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Jiang G, Wang C, Wang Y, Wang J, Xue Y, Lin Y, Hu X, Lv Y. Exogenous putrescine plays a switch-like influence on the pH stress adaptability of biofilm-based activated sludge. Appl Environ Microbiol 2024; 90:e0056924. [PMID: 38916292 PMCID: PMC11267902 DOI: 10.1128/aem.00569-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 06/04/2024] [Indexed: 06/26/2024] Open
Abstract
Microbial community adaptability to pH stress plays a crucial role in biofilm formation. This study aims to investigate the regulatory mechanisms of exogenous putrescine on pH stress, as well as enhance understanding and application for the technical measures and molecular mechanisms of biofilm regulation. Findings demonstrated that exogenous putrescine acted as a switch-like distributor affecting microorganism pH stress, thus promoting biofilm formation under acid conditions while inhibiting it under alkaline conditions. As pH decreases, the protonation degree of putrescine increases, making putrescine more readily adsorbed. Protonated exogenous putrescine could increase cell membrane permeability, facilitating its entry into the cell. Subsequently, putrescine consumed intracellular H+ by enhancing the glutamate-based acid resistance strategy and the γ-aminobutyric acid metabolic pathway to reduce acid stress on cells. Furthermore, putrescine stimulated ATPase expression, allowing for better utilization of energy in H+ transmembrane transport and enhancing oxidative phosphorylation activity. However, putrescine protonation was limited under alkaline conditions, and the intracellular H+ consumption further exacerbated alkali stress and inhibits cellular metabolic activity. Exogenous putrescine promoted the proportion of fungi and acidophilic bacteria under acidic stress and alkaliphilic bacteria under alkali stress while having a limited impact on fungi in alkaline biofilms. Increasing Bdellovibrio under alkali conditions with putrescine further aggravated the biofilm decomposition. This research shed light on the unclear relationship between exogenous putrescine, environmental pH, and pH stress adaptability of biofilm. By judiciously employing putrescine, biofilm formation could be controlled to meet the needs of engineering applications with different characteristics.IMPORTANCEThe objective of this study is to unravel the regulatory mechanism by which exogenous putrescine influences biofilm pH stress adaptability and understand the role of environmental pH in this intricate process. Our findings revealed that exogenous putrescine functioned as a switch-like distributor affecting the pH stress adaptability of biofilm-based activated sludge, which promoted energy utilization for growth and reproduction processes under acidic conditions while limiting biofilm development to conserve energy under alkaline conditions. This study not only clarified the previously ambiguous relationship between exogenous putrescine, environmental pH, and biofilm pH stress adaptability but also offered fresh insights into enhancing biofilm stability within extreme environments. Through the modulation of energy utilization, exerting control over biofilm growth and achieving more effective engineering goals could be possible.
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Affiliation(s)
- Guanyu Jiang
- School of Environmental Science and Engineering, Tianjin University, Tianjin, China
- Tianjin Key Lab of Indoor Air Environmental Quality Control, Tianjin, China
| | - Can Wang
- School of Environmental Science and Engineering, Tianjin University, Tianjin, China
- Tianjin Key Lab of Indoor Air Environmental Quality Control, Tianjin, China
| | - Yongchao Wang
- School of Environmental Science and Engineering, Tianjin University, Tianjin, China
- Tianjin Key Lab of Indoor Air Environmental Quality Control, Tianjin, China
| | - Jiayi Wang
- School of Environmental Science and Engineering, Tianjin University, Tianjin, China
- Tianjin Key Lab of Indoor Air Environmental Quality Control, Tianjin, China
| | - Yimei Xue
- School of Environmental Science and Engineering, Tianjin University, Tianjin, China
- Tianjin Key Lab of Indoor Air Environmental Quality Control, Tianjin, China
| | - Yuting Lin
- School of Environmental Science and Engineering, Tianjin University, Tianjin, China
- Tianjin Key Lab of Indoor Air Environmental Quality Control, Tianjin, China
| | - Xurui Hu
- School of Environmental Science and Engineering, Tianjin University, Tianjin, China
- Tianjin Key Lab of Indoor Air Environmental Quality Control, Tianjin, China
| | - Yahui Lv
- School of Environmental Science and Engineering, Tianjin University, Tianjin, China
- Tianjin Key Lab of Indoor Air Environmental Quality Control, Tianjin, China
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Orhan F, Akıncıoğlu A, Ceyran E. Ectoine production from a novel bacterial strain and high-purity purification with a cost-effective and single-step method. J Biotechnol 2024; 388:24-34. [PMID: 38599284 DOI: 10.1016/j.jbiotec.2024.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 03/08/2024] [Accepted: 04/05/2024] [Indexed: 04/12/2024]
Abstract
This study marks the exploration into the production of ectoine, a valuable compound with significant potential as an antioxidant, osmoprotectant, anti-inflammatory agent, and stabilizer of cell membranes, proteins, and DNA integrity. Our focus centred on investigating the presence of ectoine and optimizing its production by the novel ectoine producer bacterial strain, Piscibacillus halophilus. For the optimization of ectoine production the effects of carbon and nitrogen sources, salt, pH, agitation and incubation period were optimized by one-factor-at-a-time. We started with an initial ectoine content of 46.92 mg/L, and through a series of optimization processes, we achieved a remarkable increase, resulting in an ectoine content of 1498.2 mg/L. The bacterial species P. halophilus achieved its highest ectoine production after 48 h of incubation, with conditions set at 10 % (w/v) salinity, pH of 7.50, and an agitation speed of 160 rpm. These precise conditions were found to be the most favourable for maximizing ectoine production by this strain. Besides, we have achieved successful purification of ectoine from the crude extract through a streamlined single-step process. This purification method has delivered an exceptional level of purity, surpassing 99.15 %, and an impressive yield of over 99 %. Importantly, we accomplished this using readily available and cost-effective strong acids (HCl) and strong bases (NaOH) to arrange pH gradients. The use of acid and base in the purification process of ectoine reflects an innovative and sustainable methodology.
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Affiliation(s)
- Furkan Orhan
- Agri Ibrahim Cecen University, Art and Science Faculty, Department of Molecular Biology and Genetics, Agri 4100, Turkey; Central Research and Application Laboratory, Agri Ibrahim Cecen University, Agri, Turkey.
| | - Akın Akıncıoğlu
- Central Research and Application Laboratory, Agri Ibrahim Cecen University, Agri, Turkey; Vocational School, Agri Ibrahim Cecen University, Agri, Turkey
| | - Ertuğrul Ceyran
- Central Research and Application Laboratory, Agri Ibrahim Cecen University, Agri, Turkey
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Fan J, Liu C, Zheng J, Song Y. Dithionite promoted microbial dechlorination of hexachlorobenzene while goethite further accelerated abiotic degradation by sulfidation in paddy soil. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 259:115047. [PMID: 37220705 DOI: 10.1016/j.ecoenv.2023.115047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/17/2023] [Accepted: 05/18/2023] [Indexed: 05/25/2023]
Abstract
It is of great scientific and practical importance to explore the mechanisms of accelerated degradation of Hexachlorobenzene (HCB) in soil. Both iron oxide and dithionite may promote the reductive dechlorination of HCB, but their effects on the microbial community and the biotic and abiotic mechanisms behind it remain unclear. This study investigated the effects of goethite, dithionite, and their interaction on microbial community composition and structure, and their potential contribution to HCB dechlorination in a paddy soil to reveal the underlying mechanism. The results showed that goethite addition alone did not significantly affect HCB dechlorination because the studied soil lacked iron-reducing bacteria. In contrast, dithionite addition significantly decreased the HCB contents by 44.0-54.9%, while the coexistence of dithionite and goethite further decreased the HCB content by 57.9-69.3%. Random Forest analysis suggested that indicator taxa (Paenibacillus, Acidothermus, Haliagium, G12-WMSP1, and Frankia), Pseudomonas, richness and Shannon's index of microbial community, and immobilized Fe content were dominant driving factors for HCB dechlorination. The dithionite addition, either with or without goethite, accelerated HCB anaerobic dechlorination by increasing microbial diversity and richness as well as the relative abundance of the above specific bacterial genera. When goethite and dithionite coexist, sulfidation of goethite with dithionite could remarkably increase FeS formation and then further promote HCB dechlorination rates. Overall, our results suggested that the combined application of goethite and dithionite could be a practicable strategy for the remediation of HCB contaminated soil.
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Affiliation(s)
- Jianling Fan
- Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, Jiangsu Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, School of Environmental Science and Engineering, Nanjing University of Information Science and Technology, 219 Ningliu Road, Nanjing 210044, China
| | - Cuiying Liu
- Jiangsu Key Laboratory of Agricultural Meteorology, School of Applied Meteorology, Nanjing University of Information Science and Technology, 219 Ningliu Road, Nanjing 210044, China.
| | - Jinjin Zheng
- School of Changwang, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Yang Song
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
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Yuan C, Zhao L, Tong L, Wang L, Ke Z, Yang Y, He J. Expression and Characterization of 3,6-Dihydroxy-picolinic Acid Decarboxylase PicC of Bordetella bronchiseptica RB50. Microorganisms 2023; 11:microorganisms11040854. [PMID: 37110277 PMCID: PMC10142695 DOI: 10.3390/microorganisms11040854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 03/24/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023] Open
Abstract
Picolinic acid (PA) is a typical mono-carboxylated pyridine derivative produced by human/animals or microorganisms which could be served as nutrients for bacteria. Most Bordetella strains are pathogens causing pertussis or respiratory disease in humans and/or various animals. Previous studies indicated that Bordetella strains harbor the PA degradation pic gene cluster. However, the degradation of PA by Bordetella strains remains unknown. In this study, a reference strain of genus Bordetella, B. bronchiseptica RB50, was investigated. The organization of pic gene cluster of strain RB50 was found to be similar with that of Alcaligenes faecalis, in which the sequence similarities of each Pic proteins are between 60% to 80% except for PicB2 (47% similarity). The 3,6-dihydroxypicolinic acid (3,6DHPA) decarboxylase gene (BB0271, designated as picCRB50) of strain RB50 was synthesized and over-expressed in E. coli BL21(DE3). The PicCRB50 showed 75% amino acid similarities against known PicC from Alcaligenes faecalis. The purified PicCRB50 can efficiently transform 3,6DHPA to 2,5-dihydroxypyridine. The PicCRB50 exhibits optimal activities at pH 7.0, 35 °C, and the Km and kcat values of PicCRB50 for 3,6DHPA were 20.41 ± 2.60 μM and 7.61 ± 0.53 S−1, respectively. The present study provided new insights into the biodegradation of PA by pathogens of Bordetella spp.
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Affiliation(s)
- Cansheng Yuan
- College of Rural Revitalization, Jiangsu Open University, Nanjing 210036, China
| | - Lingling Zhao
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Lu Tong
- Suzhou Kaisiling Environmental Sci-Technology Co., Ltd., Suzhou 215413, China
| | - Lin Wang
- College of Rural Revitalization, Jiangsu Open University, Nanjing 210036, China
| | - Zhuang Ke
- College of Rural Revitalization, Jiangsu Open University, Nanjing 210036, China
| | - Ying Yang
- College of Rural Revitalization, Jiangsu Open University, Nanjing 210036, China
| | - Jian He
- College of Rural Revitalization, Jiangsu Open University, Nanjing 210036, China
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence:
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Orhan F, Ceyran E, Akincioğlu A. Optimization of ectoine production from Nesterenkonia xinjiangensis and one-step ectoine purification. BIORESOURCE TECHNOLOGY 2023; 371:128646. [PMID: 36681344 DOI: 10.1016/j.biortech.2023.128646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/13/2023] [Accepted: 01/16/2023] [Indexed: 06/17/2023]
Abstract
In the current study, the optimization of ectoine production byNesterenkonia xinjiangensisand purification of ectoine from the bacterial cell extract were performed for the first time. Various carbon sources (glucose, sucrose, maltose, lactose, mannitol, and xylose) and nitrogen sources (ammonium nitrate, ammonium phosphate, ammonium chloride, ammonium oxalate, ammonium sulphate, and ammonium acetate), were used to optimize ectoine production. Subsequently, the effects of salt, pH and, concentrations of carbon and nitrogen source on ectoine production were optimized by response surface methodology (RSM). Ultimately, high pure (over 99%) and yield (98%) of ectoine from bacterial cells extracted was obtained by a single-step process using cation exchange chromatography. This study provides information that higher ectoine production can be achieved from this bacterial isolate by optimizing the factors influencing ectoine production and thus can be used as a new and alternative ectoine producer.
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Affiliation(s)
- Furkan Orhan
- Agri Ibrahim Cecen University, Art and Science Faculty, Department of Molecular Biology and Genetics, 4100 Agri, Turkey; Central Research and Application Laboratory, Agri Ibrahim Cecen University, Agri, Turkey.
| | - Ertuğrul Ceyran
- Central Research and Application Laboratory, Agri Ibrahim Cecen University, Agri, Turkey
| | - Akın Akincioğlu
- Central Research and Application Laboratory, Agri Ibrahim Cecen University, Agri, Turkey; Vocational School, Agri Ibrahim Cecen University, Agri, Turkey
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Jiang H, Bao J, Xing Y, Cao G, Li X, Chen Q. Metabolomic and metagenomic analyses of the Chinese mitten crab Eriocheir sinensis after challenge with Metschnikowia bicuspidata. Front Microbiol 2022; 13:990737. [PMID: 36212869 PMCID: PMC9538530 DOI: 10.3389/fmicb.2022.990737] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 09/08/2022] [Indexed: 11/13/2022] Open
Abstract
Milky disease caused by Metschnikowia bicuspidata fungus has significantly harmed the Chinese mitten crab Eriocheir sinensis aquaculture industry. However, the effect of M. bicuspidata infection on the metabolism and intestinal flora of the crab remains unclear. In this study, we aimed to explore the changes in the metabolism and intestinal flora E. sinensis after 48 h of infection with M. bicuspidata, using metabolomic and metagenomic analyses. Metabolomic analysis results revealed 420 significantly different metabolites between the infected and control groups, and these metabolites were enriched in 58 metabolic pathways. M. bicuspidata infection decreased the levels of metabolites related to amino acid biosynthesis, the tricarboxylic acid cycle, as well as lysine, histidine, linolenic, arachidonic, and linoleic acid metabolism. These results indicated that M. bicuspidata infection significantly affected the energy metabolism, growth, and immunity of E. sinensis. The results of metagenomic analysis showed that the anaerobes and ascomycetes populations significantly increased and decreased, respectively, after M. bicuspidata infection. These changes in intestinal flora significantly upregulated metabolic and synthetic pathways while downregulating immunity-related pathways. The results of integrated metabolomic and metagenomic analyses showed that 55 differentially expressed genes and 28 operational taxonomic units were correlated with 420 differential metabolites. Thus, the intestinal flora changes caused by M. bicuspidata infection also affected the metabolites. This study provides novel insights into the metabolic-and intestinal microflora-based effects of M. bicuspidata infection in E. sinensis, as well as a theoretical basis for the interaction between fungi and crustaceans.
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Affiliation(s)
- Hongbo Jiang
- Aquaculture Department, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, Shenyang Agricultural University, Shenyang, China
| | - Jie Bao
- Aquaculture Department, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yuenan Xing
- Aquaculture Department, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Gangnan Cao
- Aquaculture Department, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Xiaodong Li
- Aquaculture Department, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Qijun Chen
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, Shenyang Agricultural University, Shenyang, China
- *Correspondence: Qijun Chen,
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Álvarez Márquez DE. Principales microorganismos sulfato reductores (MSR) de reactores anaerobios alimentados con efluentes ácidos, una revisión bibliográfica. REVISTA COLOMBIANA DE BIOTECNOLOGÍA 2022. [DOI: 10.15446/rev.colomb.biote.v24n1.100963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
En esta investigación bibliográfica se observa una gran variedad de especies responsables de precipitar a cuatro metales de interés (Cu, Pb, Zn y Fe). En la mayoría de las investigaciones no solamente precipitan estos metales, sino que otros elementos que están presentes en cada investigación. Los artículos aquí mencionados tienen una relación directa con el efluente proveniente de la operación unitaria de flotación. Aportan conocimiento acerca del proceso de sulfato-reducción, comprendiendo el mecanismo mediante microorganismos con características específicas, especialmente su versatilidad pues se desarrollan en diferentes ecosistemas. Se observa que varias especies, como Desulfobacter o Desulfovibrio son comunes pues tienen condiciones relativamente sencillas para desarrollarse. Los MSR son eficientes para reducir la acidez del agua (de la operación unitaria de flotación de una mina, de cocinas, de corrientes marinas, etc.). También lo son para precipitar diferentes elementos pues no requieren de algún agente externo salvo en contadas ocasiones donde debe actuar un catalizador. Hay investigaciones sobre nutrientes que deben adicionarse para incrementar su actividad. Los artículos revisados reconocieron las variables a controlar para obtener buenos resultados en la remoción de metales y su impacto en el ambiente. Es de vital importancia el desarrollo de proyectos que tomen un sistema natural como la degradación anaerobia para alcanzar un punto en el cual la tecnología y el ambiente puedan convivir logrando bienes de consumo sin causar daños irreparables a la naturaleza.
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Alvarado V, Hsu SC, Wu Z, Zhuang H, Lee PH, Guest JS. Roadmap from Microbial Communities to Individuality Modeling for Anaerobic Digestion of Sewage Sludge. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:6596-6607. [PMID: 35476456 DOI: 10.1021/acs.est.1c05258] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Biological models describing anaerobic digestion (AD) of sewage sludge have been widely applied to test various control and operation strategies. Anaerobic digestion model 1 (ADM1) provides a generic platform that includes the main processes of AD, excluding homoacetogenesis and the microbial structure. Homoacetogenic bacteria have been identified as important competitors for hydrogen consumption and acetate production. Although recent advances in meta-omics techniques have improved our characterization of AD microbial communities, conventional models treat functional groups as homogeneous and overlook the physiology and behavior of microbial individuality, limiting insights into mechanisms governing process performance. A novel microbial individuality model (MIM) that integrates kinetics, energetics, and agent-based modeling to describe a microbiome's behavior as heterogenic populations, including homoacetogenesis, was developed. The MIM was validated with two datasets from previous studies through daily biogas production, methane content, compound concentrations, and microbial relative abundance changes. The MIM identified the emergence of Methanosaeta at low concentrations of acetate. Moreover, this simulation supports experimental studies confirming that the overlooked homoacetogenesis is an important hydrogen sink in AD. Validated MIMs are expected to provide insights into syntrophic and competitive interactions among microbiomes in AD systems while testing different operational parameters in a virtual environment. The MIM offers a methodological framework to other biological treatment systems and their microbial community dynamics.
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Affiliation(s)
- Valeria Alvarado
- The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Shu-Chien Hsu
- The Hong Kong Polytechnic University, Hung Hom, Kowloon , Hong Kong
| | - Zhuoying Wu
- Imperial College London, London SW7 2AZ, United Kingdom
| | - Huichuan Zhuang
- The Hong Kong Polytechnic University, Hung Hom, Kowloon , Hong Kong
| | - Po-Heng Lee
- Imperial College London, London SW7 2AZ, United Kingdom
| | - Jeremy S Guest
- University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
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Wakamatsu T, Mizobuchi S, Mori F, Futagami T, Terada T, Morono Y. Construction of Aerobic/Anaerobic-Substrate-Induced Gene Expression Procedure for Exploration of Metagenomes From Subseafloor Sediments. Front Microbiol 2022; 12:726024. [PMID: 35095779 PMCID: PMC8793675 DOI: 10.3389/fmicb.2021.726024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 12/17/2021] [Indexed: 11/13/2022] Open
Abstract
Substrate-induced gene expression (SIGEX) is a high-throughput promoter-trap method. It is a function-based metagenomic screening tool that relies on transcriptional activation of a reporter gene green fluorescence protein (gfp) by a metagenomic DNA library upon induction with a substrate. However, its use is limited because of the relatively small size of metagenomic DNA libraries and incompatibility with screening metagenomes from anaerobic environments. In this study, these limitations of SIGEX were addressed by fine-tuning metagenome DNA library construction protocol and by using Evoglow, a green fluorescent protein that forms a chromophore even under anaerobic conditions. Two metagenomic libraries were constructed for subseafloor sediments offshore Shimokita Peninsula (Pacific Ocean) and offshore Joetsu (Japan Sea). The library construction protocol was improved by (a) eliminating short DNA fragments, (b) applying topoisomerase-based high-efficiency ligation, (c) optimizing insert DNA concentration, and (d) column-based DNA enrichment. This led to a successful construction of metagenome DNA libraries of approximately 6 Gbp for both samples. SIGEX screening using five aromatic compounds (benzoate, 3-chlorobenzoate, 3-hydroxybenzoate, phenol, and 2,4-dichlorophenol) under aerobic and anaerobic conditions revealed significant differences in the inducible clone ratios under these conditions. 3-Chlorobenzoate and 2,4-dichlorophenol led to a higher induction ratio than that for the other non-chlorinated aromatic compounds under both aerobic and anaerobic conditions. After the further screening of induced clones, a clone induced by 3-chlorobenzoate only under anaerobic conditions was isolated and characterized. The clone harbors a DNA insert that encodes putative open reading frames of unknown function. Previous aerobic SIGEX attempts succeeded in the isolation of gene fragments from anaerobes. This study demonstrated that some gene fragments require a strict in vivo reducing environment to function and may be potentially missed when screened by aerobic induction. The newly developed anaerobic SIGEX scheme will facilitate functional exploration of metagenomes from the anaerobic biosphere.
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Affiliation(s)
- Taisuke Wakamatsu
- Agricultural Sciences, Graduate School of Integrated Arts and Sciences, Kochi University, Kōchi, Japan
| | - Saki Mizobuchi
- Agricultural Sciences, Graduate School of Integrated Arts and Sciences, Kochi University, Kōchi, Japan
| | - Fumiaki Mori
- Geomicrobiology Group, Kochi Institute for Core Smaple Research, Japan Agency for Marine-Earth Science and Technology, Kōchi, Japan
| | - Taiki Futagami
- Education and Research Center for Fermentation Studies, Faculty of Agriculture, Kagoshima University, Kagoshima, Japan
| | | | - Yuki Morono
- Geomicrobiology Group, Kochi Institute for Core Smaple Research, Japan Agency for Marine-Earth Science and Technology, Kōchi, Japan
- *Correspondence: Yuki Morono,
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Tirumalai MR, Anane-Bediakoh D, Rajesh S, Fox GE. Net Charges of the Ribosomal Proteins of the S10 and spc Clusters of Halophiles Are Inversely Related to the Degree of Halotolerance. Microbiol Spectr 2021; 9:e0178221. [PMID: 34908470 PMCID: PMC8672879 DOI: 10.1128/spectrum.01782-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 11/24/2021] [Indexed: 11/20/2022] Open
Abstract
Net positive charge(s) on ribosomal proteins (r-proteins) have been reported to influence the assembly and folding of ribosomes. A high percentage of r-proteins from extremely halophilic archaea are known to be acidic or even negatively charged. Those proteins that remain positively charged are typically far less positively charged. Here, the analysis is extended to non-archaeal halophilic bacteria, eukaryotes, and halotolerant archaea. The net charges (pH 7.4) of the r-proteins that comprise the S10-spc operon/cluster from individual microbial and eukaryotic genomes were estimated and intercompared. It was observed that, as a general rule, the net charges of individual proteins remained mostly basic as the salt tolerance of the bacterial strains increased from 5 to 15%. The most striking exceptions were the extremely halophilic bacterial strains, Salinibacter ruber SD01, Acetohalobium arabaticum DSM 5501 and Selenihalanaerobacter shriftii ATCC BAA-73, which are reported to require a minimum of 18% to 21% salt for their growth. All three strains have higher numbers of acidic S10-spc cluster r-proteins than what is seen in the moderate halophiles or the halotolerant strains. Of the individual proteins, only uL2 never became acidic. uS14 and uL16 also seldom became acidic. The net negative charges on several of the S10-spc cluster r-proteins are a feature generally shared by all extremely halophilic archaea and bacteria. The S10-spc cluster r-proteins of halophilic fungi and algae (eukaryotes) were exceptions: these were positively charged despite the halophilicity of the organisms. IMPORTANCE The net charges (at pH 7.4) of the ribosomal proteins (r-proteins) that comprise the S10-spc cluster show an inverse relationship with the halophilicity/halotolerance levels in both bacteria and archaea. In non-halophilic bacteria, the S10-spc cluster r-proteins are generally basic (positively charged), while the rest of the proteomes in these strains are generally acidic. On the other hand, the whole proteomes of the extremely halophilic strains are overall negatively charged, including the S10-spc cluster r-proteins. Given that the distribution of charged residues in the ribosome exit tunnel influences cotranslational folding, the contrasting charges observed in the S10-spc cluster r-proteins have potential implications for the rate of passage of these proteins through the ribosomal exit tunnel. Furthermore, the universal protein uL2, which lies in the oldest part of the ribosome, is always positively charged irrespective of the strain/organism it belongs to. This has implications for its role in the prebiotic context.
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Affiliation(s)
- Madhan R. Tirumalai
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
| | | | - Sidharth Rajesh
- Clements High School (Class of 2023), Fort Bend Independent School District, Sugar Land, Texas, USA
| | - George E. Fox
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
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11
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Janesch E, Pereira J, Neubauer P, Junne S. Phase Separation in Anaerobic Digestion: A Potential for Easier Process Combination? FRONTIERS IN CHEMICAL ENGINEERING 2021. [DOI: 10.3389/fceng.2021.711971] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The flexibilization of bioenergy production has the potential to counteract partly other fluctuating renewable energy sources (such as wind and solar power). As a weather-independent energy source, anaerobic digestion (AD) can offer on-demand energy supply through biogas production. Separation of the stages in anaerobic digestion represents a promising strategy for the flexibilization of the fermentative part of biogas production. Segregation in two reactor systems facilitates monitoring and control of the provision of educts to the second methanogenic stage, thus controlling biogas production. Two-stage operation has proven to reach similar or even higher methane yields and biogas purities than single-stage operation in many different fields of application. It furthermore allows methanation of green hydrogen and an easier combination of material and energy use of many biogenic raw and residual biomass sources. A lot of research has been conducted in recent years regarding the process phase separation in multi-stage AD operation, which includes more than two stages. Reliable monitoring tools, coupled with effluent recirculation, bioaugmentation and simulation have the potential to overcome the current drawbacks of a sophisticated and unstable operation. This review aims to summarize recent developments, new perspectives for coupling processes for energy and material use and a system integration of AD for power-to-gas applications. Thereby, cell physiological and engineering aspects as well as the basic economic feasibility are discussed. As conclusion, monitoring and control concepts as well as suitable separation technologies and finally the data basis for techno-economic and ecologic assessments have to be improved.
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12
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Oliverio AM, Power JF, Washburne A, Cary SC, Stott MB, Fierer N. The ecology and diversity of microbial eukaryotes in geothermal springs. THE ISME JOURNAL 2018; 12:1918-1928. [PMID: 29662145 PMCID: PMC6052046 DOI: 10.1038/s41396-018-0104-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 01/18/2018] [Accepted: 03/05/2018] [Indexed: 11/09/2022]
Abstract
Decades of research into the Bacteria and Archaea living in geothermal spring ecosystems have yielded great insight into the diversity of life and organismal adaptations to extreme environmental conditions. Surprisingly, while microbial eukaryotes (protists) are also ubiquitous in many environments, their diversity across geothermal springs has mostly been ignored. We used high-throughput sequencing to illuminate the diversity and structure of microbial eukaryotic communities found in 160 geothermal springs with broad ranges in temperature and pH across the Taupō Volcanic Zone in New Zealand. Protistan communities were moderately predictable in composition and varied most strongly across gradients in pH and temperature. Moreover, this variation mirrored patterns observed for bacterial and archaeal communities across the same spring samples, highlighting that there are similar ecological constraints across the tree of life. While extreme pH values were associated with declining protist diversity, high temperature springs harbored substantial amounts of protist diversity. Although protists are often overlooked in geothermal springs and other extreme environments, our results indicate that such environments can host distinct and diverse protistan communities.
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Affiliation(s)
- Angela M Oliverio
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, 80309, USA
| | - Jean F Power
- Extremophile Research Group, GNS Science, Private Bag 2000, Taupō, 3352, New Zealand
- Thermophile Research Unit, School of Science, University of Waikato, Private Bag 3105, Hamilton, 3240, New Zealand
| | - Alex Washburne
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, 59717, USA
| | - S Craig Cary
- Thermophile Research Unit, School of Science, University of Waikato, Private Bag 3105, Hamilton, 3240, New Zealand
| | - Matthew B Stott
- Extremophile Research Group, GNS Science, Private Bag 2000, Taupō, 3352, New Zealand
| | - Noah Fierer
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA.
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, 80309, USA.
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13
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Gonzalez-Fernandez C, Barreiro-Vescovo S, de Godos I, Fernandez M, Zouhayr A, Ballesteros M. Biochemical methane potential of microalgae biomass using different microbial inocula. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:184. [PMID: 29988471 PMCID: PMC6025826 DOI: 10.1186/s13068-018-1188-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 06/25/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Microalgae biomass is regarded as a potential feedstock for bioenergy purposes through anaerobic digestion (AD). Even though AD is a well-proven technology, the use of new feedstocks requires in-depth studies. A lot of research has been conducted assessing methane yield without paying attention to the anaerobic microbiome and their activities. For such a goal, the present investigation was designed to link methane yield to those two later sludge characteristics. In this sense, different anaerobic sources were tested, namely adapted to microalgae biomass and adapted to sewage sludge. RESULTS Despite the registered differences for the anaerobic microbiome analysis and specific methane activities towards model substrates, sludge adapted to digest sewage sludge did not affect the methane yield of Chlorella sorokiniana and Scenedesmus sp. Opposite to that, sludge samples adapted to digest microalgae exhibited a concomitant increase in methane yield together with increasing digestion temperatures. More specifically, the values attained were 63.4 ± 1.5, 79.2 ± 3.1 and 108.2 ± 1.9 mL CH4 g COD in-1 for psychrophilic, mesophilic and thermophilic digestions, respectively. While psycro- and mesophilic digestion supported similar yields (most probably linked to their anaerobic microbiome resemblance), the values attained for thermophilic digestion evidenced the usefulness of having a highly specific microbiome. The relative abundance of Firmicutes, particularly Clostridia, and Proteobacteria together with an important abundance of hydrogenotrophic methanogens was highlighted in this inoculum. CONCLUSION Overall, this study showed that working with tailored anaerobic microbiome could help avoiding pretreatments devoted to methane yield enhancement.
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Affiliation(s)
| | | | | | | | | | - Mercedes Ballesteros
- Biotechnological Processes Unit, IMDEA Energy, Madrid, Spain
- Biofuels Unit, CIEMAT, Madrid, Spain
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14
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Muhammad A, Fang Y, Hou Y, Shi Z. The Gut Entomotype of Red Palm Weevil Rhynchophorus ferrugineus Olivier (Coleoptera: Dryophthoridae) and Their Effect on Host Nutrition Metabolism. Front Microbiol 2017; 8:2291. [PMID: 29209298 PMCID: PMC5702300 DOI: 10.3389/fmicb.2017.02291] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 11/06/2017] [Indexed: 12/20/2022] Open
Abstract
For invasive insects, the potential roles of gut microbiota in exploiting new food resources and spreading remain elusive. Red palm weevil (RPW), Rhynchophorus ferrugineus Olivier, is an invasive destructive pest which feeds on nutrient-poor tender tissues and has caused extensive mortality of palm trees. The microbes associated with insects can improve their nutrition assimilation. However, experimental evidence on the interactions between RPW and its gut microbiota is still absent. The aim of this study is to determine the dynamics changes and the bacterial entomotype in the RPW gut and its potential physiological roles. Here, we confirmed RPW harbors a complex gut microbiota mainly constituted by bacteria in the families Enterobacteriaceae, Lactobacillaceae, Entomoplasmataceae, and Streptococcaceae. RPW gut microbiota exhibited a highly stable microbial community with low variance in abundance across different life stages and host plants. Furthermore, the abundance of Enterobacteriaceae was markedly increased but that of Acetobacteraceae was reduced significantly after administration of antibiotics. Although no significant effects were found on the body weight gain of RPW larvae, these alterations dramatically decreased the concentration of hemolymph protein and glucose while that of hemolymph triglyceride increased. In the gut of wild-caught RPW larvae, seven bacterial species in the genera Klebsiella, Serratia, Enterobacter, and Citrobacter were shown to have an ability to degrade cellulose. Together, RPW accommodate a stable gut microbiota which can degrade plant polysaccharides and confer their host optimal adaptation to its environment by modulating its metabolism.
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Affiliation(s)
- Abrar Muhammad
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fujian, China
- Fujian Provincial Key Laboratory of Insect Ecology, College of Plant Protection, Fujian Agriculture and Forestry University, Fujian, China
| | - Ya Fang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fujian, China
- Fujian Provincial Key Laboratory of Insect Ecology, College of Plant Protection, Fujian Agriculture and Forestry University, Fujian, China
| | - Youming Hou
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fujian, China
- Fujian Provincial Key Laboratory of Insect Ecology, College of Plant Protection, Fujian Agriculture and Forestry University, Fujian, China
| | - Zhanghong Shi
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fujian, China
- Fujian Provincial Key Laboratory of Insect Ecology, College of Plant Protection, Fujian Agriculture and Forestry University, Fujian, China
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15
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Liu Z, He Z, Huang H, Ran X, Oluwafunmilayo AO, Lu Z. pH Stress-Induced Cooperation between Rhodococcus ruber YYL and Bacillus cereus MLY1 in Biodegradation of Tetrahydrofuran. Front Microbiol 2017; 8:2297. [PMID: 29209303 PMCID: PMC5702389 DOI: 10.3389/fmicb.2017.02297] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 11/07/2017] [Indexed: 11/28/2022] Open
Abstract
Microbial consortia consisting of cooperational strains exhibit biodegradation performance superior to that of single microbial strains and improved remediation efficiency by relieving the environmental stress. Tetrahydrofuran (THF), a universal solvent widely used in chemical and pharmaceutical synthesis, significantly affects the environment. As a refractory pollutant, THF can be degraded by some microbial strains under suitable conditions. There are often a variety of stresses, especially pH stress, that inhibit the THF-degradation efficiency of microbial consortia. Therefore, it is necessary to study the molecular mechanisms of microbial cooperational degradation of THF. In this study, under conditions of low pH (initial pH = 7.0) stress, a synergistic promotion of the THF degradation capability of the strain Rhodococcus ruber YYL was found in the presence of a non-THF degrading strain Bacillus cereus MLY1. Metatranscriptome analysis revealed that the low pH stress induced the strain YYL to up-regulate the genes involved in anti-oxidation, mutation, steroid and bile acid metabolism, and translation, while simultaneously down-regulating the genes involved in ATP production. In the co-culture system, strain MLY1 provides fatty acids, ATP, and amino acids for strain YYL in response to low pH stress during THF degradation. In return, YYL shares the metabolic intermediates of THF with MLY1 as carbon sources. This study provides the preliminary mechanism to understand how microbial consortia improve the degradation efficiency of refractory furan pollutants under environmental stress conditions.
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Affiliation(s)
- Zubi Liu
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Zhixing He
- College of Basic Medical Science, Zhejiang Chinese Medical University, Hangzhou, China
| | - Hui Huang
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Xuebin Ran
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | | | - Zhenmei Lu
- College of Life Sciences, Zhejiang University, Hangzhou, China
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16
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Scoma A, Coma M, Kerckhof FM, Boon N, Rabaey K. Efficient molasses fermentation under high salinity by inocula of marine and terrestrial origin. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:23. [PMID: 28163780 PMCID: PMC5282813 DOI: 10.1186/s13068-017-0701-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 01/05/2017] [Indexed: 05/14/2023]
Abstract
BACKGROUND Molasses is a dense and saline by-product of the sugar agroindustry. Its high organic content potentially fuels a myriad of renewable products of industrial interest. However, the biotechnological exploitation of molasses is mainly hampered by the high concentration of salts, an issue that is nowadays tackled through dilution. In the present study, the performance of microbial communities derived from marine sediment was compared to that of communities from a terrestrial environment (anaerobic digester sludge). The aim was to test whether adaptation to salinity represented an advantage for fermenting molasses into renewable chemicals such as volatile fatty acids (VFAs) although high sugar concentrations are uncommon to marine sediment, contrary to anaerobic digesters. RESULTS Terrestrial and marine microbial communities were enriched in consecutive batches at different initial pH values (pHi; either 6 or 7) and molasses dilutions (equivalent to organic loading rates (OLRs) of 1 or 5 gCOD L-1 d-1) to determine the best VFA production conditions. Marine communities were supplied with NaCl to maintain their native salinity. Due to molasses inherent salinity, terrestrial communities experienced conditions comparable to brackish or saline waters (20-47 mS cm-1), while marine conditions resembled brine waters (>47 mS cm-1). Enrichments at optimal conditions of OLR 5 gCOD L-1 d-1 and pHi 7 were transferred into packed-bed biofilm reactors operated continuously. The reactors were first operated at 5 gCOD L-1 d-1, which was later increased to OLR 10 gCOD L-1 d-1. Terrestrial and marine reactors had different gas production and community structures but identical, remarkably high VFA bioconversion yields (above 85%) which were obtained with conductivities up to 90 mS cm-1. COD-to-VFA conversion rates were comparable to the highest reported in literature while processing other organic leftovers at much lower salinities. CONCLUSIONS Although salinity represents a major driver for microbial community structure, proper acclimation yielded highly efficient systems treating molasses, irrespective of the inoculum origin. Selection of equivalent pathways in communities derived from different environments suggests that culture conditions select for specific functionalities rather than microbial representatives. Mass balances, microbial community composition, and biochemical analysis indicate that biomass turnover rather than methanogenesis represents the main limitation to further increasing VFA production with molasses. This information is relevant to moving towards molasses fermentation to industrial application.
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Affiliation(s)
- Alberto Scoma
- Center of Microbial Ecology and Technology (CMET), University of Gent, Coupure Links 653, 9000 Ghent, Belgium
- Center for Geomicrobiology, Aarhus University, Ny Munkegade 116, 8000 Aarhus C, Denmark
| | - Marta Coma
- Center of Microbial Ecology and Technology (CMET), University of Gent, Coupure Links 653, 9000 Ghent, Belgium
- Centre for Sustainable Chemical Technologies (CSCT), University of Bath, Claverton Down, Bath, BA2 7AY UK
| | - Frederiek-Maarten Kerckhof
- Center of Microbial Ecology and Technology (CMET), University of Gent, Coupure Links 653, 9000 Ghent, Belgium
| | - Nico Boon
- Center of Microbial Ecology and Technology (CMET), University of Gent, Coupure Links 653, 9000 Ghent, Belgium
| | - Korneel Rabaey
- Center of Microbial Ecology and Technology (CMET), University of Gent, Coupure Links 653, 9000 Ghent, Belgium
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17
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Scoma A, Coma M, Kerckhof FM, Boon N, Rabaey K. Efficient molasses fermentation under high salinity by inocula of marine and terrestrial origin. BIOTECHNOLOGY FOR BIOFUELS 2017. [PMID: 28163780 DOI: 10.1186/s13068-017-0701-8%3fsite%3dbiotechnologyforbiofuels.biomedcentral.com] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
BACKGROUND Molasses is a dense and saline by-product of the sugar agroindustry. Its high organic content potentially fuels a myriad of renewable products of industrial interest. However, the biotechnological exploitation of molasses is mainly hampered by the high concentration of salts, an issue that is nowadays tackled through dilution. In the present study, the performance of microbial communities derived from marine sediment was compared to that of communities from a terrestrial environment (anaerobic digester sludge). The aim was to test whether adaptation to salinity represented an advantage for fermenting molasses into renewable chemicals such as volatile fatty acids (VFAs) although high sugar concentrations are uncommon to marine sediment, contrary to anaerobic digesters. RESULTS Terrestrial and marine microbial communities were enriched in consecutive batches at different initial pH values (pHi; either 6 or 7) and molasses dilutions (equivalent to organic loading rates (OLRs) of 1 or 5 gCOD L-1 d-1) to determine the best VFA production conditions. Marine communities were supplied with NaCl to maintain their native salinity. Due to molasses inherent salinity, terrestrial communities experienced conditions comparable to brackish or saline waters (20-47 mS cm-1), while marine conditions resembled brine waters (>47 mS cm-1). Enrichments at optimal conditions of OLR 5 gCOD L-1 d-1 and pHi 7 were transferred into packed-bed biofilm reactors operated continuously. The reactors were first operated at 5 gCOD L-1 d-1, which was later increased to OLR 10 gCOD L-1 d-1. Terrestrial and marine reactors had different gas production and community structures but identical, remarkably high VFA bioconversion yields (above 85%) which were obtained with conductivities up to 90 mS cm-1. COD-to-VFA conversion rates were comparable to the highest reported in literature while processing other organic leftovers at much lower salinities. CONCLUSIONS Although salinity represents a major driver for microbial community structure, proper acclimation yielded highly efficient systems treating molasses, irrespective of the inoculum origin. Selection of equivalent pathways in communities derived from different environments suggests that culture conditions select for specific functionalities rather than microbial representatives. Mass balances, microbial community composition, and biochemical analysis indicate that biomass turnover rather than methanogenesis represents the main limitation to further increasing VFA production with molasses. This information is relevant to moving towards molasses fermentation to industrial application.
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Affiliation(s)
- Alberto Scoma
- Center of Microbial Ecology and Technology (CMET), University of Gent, Coupure Links 653, 9000 Ghent, Belgium
- Center for Geomicrobiology, Aarhus University, Ny Munkegade 116, 8000 Aarhus C, Denmark
| | - Marta Coma
- Center of Microbial Ecology and Technology (CMET), University of Gent, Coupure Links 653, 9000 Ghent, Belgium
- Centre for Sustainable Chemical Technologies (CSCT), University of Bath, Claverton Down, Bath, BA2 7AY UK
| | - Frederiek-Maarten Kerckhof
- Center of Microbial Ecology and Technology (CMET), University of Gent, Coupure Links 653, 9000 Ghent, Belgium
| | - Nico Boon
- Center of Microbial Ecology and Technology (CMET), University of Gent, Coupure Links 653, 9000 Ghent, Belgium
| | - Korneel Rabaey
- Center of Microbial Ecology and Technology (CMET), University of Gent, Coupure Links 653, 9000 Ghent, Belgium
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18
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Venkiteshwaran K, Bocher B, Maki J, Zitomer D. Relating Anaerobic Digestion Microbial Community and Process Function. Microbiol Insights 2016; 8:37-44. [PMID: 27127410 PMCID: PMC4841157 DOI: 10.4137/mbi.s33593] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 01/19/2016] [Accepted: 01/25/2016] [Indexed: 01/01/2023] Open
Abstract
Anaerobic digestion (AD) involves a consortium of microorganisms that convert substrates into biogas containing methane for renewable energy. The technology has suffered from the perception of being periodically unstable due to limited understanding of the relationship between microbial community structure and function. The emphasis of this review is to describe microbial communities in digesters and quantitative and qualitative relationships between community structure and digester function. Progress has been made in the past few decades to identify key microorganisms influencing AD. Yet, more work is required to realize robust, quantitative relationships between microbial community structure and functions such as methane production rate and resilience after perturbations. Other promising areas of research for improved AD may include methods to increase/control (1) hydrolysis rate, (2) direct interspecies electron transfer to methanogens, (3) community structure-function relationships of methanogens, (4) methanogenesis via acetate oxidation, and (5) bioaugmentation to study community-activity relationships or improve engineered bioprocesses.
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Affiliation(s)
- Kaushik Venkiteshwaran
- Department of Civil, Construction and Environmental Engineering, Marquette University, Milwaukee, WI, USA
| | | | - James Maki
- Department of Biological Sciences, Marquette University, Milwaukee, WI, USA
| | - Daniel Zitomer
- Department of Civil, Construction and Environmental Engineering, Marquette University, Milwaukee, WI, USA
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19
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Zabetakis KM, Niño de Guzmán GT, Torrents A, Yarwood S. Toxicity of zero-valent iron nanoparticles to a trichloroethylene-degrading groundwater microbial community. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2015; 50:794-805. [PMID: 26030685 DOI: 10.1080/10934529.2015.1019796] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The microbiological impact of zero-valent iron used in the remediation of groundwater was investigated by exposing a trichloroethylene-degrading anaerobic microbial community to two types of iron nanoparticles. Changes in total bacterial and archaeal population numbers were analyzed using qPCR and were compared to results from a blank and negative control to assess for microbial toxicity. Additionally, the results were compared to those of samples exposed to silver nanoparticles and iron filings in an attempt to discern the source of toxicity. Statistical analysis revealed that the three different iron treatments were equally toxic to the total bacteria and archaea populations, as compared with the controls. Conversely, the silver nanoparticles had a limited statistical impact when compared to the controls and increased the microbial populations in some instances. Therefore, the findings suggest that zero-valent iron toxicity does not result from a unique nanoparticle-based effect.
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Affiliation(s)
- Kara M Zabetakis
- a Marine-Estuarine-Environmental Sciences Department , University of Maryland , College Park , Maryland , USA
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20
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Jia S, Zhang X, Zhang G, Yin A, Zhang S, Li F, Wang L, Zhao D, Yun Q, Tala, Wang J, Sun G, Baabdullah M, Yu X, Hu S, Al-Mssallem IS, Yu J. Seasonally variable intestinal metagenomes of the red palm weevil (Rhynchophorus ferrugineus). Environ Microbiol 2013; 15:3020-9. [PMID: 24102776 PMCID: PMC4253082 DOI: 10.1111/1462-2920.12262] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Revised: 06/26/2013] [Accepted: 08/23/2013] [Indexed: 11/29/2022]
Abstract
The intestinal microbes residing in the red palm weevil (RPW, Rhynchophorus ferrugineus) larva consume tender interior fibrous tissues of date palm trunks. The understanding of such microbiota at molecular level provides vital clues for the biological control of this devastating pest. Using pyrosequencing and shotgun strategy, we first study taxonomic profiles of the microbiota sampled at different months (March, July and November), and then confirm the impact of high-temperature stress on the microbial populations based on data from 16S rRNA amplicons using both field and laboratory samples. We further identify Klebsiella pneumoniae in November and Lactococcus lactis in July as the dominant species of the microbiota. We find that the RPW gut microbiota degrades polysaccharides and sucrose with hydrolases and that different active bacterial species in November and July are responsible for the symbiotic relationship between the microbiota and the host. Our results provide vital information for pest control and cellulolytic bacterial species characterization.
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Affiliation(s)
- Shangang Jia
- Joint Center for Genomics Research, King Abdulaziz City for Science and Technology and Chinese Academy of Sciences, Riyadh, Kingdom of Saudi Arabia.,CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Xiaowei Zhang
- Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology (KACST) and Chinese Academy of Sciences (CAS), Riyadh, Kingdom of Saudi Arabia.,CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Guangyu Zhang
- Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology (KACST) and Chinese Academy of Sciences (CAS), Riyadh, Kingdom of Saudi Arabia.,CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - An Yin
- Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology (KACST) and Chinese Academy of Sciences (CAS), Riyadh, Kingdom of Saudi Arabia.,CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Sun Zhang
- Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology (KACST) and Chinese Academy of Sciences (CAS), Riyadh, Kingdom of Saudi Arabia.,CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Fusen Li
- Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology (KACST) and Chinese Academy of Sciences (CAS), Riyadh, Kingdom of Saudi Arabia.,CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Lei Wang
- Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology (KACST) and Chinese Academy of Sciences (CAS), Riyadh, Kingdom of Saudi Arabia.,CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Duojun Zhao
- Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology (KACST) and Chinese Academy of Sciences (CAS), Riyadh, Kingdom of Saudi Arabia.,CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Quanzheng Yun
- Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology (KACST) and Chinese Academy of Sciences (CAS), Riyadh, Kingdom of Saudi Arabia.,CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Tala
- Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology (KACST) and Chinese Academy of Sciences (CAS), Riyadh, Kingdom of Saudi Arabia.,CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Jixiang Wang
- Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology (KACST) and Chinese Academy of Sciences (CAS), Riyadh, Kingdom of Saudi Arabia.,CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Gaoyuan Sun
- Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology (KACST) and Chinese Academy of Sciences (CAS), Riyadh, Kingdom of Saudi Arabia.,CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Mohammed Baabdullah
- Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology (KACST) and Chinese Academy of Sciences (CAS), Riyadh, Kingdom of Saudi Arabia
| | - Xiaoguang Yu
- Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology (KACST) and Chinese Academy of Sciences (CAS), Riyadh, Kingdom of Saudi Arabia.,CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Songnian Hu
- Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology (KACST) and Chinese Academy of Sciences (CAS), Riyadh, Kingdom of Saudi Arabia.,CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Ibrahim S Al-Mssallem
- Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology (KACST) and Chinese Academy of Sciences (CAS), Riyadh, Kingdom of Saudi Arabia.,Department of Biotechnology, College of Agriculture and Food Sciences, King Faisal University, Hofuf, Kingdom of Saudi Arabia
| | - Jun Yu
- Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology (KACST) and Chinese Academy of Sciences (CAS), Riyadh, Kingdom of Saudi Arabia.,CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
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Liu G, Bettegowda C, Qiao Y, Staedtke V, Chan KWY, Bai R, Li Y, Riggins GJ, Kinzler KW, Bulte JWM, McMahon MT, Gilad AA, Vogelstein B, Zhou S, van Zijl PCM. Noninvasive imaging of infection after treatment with tumor-homing bacteria using Chemical Exchange Saturation Transfer (CEST) MRI. Magn Reson Med 2013; 70:1690-8. [PMID: 24123389 DOI: 10.1002/mrm.24955] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 08/12/2013] [Accepted: 08/22/2013] [Indexed: 12/27/2022]
Abstract
PURPOSE To develop a noninvasive MRI method for determining the germination and infection of tumor-homing bacteria in bacteriolytic cancer therapy using endogenous CEST contrast. METHODS The CEST parameters of the anaerobic gram-positive bacterium Clostridium novyi-NT (C. novyi-NT) were first characterized in vitro, then used to detect C. novyi-NT germination and infection in subcutaneous CT26 colorectal tumor-bearing mice (n = 6) after injection of 300 million bacterial spores. Lipopolysacharide (LPS) injected mice were used to exclude that the changes of CEST MRI were due to inflammation. RESULTS CEST contrast was observed over a broad frequency range for bacterial suspensions in vitro, with the maximum contrast around 2.6 ppm from the water resonance. No signal could be detected for bacterial spores, demonstrating the specificity for germination. In vivo, a significant elevation of CEST contrast was identified in C. novyi-NT infected tumors as compared to those before bacterial germination and infection (P < 0.05; n = 6). No significant change was observed in tumors with LPS-induced sterile inflammation (P > 0.05; n = 4). CONCLUSION Endogenous bacterial CEST contrast (bacCEST) can be used to monitor the germination and proliferation of the therapeutic bacterium C. novyi-NT without a need for exogenous cell labeling probes.
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Affiliation(s)
- Guanshu Liu
- F.M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, Maryland, USA; Department of Radiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Bayraktarov E, Price RE, Ferdelman TG, Finster K. The pH and pCO2 dependence of sulfate reduction in shallow-sea hydrothermal CO2 - venting sediments (Milos Island, Greece). Front Microbiol 2013; 4:111. [PMID: 23658555 PMCID: PMC3647119 DOI: 10.3389/fmicb.2013.00111] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 04/17/2013] [Indexed: 11/13/2022] Open
Abstract
Microbial sulfate reduction (SR) is a dominant process of organic matter mineralization in sulfate-rich anoxic environments at neutral pH. Recent studies have demonstrated SR in low pH environments, but investigations on the microbial activity at variable pH and CO2 partial pressure are still lacking. In this study, the effect of pH and pCO2 on microbial activity was investigated by incubation experiments with radioactive (35)S targeting SR in sediments from the shallow-sea hydrothermal vent system of Milos, Greece, where pH is naturally decreased by CO2 release. Sediments differed in their physicochemical characteristics with distance from the main site of fluid discharge. Adjacent to the vent site (T ~40-75°C, pH ~5), maximal sulfate reduction rates (SRR) were observed between pH 5 and 6. SR in hydrothermally influenced sediments decreased at neutral pH. Sediments unaffected by hydrothermal venting (T ~26°C, pH ~8) expressed the highest SRR between pH 6 and 7. Further experiments investigating the effect of pCO2 on SR revealed a steep decrease in activity when the partial pressure increased from 2 to 3 bar. Findings suggest that sulfate reducing microbial communities associated with hydrothermal vent system are adapted to low pH and high CO2, while communities at control sites required a higher pH for optimal activity.
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Affiliation(s)
- Elisa Bayraktarov
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology Bremen, Germany
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Strobel HJ, Caldwell FC, Dawson KA. Carbohydrate Transport by the Anaerobic Thermophile Clostridium thermocellum LQRI. Appl Environ Microbiol 2010; 61:4012-5. [PMID: 16535164 PMCID: PMC1388600 DOI: 10.1128/aem.61.11.4012-4015.1995] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Clostridium thermocellum is an anaerobic thermophilic bacterium which degrades cellulose and ferments the resulting glucose, cellobiose, and cellodextrins predominantly to ethanol. However, relatively little information was available on carbohydrate uptake by this bacterium. Washed cells internalized intact oligomers as large as cellopentaose. Since cellobiose and cellodextrin phosphorylase activities were detected in the cytosol and were not associated with cell membranes, phosphorylation of carbohydrates occurred intracellularly. Kinetic studies indicated that cellobiose and larger cellodextrins were taken up by a common uptake system while glucose entered via a separate mechanism. When cells were treated with metabolic inhibitors including iodoacetate and arsenate, the uptake of radiolabeled glucose or cellobiose was reduced by as much as 90%, and this reduction was associated with a 95% decline in intracellular ATP content. A combination of the ionophores nigericin and valinomycin abolished the proton-motive force but only slightly decreased transport and ATP. These results suggested that the two modes of carbohydrate transport in C. thermocellum were ATP dependent. This work is the first demonstration of cellodextrin transport by a cellulolytic bacterium.
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Ravot G, Ollivier B, Magot M, Patel B, Crolet J, Fardeau M, Garcia J. Thiosulfate reduction, an important physiological feature shared by members of the order thermotogales. Appl Environ Microbiol 2010; 61:2053-5. [PMID: 16535035 PMCID: PMC1388453 DOI: 10.1128/aem.61.5.2053-2055.1995] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Several members of the order Thermotogales in the domain Bacteria, viz., Thermotoga neapolitana, Thermotoga maritima, Thermosipho africanus, Fervidobacterium islandicum, and Thermotoga strain SEBR 2665, an isolate from an oil well, reduced thiosulfate to sulfide. This reductive process enhanced cellular yields and growth rates of all the members but was more significant with the two hyperthermophiles T. neapolitana and T. maritima. This is the first report of such an occurrence in this group of thermophilic and hyperthermophilic anaerobic bacteria. The results suggest that thiosulfate reduction is important in the geochemical cycling of sulfur in anaerobic thermal environments such as the slightly acidic and neutral-pH volcanic hot springs and oil reservoirs.
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Natural competence in Thermoanaerobacter and Thermoanaerobacterium species. Appl Environ Microbiol 2010; 76:4713-9. [PMID: 20472726 DOI: 10.1128/aem.00402-10] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Low-G+C thermophilic obligate anaerobes in the class Clostridia are considered among the bacteria most resistant to genetic engineering due to the difficulty of introducing foreign DNA, thus limiting the ability to study and exploit their native hydrolytic and fermentative capabilities. Here, we report evidence of natural genetic competence in 13 Thermoanaerobacter and Thermoanaerobacterium strains previously believed to be difficult to transform or genetically recalcitrant. In Thermoanaerobacterium saccharolyticum JW/SL-YS485, natural competence-mediated DNA incorporation occurs during the exponential growth phase with both replicating plasmid and homologous recombination-based integration, and circular or linear DNA. In T. saccharolyticum, disruptions of genes similar to comEA, comEC, and a type IV pilus (T4P) gene operon result in strains unable to incorporate further DNA, suggesting that natural competence occurs via a conserved Gram-positive mechanism. The relative ease of employing natural competence for gene transfer should foster genetic engineering in these industrially relevant organisms, and understanding the mechanisms underlying natural competence may be useful in increasing the applicability of genetic tools to difficult-to-transform organisms.
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Mäkinen AE, Kaksonen AH, Puhakka JA. Thermovorax subterraneus, gen. nov., sp. nov., a thermophilic hydrogen-producing bacterium isolated from geothermally active underground mine. Extremophiles 2009; 13:505-10. [PMID: 19305944 DOI: 10.1007/s00792-009-0235-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2008] [Accepted: 02/26/2009] [Indexed: 11/28/2022]
Abstract
A thermophilic, rod-shaped, motile, Gram-positive, spore-forming bacterium strain 70B(T) was isolated from a geothermally active underground mine in Japan. The temperature and pH range for growth was 50-81 degrees C (optimum 71 degrees C) and 6.2-9.8 (optimum pH 7-7.5), respectively. Growth occurred in the presence 0-2% NaCl (optimum 1% NaCl). Strain 70B(T) could utilize glucose, fructose, mannose, mannitol, pyruvate, cellobiose and tryptone as substrates. Thiosulfate was used as electron acceptor. Major whole-cell fatty acids were iso-C(15:0), C(16:0) DMA (dimethyl acetal), C(16:0) and anteiso-C(15:0). The G+C mol% of the DNA was 44.2%. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the closest relatives of strain 70B(T) were Thermosediminibacter oceani DSM 16646(T) (94% similarity) and Thermosediminibacter litoriperuensis DSM 16647 (93% similarity). The phenotypic, chemotaxonomic and phylogenetic properties suggest that strain 70B(T) represents a novel species in a new genus, for which the name Thermovorax subterraneus gen. nov., sp. nov. is proposed. The type strain of Thermovorax subterraneus is 70B(T) (=DSM 21563 = JCM 15541).
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Affiliation(s)
- Annukka E Mäkinen
- Department of Chemistry and Bioengineering, Tampere University of Technology, P.O. Box 541, 33101, Tampere, Finland.
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Tanaka S, Suda Y, Ikeda K, Ono M, Miyasaka H, Watanabe M, Sasaki K, Hirata K. A novel gene with antisalt and anticadmium stress activities from a halotolerant marine green alga Chlamydomonas sp. W80. FEMS Microbiol Lett 2007; 271:48-52. [PMID: 17391362 DOI: 10.1111/j.1574-6968.2007.00696.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
A novel gene with antistress activities against both salt (NaCl) and cadmium stresses was isolated from the cDNA library of halotolerant green alga Chlamydomonas sp. strain W80 by a functional expression screening with Escherichia coli. The C-terminal region of this protein is responsible for the antistress activity, because N-terminal truncated clone of this gene retains the antistress activity, and the C-terminal truncated clone loses the activity. In the C-terminal region, there is a histidine and aspartic acid-rich domain (HD-rich domain).
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Affiliation(s)
- Satoshi Tanaka
- The Kansai Electric Power Co, Environmental Research Center, Kyoto, Japan
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Bezirtzoglou E, Panagiou A, Savvaidis I, Maipa V. Distribution of Clostridium perfringens in polluted lake environments. Anaerobe 2007; 3:169-72. [PMID: 16887584 DOI: 10.1006/anae.1997.0101] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/1996] [Accepted: 05/02/1997] [Indexed: 11/22/2022]
Abstract
Many of the directives that relate to the prevention of pollution or the improvement of fresh water also relate to lake waters since lake waters ultimately inherit much of the pollution that enters into fresh water. In order to determine the influence of the water depth on Clostridium perfringens, we utilised a new medium, lactose-sulfite (LS) broth, suggested for rapid enumeration and identification of C. perfringens. Duplicate samples were collected at each one of the following sites of the polluted station: surface, 60 cm, 90 cm and bottom (1.18 cm). Membrane filtration equipment was used. All samples were alternatively passed through two membrane filters, the first (20-25 microm pore size) was used for retention of the abundant phytoplankton and the second (porosity 0.45 microm) for C. perfringens. Membranes were placed into the first tube of ten-fold dilutions from 10(1) to 10(4) and incubated aerobically in a waterbath at 46 degrees C for 24 h. The numbers of C. perfringens fluctuated depending on the water depth. Vegetative forms were found only in the bottom sampling; they were never found in surface, 60 cm and 90 cm sampling sites. Sporulated forms were found in all sampling sites with the exception of the surface sampling. Clostridium perfringens as an anaerobic bacterium never occurred in the surface waters in vegetative or spore forms, even if the waters were extremely polluted by domestic or industrial activities. Vegetative forms occurred only in the bottom samples but spore forms which are more resistant to various environmental effects occurred in all depths except for the surface.
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Affiliation(s)
- E Bezirtzoglou
- Department of Microbiology, University of Ioannina, Medical School, Ioannina, Greece
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29
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Bonch-Osmolovskaya EA, Miroshnichenko ML, Lebedinsky AV, Chernyh NA, Nazina TN, Ivoilov VS, Belyaev SS, Boulygina ES, Lysov YP, Perov AN, Mirzabekov AD, Hippe H, Stackebrandt E, L'Haridon S, Jeanthon C. Radioisotopic, culture-based, and oligonucleotide microchip analyses of thermophilic microbial communities in a continental high-temperature petroleum reservoir. Appl Environ Microbiol 2003; 69:6143-51. [PMID: 14532074 PMCID: PMC201201 DOI: 10.1128/aem.69.10.6143-6151.2003] [Citation(s) in RCA: 142] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2003] [Accepted: 08/01/2003] [Indexed: 11/20/2022] Open
Abstract
Activity measurements by radioisotopic methods and cultural and molecular approaches were used in parallel to investigate the microbial biodiversity and its physiological potential in formation waters of the Samotlor high-temperature oil reservoir (Western Siberia, Russia). Sulfate reduction with rates not exceeding 20 nmol of H(2)S liter(-1) day(-1) occurred at 60 and 80 degrees C. In upper horizons (AB, A, and B), methanogenesis (lithotrophic and/or acetoclastic) was detected only in wells in which sulfate reduction did not occur. In some of the wells from deeper (J) horizons, high-temperature sulfate reduction and methanogenesis occurred simultaneously, the rate of lithotrophic methanogenesis exceeding 80 nmol of CH(4) liter(-1) day(-1). Enrichment cultures indicated the presence of diverse physiological groups representing aerobic and anaerobic thermophiles and hyperthermophiles; fermentative organotrophs were predominant. Phylogenetic analyses of 15 isolates identified representatives of the genera Thermotoga, Thermoanaerobacter, Geobacillus, Petrotoga, Thermosipho, and Thermococcus, the latter four being represented by new species. Except for Thermosipho, the isolates were members of genera recovered earlier from similar habitats. DNA obtained from three samples was hybridized with a set of oligonucleotide probes targeting selected microbial groups encompassing key genera of thermophilic bacteria and archaea. Oligonucleotide microchip analyses confirmed the cultural data but also revealed the presence of several groups of microorganisms that escaped cultivation, among them representatives of the Aquificales/Desulfurobacterium-Thermovibrio cluster and of the genera Desulfurococcus and Thermus, up to now unknown in this habitat. The unexpected presence of these organisms suggests that their distribution may be much wider than suspected.
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Vallero MVG, Hulshoff Pol LW, Lettinga G, Lens PNL. Effect of NaCl on thermophilic (55 degrees C) methanol degradation in sulfate reducing granular sludge reactors. WATER RESEARCH 2003; 37:2269-2280. [PMID: 12727235 DOI: 10.1016/s0043-1354(03)00024-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The effect of NaCl on thermophilic (55 degrees C) methanol conversion in the presence of excess of sulfate (COD/SO(4)(2-)=0.5) was investigated in two 6.5L lab-scale upflow anaerobic sludge bed reactors inoculated with granular sludge previously not adapted to NaCl. Methanol was almost completely used for sulfate reduction in the absence of NaCl when operating at an organic loading rate of 5 g CODL(-1)day(-1) and a hydraulic retention time of 10h. The almost fully sulfidogenic sludge consisted of both granules and flocs developed after approximately 100 days in both reactors. Sulfate reducing bacteria (SRB) outcompeted methane producing archaea (MPA) for methanol, but acetate represented a side-product, accounting for maximal 25% of the total COD converted. Either MPA or SRB did not use acetate as substrate in activity tests. High NaCl concentrations (25 gL(-1)) completely inhibited methanol degradation, whereas low salt concentrations (2.5 g NaClL(-1)) provoked considerable changes in the metabolic fate of methanol. The MPA were most sensitive towards the NaCl shock (25 gL(-1)). In contrast, the addition of 2.5 gL(-1) of NaCl stimulated MPA and homoacetogenic bacteria.
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Affiliation(s)
- M V G Vallero
- Department of Environmental Technology, Wageningen Agricultural University, Biotechnion-Bomenweg 2, PO Box 8129, Wageningen 6700 EV, The Netherlands
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Marion GM, Fritsen CH, Eicken H, Payne MC. The search for life on Europa: limiting environmental factors, potential habitats, and Earth analogues. ASTROBIOLOGY 2003; 3:785-811. [PMID: 14987483 DOI: 10.1089/153110703322736105] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The putative ocean of Europa has focused considerable attention on the potential habitats for life on Europa. By generally clement Earth standards, these Europan habitats are likely to be extreme environments. The objectives of this paper were to examine: (1) the limits for biological activity on Earth with respect to temperature, salinity, acidity, desiccation, radiation, pressure, and time; (2) potential habitats for life on Europa; and (3) Earth analogues and their limitations for Europa. Based on empirical evidence, the limits for biological activity on Earth are: (1) the temperature range is from 253 to 394 K; (2) the salinity range is a(H2O) = 0.6-1.0; (3) the desiccation range is from 60% to 100% relative humidity; (4) the acidity range is from pH 0 to 13; (5) microbes such as Deinococcus are roughly 4,000 times more resistant to ionizing radiation than humans; (6) the range for hydrostatic pressure is from 0 to 1,100 bars; and (7) the maximum time for organisms to survive in the dormant state may be as long as 250 million years. The potential habitats for life on Europa are the ice layer, the brine ocean, and the seafloor environment. The dual stresses of lethal radiation and low temperatures on or near the icy surface of Europa preclude the possibility of biological activity anywhere near the surface. Only at the base of the ice layer could one expect to find the suitable temperatures and liquid water that are necessary for life. An ice layer turnover time of 10 million years is probably rapid enough for preserving in the surface ice layers dormant life forms originating from the ocean. Model simulations demonstrate that hypothetical oceans could exist on Europa that are too cold for biological activity (T < 253 K). These simulations also demonstrate that salinities are high, which would restrict life to extreme halophiles. An acidic ocean (if present) could also potentially limit life. Pressure, per se, is unlikely to directly limit life on Europa. But indirectly, pressure plays an important role in controlling the chemical environments for life. Deep ocean basins such as the Mariana Trench are good analogues for the cold, high-pressure ocean of Europa. Many of the best terrestrial analogues for potential Europan habitats are in the Arctic and Antarctica. The six factors likely to be most important in defining the environments for life on Europa and the focus for future work are liquid water, energy, nutrients, low temperatures, salinity, and high pressures.
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Burdette DS, Jung SH, Shen GJ, Hollingsworth RI, Zeikus JG. Physiological function of alcohol dehydrogenases and long-chain (C(30)) fatty acids in alcohol tolerance of Thermoanaerobacter ethanolicus. Appl Environ Microbiol 2002; 68:1914-8. [PMID: 11916712 PMCID: PMC123834 DOI: 10.1128/aem.68.4.1914-1918.2002] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2001] [Accepted: 01/20/2002] [Indexed: 11/20/2022] Open
Abstract
A mutant strain (39E H8) of Thermoanaerobacter ethanolicus that displayed high (8% [vol/vol]) ethanol tolerance for growth was developed and characterized in comparison to the wild-type strain (39E), which lacks alcohol tolerance (<1.5% [vol/vol]). The mutant strain, unlike the wild type, lacked primary alcohol dehydrogenase and was able to increase the percentage of transmembrane fatty acids (i.e., long-chain C(30) fatty acids) in response to increasing levels of ethanol. The data support the hypothesis that primary alcohol dehydrogenase functions primarily in ethanol consumption, whereas secondary alcohol dehydrogenase functions in ethanol production. These results suggest that improved thermophilic ethanol fermentations at high alcohol levels can be developed by altering both cell membrane composition (e.g., increasing transmembrane fatty acids) and the metabolic machinery (e.g., altering primary alcohol dehydrogenase and lactate dehydrogenase activities).
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Affiliation(s)
- D S Burdette
- Department of Biochemistry, Michigan State University, East Lansing, Michigan 48824-1319, USA
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Vieille C, Zeikus GJ. Hyperthermophilic enzymes: sources, uses, and molecular mechanisms for thermostability. Microbiol Mol Biol Rev 2001; 65:1-43. [PMID: 11238984 PMCID: PMC99017 DOI: 10.1128/mmbr.65.1.1-43.2001] [Citation(s) in RCA: 1392] [Impact Index Per Article: 60.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Enzymes synthesized by hyperthermophiles (bacteria and archaea with optimal growth temperatures of > 80 degrees C), also called hyperthermophilic enzymes, are typically thermostable (i.e., resistant to irreversible inactivation at high temperatures) and are optimally active at high temperatures. These enzymes share the same catalytic mechanisms with their mesophilic counterparts. When cloned and expressed in mesophilic hosts, hyperthermophilic enzymes usually retain their thermal properties, indicating that these properties are genetically encoded. Sequence alignments, amino acid content comparisons, crystal structure comparisons, and mutagenesis experiments indicate that hyperthermophilic enzymes are, indeed, very similar to their mesophilic homologues. No single mechanism is responsible for the remarkable stability of hyperthermophilic enzymes. Increased thermostability must be found, instead, in a small number of highly specific alterations that often do not obey any obvious traffic rules. After briefly discussing the diversity of hyperthermophilic organisms, this review concentrates on the remarkable thermostability of their enzymes. The biochemical and molecular properties of hyperthermophilic enzymes are described. Mechanisms responsible for protein inactivation are reviewed. The molecular mechanisms involved in protein thermostabilization are discussed, including ion pairs, hydrogen bonds, hydrophobic interactions, disulfide bridges, packing, decrease of the entropy of unfolding, and intersubunit interactions. Finally, current uses and potential applications of thermophilic and hyperthermophilic enzymes as research reagents and as catalysts for industrial processes are described.
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Affiliation(s)
- C Vieille
- Biochemistry Department, Michigan State University, East Lansing, Michigan 48824, USA
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Mai V, Wiegel J. Advances in development of a genetic system for Thermoanaerobacterium spp.: expression of genes encoding hydrolytic enzymes, development of a second shuttle vector, and integration of genes into the chromosome. Appl Environ Microbiol 2000; 66:4817-21. [PMID: 11055929 PMCID: PMC92385 DOI: 10.1128/aem.66.11.4817-4821.2000] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Despite recent success in transforming various thermophilic gram-type-positive anaerobes with plasmid DNA, use of shuttle vectors for the expression of genes other than antibiotic resistance markers has not previously been described. We constructed new vectors in order to express heterologous hydrolytic enzymes in our model system, Thermoanaerobacterium saccharolyticum JW/SL-YS485. Transformed Thermoanaerobacterium expressed active enzyme, indicating that this system may function as an alternate expression host, especially for genes with a thermophilic origin. To develop further the genetic system for T. saccharolyticum JW/SL-YS485, two improved Escherichia coli-Thermoanaerobacterium shuttle vectors, pRKM1 and pRUKM, were constructed. Furthermore, the kanamycin resistance cassette alone and the kanamycin resistance cassette plus the cellobiohydrolase gene (cbhA) from Clostridium thermocellum JW20 were integrated into the xylanase gene (xynA) region of the Thermoanaerobacterium chromosome via homologous recombination using pUC-based suicide vectors pUXK and pUXKC.
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Affiliation(s)
- V Mai
- Department of Microbiology and Center for Biological Resource Recovery, University of Georgia, Athens, Georgia 30602, USA
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Abstract
Examination of microbial diversity in environments of increasing salt concentrations indicates that certain types of dissimilatory metabolism do not occur at the highest salinities. Examples are methanogenesis for H2 + CO2 or from acetate, dissimilatory sulfate reduction with oxidation of acetate, and autotrophic nitrification. Occurrence of the different metabolic types is correlated with the free-energy change associated with the dissimilatory reactions. Life at high salt concentrations is energetically expensive. Most bacteria and also the methanogenic Archaea produce high intracellular concentrations of organic osmotic solutes at a high energetic cost. All halophilic microorganisms expend large amounts of energy to maintain steep gradients of NA+ and K+ concentrations across their cytoplasmic membrane. The energetic cost of salt adaptation probably dictates what types of metabolism can support life at the highest salt concentrations. Use of KCl as an intracellular solute, while requiring far-reaching adaptations of the intracellular machinery, is energetically more favorable than production of organic-compatible solutes. This may explain why the anaerobic halophilic fermentative bacteria (order Haloanaerobiales) use this strategy and also why halophilic homoacetogenic bacteria that produce acetate from H2 + CO2 exist whereas methanogens that use the same substrates in a reaction with a similar free-energy yield do not.
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Affiliation(s)
- A Oren
- Division of Microbial and Molecular Ecology, Institute of Life Sciences, and the Moshe Shilo Minerva Center for Marine Biogeochemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel.
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Purcarea C, Evans DR, Hervé G. Channeling of carbamoyl phosphate to the pyrimidine and arginine biosynthetic pathways in the deep sea hyperthermophilic archaeon Pyrococcus abyssi. J Biol Chem 1999; 274:6122-9. [PMID: 10037695 DOI: 10.1074/jbc.274.10.6122] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The kinetics of the coupled reactions between carbamoyl-phosphate synthetase (CPSase) and both aspartate transcarbamoylase (ATCase) and ornithine transcarbamoylase (OTCase) from the deep sea hyperthermophilic archaeon Pyrococcus abyssi demonstrate the existence of carbamoyl phosphate channeling in both the pyrimidine and arginine biosynthetic pathways. Isotopic dilution experiments and coupled reaction kinetics analyzed within the context of the formalism proposed by Ovádi et al. (Ovádi, J., Tompa, P., Vertessy, B., Orosz, F., Keleti, T., and Welch, G. R. (1989) Biochem. J. 257, 187-190) are consistent with a partial channeling of the intermediate at 37 degrees C, but channeling efficiency increases dramatically at elevated temperatures. There is no preferential partitioning of carbamoyl phosphate between the arginine and pyrimidine biosynthetic pathways. Gel filtration chromatography at high and low temperature and in the presence and absence of substrates did not reveal stable complexes between P. abyssi CPSase and either ATCase or OTCase. Thus, channeling must occur during the dynamic association of coupled enzymes pairs. The interaction of CPSase-ATCase was further demonstrated by the unexpectedly weak inhibition of the coupled reaction by the bisubstrate analog, N-(phosphonacetyl)-L-aspartate (PALA). The anomalous effect of PALA suggests that, in the coupled reaction, the effective concentration of carbamoyl phosphate in the vicinity of the ATCase active site is 96-fold higher than the concentration in the bulk phase. Channeling probably plays an essential role in protecting this very unstable intermediate of metabolic pathways performing at extreme temperatures.
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Affiliation(s)
- C Purcarea
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, Michigan 48201, USA
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Han CJ, Kelly RM. Biooxidation capacity of the extremely thermoacidophilic archaeon metallosphaera sedula under bioenergetic challenge. Biotechnol Bioeng 1998; 58:617-24. [PMID: 10099299 DOI: 10.1002/(sici)1097-0290(19980620)58:6<617::aid-bit7>3.0.co;2-l] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The biooxidation capacity of an extremely thermoacidophilic archaeon Metallosphaera sedula (DSMZ 5348) was examined under bioenergetic challenges imparted by thermal or chemical stress in regard to its potential use in microbial bioleaching processes. Within the normal growth temperature range of M. sedula (70-79 degrees C) at pH 2.0, upward temperature shifts resulted in bioleaching rates that followed an Arrhenius-like dependence. When the cells were subjected to supraoptimal temperatures through gradual thermal acclimation at 81 degrees C (Han et al., 1997), cell densities were reduced but 3 to 5 times faster specific leaching rates (Fe3+ released from iron pyrite/cell/h) could be achieved by the stressed cells compared to cells at 79 degrees C and 73 degrees C, respectively. The respiration capacity of M. sedula growing at 74 degrees C was challenged by poisoning the cells with uncouplers to generate chemical stress. When the protonophore 2,4-dinitrophenol (5-10 μM) was added to a growing culture of M. sedula on iron pyrite, there was little effect on specific leaching rates compared to a culture with no protonophore at 74 degrees C; 25 μM levels proved to be toxic to M. sedula. However, a significant stimulation in specific rate was observed when the cells were subjected to 1 μM nigericin (+135%) and 2 μM (+63%); 5 μM levels of the ionophore completely arrested cell growth. The ionophore effect was further investigated in continuous culture growing on ferrous sulfate at 74 degrees C. When 1 μM nigericin was added as a pulse to a continuous culture, a 30% increase in specific iron oxidation rate was observed for short intervals, indicating a potential positive impact on leaching when periodic chemical stress is applied. This study suggests that biooxidation rates can be increased by strategic exposure of extreme thermoacidophiles to chemical or thermal stress, and this approach should be considered for improving process performance. Copyright 1998 John Wiley & Sons, Inc.
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Affiliation(s)
- CJ Han
- Department of Chemical Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905, USA
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Abstract
The moderately halophilic heterotrophic aerobic bacteria form a diverse group of microorganisms. The property of halophilism is widespread within the bacterial domain. Bacterial halophiles are abundant in environments such as salt lakes, saline soils, and salted food products. Most species keep their intracellular ionic concentrations at low levels while synthesizing or accumulating organic solutes to provide osmotic equilibrium of the cytoplasm with the surrounding medium. Complex mechanisms of adjustment of the intracellular environments and the properties of the cytoplasmic membrane enable rapid adaptation to changes in the salt concentration of the environment. Approaches to the study of genetic processes have recently been developed for several moderate halophiles, opening the way toward an understanding of haloadaptation at the molecular level. The new information obtained is also expected to contribute to the development of novel biotechnological uses for these organisms.
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Affiliation(s)
- A Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, 41012 Seville, Spain.
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Holst O, Manelius Å, Krahe M, Märkl H, Raven N, Sharp R. Thermophiles and fermentation technology. ACTA ACUST UNITED AC 1997. [DOI: 10.1016/s0300-9629(97)00002-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Ravot G, Ollivier B, Fardeau ML, Patel BK, Andrews KT, Magot M, Garcia JL. L-alanine production from glucose fermentation by hyperthermophilic members of the domains bacteria and Archaea: a remnant of an ancestral metabolism? Appl Environ Microbiol 1996; 62:2657-9. [PMID: 8779604 PMCID: PMC168047 DOI: 10.1128/aem.62.7.2657-2659.1996] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
New members of the order Thermotogales were isolated from nonvolcanically heated geothermal environments, including oil fields and waters of the Great Artesian Basin of Australia, thereby extending their known habitats, previously recognized primarily as volcanic. The hyperthermophilic and thermophilic members of Thermotogales of volcanic origin, together with the recently described nonvolcanic species of this order and three new isolates described in this paper, were all found to produce L-alanine from glucose fermentation, in addition to acetate, lactate, CO2 and H2. L-alanine production from glucose is a trait in common with Pyrococcus furiosus and Thermococcus profundus. We propose that L-alanine production from sugar fermentation be regarded as an ancestral metabolic characteristic.
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Affiliation(s)
- G Ravot
- Laboratoire ORSTOM de Microbiologie des Anaérobies, Université de Provence, Marseille, France
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Fardeau ML, Faudon C, Cayol JL, Magot M, Patel BK, Ollivier B. Effect of thiosulphate as electron acceptor on glucose and xylose oxidation by Thermoanaerobacter finnii and a Thermoanaerobacter sp. isolated from oil field water. Res Microbiol 1996; 147:159-65. [PMID: 8761734 DOI: 10.1016/0923-2508(96)80215-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
During glucose and xylose fermentation, Thermoanaerobacter finnii was observed to produce lactate, acetate, H2 and CO2, with ethanol being the major end product. Thermoanaerobacter strain SEBR 5268, an isolate from an oil field, also produced a similar range of end products from glucose and xylose fermentation, with the exception that both ethanol and lactate were the major products of sugar metabolism. Both these strains were able to reduce thiosulphate to sulphide in the presence of these two substrates, with acetate being the dominant metabolite in that case. In addition, a faster growth rate and increased cell yield were obtained in the presence of thiosulphate, than in its absence. The higher concentrations of acetate produced in the presence of thiosulphate rather than without any electron acceptor indicated that more ATP was generated from substrate-level phosphorylation. These results have implications for our understanding of the breakdown of carbohydrates present in organic matter found in the natural ecological niches of Thermoanaerobacter species (sulphide-, elemental sulphur- or sulphate-rich thermal hot springs and oil fields).
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Affiliation(s)
- M L Fardeau
- Laboratoire de Microbiologie ORSTOM, Université de Provence, CESB-ESIL, Marseille, France
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42
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Kozyavkin SA, Pushkin AV, Eiserling FA, Stetter KO, Lake JA, Slesarev AI. DNA enzymology above 100 degrees C. Topoisomerase V unlinks circular DNA at 80-122 degrees C. J Biol Chem 1995; 270:13593-5. [PMID: 7775408 DOI: 10.1074/jbc.270.23.13593] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The widespread application of polymerase chain reaction and related techniques in biology and medicine has led to a heightened interest in thermophilic enzymes of DNA metabolism. Some of these enzymes are stable for hours at 100 degrees C, but no enzymatic activity on duplex DNA at temperatures above 100 degrees C has so far been demonstrated. Recently, we isolated topoisomerase V from the hyperthermophile Methanopyrus kandleri, which grows up to 110 degrees C. This novel enzyme is similar to eukaryotic topoisomerase I and acts on duplex DNA regions. We now show that topoisomerase V catalyzes the unlinking of double-stranded circular DNA at temperatures up to 122 degrees C. In this in vitro system, maximal DNA unlinking occurs at 108 degrees C and corresponds to complementary strands being linked at most once. These results further imply that in the presence of sufficient positive supercoiling DNA can exist as a double helix even at 122 degrees C.
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Affiliation(s)
- S A Kozyavkin
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland, 20892-0540, USA
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Ciulla R, Krishnan S, Roberts MF. Internalization of Sucrose by Methanococcus thermolithotrophicus. Appl Environ Microbiol 1995; 61:421-9. [PMID: 16534924 PMCID: PMC1388342 DOI: 10.1128/aem.61.2.421-429.1995] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
When sucrose is present in the external medium, it is internalized by Methanococcus thermolithotrophicus. Sucrose internalization, as determined by both natural abundance (sup13)C nuclear magnetic resonance spectroscopy and [(sup14)C]sucrose uptake, is directly proportional to external sucrose levels. The uptake is energy independent and exhibits kinetic behavior consistent with a simple passive diffusion process. In the presence of 0.2 M sucrose, methanogenesis is inhibited as the NaCl concentration in the external medium is increased. Growth, as determined by protein content, is inhibited by 0.2 M sucrose when the external NaCl concentration is 1.4 M. These results are important because they show that (i) sucrose cannot be used as a noncharged solute to replace NaCl in experiments to evaluate how external osmotic strength affects the internal solute composition of M. thermolithotrophicus, and (ii) sucrose cannot be used as an impermeable marker for the extracellular volume in experiments to measure the intracellular volume of M. thermolithotrophicus.
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Prieur D, Erauso G, Jeanthon C. Hyperthermophilic life at deep-sea hydrothermal vents. PLANETARY AND SPACE SCIENCE 1995; 43:115-122. [PMID: 11538423 DOI: 10.1016/0032-0633(94)00143-f] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The discovery of deep-sea hydrothermal vents in 1977 considerably modified the views on deep-sea biology. For the first time, an ecosystem totally based on primary production achieved by chemosynthetic bacteria was discovered. Besides the warm vents where dense invertebrate communities and their symbiotic bacteria are located, the "black smokers" venting fluids at temperatures up to 350 degrees C were also investigated by microbiologists. Several strains of hyperthermophilic Archaea (methanogens, sulfate-reducers, sulfur-reducers) were isolated from smokers and surrounding materials. Deep-sea isolates that have been totally described, have been assigned to new species, within genera previously found in coastal geothermally heated environments. However, some species appear to exist in both deep and shallow ecosystems. Some deep-sea hyperthermophiles appear to be adapted to hydrostatic pressure and showed a barophilic response. The distribution of hyperthermophiles in the hot ecosystems of the planet, and their adaptation to pressure are presented and discussed.
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Affiliation(s)
- D Prieur
- CNRS, Station Biologique, Roscoff, France
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Fetzner S, Lingens F. Bacterial dehalogenases: biochemistry, genetics, and biotechnological applications. Microbiol Rev 1994; 58:641-85. [PMID: 7854251 PMCID: PMC372986 DOI: 10.1128/mr.58.4.641-685.1994] [Citation(s) in RCA: 148] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
This review is a survey of bacterial dehalogenases that catalyze the cleavage of halogen substituents from haloaromatics, haloalkanes, haloalcohols, and haloalkanoic acids. Concerning the enzymatic cleavage of the carbon-halogen bond, seven mechanisms of dehalogenation are known, namely, reductive, oxygenolytic, hydrolytic, and thiolytic dehalogenation; intramolecular nucleophilic displacement; dehydrohalogenation; and hydration. Spontaneous dehalogenation reactions may occur as a result of chemical decomposition of unstable primary products of an unassociated enzyme reaction, and fortuitous dehalogenation can result from the action of broad-specificity enzymes converting halogenated analogs of their natural substrate. Reductive dehalogenation either is catalyzed by a specific dehalogenase or may be mediated by free or enzyme-bound transition metal cofactors (porphyrins, corrins). Desulfomonile tiedjei DCB-1 couples energy conservation to a reductive dechlorination reaction. The biochemistry and genetics of oxygenolytic and hydrolytic haloaromatic dehalogenases are discussed. Concerning the haloalkanes, oxygenases, glutathione S-transferases, halidohydrolases, and dehydrohalogenases are involved in the dehalogenation of different haloalkane compounds. The epoxide-forming halohydrin hydrogen halide lyases form a distinct class of dehalogenases. The dehalogenation of alpha-halosubstituted alkanoic acids is catalyzed by halidohydrolases, which, according to their substrate and inhibitor specificity and mode of product formation, are placed into distinct mechanistic groups. beta-Halosubstituted alkanoic acids are dehalogenated by halidohydrolases acting on the coenzyme A ester of the beta-haloalkanoic acid. Microbial systems offer a versatile potential for biotechnological applications. Because of their enantiomer selectivity, some dehalogenases are used as industrial biocatalysts for the synthesis of chiral compounds. The application of dehalogenases or bacterial strains in environmental protection technologies is discussed in detail.
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Affiliation(s)
- S Fetzner
- Institut für Mikrobiologie der Universität Hohenheim, Stuttgart, Germany
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Abstract
New obligately anaerobic bacteria are being discovered at an accelerating rate and it is becoming very evident that the diversity of anoxic biotransformations has been greatly underestimated. Furthermore, among contemporary anaerobes there are many that thrive in extreme environments including, for example, an impressive array of both archaebacterial and eubacterial hyperthermophiles. Free energy for growth and reproduction may be conserved not only via fermentations but also by anoxygenic photophosphorylation and other modes of creating transmembrane proton potential. Thus forms of anaerobic respiration in which various inorganic oxidants (or indeed carbon dioxide) serve as terminal electron acceptors have greatly extended the natural habitats in which such organisms may predominate. Anaerobic bacteria are, however, often found in nature as members of close microbial communities (consortia) that, although sustained by syntrophic and other relations between component species, are liable to alter their composition and character in response to environmental changes, e.g., availability of terminal oxidants. It follows that the biotechnological exploitation of obligately anaerobic bacteria must be informed by knowledge both of their biochemical capacities and of their normal environmental roles. It is against this background that illustrative examples of the activities of anaerobic bacteria are considered under three heads: 1. Biodegradation/Bioremediation, with special reference to the anaerobic breakdown of aromatic and/or halogenated organic substances; 2. Biosynthesis/Bioproduction, encompassing normal and modified fermentations; and 3. Biotransformations, accomplished by whole or semipermeabilized organisms or by enzymes derived therefrom, with particular interest attaching to the production of chiral compounds by a number of procedures, including electromicrobial reduction.
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Affiliation(s)
- J G Morris
- Institute of Biological Sciences, University of Wales, Penglais, Aberystwyth, UK
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47
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Abstract
Strictly anaerobic halophiles, namely fermentative, sulfate-reducing, homoacetogenic, phototrophic, and methanogenic bacteria are involved in the oxidation of organic carbon in hypersaline environments. To date, six anaerobic fermentative genera, containing nine species, have been described. Two of them are homoacetogens. Six species belong to the family Haloanaerobiaceae, as indicated by their unique 16S rRNA oligonucleotide sequences. Desulfohalobium retbaense and Desulfovibrio halophilus represent the only two moderately halophilic sulfate reducers so far reported. Among anoxygenic phototrophic anaerobes, a few purple bacteria with optimal growth at salinities between 6 and 11% NaCl have been isolated from hypersaline habitats. They belong to the genera Rhodospirillum, Chromatium, Thiocapsa, and Ectothiorhodospira. The commonest organisms isolated so far are Chromatium salexigens, Thiocapsa halophila, and Rhodospirillum salinarum. Extremely halophilic purple bacteria have most commonly been isolated from alkaline brines and require about 20 to 25% NaCl for optimal growth. They belong to the family Ectothiorodhospiraceae. Their osmoregulation involves synthesis or uptake of compatible solutes such as glycine-betaine that accumulate in their cytoplasm. The existence of methanogens in hypersaline environments is related to the presence of noncompetitive substrates such as methylamines, which originate mainly from the breakdown of osmoregulatory amines. Methanogenesis probably does not contribute to the mineralization of carbohydrates at NaCl concentrations higher than 15%. Above this concentration, sulfate reduction is probably the main way to oxidize H2 (although at rates too low to use up all the H2 formed) and occupies a terminal function kn the degradation of carbohydrates. Three genera and five species of halophilic methylotrophic methanogens have been reported. A bloom of phototrophic bacteria in the marine salterns of Salins-de-Giraud, located on the Mediterranean French coast in the Rhone Delta, is also described.
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Affiliation(s)
- B Ollivier
- Laboratoire de Microbiologie ORSTOM, Université de Provence, Marseille, France
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