiency of liquid industrial wastes increases when using bioreactors colonized by microbial biofilms. High concentrations of proteins derived from the fish processing industry lead to the production of ammonia, which inhibits methane production. Two bioreactors were constructed to compare methanogenic activity: one enriched with mMPA (methylaminotrofic methane production archaea) consortia (control bioreactor), and the second with NH3 tolerant consortia (treatment bioreactor). Ammonia tolerant activity was assessed by applying an ammonia shock (755 mg NH3/L). Methane production, consumption of total organic carbon (TOC) and the taxonomic composition of bacteria and archaea was evaluated using 16S rDNA in the acclimatization, ammonia shock, and recovery phases.The ammonia shock significantly affected both methane production and the consumption of TOC in the control reactor (p < 0.05) and taxonomical composition of the microbial consortia (OTU). These values remained constant in the treatment reactor. The analysis of biofilm composition showed a predominance of Methanosarcinaceae (Methanomethylovorans sp., and probably two different species of Methanosarcina sp.) in bioreactors. These results demonstrate that using acclimated biofilms enriched with ammonia tolerant methanogens control the inhibitory effect of ammonia on methanogenesis.
Collapse
Affiliation(s)
- Manuel Alarcón-Vivero
- Instituto de Acuicultura, Universidad Austral de Chile (UACh), Sede Puerto Montt, Puerto Montt, Chile
| | - Nathaly Ruiz-Tagle Moena
- Lab. Biopelículas y Microbiología Ambiental, Centro de Biotecnología, Universidad de Concepción, Concepción, Chile
| | - Fidelina Gonzalez
- Departamento de Biología Celular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | | | - Estrella Aspé
- Departamento de Ingeniería Química, Facultad de Ingeniería, Universidad de Concepción, Concepción, Chile
| | - Homero Urrutia Briones
- Lab. Biopelículas y Microbiología Ambiental, Centro de Biotecnología, Universidad de Concepción, Concepción, Chile.,Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Katherine Sossa Fernandez
- Lab. Biopelículas y Microbiología Ambiental, Centro de Biotecnología, Universidad de Concepción, Concepción, Chile. .,Facultad de Ciencias Forestales, Universidad de Concepción, Concepción, Chile.
| |
Collapse
|
4
|
Wang B, Li H, Liu T, Guo J. Enhanced removal of cephalexin and sulfadiazine in nitrifying membrane-aerated biofilm reactors. CHEMOSPHERE 2021; 263:128224. [PMID: 33297180 DOI: 10.1016/j.chemosphere.2020.128224] [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: 06/29/2020] [Revised: 08/27/2020] [Accepted: 08/30/2020] [Indexed: 05/06/2023]
Abstract
Nitrification process has been reported to be capable of degrading various pharmaceuticals due to the cometabolism of ammonia-oxidizing bacteria (AOB). The membrane aerated biofilm reactor (MABR) is an emerging configuration in wastewater treatment with advantages of high nitrification rate and low energy consumption. However, there are very few studies investigating the degradation of antibiotics at environmentally relevant levels in nitrifying MABR systems. In this study, the removal of two widely used antibiotics, cephalexin (CFX) and sulfadiazine (SDZ), was evaluated in two independent MABRs with nitrifying biofilms. The impacts of CFX and SDZ exposure on the nitrification performance and microbial community structure within biofilms were also investigated. The results showed that nitrifying biofilms were very efficient in removing CFX (94.6%) and SDZ (75.4%) with an initial concentration of 100 μg/L when hydraulic retention time (HRT) was 4 h in the reactors. When HRT decreased from 4 h to 3 h, the removal rates of CFX and SDZ increased significantly from 23.4 ± 1.0 μg/(L·h) and 18.7 ± 1.1 μg/(L·h), respectively, to 27.7 ± 1.3 μg/(L·h) (p<0.01) and 20.8 ± 2.4 μg/(L·h) (p<0.05), while the removal efficiencies decreased to 86.0% and 61.5%, respectively. Despite the exposure to CFX and SDZ, the nitrification performance was not affected, and microbial community structure within biofilms also remained relatively stable. This study shows that nitrifying MABR process is a promising option for the efficient removal of antibiotics from domestic wastewater.
Collapse
Affiliation(s)
- Bingzheng Wang
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD, 4072, Australia
| | - Huayu Li
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD, 4072, Australia; Beijing Key Laboratory of Aqueous Typical Pollutants Control and Water Quality Safeguard, Department of Municipal and Environmental Engineering, Beijing Jiaotong University, Beijing, 100044, China
| | - Tao Liu
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD, 4072, Australia
| | - Jianhua Guo
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD, 4072, Australia.
| |
Collapse
|
5
|
Stahl DA. The path leading to the discovery of the ammoniaoxidizing archaea. Environ Microbiol 2020; 22:4507-4519. [PMID: 32955155 DOI: 10.1111/1462-2920.15239] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 09/16/2020] [Indexed: 11/28/2022]
Affiliation(s)
- David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, 98195, USA
| |
Collapse
|
6
|
Liu T, Guo J, Hu S, Yuan Z. Model-based investigation of membrane biofilm reactors coupling anammox with nitrite/nitrate-dependent anaerobic methane oxidation. ENVIRONMENT INTERNATIONAL 2020; 137:105501. [PMID: 32032775 DOI: 10.1016/j.envint.2020.105501] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 01/13/2020] [Accepted: 01/16/2020] [Indexed: 05/28/2023]
Abstract
An innovative process coupling anaerobic ammonium oxidation (anammox) with nitrite/nitrate-dependent anaerobic methane oxidation (n-DAMO) in membrane biofilm reactors (MBfRs) has been developed to achieve high-level nitrogen removal from both sidestream (i.e., anaerobic digestion liquor) and mainstream (i.e., domestic strength) wastewater. In this study, a 1D biofilm model embedding the n-DAMO and anammox reactions was developed to facilitate further understanding of the process and its optimization. The model was calibrated and validated using comprehensive data sets from two independent MBfRs, treating sidestream- and mainstream-strength wastewater, respectively. Modelling results revealed a unique biofilm stratification. While anammox bacteria dominated throughout the biofilm, n-DAMO archaea (coupling nitrate reduction with anaerobic methane oxidation) only occurred at the inner layer and n-DAMO bacteria (coupling nitrite reduction with anaerobic methane oxidation) spread more evenly with a slightly higher fraction in the outer layer. The established MBfRs were robust against dynamic influent flowrates and nitrite/ammonium ratios. Thicker biofilms were beneficial for not only the total nitrogen (TN) removal but also the system robustness. Additionally, a positive correlation between the nitrogen removal efficiency and the residual methane emission was observed, as a result of higher methane partial pressure required. However, there was a threshold of methane partial pressure, above which the residual methane increased but nitrogen removal efficiency was stable. Meanwhile, thicker biofilms were also favorable to achieve less residual methane emission. Simulation results also suggested the feasibility of methane-based MBfRs to polish mainstream anammox effluent to meet a stringent N discharge standard (e.g., TN < 5 mg/L).
Collapse
Affiliation(s)
- Tao Liu
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Jianhua Guo
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Shihu Hu
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Zhiguo Yuan
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Queensland 4072, Australia.
| |
Collapse
|
7
|
Westphal A, Eichinger F, Eichinger L, Würdemann H. Change in the microbial community of saline geothermal fluids amended with a scaling inhibitor: effects of heat extraction and nitrate dosage. Extremophiles 2019; 23:283-304. [PMID: 30778766 DOI: 10.1007/s00792-019-01080-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 01/29/2019] [Indexed: 11/27/2022]
Abstract
Geothermal plants are often affected by corrosion caused by microbial metabolites such as H2S. In the Bad Blumau (Austria) geothermal system, an increase in microbially produced H2S was observed in the hot (107 °C) and scaling inhibitor-amended saline fluids and in fluids that had cooled down (45 °C). Genetic fingerprinting and quantification revealed the dominance, increasing abundance and diversity of sulfate reducers such as Desulfotomaculum spp. that accompanied the cooling and processing of the geothermal fluids. In addition, a δ34S isotopic signature showed the microbial origin of the H2S that has been produced either chemolithotrophically or chemoorganotrophically. A nitrate addition test in a test pipe as a countermeasure against the microbial H2S formation caused a shift from a biocenosis dominated by bacteria of the phylum Firmicutes to a community of Firmicutes and Proteobacteria. Nitrate supported the growth of nitrate-reducing sulfur-oxidizing Thiobacillus thioparus, which incompletely reduced nitrate to nitrite. The addition of nitrate led to a change in the composition of the sulfate-reducing community. As a result, representatives of nitrate- and nitrite-reducing SRB, such as Desulfovibrio and Desulfonatronum, emerged as additional community members. The interaction of sulfate-reducing bacteria and nitrate-reducing sulfur-oxidizing bacteria (NR-SOB) led to the removal of H2S, but increased the corrosion rate in the test pipe.
Collapse
Affiliation(s)
- Anke Westphal
- Section 5.3 Geomicrobiology, GFZ German Research Centre for Geosciences, Telegrafenberg, 14473, Potsdam, Germany
| | | | - Lorenz Eichinger
- HYDROISOTOP GmbH, Woelkestr. 9, 85301, Schweitenkirchen, Germany
| | - Hilke Würdemann
- Section 5.3 Geomicrobiology, GFZ German Research Centre for Geosciences, Telegrafenberg, 14473, Potsdam, Germany. .,Department of Engineering and Natural Sciences, University of Applied Science Merseburg, Eberhard-Leibnitz-Str. 2, 06217, Merseburg, Germany.
| |
Collapse
|
8
|
Meeroff DE, Shaha B, Bloetscher F, Esiobu N, Mercer B, McCorquordale D, Kari R, Bennett M. Characterization of Biofilms and Mineralogical Scale in Underground Injection Well Disposal of Landfill Leachate and Industrial Wastewater Streams. ACTA ACUST UNITED AC 2019. [DOI: 10.4236/gep.2019.711006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
9
|
Kannan P, Su SS, Mannan MS, Castaneda H, Vaddiraju S. A Review of Characterization and Quantification Tools for Microbiologically Influenced Corrosion in the Oil and Gas Industry: Current and Future Trends. Ind Eng Chem Res 2018. [DOI: 10.1021/acs.iecr.8b02211] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Pranav Kannan
- Mary Kay O’Connor Process Safety Center, Texas A&M University System, 3122 TAMU, College Station, Texas 77843-3122, United States
- Artie McFerrin Department of Chemical Engineering, Texas A&M University System, 3122 TAMU, College Station, Texas 77843-3122, United States
| | - Shei Sia Su
- National Corrosion and Materials Reliability Laboratory, Texas A&M University, College Station, Texas 77843-3003, United States
- Materials Science and Engineering Department, Texas A&M University, College Station, Texas 77843-3003, United States
| | - M. Sam Mannan
- Mary Kay O’Connor Process Safety Center, Texas A&M University System, 3122 TAMU, College Station, Texas 77843-3122, United States
- Artie McFerrin Department of Chemical Engineering, Texas A&M University System, 3122 TAMU, College Station, Texas 77843-3122, United States
| | - Homero Castaneda
- National Corrosion and Materials Reliability Laboratory, Texas A&M University, College Station, Texas 77843-3003, United States
- Materials Science and Engineering Department, Texas A&M University, College Station, Texas 77843-3003, United States
| | - Sreeram Vaddiraju
- Mary Kay O’Connor Process Safety Center, Texas A&M University System, 3122 TAMU, College Station, Texas 77843-3122, United States
- Artie McFerrin Department of Chemical Engineering, Texas A&M University System, 3122 TAMU, College Station, Texas 77843-3122, United States
| |
Collapse
|
10
|
Jia Y, Khanal SK, Zhang H, Chen GH, Lu H. Sulfamethoxazole degradation in anaerobic sulfate-reducing bacteria sludge system. WATER RESEARCH 2017; 119:12-20. [PMID: 28433879 DOI: 10.1016/j.watres.2017.04.040] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 03/23/2017] [Accepted: 04/15/2017] [Indexed: 06/07/2023]
Abstract
Sulfamethoxazole (SMX) is one of the most commonly used antibiotics. SMX degradation in sulfate-reducing bacteria (SRB) sludge systems has not been reported so far. This research investigated the SMX degradation using SRB sludge in a sulfate-reducing up-flow sludge bed reactor. Moreover, the mechanisms and kinetics of SMX removal were also investigated using SRB sludge via a series of batch experiments. The results showed that SMX removal was characterized by a rapid sorption onto SRB sludge, and desorption from SRB sludge to aqueous phase until achieving equilibrium, and then followed by slow biodegradation. Biodegradation was the dominant route for SMX removal. The sorption process conformed well to a pseudo-second-order kinetic model, meaning that the sorption occurred primarily via a chemical sorption process. The removal of SMX followed the pseudo-zero-order kinetic model with a specific removal rate of 13.2 ± 0.1 μg/L/d at initial SMX concentration 100 μg/L in batch tests. Based on the analysis of metabolites, most of the SMX biotransformation products' structures altered in the isoxazole ring, which were significantly different from that produced by aerobic and anaerobic sludge systems. Thus, SRB sludge system could play an important role in SMX biodegradation, especially in Sulfate-reduction Autotrophic denitrification and Nitrification Integrated (SANI) process for sewage treatment.
Collapse
Affiliation(s)
- Yanyan Jia
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology (Sun Yat-sen University), Guangzhou, 510275, China
| | - Samir Kumar Khanal
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, USA
| | - Huiqun Zhang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology (Sun Yat-sen University), Guangzhou, 510275, China
| | - Guang-Hao Chen
- Department of Civil and Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Hui Lu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology (Sun Yat-sen University), Guangzhou, 510275, China.
| |
Collapse
|
11
|
Costa AM, Mergulhão FJ, Briandet R, Azevedo NF. It is all about location: how to pinpoint microorganisms and their functions in multispecies biofilms. Future Microbiol 2017; 12:987-999. [PMID: 28745517 DOI: 10.2217/fmb-2017-0053] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Multispecies biofilms represent the dominant mode of life for the vast majority of microorganisms. Bacterial spatial localization in such biostructures governs ecological interactions between different populations and triggers the overall community functions. Here, we discuss the pros and cons of fluorescence-based techniques used to decipher bacterial species patterns in biofilms at single cell level, including fluorescence in situ hybridization and the use of genetically modified bacteria that express fluorescent proteins, reporting the significant improvements of those techniques. The development of tools for spatial and temporal study of multispecies biofilms will allow live imaging and spatial localization of cells in naturally occurring biofilms coupled with metabolic information, increasing insight of microbial community and the relation between its structure and functions.
Collapse
Affiliation(s)
- Angela M Costa
- LEPABE, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal.,i3S - Instituto de Investigação e Inovação em Saúde, University of Porto, Portugal.,INEB - Institute of Biomedical Engineering, University of Porto, Porto, Portugal
| | - Filipe J Mergulhão
- LEPABE, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Romain Briandet
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Nuno F Azevedo
- LEPABE, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| |
Collapse
|
12
|
Martínez-Porchas M, Vargas-Albores F. An efficient strategy using k-mers to analyse 16S rRNA sequences. Heliyon 2017; 3:e00370. [PMID: 28795166 PMCID: PMC5537200 DOI: 10.1016/j.heliyon.2017.e00370] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 07/11/2017] [Accepted: 07/21/2017] [Indexed: 11/28/2022] Open
Abstract
The use of k-mers has been a successful strategy for improving metagenomics studies, including taxonomic classifications, or de novo assemblies, and can be used to obtain sequences of interest from the available databases. The aim of this manuscript was to propose a simple but efficient strategy to generate k-mers and to use them to obtain and analyse in silico 16S rRNA sequence fragments. A total of 513,309 bacterial sequences contained in the SILVA database were considered for the study, and homemade PHP scripts were used to search for specific nucleotide chains, recover fragments of bacterial sequences, make calculations and organize information. Consensus sequences matching conserved regions were constructed by aligning most of the primers used in the literature. Sequences of k nucleotides (9- to 15-mers) were extracted from the generated primer contigs. Frequency analysis revealed that k-mer size was inversely proportional to the occurrence of k-mers in the different conserved regions, suggesting a stringency relationship; high numbers of duplicate reactions were observed with short k-mers, and a lower proportion of sequences were obtained with large ones, with the best results obtained using 12-mers. Using 12-mers with the proposed method to obtain and study sequences was found to be a reliable approach for the analysis of 16S rRNA sequences and this strategy may probably be extended to other biomarkers. Furthermore, additional applications such as evaluating the degree of conservation and designing primers and other calculations are proposed as examples.
Collapse
Affiliation(s)
| | - Francisco Vargas-Albores
- Centro de Investigación en Alimentación y Desarrollo, A. C. Km 0.6 Carretera a La Victoria. Hermosillo, Sonora, México
| |
Collapse
|
13
|
Martinez-Porchas M, Villalpando-Canchola E, Ortiz Suarez LE, Vargas-Albores F. How conserved are the conserved 16S-rRNA regions? PeerJ 2017; 5:e3036. [PMID: 28265511 PMCID: PMC5333541 DOI: 10.7717/peerj.3036] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 01/26/2017] [Indexed: 12/20/2022] Open
Abstract
The 16S rRNA gene has been used as master key for studying prokaryotic diversity in almost every environment. Despite the claim of several researchers to have the best universal primers, the reality is that no primer has been demonstrated to be truly universal. This suggests that conserved regions of the gene may not be as conserved as expected. The aim of this study was to evaluate the conservation degree of the so-called conserved regions flanking the hypervariable regions of the 16S rRNA gene. Data contained in SILVA database (release 123) were used for the study. Primers reported as matches of each conserved region were assembled to form contigs; sequences sizing 12 nucleotides (12-mers) were extracted from these contigs and searched into the entire set of SILVA sequences. Frequency analysis shown that extreme regions, 1 and 10, registered the lowest frequencies. 12-mer frequencies revealed segments of contigs that were not as conserved as expected (≤90%). Fragments corresponding to the primer contigs 3, 4, 5b and 6a were recovered from all sequences in SILVA database. Nucleotide frequency analysis in each consensus demonstrated that only a small fraction of these so-called conserved regions is truly conserved in non-redundant sequences. It could be concluded that conserved regions of the 16S rRNA gene exhibit considerable variation that has to be considered when using this gene as biomarker.
Collapse
|
14
|
Pozo G, Jourdin L, Lu Y, Keller J, Ledezma P, Freguia S. Cathodic biofilm activates electrode surface and achieves efficient autotrophic sulfate reduction. Electrochim Acta 2016. [DOI: 10.1016/j.electacta.2016.07.100] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
15
|
Ye C, Yang X, Zhao FJ, Ren L. The shift of the microbial community in activated sludge with calcium treatment and its implication to sludge settleability. BIORESOURCE TECHNOLOGY 2016; 207:11-18. [PMID: 26868150 DOI: 10.1016/j.biortech.2016.01.135] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 01/27/2016] [Accepted: 01/31/2016] [Indexed: 06/05/2023]
Abstract
The sludge settleability is of prime importance for the activated sludge process. The effect of calcium ion on the biological performance of sludge was investigated in a lab-scale activated sludge system with varying Ca(2+) concentration. Results indicated that addition of 150mg/L Ca(2+) to the influent significantly improved the settling characteristics and metabolic reactivity of activated sludge in the bioreactors. Analyses using denaturing gradient gel electrophoresis (DGGE) and 16S rRNA sequencing showed that a significant difference in the presence of certain bacterial groups between the sludge systems with 150mg/L Ca(2+) and those with 0-100mg/L Ca(2+) addition. Ca(2+) also increased the production of the extracellular polymeric substance (EPS) and facilitated the development of microbial cluster in the bioreactor. Study showed that an addition of 150mg/L Ca(2+) to the influent provides a simple approach to improve the settling properties of activated sludge and maintain high pollutant removal efficiency.
Collapse
Affiliation(s)
- Chengchen Ye
- Jiangsu Key Laboratory for Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xinping Yang
- Jiangsu Key Laboratory for Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Fang-Jie Zhao
- Jiangsu Key Laboratory for Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China; Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
| | - Lifei Ren
- Jiangsu Key Laboratory for Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| |
Collapse
|
16
|
Karunakaran E, Vernon D, Biggs CA, Saul A, Crawford D, Jensen H. Enumeration of sulphate-reducing bacteria for assessing potential for hydrogen sulphide production in urban drainage systems. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2016; 73:3087-3094. [PMID: 27332857 DOI: 10.2166/wst.2016.026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Urban drainage structures have increasing demands which can lead to increasing hydrogen sulphide related problems forming in places where they have not previously been prevalent. This puts pressure on the methods currently used to monitor and diagnose these problems and more sophisticated methods may be needed for identifying the origin of the problems. Molecular microbiological techniques, such as quantitative polymerase chain reaction, offer a potential alternative for identifying and quantifying bacteria likely to be causing the production of hydrogen sulphide, information that, when combined with an appropriate sampling programme, can then be used to identify the potentially most effective remediation technique. The application of these methods in urban drainage systems is, however, not always simple, but good results can be achieved. In this study bacteria producing hydrogen sulphide were quantified in three small combined sewer overflow storage tanks. Bacterial counts were compared between wastewater, biofilms and sediments. Similar numbers were found in the wastewater and biofilms, with the numbers in the sediments being lower. If remediation methods for hydrogen sulphide are deemed necessary in the tanks, methods that target both the wastewater and the biofilms should therefore be considered.
Collapse
Affiliation(s)
- Esther Karunakaran
- Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield S1 3JD, UK E-mail:
| | - Dejan Vernon
- Innovation, Thames Water, Reading STW, Reading RG2 0RP, UK
| | - Catherine A Biggs
- Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield S1 3JD, UK E-mail:
| | - Adrian Saul
- Department of Civil and Structural Engineering, University of Sheffield, Mappin Street, Sheffield S1 3JD, UK
| | - David Crawford
- Thames Tideway Tunnel Limited, North Wharf Road, London W2 1AF, UK
| | - Henriette Jensen
- Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield S1 3JD, UK E-mail:
| |
Collapse
|
17
|
Hao T, Luo J, Wei L, Mackey HR, Liu R, Rey Morito G, Chen GH. Physicochemical and biological characterization of long-term operated sulfate reducing granular sludge in the SANI® process. WATER RESEARCH 2015; 71:74-84. [PMID: 25600299 DOI: 10.1016/j.watres.2014.12.051] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2014] [Revised: 09/26/2014] [Accepted: 12/29/2014] [Indexed: 06/04/2023]
Abstract
The SANI(®) process (Sulfate reduction, Autotrophic denitrification and Nitrification Integrated) is a treatment system with low energy demands. The major bioreactor of this new technology is a sulfate-reducing up-flow sludge bed (SRUSB) that converts organics and provides electron donors for subsequent autotrophic denitrification. This research characterizes the granules inside the SRUSB, with the aim of improving its efficiency, maximizing its operational flexibility, and minimizing its footprint. The unique sulfate-reducing bacteria (SRB) granules serving in the SRUSB were found to increase the resilience and compactness of the SRUSB. The granules, with a compact and porous structure, showed high cohesion resisting breakage with a shear force G > 3400 s(-1). The hydrophobicity of the external surface of the mature granules remained stable at around 70% and acid volatile sulfide (AVS) accumulated at the bottom of the SRUSB. 16s rRNA gene analysis of the microbial communities revealed that Desulfobulbus (42.1%), Prosthecochloris (19%) and Trichococcus (12%) dominated the mature granular sludge. Fluorescence in situ hybridization (FISH) further showed that SRB organisms were located internally and then surrounded by non-SRB. According to the FISH results, the spatial distribution of extracellular polymeric substances (EPS) displayed protein and α-polysaccharides in the exterior and β-polysaccharide in the core of the granules. Such biological structure suggests that each SRB granule acts as an efficient and independent unit, capable of achieving both fermentation and organic conversion. The present investigation sheds light on the physicochemical and biological characteristics of the SRB granulate. This information provides valuable information for scaling-up the SANI(®) process to treat real saline sewage in Hong Kong.
Collapse
Affiliation(s)
- Tianwei Hao
- Department of Civil & Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Jinghai Luo
- Department of Civil & Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Li Wei
- Department of Civil & Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Hamish R Mackey
- Department of Civil & Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Rulong Liu
- Department of Civil & Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Guillermo Rey Morito
- Department of Civil & Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Guang-Hao Chen
- Department of Civil & Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong; SYSU-HKUST Research Centre for Innovative Environmental Technology, Sun Yat-sen University, Guangzhou, China.
| |
Collapse
|
18
|
Lienen T, Kleyböcker A, Verstraete W, Würdemann H. Moderate temperature increase leads to disintegration of floating sludge and lower abundance of the filamentous bacterium Microthrix parvicella in anaerobic digesters. WATER RESEARCH 2014; 65:203-212. [PMID: 25117937 DOI: 10.1016/j.watres.2014.07.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 06/21/2014] [Accepted: 07/12/2014] [Indexed: 06/03/2023]
Abstract
Filamentous bacteria such as Microthrix parvicella can cause serious foaming and floating sludge problems in anaerobic digesters fed with sewage sludge. The sewage sludge and oil co-fermenting laboratory-scale biogas digesters in this study were fed with substrates from a foaming-prone full-scale biogas plant containing the filamentous bacterium M. parvicella. At 37 °C, in both pneumatically mixed digesters a highly viscous and approximately 3 cm thick floating sludge was observed. A gradual increase of the temperature from 37 °C to 56 °C led to a significant decrease in the floating sludge thickness, which correlated with a strong decrease in the abundance of M. parvicella in the digestate. Furthermore, the stepwise temperature increase allowed for an adaption of the microbial community and prevented process failure. The study indicates that already a moderate temperature increase from 37 °C to 41 °C might help to control the M. parvicella abundance in full-scale biogas plants.
Collapse
Affiliation(s)
- T Lienen
- GFZ German Research Centre for Geosciences, Section 4.5 Geomicrobiology, 14473 Potsdam, Germany.
| | - A Kleyböcker
- GFZ German Research Centre for Geosciences, Section 4.5 Geomicrobiology, 14473 Potsdam, Germany.
| | - W Verstraete
- LabMET, Ghent University, Coupure Links 653, B-9000 Gent, Belgium.
| | - H Würdemann
- GFZ German Research Centre for Geosciences, Section 4.5 Geomicrobiology, 14473 Potsdam, Germany.
| |
Collapse
|
19
|
Flahou B, Modrý D, Pomajbíková K, Petrželková KJ, Smet A, Ducatelle R, Pasmans F, Sá RM, Todd A, Hashimoto C, Mulama M, Kiang J, Rossi M, Haesebrouck F. Diversity of zoonotic enterohepatic Helicobacter species and detection of a putative novel gastric Helicobacter species in wild and wild-born captive chimpanzees and western lowland gorillas. Vet Microbiol 2014; 174:186-94. [PMID: 25248691 DOI: 10.1016/j.vetmic.2014.08.032] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 08/26/2014] [Accepted: 08/30/2014] [Indexed: 02/01/2023]
Abstract
A number of Helicobacter species cause gastrointestinal or hepatic disease in humans, including H. pylori, gastric non-H. pylori helicobacters from animal origin and enterohepatic Helicobacter species. Little is known on the presence of Helicobacter species in great apes, our closest living relatives and potential reservoirs of microorganisms that might emerge in humans. The aim of the present study was to investigate the presence of gastric and enterohepatic Helicobacter species in African chimpanzees and gorillas. Fresh fecal samples were collected from wild endangered chimpanzees and critically endangered western lowland gorillas from different African National Parks, as well as wild-born captive animals from primate sanctuaries. Intact Helicobacter bacteria were demonstrated in feces by fluorescence in situ hybridization. Screening using a Helicobacter genus-specific PCR revealed the presence of Helicobacter DNA in the majority of animals in all groups. Cloning and sequencing of 16S rRNA gene fragments revealed a high homology to sequences from various zoonotic enterohepatic Helicobacter species, including H. cinaedi and H. canadensis. A number of gorillas and chimpanzees also tested positive using PCR assays designed to amplify part of the ureAB gene cluster and the hsp60 gene of gastric helicobacters. Phylogenetic analysis revealed the presence of a putative novel zoonotic gastric Helicobacter taxon/species. For this species, we propose the name 'Candidatus Helicobacter homininae', pending isolation and further genetic characterization. The presence of several Helicobacter species not only implies a possible health threat for these endangered great apes, but also a possible zoonotic transmission of gastric and enterohepatic helicobacters from these primate reservoirs to humans.
Collapse
Affiliation(s)
- Bram Flahou
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium.
| | - David Modrý
- Department of Pathology and Parasitology, Faculty of Veterinary Medicine, University of Brno, Palackeho 1-3, 612 42 Brno, Czech Republic; Biology Center, Institute of Parasitology, Academy of Sciences of the Czech Republic, Branišovská 31, CZ-370 05 České Budějovice, Czech Republic; CEITEC, Central European Institute of Technology, University of Veterinary and Pharmaceutical Sciences, Hudcova 70, 621 00 Brno, Czech Republic
| | - Kateřina Pomajbíková
- Department of Pathology and Parasitology, Faculty of Veterinary Medicine, University of Brno, Palackeho 1-3, 612 42 Brno, Czech Republic; Biology Center, Institute of Parasitology, Academy of Sciences of the Czech Republic, Branišovská 31, CZ-370 05 České Budějovice, Czech Republic
| | - Klára J Petrželková
- Department of Pathology and Parasitology, Faculty of Veterinary Medicine, University of Brno, Palackeho 1-3, 612 42 Brno, Czech Republic; Biology Center, Institute of Parasitology, Academy of Sciences of the Czech Republic, Branišovská 31, CZ-370 05 České Budějovice, Czech Republic; Department of Mammal Ecology, Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Kvetna 8, 603 65 Brno, Czech Republic; Liberec ZOO, Masarykova 1347/31, 460 01 Liberec, Czech Republic
| | - Annemieke Smet
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Richard Ducatelle
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Frank Pasmans
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Rui M Sá
- Department of Pathology and Parasitology, Faculty of Veterinary Medicine, University of Brno, Palackeho 1-3, 612 42 Brno, Czech Republic; Centre for Research in Anthropology, ISCTE-Instituto Universitário de Lisboa, Av. Forças Armadas, 1649-026 Lisboa, Portugal
| | - Angelique Todd
- WWF, Dzanga Sangha Protected Areas, Bangui, Central African Republic
| | - Chie Hashimoto
- Primate Research Institute, Kyoto University, Kanrin, Inuyama, Aichi 484-8506, Japan
| | - Martin Mulama
- Sweetwaters Chimpanzee Sanctuary, Ol Pejeta Conservancy, 10400 Nanyuki, Kenya
| | | | - Mirko Rossi
- Department of Food Health and Environmental Hygiene, Faculty of Veterinary Medicine, University of Helsinki, PO Box 66 (Agnes Sjöberginkatu 2), FI-00014 Helsinki, Finland
| | - Freddy Haesebrouck
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| |
Collapse
|
20
|
Madden P, Al-Raei AM, Enright AM, Chinalia FA, de Beer D, O'Flaherty V, Collins G. Effect of sulfate on low-temperature anaerobic digestion. Front Microbiol 2014; 5:376. [PMID: 25120534 PMCID: PMC4110509 DOI: 10.3389/fmicb.2014.00376] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 07/03/2014] [Indexed: 11/13/2022] Open
Abstract
The effect of sulfate addition on the stability of, and microbial community behavior in, low-temperature anaerobic expanded granular sludge bed-based bioreactors was investigated at 15°C. Efficient bioreactor performance was observed, with chemical oxygen demand (COD) removal efficiencies of >90%, and a mean SO2−4 removal rate of 98.3%. In situ methanogensis appeared unaffected at a COD: SO2−4 influent ratio of 8:1, and subsequently of 3:1, and was impacted marginally only when the COD: SO2−4 ratio was 1:2. Specific methanogenic activity assays indicated a complex set of interactions between sulfate-reducing bacteria (SRB), methanogens and homoacetogenic bacteria. SO2−4 addition resulted in predominantly acetoclastic, rather than hydrogenotrophic, methanogenesis until >600 days of SO2−4-influenced bioreactor operation. Temporal microbial community development was monitored by denaturation gradient gel electrophoresis (DGGE) of 16S rRNA genes. Fluorescence in situ hybridizations (FISH), qPCR and microsensor analysis were combined to investigate the distribution of microbial groups, and particularly SRB and methanogens, along the structure of granular biofilms. qPCR data indicated that sulfidogenic genes were present in methanogenic and sulfidogenic biofilms, indicating the potential for sulfate reduction even in bioreactors not exposed to SO2−4. Although the architecture of methanogenic and sulfidogenic granules was similar, indicating the presence of SRB even in methanogenic systems, FISH with rRNA targets found that the SRB were more abundant in the sulfidogenic biofilms. Methanosaeta species were the predominant, keystone members of the archaeal community, with the complete absence of the Methanosarcina species in the experimental bioreactor by trial conclusion. Microsensor data suggested the ordered distribution of sulfate reduction and sulfide accumulation, even in methanogenic granules.
Collapse
Affiliation(s)
- Pádhraig Madden
- Microbiology, School of Natural Sciences, National University of Ireland Galway Galway, Ireland
| | - Abdul M Al-Raei
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology Bremen, Germany
| | - Anne M Enright
- Microbiology, School of Natural Sciences, National University of Ireland Galway Galway, Ireland
| | - Fabio A Chinalia
- Centre for Resource Management and Efficiency, School of Applied Science, Cranfield University Bedfordshire, UK
| | - Dirk de Beer
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology Bremen, Germany
| | - Vincent O'Flaherty
- Microbiology, School of Natural Sciences, National University of Ireland Galway Galway, Ireland ; Ryan Institute for Environmental, Marine and Energy Research, National University of Ireland Galway Galway, Ireland
| | - Gavin Collins
- Microbiology, School of Natural Sciences, National University of Ireland Galway Galway, Ireland ; Ryan Institute for Environmental, Marine and Energy Research, National University of Ireland Galway Galway, Ireland ; Infrastructure and Environment, School of Engineering, University of Glasgow UK
| |
Collapse
|
21
|
Liu H, Tan S, Sheng Z, Liu Y, Yu T. Bacterial community structure and activity of sulfate reducing bacteria in a membrane aerated biofilm analyzed by microsensor and molecular techniques. Biotechnol Bioeng 2014; 111:2155-62. [PMID: 24890472 DOI: 10.1002/bit.25277] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 04/23/2014] [Accepted: 04/29/2014] [Indexed: 11/07/2022]
Abstract
The activities and vertical spatial distribution of sulfate reducing bacteria (SRB) in an oxygen (O2 )-based membrane aerated biofilm (MAB) were investigated using microsensor (O2 and H2 S) measurements and molecular techniques (polymerase chain reaction-denaturing gradient gel electrophoresis [PCR-DGGE] and fluorescence in situ hybridization [FISH]). The O2 concentration profile revealed that O2 penetrated from the bottom (substratum) of the gas permeable membrane, and was gradually consumed within the biofilm until it was completely depleted near the biofilm/bulk liquid interface, indicating oxic and anoxic zone in the MAB. The H2 S concentration profile showed that H2 S production was found in the upper 285 µm of the biofilm, indicating a high activity of SRB in this region. The results from DGGE of the PCR-amplified dissimilatory sulfite reductase subunit B (dsrB) gene and FISH showed an uneven spatial distribution of SRB. The maximum SRB biomass was located in the upper biofilm. The information from the molecular analysis can be supplemented with that from microsensor measurements to better understand the microbial community and activity of SRB in the MAB.
Collapse
Affiliation(s)
- Hong Liu
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta, Canada, T6G 2W2
| | | | | | | | | |
Collapse
|
22
|
Krüger M, Shehata AA, Grosse-Herrenthey A, Ständer N, Schrödl W. Relationship between gastrointestinal dysbiosis and Clostridium botulinum in dairy cows. Anaerobe 2014; 27:100-5. [PMID: 24747040 DOI: 10.1016/j.anaerobe.2014.03.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 03/25/2014] [Accepted: 03/27/2014] [Indexed: 01/16/2023]
Abstract
The gastrointestinal tract is a balanced ecosystem that can get out of balance and predisposed to clostridial diseases or other pathological conditions. The objective of the present study was to evaluate the gut microbiota in dairy cows suffering from chronic botulism. Cows were investigated for Clostridium (C.) botulinum in faeces and rumen fluids. In order to study the relationship between botulism and gastrointestinal microbiota, faeces and rumen fluid were tested for bacterial composition using conventional microbiological culture techniques and fluorescence in situ hybridization (FISH). Protozoa were analyzed in rumen fluid microscopically. The presence of C. botulinum was associated with specific changes in the faecal microbiota, especially a significant reduction of total aerobic bacteria, total anaerobic bacteria, enterococci, Clostridium perfringens and yeast and fungi. Also C. botulinum positive rumen fluid had significantly more Bacteroides spp., C. histolyticum group, Alfa- proteobacteria, Gammaproteobacteria, and sulfate-reducing bacteria; as well as significantly fewer Euryaracheota, and the protozoa Epidinium spp. Dasytricha spp., Diplodiniinae spp. and Ophryoscolex spp. In conclusion, C. botulinum is common in dairy cows in Germany but the incidence of botulism is associated with microbial changes and composition in the gastrointestinal tract. Bacteria, yeast and protozoa appear to be crucial in the colonization process; however, the chronology of these events and role of each microbial group needs further evaluation.
Collapse
Affiliation(s)
- Monika Krüger
- Institute of Bacteriology and Mycology, Faculty of Veterinary Medicine, Leipzig University, An den Tierkliniken 29, 04103 Leipzig, Germany
| | - Awad A Shehata
- Institute of Bacteriology and Mycology, Faculty of Veterinary Medicine, Leipzig University, An den Tierkliniken 29, 04103 Leipzig, Germany; Avian and Rabbit Diseases Department, Faculty of Veterinary Medicine, Sadat City University, Egypt.
| | - Anke Grosse-Herrenthey
- Institute of Bacteriology and Mycology, Faculty of Veterinary Medicine, Leipzig University, An den Tierkliniken 29, 04103 Leipzig, Germany
| | - Norman Ständer
- Institute of Bacteriology and Mycology, Faculty of Veterinary Medicine, Leipzig University, An den Tierkliniken 29, 04103 Leipzig, Germany
| | - Wieland Schrödl
- Institute of Bacteriology and Mycology, Faculty of Veterinary Medicine, Leipzig University, An den Tierkliniken 29, 04103 Leipzig, Germany
| |
Collapse
|
23
|
Liang R, Grizzle RS, Duncan KE, McInerney MJ, Suflita JM. Roles of thermophilic thiosulfate-reducing bacteria and methanogenic archaea in the biocorrosion of oil pipelines. Front Microbiol 2014; 5:89. [PMID: 24639674 PMCID: PMC3944610 DOI: 10.3389/fmicb.2014.00089] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2013] [Accepted: 02/18/2014] [Indexed: 11/13/2022] Open
Abstract
Thermophilic sulfide-producing microorganisms from an oil pipeline network were enumerated with different sulfur oxyanions as electron acceptors at 55°C. Most-probable number (MPN) analysis showed that thiosulfate-reducing bacteria were the most numerous sulfidogenic microorganisms in pipeline inspection gauge (PIG) scrapings. Thiosulfate-reducing and methanogenic enrichments were obtained from the MPN cultures that were able to use yeast extract as the electron donor. Molecular analysis revealed that both enrichments harbored the same dominant bacterium, which belonged to the genus Anaerobaculum. The dominant archaeon in the methanogenic enrichment was affiliated with the genus Methanothermobacter. With yeast extract as the electron donor, the general corrosion rate by the thiosulfate-reducing enrichment (8.43 ± 1.40 milli-inch per year, abbreviated as mpy) was about 5.5 times greater than the abiotic control (1.49 ± 0.15 mpy), while the comparable measures for the methanogenic culture were 2.03 ± 0.49 mpy and 0.62 ± 0.07 mpy, respectively. Total iron analysis in the cultures largely accounted for the mass loss of iron measured in the weight loss determinations. Profilometry analysis of polished steel coupons incubated in the presence of the thiosulfate-reducing enrichment revealed 59 pits over an area of 71.16 mm(2), while only 6 pits were evident in the corresponding methanogenic incubations. The results show the importance of thiosulfate-utilizing, sulfide-producing fermentative bacteria such as Anaerobaculum sp. in the corrosion of carbon steel, but also suggest that Anaerobaculum sp. are of far less concern when growing syntrophically with methanogens.
Collapse
Affiliation(s)
| | | | | | | | - Joseph M. Suflita
- Department of Microbiology and Plant Biology, OU Biocorrosion Center, University of OklahomaNorman, OK, USA
| |
Collapse
|
24
|
Lienen T, Kleyböcker A, Verstraete W, Würdemann H. Foam formation in a downstream digester of a cascade running full-scale biogas plant: Influence of fat, oil and grease addition and abundance of the filamentous bacterium Microthrix parvicella. BIORESOURCE TECHNOLOGY 2014; 153:1-7. [PMID: 24321688 DOI: 10.1016/j.biortech.2013.11.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Revised: 10/30/2013] [Accepted: 11/01/2013] [Indexed: 06/03/2023]
Abstract
The microbial community composition in a full-scale biogas plant fed with sewage sludge and fat, oil and grease (FOG) was investigated over a 15-month period, including two foam formation events. Addition of FOG as a substrate in the biogas plant together with high abundances of Microthrix parvicella were found to promote foam formation in the downstream digester of a cascade of two biogas digesters. Genetic fingerprinting and quantitative PCR (qPCR) indicated a higher abundance of M. parvicella in the digester, when the digestion process was accompanied by excessive foaming relative to the reference digesters without disturbance. The creation of foam depended on the introduced proportion of FOG and the abundance of M. parvicella. Furthermore, shifts in the abundance of M. parvicella in the biogas plant were observed within the 15-month monitoring period corresponding to its seasonal abundance in the sludge of the wastewater treatment plant (WWTP).
Collapse
Affiliation(s)
- T Lienen
- GFZ German Research Centre for Geosciences, Section 4.5 Geomicrobiology, 14473 Potsdam, Germany.
| | - A Kleyböcker
- GFZ German Research Centre for Geosciences, Section 4.5 Geomicrobiology, 14473 Potsdam, Germany.
| | - W Verstraete
- LabMET, Ghent University, Coupure Links 653, B-9000 Gent, Belgium.
| | - H Würdemann
- GFZ German Research Centre for Geosciences, Section 4.5 Geomicrobiology, 14473 Potsdam, Germany.
| |
Collapse
|
25
|
Hao T, Wei L, Lu H, Chui H, Mackey HR, van Loosdrecht MCM, Chen G. Characterization of sulfate-reducing granular sludge in the SANI(®) process. WATER RESEARCH 2013; 47:7042-7052. [PMID: 24200003 DOI: 10.1016/j.watres.2013.07.052] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Revised: 07/12/2013] [Accepted: 07/18/2013] [Indexed: 06/02/2023]
Abstract
Hong Kong practices seawater toilet flushing covering 80% of the population. A sulfur cycle-based biological nitrogen removal process, the Sulfate reduction, Autotrophic denitrification and Nitrification Integrated (SANI(®)) process, had been developed to close the loop between the hybrid water supply and saline sewage treatment. To enhance this novel process, granulation of a Sulfate-Reducing Up-flow Sludge Bed (SRUSB) reactor has recently been conducted for organic removal and provision of electron donors (sulfide) for subsequent autotrophic denitrification, with a view to minimizing footprint and maximizing operation resilience. This further study was focused on the biological and physicochemical characteristics of the granular sulfate-reducing sludge. A lab-scale SRUSB reactor seeded with anaerobic digester sludge was operated with synthetic saline sewage for 368 days. At 1 h nominal hydraulic retention time (HRT) and 6.4 kg COD/m(3)-d organic loading rate, the SRUSB reactor achieved 90% COD and 75% sulfate removal efficiencies. Granular sludge was observed within 30 days, and became stable after 4 months of operation with diameters of 400-500 μm, SVI5 of 30 ml/g, and extracellular polymeric substances of 23 mg carbohydrate/g VSS. Fluorescence in situ hybridization (FISH) analysis revealed that the granules were enriched with abundant sulfate-reducing bacteria (SRB) as compared with the seeding sludge. Pyrosequencing analysis of the 16S rRNA gene in the sulfate-reducing granules on day 90 indicated that the microbial community consisted of a diverse SRB genera, namely Desulfobulbus (18.1%), Desulfobacter (13.6%), Desulfomicrobium (5.6%), Desulfosarcina (0.73%) and Desulfovibrio (0.6%), accounting for 38.6% of total operational taxonomic units at genera level, with no methanogens detected. The microbial population and physicochemical properties of the granules well explained the excellent performance of the granular SRUSB reactor.
Collapse
Affiliation(s)
- Tianwei Hao
- Department of Civil & Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | | | | | | | | | | | | |
Collapse
|
26
|
Coldham T, Rose K, O’Rourke J, Neilan BA, Dalton H, Lee A, Mitchell H. Detection of Helicobacter species in the gastrointestinal tract of ringtail possum and koala: Possible influence of diet, on the gut microbiota. Vet Microbiol 2013; 166:429-37. [DOI: 10.1016/j.vetmic.2013.06.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2012] [Revised: 05/21/2013] [Accepted: 06/19/2013] [Indexed: 10/26/2022]
|
27
|
Zielińska M, Cydzik-Kwiatkowska A, Zieliński M, Dębowski M. Impact of temperature, microwave radiation and organic loading rate on methanogenic community and biogas production during fermentation of dairy wastewater. BIORESOURCE TECHNOLOGY 2013; 129:308-314. [PMID: 23262005 DOI: 10.1016/j.biortech.2012.11.093] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Revised: 11/19/2012] [Accepted: 11/20/2012] [Indexed: 06/01/2023]
Abstract
This study analyzed dairy wastewater fermentation in convection- and microwave-heated hybrid reactors at loadings of 1 and 2 kg COD/(m3 d) and temperatures of 35 and 55 °C. The biomass was investigated at a molecular level to determine the links between the operational parameters of anaerobic digestion and methanogenic Archaea structure. The highest production of biogas with methane content of ca. 67% was noted in the mesophilic microwave-heated reactors. The production of methane-rich biogas and the overall diversity of Archaea was determined by Methanosarcinaceae presence. The temperature and the application of microwaves were the main factors explaining the variations in the methanogen community. At 35 °C, the microwave heating stimulated the growth of highly diverse methanogen assemblages, promoting Methanosarcina barkeri presence and excluding Methanosarcina harudinacea from the biomass. A temperature increase to 55 °C lowered Methanosarcinaceae abundance and induced a replacement of Methanoculleus palmolei by Methanosarcina thermophila.
Collapse
Affiliation(s)
- Magdalena Zielińska
- Department of Environmental Biotechnology, University of Warmia and Mazury in Olsztyn, Słoneczna 45G, 10-709 Olsztyn, Poland.
| | | | | | | |
Collapse
|
28
|
Cocoa modulatory effect on rat faecal microbiota and colonic crosstalk. Arch Biochem Biophys 2012; 527:105-12. [PMID: 22663919 DOI: 10.1016/j.abb.2012.05.015] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Revised: 05/14/2012] [Accepted: 05/21/2012] [Indexed: 11/21/2022]
Abstract
Previous studies have reported the effect of a cocoa-enriched diet on the intestinal immune system in rats. Cocoa contains fibre and polyphenols that can directly influence the intestinal ecosystem and its relationship with the immune system. The aim of this study was to evaluate the effects of a cocoa-enriched diet on gut microbiota, toll-like receptor (TLR) expression and immunoglobulin (Ig) A (IgA) intestinal secretion in rats. Four-week-old Wistar rats were fed a standard or cocoa diet for 6 weeks. Faecal samples were collected before the beginning of the diet and at the end of the study. After the nutritional intervention, colon samples were obtained to quantify TLR and IgA gene expression and IgA protein. Microbiota composition was characterized by fluorescent in situ hybridization (FISH) coupled to flow cytometry (FCM) analysis using specific probes directed to 16S rRNA of the main bacteria genus present in rat intestine. The cocoa dietary intervention resulted in a differential TLR pattern and a decrease in the intestinal IgA secretion and IgA-coating bacteria. Moreover there was a significant decrease in the proportion of Bacteroides, Clostridium and Staphylococcus genera in the faeces of cocoa-fed animals. In conclusion, cocoa intake affects the growth of certain species of gut microbiota in rats and is associated with changes in the TLR pattern which could be responsible for the changes observed in the intestinal immune system.
Collapse
|
29
|
Kristiansen A, Saunders AM, Hansen AA, Nielsen PH, Nielsen JL. Community structure of bacteria and fungi in aerosols of a pig confinement building. FEMS Microbiol Ecol 2012; 80:390-401. [PMID: 22242889 DOI: 10.1111/j.1574-6941.2012.01305.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Revised: 12/29/2011] [Accepted: 01/04/2012] [Indexed: 11/28/2022] Open
Abstract
Modern intensive husbandry practices can create poor indoor air quality, with high levels of airborne dust, endotoxins, ammonia, and microorganisms. Air in a sow breeding barn was investigated to determine the biomass composition of bioaerosols using molecular methods supplemented with microscopic and cultivation-dependent approaches. A total of 2.7 ± 0.7 × 10(7) bacterial cells m(-3) air and 1.2 ± 0.3 × 10(6) fungi spores m(-3) were detected, corresponding to the fungal biovolume constituted 98% of the total microbial biovolume (fungal and bacterial). Fifty-two percent of all 4',6-diamidino-2-phenyl indole-stained cells were detectable with fluorescence in situ hybridization (FISH) with a general bacterial probe mixture. Quantitative FISH of the bacterial consortium revealed Firmicutes as the dominant group with Streptococcus as the major genus, while Actinobacteria constituted 10% of the detectable bacteria. Additionally, the study revealed an abundant and diverse fungal community including species not previously found in similar environments. The most abundant fungal 18S rRNA gene clone sequences identified affiliated with the Aspergillus-Eurotium cluster, but among others, species of Wallemia, Mucorales, and Russulales were detected. For both fungi and anaerobic bacteria, a hitherto undescribed diversity was found in bioaerosols from a modern sow breeding barn, which potentially could create poor indoor air quality, although their effect on the health of farmworkers and stock still is not resolved.
Collapse
Affiliation(s)
- Anja Kristiansen
- Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Aalborg, Denmark
| | | | | | | | | |
Collapse
|
30
|
Hanajima D, Fukumoto Y, Yasuda T, Suzuki K, Maeda K, Morioka R. Bacterial community dynamics in aerated cow manure slurry at different aeration intensities. J Appl Microbiol 2011; 111:1416-25. [PMID: 21920002 DOI: 10.1111/j.1365-2672.2011.05151.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AIMS This study aimed to characterize microbial community dynamics in aerated cow manure slurry at different aeration intensities. METHODS AND RESULTS Batch aerobic treatments were set up in 5-l jar fermentor, each containing 3 l of manure slurry; the slurries were subjected to low, medium and high (50, 150 and 250 ml min(-1), respectively) aeration for 9 days. Microbial community composition was determined using terminal restriction fragment length polymorphism and a clone library targeting 16S rRNA genes. High and medium aeration accelerated organic carbon degradation in parallel with the degree of aeration intensity; however, 90% of the initial total organic carbon was retained during low-aeration treatment. During the active stages of organic carbon decomposition, clones belonging to the class Bacilli accumulated. Moreover, Bacilli accumulation occurred earlier under high aeration than under medium aeration. CONCLUSIONS Organic matter degradation was mainly governed by a common microbial assemblage consisting of many lineages belonging to the class Bacilli. The timing of community development differed depending on aeration intensity. SIGNIFICANCE AND IMPACT OF THE STUDY This study reports on changes in several environmentally important parameters and the principal microbial assemblage during the pollution-reducing phase of cattle manure aeration treatment.
Collapse
Affiliation(s)
- D Hanajima
- Waste Recycling Research Team, National Agricultural Research Center for Hokkaido Region, Sapporo, Hokkaido, Japan.
| | | | | | | | | | | |
Collapse
|
31
|
Becker JC, Groeger AW, Nowlin WH, Chumchal MM, Hahn D. Spatial variability in the speciation and bioaccumulation of mercury in an arid subtropical reservoir ecosystem. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2011; 30:2300-2311. [PMID: 21769922 DOI: 10.1002/etc.626] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Revised: 05/10/2011] [Accepted: 06/05/2011] [Indexed: 05/31/2023]
Abstract
Patterns of spatial variation of mercury and methylmercury (MeHg) were examined in sediments and muscle tissue of largemouth bass (Micropterus salmoides) from Amistad International Reservoir, a large and hydrologically complex subtropical water body in the Rio Grande drainage. The distributions of both Hg and MeHg were compared with environmental and biological factors known to influence production of MeHg. The highest concentrations of total Hg (THg) in sediment were found in the Rio Grande arm of the reservoir, whereas MeHg was highest at sites in the Devils River arm and inundated Pecos River (often more than 3.0 ng/g). Conditions in the sediments of the Devils River arm and Pecos River channel were likely more favorable to the production of MeHg, with higher sediment porewater dissolved organic carbon, and porewater sulfate levels in the optimal range for methylation. Although the detection of different groups of sulfate-reducing bacteria by polymerase chain reaction (PCR) was generally correlated with MeHg concentrations, bacterial counts via fluorescent in situ hybridization (FISH) did not correlate with MeHg. A sample of 156 largemouth bass (<30 cm) showed a spatial pattern similar to that of MeHg in sediments, where fish from the Devils River arm of the reservoir had higher muscle Hg concentrations than those collected in the Rio Grande arm. In 88 bass of legal sport fishing size (>35 cm), 77% exceeded the 0.3 mg/kg U.S. Environmental Protection Agency screening value. This study shows that significant variation in sediment MeHg and biotic Hg concentration can exist within lakes and reservoirs and that it can correspond to variation in environmental conditions and Hg methylation.
Collapse
Affiliation(s)
- Jesse C Becker
- Department of Biology, Texas State University-San Marcos, Aquatic Station, San Marcos, Texas, USA.
| | | | | | | | | |
Collapse
|
32
|
Kan J, Chellamuthu P, Obraztsova A, Moore JE, Nealson KH. Diverse bacterial groups are associated with corrosive lesions at a Granite Mountain Record Vault (GMRV). J Appl Microbiol 2011; 111:329-37. [PMID: 21599813 DOI: 10.1111/j.1365-2672.2011.05055.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIMS This study applied culture-dependent and molecular approaches to examine the bacterial communities at corrosion sites at Granite Mountain Record Vault (GMRV) in Utah, USA, with the goal of understanding the role of microbes in these unexpected corrosion events. METHODS AND RESULTS Samples from corroded steel chunks, rock particles and waters around the corrosion pits were collected for bacterial isolation and molecular analyses. Bacteria cultivated from these sites were identified as members of Alphaproteobacteria, Gammaproteobacteria, Firmicutes and Actinobacteria. In addition, molecular genetic characterization of the communities via nested-polymerase chain reaction-denaturing gradient gel electrophoresis (DGGE) indicated the presence of a broad spectrum of bacterial groups, including Alphaproteobacteria, Betaproteobacteria, Deltaproteobacteria, Actinobacteria, Firmicutes and Bacteroidetes. However, neither cultivation nor molecular approaches identified sulfate-reducing bacteria (SRB), the bacteria commonly implicated as causative organisms were found associated with corrosive lesions in a process referred to as microbially influenced corrosion (MIC). The high diversity of bacterial groups at the corrosion sites in comparison with that seen in the source waters suggested to us a role for the microbes in corrosion, perhaps being an expression of a redox-active group of microbes transferring electrons, harvesting energy and producing biomass. CONCLUSIONS The corrosion sites contained highly diverse microbial communities, consistent with the involvement of microbial activities along the redox gradient at corrosion interface. We hypothesize an electron transport model for MIC, involving diverse bacterial groups such as acid-producing bacteria (APB), SRB, sulfur-oxidizing bacteria (SOB), metal-reducing bacteria (MRB) and metal-oxidizing bacteria (MOB). SIGNIFICANCE AND IMPACT OF THE STUDY The characterization of micro-organisms that influence metal-concrete corrosion at GMRV has significant implications for corrosion control in high-altitude freshwater environments. MIC provides a potential opportunity to further our understandings of extracellular electron transfer and interspecies communications.
Collapse
Affiliation(s)
- J Kan
- Department of Earth Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | | | | | | | | |
Collapse
|
33
|
Detection, isolation, and characterization of helicobacter species from the gastrointestinal tract of the brushtail possum. Appl Environ Microbiol 2011; 77:1581-7. [PMID: 21216901 DOI: 10.1128/aem.01960-10] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The presence of Helicobacter species in Australian marsupials was examined systematically using microscopy, culture, and PCR in different regions of the gastrointestinal tract (GIT) and in the liver of brushtail possums (BTPs) (Trichosurus vulpecula), a common Australian marsupial that feeds on eucalyptus leaves. The spatial distribution of Helicobacter species in the GIT sections also was examined microscopically in silver-stained sections and by fluorescent in situ hybridization (FISH) using a Helicobacter genus-specific probe. Helicobacter species were found colonizing the lower bowel of all BTPs studied. Good agreement was observed between the detection of Helicobacter species using culture and PCR, which was supported by the microscopic examination of silver-stained sections and FISH. The lower bowel of BTPs were colonized by one to three morphologically different (a comma-shaped species with no apparent flagella, a fusiform-shaped species entwined with periplasmic fibers and a bipolar sheathed flagella, and an S-shaped species with bipolar sheathed flagella) and potentially novel Helicobacter species, as well as in one case with a potentially novel Campylobacter species, which was a tightly coiled rod with bipolar unsheathed flagella. The isolation and characterization of these Helicobacter species in BTPs provides important information regarding the specific natural niche of these bacteria and their corelationship within their host, and it increases our understanding of the ecology of Helicobacter species.
Collapse
|
34
|
Zhao YG, Li XW, Wang JC, Bai J, Tian WJ. Performance of a sulfidogenic bioreactor and bacterial community shifts under different alkalinity levels. BIORESOURCE TECHNOLOGY 2010; 101:9190-9196. [PMID: 20688512 DOI: 10.1016/j.biortech.2010.07.055] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2010] [Revised: 06/16/2010] [Accepted: 07/14/2010] [Indexed: 05/29/2023]
Abstract
The performance of a sulfidogenic bioreactor and the response of bacterial populations to influent alkalinity changes were investigated. The bioreactor reached 40% of sulfate removal efficiency (SRE) with 0 mg l(-1) of alkalinity, and single-stranded conformation polymorphism profiles showed that some members of Bacteroides, Dysgonomonas, Sporobacter, Quinella, and Citrobacter became dominant populations. 16S rRNA gene library analysis indicated that the Actinobacteria group increased from 0% in seed to 23% in sludge. An increase in alkalinity to 1300 mg l(-1) led to a rapid increase of SRE to 65% and changes in the bacterial community. Sequences representing Dysgonomonas, Raoultella, Kluyvera, and Phascolarctobacterium were now found. When alkalinity was deceased to 0 mg l(-1), SRE dropped and the bands representing Raoultella, Kluyvera, and Phascolarctobacterium disappeared, while bands representing Clostridium appeared. A second cycle of low/high alkalinity did not result in obvious changes to the bacterial community. These results indicate that the sulfidogenic bioreactor favored higher influent alkalinity and that the different functional microbial populations responded well to the alkalinity changes.
Collapse
Affiliation(s)
- Yang-Guo Zhao
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China.
| | | | | | | | | |
Collapse
|
35
|
Lanthier M, Scott A, Zhang Y, Cloutier M, Durie D, Henderson V, Wilkes G, Lapen D, Topp E. Distribution of selected virulence genes and antibiotic resistance in Enterococcus species isolated from the South Nation River drainage basin, Ontario, Canada. J Appl Microbiol 2010; 110:407-21. [DOI: 10.1111/j.1365-2672.2010.04893.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
36
|
Kumaraswamy R, Ebert S, Gray MR, Fedorak PM, Foght JM. Molecular- and cultivation-based analyses of microbial communities in oil field water and in microcosms amended with nitrate to control H2S production. Appl Microbiol Biotechnol 2010; 89:2027-38. [DOI: 10.1007/s00253-010-2974-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2010] [Revised: 10/18/2010] [Accepted: 10/18/2010] [Indexed: 11/29/2022]
|
37
|
Rinker K, Han C, Kelly R. Continuous culture as a tool for investigating the growth physiology of heterotrophic hyperthermophiles and extreme thermoacidophiles. J Appl Microbiol 2010; 85 Suppl 1:118S-127S. [DOI: 10.1111/j.1365-2672.1998.tb05290.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
38
|
Lanthier M, Scott A, Lapen DR, Zhang Y, Topp E. Frequency of virulence genes and antibiotic resistances inEnterococcusspp. isolates from wastewater and feces of domesticated mammals and birds, and wildlife. Can J Microbiol 2010; 56:715-29. [DOI: 10.1139/w10-046] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Enterococci are gastrointestinal tract residents and also an important cause of nosocomial infections. To understand which species, virulence determinants, and antibiotic resistances are prevalent in enterococci shed by various hosts groups, a total of 1460 strains isolated from 144 fecal samples obtained from wastewater, domesticated mammals and birds, and wildlife were characterized. Identification of isolates to the species level showed that Enterococcus faecalis was dominant in domesticated mammals and birds and wildlife feces, whereas Enterococcus faecium was dominant among wastewater isolates, and that no single Enterococcus species could be associated with a specific host group. The frequency of 12 virulence determinants was evaluated among isolates, but no single virulence determinant could be associated with a specific host group. Resistance to 12 antibiotics was evaluated among isolates, and it was shown that the highest frequency of resistance at breakpoint concentration was found in domesticated mammals and birds (P ≤ 0.05 for 4 antibiotics). Our results suggests that (1) species identification and virulence typing of Enterococcus spp. isolates are not useful for the identification of the host groups responsible for fecal contamination of water by microbial source tracking and that (2) antibiotic use for clinical, veterinary, or animal husbandry practices is promoting resistance.
Collapse
Affiliation(s)
- Martin Lanthier
- Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON K1A 0C6, Canada
- Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, 1391 Sanford Street, London, ON N5V 4T3, Canada
| | - Andrew Scott
- Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON K1A 0C6, Canada
- Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, 1391 Sanford Street, London, ON N5V 4T3, Canada
| | - David R. Lapen
- Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON K1A 0C6, Canada
- Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, 1391 Sanford Street, London, ON N5V 4T3, Canada
| | - Yun Zhang
- Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON K1A 0C6, Canada
- Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, 1391 Sanford Street, London, ON N5V 4T3, Canada
| | - Edward Topp
- Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON K1A 0C6, Canada
- Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, 1391 Sanford Street, London, ON N5V 4T3, Canada
| |
Collapse
|
39
|
Hahn D, Amann RI, Zeyer J. Whole-Cell Hybridization of Frankia Strains with Fluorescence- or Digoxigenin-Labeled, 16S rRNA-Targeted Oligonucleotide Probes. Appl Environ Microbiol 2010; 59:1709-16. [PMID: 16348948 PMCID: PMC182149 DOI: 10.1128/aem.59.6.1709-1716.1993] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Whole-cell hybridization with non-radioactively labeled oligonucleotide probes was used to detect and identify Frankia strains in pure cultures and in nodules. Digoxigenin-labeled probes, which were detected with antibody-alkaline phosphatase conjugates, were more suitable for in situ detection of Frankia strains than fluorescent probes since the sensitivity of the former was higher and problems arising from the autofluorescence of cells and plant material were avoided. Successful detection of Frankia strains in paraformaldehyde-fixed cell material with digoxigenin-labeled oligonucleotide probes depended on pretreatments to permeabilize the cells. Specific hybridization signals on vesicles were obtained after lysozyme pretreatment (1 mg ml for 30 min at 20 degrees C). Reliable penetration of the antibody-enzyme conjugate into hyphae required additional washing with the detergent Nonidet P-40 (0.1%) and toluene (1% in ethanol) after lysozyme treatment. Identification of Frankia vesicles in nodule homogenates was possible only after the removal of the polysaccharide capsule surrounding the vesicles. Incubation with H(2)O(2) (15% in water for 1 h at room temperature) before lysozyme and detergent treatments was found to facilitate specific hybridization. No filaments or spores could be detected in nodule homogenates. This technique should be a powerful tool in the identification of Frankia isolates, in the characterization of as-yet-uncultured nodule populations, and in the confirmation of the origin of unusual Frankia isolates.
Collapse
Affiliation(s)
- D Hahn
- Eidgenössische Technische Hochschule Zürich, Institute of Terrestrial Ecology and Soil Biology, Grabenstrasse 3, CH-8952 Schlieren, Switzerland, and Lehrstuhl für Mikrobiologie, Technische Universität München, D-8000 Munich 2, Germany
| | | | | |
Collapse
|
40
|
Shen Y, Stehmeier LG, Voordouw G. Identification of hydrocarbon-degrading bacteria in soil by reverse sample genome probing. Appl Environ Microbiol 2010; 64:637-45. [PMID: 16349504 PMCID: PMC106095 DOI: 10.1128/aem.64.2.637-645.1998] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacteria with limited genomic cross-hybridization were isolated from soil contaminated with C5+, a mixture of hydrocarbons, and identified by partial 16S rRNA sequencing. Filters containing denatured genomic DNAs were used in a reverse sample genome probe (RSGP) procedure for analysis of the effect of an easily degradable compound (toluene) and a highly recalcitrant compound (dicyclopentadiene [DCPD]) on community composition. Hybridization with labeled total-community DNA isolated from soil exposed to toluene indicated enrichment of several Pseudomonas spp., which were subsequently found to be capable of toluene mineralization. Hybridization with labeled total-community DNA isolated from soil exposed to DCPD indicated enrichment of a Pseudomonas sp. or a Sphingomonas sp. These two bacteria appeared capable of producing oxygenated DCPD derivatives in the soil environment, but mineralization could not be shown. These results demonstrate that bacteria, which metabolize degradable or recalcitrant hydrocarbons, can be identified by the RSGP procedure.
Collapse
Affiliation(s)
- Y Shen
- Department of Biological Sciences, The University of Calgary, Calgary, Alberta, Canada T2N 1N4, and NOVA Research and Technology Centre, Calgary, Alberta, Canada T2E 7K7
| | | | | |
Collapse
|
41
|
Moller S, Kristensen CS, Poulsen LK, Carstensen JM, Molin S. Bacterial growth on surfaces: automated image analysis for quantification of growth rate-related parameters. Appl Environ Microbiol 2010; 61:741-8. [PMID: 16534939 PMCID: PMC1388357 DOI: 10.1128/aem.61.2.741-748.1995] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A fast routine method for estimating bacterial cell growth rates by using the metachromatic dye acridine orange is described. The method allows simultaneous estimates of cellular RNA and DNA contents of single cells. Acridine orange staining can be used as a nonspecific supplement to quantitative species-specific hybridizations with fluorescence-labelled ribosomal probes to estimate the single-cell concentration of RNA. By automated analysis of digitized images of stained cells, we determined four independent growth rate-related parameters: cellular RNA and DNA contents, cell volume, and the frequency of dividing cells in a cell population. These parameters were used to compare physiological states of liquid-suspended and surface-growing Pseudomonas putida KT2442 in chemostat cultures. The major finding is that the correlation between substrate availability and cellular growth rate found for the free-living cells was not observed for the surface-bound cells; in contrast, the data indicate an almost constant growth rate for attached cells which was independent of the dilution rate in the chemostat.
Collapse
|
42
|
Voordouw G, Voordouw JK, Jack TR, Foght J, Fedorak PM, Westlake DW. Identification of distinct communities of sulfate-reducing bacteria in oil fields by reverse sample genome probing. Appl Environ Microbiol 2010; 58:3542-52. [PMID: 16348801 PMCID: PMC183142 DOI: 10.1128/aem.58.11.3542-3552.1992] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Thirty-five different standards of sulfate-reducing bacteria, identified by reverse sample genome probing and defined as bacteria with genomes showing little or no cross-hybridization, were in part characterized by Southern blotting, using 16S rRNA and hydrogenase gene probes. Samples from 56 sites in seven different western Canadian oil field locations were collected and enriched for sulfate-reducing bacteria by using different liquid media containing one of the following carbon sources: lactate, ethanol, benzoate, decanoate, propionate, or acetate. DNA was isolated from the enrichments and probed by reverse sample genome probing using master filters containing denatured chromosomal DNAs from the 35 sulfate-reducing bacterial standards. Statistical analysis of the microbial compositions at 44 of the 56 sites indicated the presence of two distinct communities of sulfate-reducing bacteria. The discriminating factor between the two communities was the salt concentration of the production waters, which were either fresh water or saline. Of 34 standards detected, 10 were unique to the fresh water and 18 were unique to the saline oil field environment, while only 6 organisms were cultured from both communities.
Collapse
Affiliation(s)
- G Voordouw
- Division of Biochemistry, Department of Biological Sciences, The University of Calgary, Calgary, Alberta, Canada T2N 1N4; NOVA HUSKY Research Corporation, Calgary, Alberta, Canada T2E 7K7 ; and Department of Microbiology, University of Alberta, Edmonton, Alberta, Canada T6G 2E9
| | | | | | | | | | | |
Collapse
|
43
|
Fleminger G, Shabtai Y. Direct and Rapid Analysis of the Adhesion of Bacteria to Solid Surfaces: Interaction of Fluorescently Labeled Rhodococcus Strain GIN-1 (NCIMB 40340) Cells with Titanium-Rich Particles. Appl Environ Microbiol 2010; 61:4357-61. [PMID: 16535188 PMCID: PMC1388653 DOI: 10.1128/aem.61.12.4357-4361.1995] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A fluorimetric assay which enables direct and accurate analysis of the adhesion of bacteria to solid particles was developed. The assay is based on labeling of the bacteria with fluorescamine, which reacts with primary amino groups on the cell surface to yield a yellow fluorescence that is easily detectable by both fluorescence microscopy and spectrofluorimetry. As an example, fluorescent labeling of Rhodococcus strain GIN-1 (NCIMB 40340) cells enabled the detection and quantitative determination of their adsorption to TiO(inf2) and coal fly ash particles. Exposure of the cells to 10% acetone during the labeling reaction affected neither their viability nor their ability to adhere to these particles. Only a small fraction (;sim2%) of the total cell protein was labeled by fluorescamine upon staining of intact bacterial cells, which may indicate preferential labeling of certain proteins. Specificity studies carried out with the fluorescence assay confirmed previous findings that Rhodococcus strain GIN-1 cells possess high affinities for TiO(inf2), ZnO, and coal fly ash and low affinities for other metal oxides. In principle, the newly developed fluorimetric assay may be used for determination of cell adhesion to any solid matrix by either microscopic examination or epifluorescence measurements. In the present work, the adhesion of several other microorganisms to TiO(inf2) particles was tested as well, but their ability to adhere to these particles was significantly lower than that of Rhodococcus strain GIN-1 cells.
Collapse
|
44
|
Raskin L, Rittmann BE, Stahl DA. Competition and coexistence of sulfate-reducing and methanogenic populations in anaerobic biofilms. Appl Environ Microbiol 2010; 62:3847-57. [PMID: 16535428 PMCID: PMC1388966 DOI: 10.1128/aem.62.10.3847-3857.1996] [Citation(s) in RCA: 180] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The microbial population structure and function of natural anaerobic communities maintained in laboratory fixed-bed biofilm reactors were tracked before and after a major perturbation, which involved the addition of sulfate to the influent of a reactor that had previously been fed only glucose (methanogenic), while sulfate was withheld from a reactor that had been fed both glucose and sulfate (sulfidogenic). The population structure, determined by using phylogenetically based oligonucleotide probes for methanogens and sulfate-reducing bacteria, was linked to the functional performance of the biofilm reactors. Before the perturbation, the methanogenic reactor contained up to 25% methanogens as well as 15% sulfate-reducing bacteria, even though sulfate was not present in the influent of this reactor. Methanobacteriales and Desulfovibrio spp. were the most abundant methanogens and sulfate-reducing bacteria, respectively. The presence of sulfate-reducing bacteria (primarily Desulfovibrio spp. and Desulfobacterium spp.) in the absence of sulfate may be explained by their ability to function as proton-reducing acetogens and/or fermenters. Sulfate reduction began immediately following the addition of sulfate consistent with the presence of significant levels of sulfate-reducing bacteria in the methanogenic reactor, and levels of sulfate-reducing bacteria increased to a new steady-state level of 30 to 40%; coincidentally, effluent acetate concentrations decreased. Notably, some sulfate-reducing bacteria (Desulfococcus/Desulfosarcina/Desulfobotulus group) were more competitive without sulfate. Methane production decreased immediately following the addition of sulfate; this was later followed by a decrease in the relative concentration of methanogens, which reached a new steady-state level of approximately 8%. The changeover to sulfate-free medium in the sulfidogenic reactor did not cause a rapid shift to methanogenesis. Methane production and a substantial increase in the levels of methanogens were observed only after approximately 50 days following the perturbation.
Collapse
|
45
|
Hahn D, Amann RI, Zeyer J. Detection of mRNA in streptomyces cells by whole-cell hybridization with digoxigenin-labeled probes. Appl Environ Microbiol 2010; 59:2753-7. [PMID: 16349031 PMCID: PMC182355 DOI: 10.1128/aem.59.8.2753-2757.1993] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Detection of mRNA of the thiostrepton resistance gene (tsr) harbored by plasmid pIJ673 in Streptomyces violacelatus was achieved by whole-cell hybridization with digoxigenin-labeled in vitro transcripts followed by an antibody-alkaline phosphatase detection of the digoxigenin reporter molecule. Prior to hybridization, the cells had to be permeabilized by lysozyme, the detergent Nonidet P-40, and toluene. The permeability of the S. violacelatus cells for probes and the antibody-alkaline phosphatase conjugate was demonstrated by hybridization with digoxigenin-labeled, 16S rRNA-targeted oligonucleotides.
Collapse
Affiliation(s)
- D Hahn
- Institute of Terrestrial Ecology, Soil Biology, Eidgenössische Technische Hochschule Zürich, Grabenstrasse 3, CH-8952 Schlieren, Switzerland, and Lehrstuhl für Mikrobiologie, Technische Universität München, Arcisstrasse 21, D-8000 Munich 2, Germany
| | | | | |
Collapse
|
46
|
Telang AJ, Ebert S, Foght JM, Westlake D, Jenneman GE, Gevertz D, Voordouw G. Effect of nitrate injection on the microbial community in an oil field as monitored by reverse sample genome probing. Appl Environ Microbiol 2010; 63:1785-93. [PMID: 16535595 PMCID: PMC1389150 DOI: 10.1128/aem.63.5.1785-1793.1997] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The reverse sample genome probe (RSGP) method, developed for monitoring the microbial community in oil fields with a moderate subsurface temperature, has been improved by (i) isolation of a variety of heterotrophic bacteria and inclusion of their genomes on the oil field master filter and (ii) use of phosphorimaging technology for the rapid quantitation of hybridization signals. The new master filter contains the genomes of 30 sulfate-reducing, 1 sulfide-oxidizing, and 16 heterotrophic bacteria. Most have been identified by partial 16S rRNA sequencing. Use of improved RSGP in monitoring the effect of nitrate injection in an oil field indicated that the sulfide-oxidizing, nitrate-reducing isolate CVO (a Campylobacter sp.) becomes the dominant community component immediately after injection. No significant enhancement of other community members, including the sulfate-reducing bacteria, was observed. The elevated level of CVO decayed at most sampling sites within 30 days after nitrate injection was terminated. Chemical analyses indicated a corresponding decrease and subsequent increase in sulfide concentrations. Thus, transient injection of a higher potential electron acceptor into an anaerobic subsurface system can have desirable effects (i.e., reduction of sulfide levels) without a permanent adverse influence on the resident microbial community.
Collapse
|
47
|
Lomakina AV, Pavlova ON, Shubenkova OV, Zemskaya TI. Diversity of cultured aerobic organisms in the areas of natural oil seepage on Lake Baikal. BIOL BULL+ 2009. [DOI: 10.1134/s1062359009050021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
48
|
Wagner ID, Ahmed S, Zhao W, Zhang CL, Romanek CS, Rohde M, Wiegel J. Caldanaerovirga acetigignens gen. nov., sp. nov., an anaerobic xylanolytic, alkalithermophilic bacterium isolated from Trego Hot Spring, Nevada, USA. Int J Syst Evol Microbiol 2009; 59:2685-91. [DOI: 10.1099/ijs.0.005207-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
|
49
|
Lo HM, Liu MH, Pai TY, Liu WF, Lin CY, Wang SC, Banks CJ, Hung CH, Chiang CF, Lin KC, Chen PH, Chen JK, Chiu HY, Su MH, Kurniawan TA, Wu KC, Hsieh CY, Hsu HS. Biostabilization assessment of MSW co-disposed with MSWI fly ash in anaerobic bioreactors. JOURNAL OF HAZARDOUS MATERIALS 2009; 162:1233-1242. [PMID: 18653282 DOI: 10.1016/j.jhazmat.2008.06.028] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2007] [Revised: 05/03/2008] [Accepted: 06/09/2008] [Indexed: 05/26/2023]
Abstract
Municipal solid waste incinerator (MSWI) fly ash has been examined for possible use as landfill interim cover. For this aim, three anaerobic bioreactors, 1.2m high and 0.2m in diameter, were used to assess the co-digestion or co-disposal performance of MSW and MSWI fly ash. Two bioreactors contained ratios of 10 and 20 g fly ash per liter of MSW (or 0.2 and 0.4 g g(-1) VS, that is, 0.2 and 0.4 g fly ash per gram volatile solids (VS) of MSW). The remaining bioreactor was used as control, without fly ash addition. The results showed that gas production rate was enhanced by the appropriate addition of MSWI fly ash, with a rate of approximately 6.5l day(-1)kg(-1)VS at peak production in the ash-added bioreactors, compared to approximately 4l day(-1)kg(-1)VS in control. Conductivity, alkali metals and VS in leachate were higher in the fly ash-added bioreactors compared to control. The results show that MSW decomposition was maintained throughout at near-neutral pH and might be improved by release of alkali and trace metals from fly ash. Heavy metals exerted no inhibitory effect on MSW digestion in all three bioreactors. These phenomena indicate that proper amounts of MSWI fly ash, co-disposed or co-digested with MSW, could facilitate bacterial activity, digestion efficiency and gas production rates.
Collapse
Affiliation(s)
- H M Lo
- Department of Environmental Engineering and Management, Chaoyang University of Technology, 168, Jifong East Road, Wufong, Taichung County, Taiwan.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
50
|
Kumar M, Wu PC, Tsai JC, Lin JG. Biodegradation of soil-applied polycyclic aromatic hydrocarbons by sulfate-reducing bacterial consortium. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2009; 44:12-20. [PMID: 19085590 DOI: 10.1080/10934520802515178] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
In the present study, the potential of polycyclic aromatic hydrocarbons (PAHs) biodegradation by sulfate-reducing bacterial consortium enriched from piggery wastewater was investigated. The batch experiments of soil-applied PAH biodegradation were conducted with a mixture of PAHs, i.e., naphthalene, fluorene, phenanthrene, fluoranthene and pyrene, at a concentration of 50 mu g of each PAH per g of soil. A central composite design (CCD) was applied to determine the experimental conditions of each batch assay. The pH, biomass and ethanol concentrations were selected as independent variables and the PAH removal percentage was considered as a dependent variable. The optimal conditions for PAH biodegradation were found to be a pH between 4 and 6.5, an ethanol concentration less than 35 mg/L and a biomass concentration greater than 65 mg/L. Bench scale experiments were carried out at the optimal conditions. At the end of experiment (27 d), total PAH removals by biodegradation and volatilization were around 74% and 20%, respectively. The order of PAH removal was naphthalene, phenanthrene, fluorene, fluoranthene, and pyrene. Throughout the study, PAH biodegradation was in good correlation with sulfate reduction. Results of the kinetics study indicated a competitive inhibition between PAHs investigated.
Collapse
Affiliation(s)
- Mathava Kumar
- Institute of Environmental Engineering, National Chiao Tung University, Hsinchu, Taiwan
| | | | | | | |
Collapse
|