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Burch TR, Spencer SK, Borchardt SS, Larson RA, Borchardt MA. Fate of Manure-Borne Pathogens during Anaerobic Digestion and Solids Separation. JOURNAL OF ENVIRONMENTAL QUALITY 2018; 47:336-344. [PMID: 29634802 PMCID: PMC7166490 DOI: 10.2134/jeq2017.07.0285] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Anaerobic digestion can inactivate zoonotic pathogens present in cattle manure, which reduces transmission of these pathogens from farms to humans through the environment. However, the variability of inactivation across farms and over time is unknown because most studies have examined pathogen inactivation under ideal laboratory conditions or have focused on only one or two full-scale digesters at a time. In contrast, we sampled seven full-scale digesters treating cattle manure in Wisconsin for 9 mo on a biweekly basis ( = 118 pairs of influent and effluent samples) and used real-time quantitative polymerase chain reaction to analyze these samples for 19 different microbial genetic markers. Overall, inactivation of pathogens and fecal indicators was highly variable. When aggregated across digester and season, log-removal values for several representative microorganisms-bovine , -like CowM3, and bovine polyomavirus-were 0.78 ± 0.34, 0.70 ± 0.50, and 0.53 ± 0.58, respectively (mean ± SD). These log-removal values were up to two times lower than expected based on the scientific literature. Thus, our study indicates that full-scale anaerobic digestion of cattle manure requires optimization with regard to pathogen inactivation. Future studies should focus on identifying the potential causes of this suboptimal performance (e.g., overloading, poor mixing, poor temperature control). Our study also examined the fate of pathogens during manure separation and found that the majority of microbes we detected ended up in the liquid fraction of separated manure. This finding has important implications for the transmission of zoonotic pathogens through the environment to humans.
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Affiliation(s)
| | | | - Spencer S. Borchardt
- Wisconsin Water Science Center, USGS2615 Yellowstone Dr.MarshfieldWI54449
- Present address:
Kimley Horn and Associates2550 University Ave. W. Suite 238NSaint PaulMN55114
| | - Rebecca A. Larson
- Dep. of Biological Systems EngineeringUniv. of Wisconsin–Madison460 Henry Mall, Room 232EMadisonWI53706
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Bacterial reduction in sealed caries lesions is strain- and material-specific. Sci Rep 2018; 8:3767. [PMID: 29491366 PMCID: PMC5830646 DOI: 10.1038/s41598-018-21842-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 02/13/2018] [Indexed: 12/19/2022] Open
Abstract
Sealing can arrest caries lesions. We aimed to evaluate if sealing effects and kinetics are bacterial-strain and sealing-material specific. Human dentin discs were mounted in a dual-chamber device. Caries lesions were induced chemically and contaminated with either Lactobacillus rhamnosus (LR) or Streptococcus sobrinus (SS). For (1) kinetics assessment, the initial bacterial load and the sealing period were varied, and lesions sealed using a self-etch adhesive and composite. For (2) comparing materials, six sealing protocols (#1-#6) were evaluated: 1# Self-etch adhesive plus composite placed without a liner, or #2 calcium hydroxide, or #3 mineral trioxide aggregate, or #4 Biodentine liners; #5 antibacterial adhesive plus composite; #6 glass ionomer cement. Pulpal fluid flow was simulated during sealing. The outcome was the number of surviving bacteria (CFU) per g dentin. For LR, bacterial survival increased significantly with increasing initial bacterial load and decreased with longer sealing periods. The relative reduction followed a first-order kinetics. More LR survived under calcium hydroxide or MTA than other materials (p < 0.001). For SS, nearly no bacteria survived sealing regardless of sealing period, initial bacterial load or sealing material. In conclusion, sealing effects and kinetics were strain- and material-specific.
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Fowler AC, Winstanley HF. Microbial dormancy and boom-and-bust population dynamics under starvation stress. Theor Popul Biol 2018; 120:114-120. [PMID: 29447840 DOI: 10.1016/j.tpb.2018.02.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 01/20/2018] [Accepted: 02/05/2018] [Indexed: 11/16/2022]
Abstract
We propose a model for the growth of microbial populations in the presence of a rate-limiting nutrient which accounts for the switching of cells to a dormant phase at low densities in response to decreasing concentration of a putative biochemical signal. We then show that in conditions of nutrient starvation, self-sustained oscillations can occur, thus providing a natural explanation for such phenomena as plankton blooms. However, unlike results of previous studies, the microbial population minima do not become unrealistically small, being buffered during minima by an increased dormant phase population. We also show that this allows microbes to survive in extreme environments for very long periods, consistent with observation. The mechanism provides a natural vehicle for other such sporadic outbreaks, such as viral epidemics.
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Affiliation(s)
- A C Fowler
- MACSI, University of Limerick, Limerick, Ireland; OCIAM, University of Oxford, Oxford, UK.
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54
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Bokulich NA, Bamforth CW, Mills DA. A Review of Molecular Methods for Microbial Community Profiling of Beer and Wine. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2018. [DOI: 10.1094/asbcj-2012-0709-01] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Nicholas A. Bokulich
- Department of Viticulture and Enology and Department of Food Science and Technology
| | | | - David A. Mills
- Department of Viticulture and Enology and Department of Food Science and Technology, University of California, Davis 95616
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Ojha KS, Burgess CM, Duffy G, Kerry JP, Tiwari BK. Integrated phenotypic-genotypic approach to understand the influence of ultrasound on metabolic response of Lactobacillus sakei. PLoS One 2018; 13:e0191053. [PMID: 29370210 PMCID: PMC5784923 DOI: 10.1371/journal.pone.0191053] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 12/27/2017] [Indexed: 11/18/2022] Open
Abstract
The lethal effects of soundwaves on a range of microorganisms have been known for almost a century whereas, the use of ultrasound to promote or control their activity is much more recent. Moreover, the fundamental molecular mechanism influencing the behaviour of microorganisms subjected to ultrasonic waves is not well established. In this study, we investigated the influence of ultrasonic frequencies of 20, 45, 130 and 950 kHz on growth kinetics of Lactobacillus sakei. A significant increase in the growth rate of L. sakei was observed following ultrasound treatment at 20 kHz despite the treatment yielding a significant reduction of ca. 3 log cfu/mL in cells count. Scanning electron microscopy showed that ultrasound caused significant changes on the cell surface of L. sakei culture with the formation of pores "sonoporation". Phenotypic microarrays showed that all ultrasound treated L. sakei after exposure to various carbon, nitrogen, phosphorus and sulphur sources had significant variations in nutrient utilisation. Integration of this phenotypic data with the genome of L. sakei revealed that various metabolic pathways were being influenced by the ultrasound treatments. Results presented in this study showed that the physiological response of L. sakei in response to US is frequency dependent and that it can influence metabolic pathways. Hence, ultrasound treatments can be employed to modulate microbial activity for specialised applications.
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Affiliation(s)
- K Shikha Ojha
- Food Chemistry and Technology, Teagasc Food Research Centre, Dublin, Ireland
| | | | | | - Joseph P Kerry
- Food Packaging Group, University College Cork, Cork, Ireland
| | - Brijesh K Tiwari
- Food Chemistry and Technology, Teagasc Food Research Centre, Dublin, Ireland
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Couto JM, McGarrity A, Russell J, Sloan WT. The effect of metabolic stress on genome stability of a synthetic biology chassis Escherichia coli K12 strain. Microb Cell Fact 2018; 17:8. [PMID: 29357936 PMCID: PMC5776760 DOI: 10.1186/s12934-018-0858-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 01/15/2018] [Indexed: 12/14/2022] Open
Abstract
Background Synthetic organism-based biotechnologies are increasingly being proposed for environmental applications, such as in situ sensing. Typically, the novel function of these organisms is delivered by compiling genetic fragments in the genome of a chassis organism. To behave predictably, these chassis are designed with reduced genomes that minimize biological complexity. However, in these proposed applications it is expected that even when contained within a device, organisms will be exposed to fluctuating, often stressful, conditions and it is not clear whether their genomes will retain stability. Results Here we employed a chemostat design which enabled us to maintained two strains of E. coli K12 under sustained starvation stress: first the reduced genome synthetic biology chassis MDS42 and then, the control parent strain MG1655. We estimated mutation rates and utilised them as indicators of an increase in genome instability. We show that within 24 h the spontaneous mutation rate had increased similarly in both strains, destabilizing the genomes. High rates were maintained for the duration of the experiment. Growth rates of a cohort of randomly sampled mutants from both strains were utilized as a proxy for emerging phenotypic, and by association genetic variation. Mutant growth rates were consistently less than rates in non-mutants, an indicator of reduced fitness and the presence of mildly deleterious mutations in both the strains. In addition, the effect of these mutations on the populations as a whole varied by strain. Conclusions Overall, this study shows that genome reductions in the MDS42 did not stabilize the chassis under metabolic stress. Over time, this could compromise the effectiveness of synthetic organisms built on chassis in environmental applications. Electronic supplementary material The online version of this article (10.1186/s12934-018-0858-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jillian M Couto
- Division of Infrastructure and Environment, School of Engineering, University of Glasgow, Rankine Building, Level 5, Glasgow, G12 8QQ, UK.
| | - Anne McGarrity
- Division of Infrastructure and Environment, School of Engineering, University of Glasgow, Rankine Building, Level 5, Glasgow, G12 8QQ, UK
| | - Julie Russell
- Division of Infrastructure and Environment, School of Engineering, University of Glasgow, Rankine Building, Level 5, Glasgow, G12 8QQ, UK
| | - William T Sloan
- Division of Infrastructure and Environment, School of Engineering, University of Glasgow, Rankine Building, Level 5, Glasgow, G12 8QQ, UK
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Wasai S, Kanno N, Matsuura K, Haruta S. Increase of Salt Tolerance in Carbon-Starved Cells of Rhodopseudomonas palustris Depending on Photosynthesis or Respiration. Microorganisms 2018; 6:microorganisms6010004. [PMID: 29316629 PMCID: PMC5874618 DOI: 10.3390/microorganisms6010004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 12/22/2017] [Accepted: 01/03/2018] [Indexed: 12/26/2022] Open
Abstract
Bacteria in natural environments are frequently exposed to nutrient starvation and survive against environmental stresses under non-growing conditions. In order to determine the energetic influence on survivability during starvation, changes in salt tolerance were investigated using the purple photosynthetic bacterium Rhodopseudomonas palustris after carbon starvation under photosynthetic conditions in comparison with anaerobic and aerobic dark conditions. Tolerance to a treatment with high concentration of salt (2.5 M NaCl for 1 h) was largely increased after starvation under anaerobically light and aerobically dark conditions. The starved cells under the conditions of photosynthesis or aerobic respiration contained high levels of cellular ATP, but starvation under the anaerobic dark conditions resulted in a decrease of cellular ATP contents. To observe the large increase of the salt tolerance, incubation of starved cells for more than 18 h under illumination was needed. These results suggest that the ATP-dependent rearrangement of cells induced salt tolerance.
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Affiliation(s)
- Sawa Wasai
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan.
| | - Nanako Kanno
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan.
| | - Katsumi Matsuura
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan.
| | - Shin Haruta
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan.
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Edrada-Ebel R, Ævarsson A, Polymenakou P, Hentschel U, Carettoni D, Day J, Green D, Hreggviðsson GÓ, Harvey L, McNeil B. SeaBioTech: From Seabed to Test-Bed: Harvesting the Potential of Marine Biodiversity for Industrial Biotechnology. GRAND CHALLENGES IN MARINE BIOTECHNOLOGY 2018. [DOI: 10.1007/978-3-319-69075-9_12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Wang L, Liu Z, Dai S, Yan J, Wise MJ. The Sit-and-Wait Hypothesis in Bacterial Pathogens: A Theoretical Study of Durability and Virulence. Front Microbiol 2017; 8:2167. [PMID: 29209284 PMCID: PMC5701638 DOI: 10.3389/fmicb.2017.02167] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Accepted: 10/23/2017] [Indexed: 12/20/2022] Open
Abstract
The intriguing sit-and-wait hypothesis predicts that bacterial durability in the external environment is positively correlated with their virulence. Since its first proposal in 1987, the hypothesis has been spurring debates in terms of its validity in the field of bacterial virulence. As a special case of the vector-borne transmission versus virulence tradeoff, where vector is now replaced by environmental longevity, there are only sporadic studies over the last three decades showing that environmental durability is possibly linked with virulence. However, no systematic study of these works is currently available and epidemiological analysis has not been updated for the sit-and-wait hypothesis since the publication of Walther and Ewald's (2004) review. In this article, we put experimental evidence, epidemiological data and theoretical analysis together to support the sit-and-wait hypothesis. According to the epidemiological data in terms of gain and loss of virulence (+/-) and durability (+/-) phenotypes, we classify bacteria into four groups, which are: sit-and-wait pathogens (++), vector-borne pathogens (+-), obligate-intracellular bacteria (--), and free-living bacteria (-+). After that, we dive into the abundant bacterial proteomic data with the assistance of bioinformatics techniques in order to investigate the two factors at molecular level thanks to the fast development of high-throughput sequencing technology. Sequences of durability-related genes sourced from Gene Ontology and UniProt databases and virulence factors collected from Virulence Factor Database are used to search 20 corresponding bacterial proteomes in batch mode for homologous sequences via the HMMER software package. Statistical analysis only identified a modest, and not statistically significant correlation between mortality and survival time for eight non-vector-borne bacteria with sit-and-wait potentials. Meanwhile, through between-group comparisons, bacteria with higher host-mortality are significantly more durable in the external environment. The results of bioinformatics analysis correspond well with epidemiological data, that is, non-vector-borne pathogens with sit-and-wait potentials have higher number of virulence and durability genes compared with other bacterial groups. However, the conclusions are constrained by the relatively small bacterial sample size and non-standardized experimental data.
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Affiliation(s)
- Liang Wang
- School of Medical Informatics, Xuzhou Medical University, Xuzhou, China
| | - Zhanzhong Liu
- Department of Clinical Pharmacology, Xuzhou Infectious Diseases Hospital, Xuzhou, China
| | - Shiyun Dai
- School of Anaesthesia, Xuzhou Medical University, Xuzhou, China
| | - Jiawei Yan
- Clinical Laboratory of Tuberculosis, Xuzhou Infectious Diseases Hospital, Xuzhou, China
| | - Michael J. Wise
- School of Computer Science and Software Engineering, University of Western Australia, Perth, WA, Australia
- The Marshall Centre for Infectious Diseases Research and Training, University of Western Australia, Perth, WA, Australia
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60
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Svenningsen NB, Damgaard M, Rasmussen M, Pérez-Pantoja D, Nybroe O, Nicolaisen MH. Cupriavidus pinatubonensis AEO106 deals with copper-induced oxidative stress before engaging in biodegradation of the herbicide 4-chloro-2-methylphenoxyacetic acid. BMC Microbiol 2017; 17:211. [PMID: 29084513 PMCID: PMC5663122 DOI: 10.1186/s12866-017-1119-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 10/19/2017] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Microbial degradation of phenoxy acid (PA) herbicides in agricultural soils is important to minimize herbicide leaching to groundwater reservoirs. Degradation may, however, be hampered by exposure of the degrader bacteria to toxic metals as copper (Cu) in the soil environment. Exposure to Cu leads to accumulation of intracellular reactive oxygen species (ROS) in some bacteria, but it is not known how Cu-derived ROS and an ensuing oxidative stress affect the degradation of PA herbicides. Based on the previously proposed paradigm that bacteria deal with environmental stress before they engage in biodegradation, we studied how the degradation of the PA herbicide 2-methyl-4-chlorophenoxyacetic acid (MCPA) by the model PA degrader Cupriavidus pinatubonensis AEO106 was affected by Cu exposure. RESULTS Exposure of C. pinatubonensis in batch culture to sublethal concentrations of Cu increased accumulation of ROS measured by the oxidant sensing probe 2,7-dichlorodihydrofluorescein diacetate and flow cytometry, and resulted in upregulation of a gene encoding a protein belong to the Ohr/OsmC protein family. The ohr/osmC gene was also highly induced by H2O2 exposure suggesting that it is involved in the oxidative stress response in C. pinatubonensis. The increased ROS accumulation and increased expression of the oxidative stress defense coincided with a delay in the catabolic performance, since both expression of the catabolic tfdA gene and MCPA mineralization were delayed compared to unexposed control cells. CONCLUSIONS The current study suggests that Cu-induced ROS accumulation in C. pinatubonensis activates a stress response involving the product of the ohr/osmC gene. Further, the stress response is launched before induction of the catabolic tfdA gene and mineralization occurs.
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Affiliation(s)
- Nanna Bygvraa Svenningsen
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, Denmark
| | - Mette Damgaard
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, Denmark
| | - Maria Rasmussen
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, Denmark
| | - Danilo Pérez-Pantoja
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación, Universidad Tecnológica Metropolitana, Ignacio Valdivieso 2409, San Joaquín, Santiago, Chile
| | - Ole Nybroe
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, Denmark
| | - Mette Haubjerg Nicolaisen
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, Denmark.
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Castro-Rosas J, Gómez-Aldapa CA, Villagómez Ibarra JR, Santos-López EM, Rangel-Vargas E. Heat resistance of viable but non-culturable Escherichia coli cells determined by differential scanning calorimetry. FEMS Microbiol Lett 2017; 364:4108096. [PMID: 28967946 DOI: 10.1093/femsle/fnx188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 08/30/2017] [Indexed: 11/14/2022] Open
Abstract
Several reports have suggested that the viable but non-culturable (VBNC) state is a resistant form of bacterial cells that allows them to remain in a dormant form in the environment. Nevertheless, studies on the resistance of VBNC bacterial cells to ecological factors are limited, mainly because techniques that allow this type of evaluation are lacking. Differential scanning calorimetry (DSC) has been used to study the thermal resistance of culturable bacteria but has never been used to study VBNC cells. In this work, the heat resistance of Escherichia coli cells in the VBNC state was studied using the DSC technique. The VBNC state was induced in E. coli ATCC 25922 by suspending bacterial cells in artificial sea water, followed by storage at 3 ± 2°C for 110 days. Periodically, the behaviour of E. coli cells was monitored by plate counts, direct viable counts and DSC. The entire bacterial population entered the VBNC state after 110 days of storage. The results obtained with DSC suggest that the VBNC state does not confer thermal resistance to E. coli cells in the temperature range analysed here.
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Affiliation(s)
- Javier Castro-Rosas
- Área Académica de Química. Instituto de Ciencias Básicas e Ingeniería, Universidad Autónoma del Estado de Hidalgo, Ciudad del Conocimiento, Carretera Pachuca-Tulancingo km. 4.5. Mineral de la Reforma, Hgo., C.P. 42184. México
| | - Carlos Alberto Gómez-Aldapa
- Área Académica de Química. Instituto de Ciencias Básicas e Ingeniería, Universidad Autónoma del Estado de Hidalgo, Ciudad del Conocimiento, Carretera Pachuca-Tulancingo km. 4.5. Mineral de la Reforma, Hgo., C.P. 42184. México
| | - José Roberto Villagómez Ibarra
- Área Académica de Química. Instituto de Ciencias Básicas e Ingeniería, Universidad Autónoma del Estado de Hidalgo, Ciudad del Conocimiento, Carretera Pachuca-Tulancingo km. 4.5. Mineral de la Reforma, Hgo., C.P. 42184. México
| | - Eva María Santos-López
- Área Académica de Química. Instituto de Ciencias Básicas e Ingeniería, Universidad Autónoma del Estado de Hidalgo, Ciudad del Conocimiento, Carretera Pachuca-Tulancingo km. 4.5. Mineral de la Reforma, Hgo., C.P. 42184. México
| | - Esmeralda Rangel-Vargas
- Área Académica de Química. Instituto de Ciencias Básicas e Ingeniería, Universidad Autónoma del Estado de Hidalgo, Ciudad del Conocimiento, Carretera Pachuca-Tulancingo km. 4.5. Mineral de la Reforma, Hgo., C.P. 42184. México
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Almatroudi A, Tahir S, Hu H, Chowdhury D, Gosbell IB, Jensen SO, Whiteley GS, Deva AK, Glasbey T, Vickery K. Staphylococcus aureus dry-surface biofilms are more resistant to heat treatment than traditional hydrated biofilms. J Hosp Infect 2017; 98:161-167. [PMID: 28919336 DOI: 10.1016/j.jhin.2017.09.007] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 09/11/2017] [Indexed: 01/07/2023]
Abstract
BACKGROUND The importance of biofilms to clinical practice is being increasingly realized. Biofilm tolerance to antibiotics is well described but limited work has been conducted on the efficacy of heat disinfection and sterilization against biofilms. AIM To test the susceptibility of planktonic, hydrated biofilm and dry-surface biofilm forms of Staphylococcus aureus, to dry-heat and wet-heat treatments. METHODS S. aureus was grown as both hydrated biofilm and dry-surface biofilm in the CDC biofilm generator. Biofilm was subjected to a range of temperatures in a hot-air oven (dry heat), water bath or autoclave (wet heat). FINDINGS Dry-surface biofilms remained culture positive even when treated with the harshest dry-heat condition of 100°C for 60min. Following autoclaving samples were culture negative but 62-74% of bacteria in dry-surface biofilms remained alive as demonstrated by live/dead staining and confocal microscopy. Dry-surface biofilms subjected to autoclaving at 121°C for up to 30min recovered and released planktonic cells. Recovery did not occur following autoclaving for longer or at 134°C, at least during the time-period tested. Hydrated biofilm recovered following dry-heat treatment up to 100°C for 10min but failed to recover following autoclaving despite the presence of 43-60% live cells as demonstrated by live/dead staining. CONCLUSION S. aureus dry-surface biofilms are less susceptible to killing by dry heat and steam autoclaving than hydrated biofilms, which are less susceptible to heat treatment than planktonic suspensions.
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Affiliation(s)
- A Almatroudi
- Surgical Infection Research Group, Faculty of Medicine and Health Sciences, Macquarie University, New South Wales, Australia; Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Qassim, Saudi Arabia
| | - S Tahir
- Surgical Infection Research Group, Faculty of Medicine and Health Sciences, Macquarie University, New South Wales, Australia
| | - H Hu
- Surgical Infection Research Group, Faculty of Medicine and Health Sciences, Macquarie University, New South Wales, Australia
| | - D Chowdhury
- Surgical Infection Research Group, Faculty of Medicine and Health Sciences, Macquarie University, New South Wales, Australia
| | - I B Gosbell
- Antibiotic Resistance and Mobile Elements Group, Ingham Institute for Applied Medical Research, Liverpool, New South Wales, Australia; Medical Sciences Research Group, School of Medicine, Western Sydney University, New South Wales, Australia; Department of Microbiology & Infectious Diseases, Sydney South West Pathology Service, Liverpool, New South Wales Health Pathology, New South Wales, Australia
| | - S O Jensen
- Antibiotic Resistance and Mobile Elements Group, Ingham Institute for Applied Medical Research, Liverpool, New South Wales, Australia; Medical Sciences Research Group, School of Medicine, Western Sydney University, New South Wales, Australia
| | - G S Whiteley
- Medical Sciences Research Group, School of Medicine, Western Sydney University, New South Wales, Australia; Whiteley Corporation, North Sydney, New South Wales, Australia
| | - A K Deva
- Surgical Infection Research Group, Faculty of Medicine and Health Sciences, Macquarie University, New South Wales, Australia
| | - T Glasbey
- Whiteley Corporation, North Sydney, New South Wales, Australia
| | - K Vickery
- Surgical Infection Research Group, Faculty of Medicine and Health Sciences, Macquarie University, New South Wales, Australia.
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Brouchkov A, Kabilov M, Filippova S, Baturina O, Rogov V, Galchenko V, Mulyukin A, Fursova O, Pogorelko G. Bacterial community in ancient permafrost alluvium at the Mammoth Mountain (Eastern Siberia). Gene 2017; 636:48-53. [PMID: 28916375 DOI: 10.1016/j.gene.2017.09.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 09/07/2017] [Accepted: 09/11/2017] [Indexed: 09/30/2022]
Abstract
Permanently frozen (approx. 3.5Ma) alluvial Neogene sediments exposed in the Aldan river valley at the Mammoth Mountain (Eastern Siberia) are unique, ancient, and poorly studied permafrost environments. So far, the structure of the indigenous bacterial community has remained unknown. Use of 16S metagenomic analysis with total DNA isolation using DNA Spin Kit for Soil (MO-Bio) and QIAamp DNA Stool Mini Kit (Qiagen) has revealed the major and minor bacterial lineages in the permafrost alluvium sediments. In sum, 61 Operational Taxonomic Units (OTUs) with 31,239 reads (Qiagen kit) and 15,404 reads (Mo-Bio kit) could be assigned to the known taxa. Only three phyla, Bacteroidetes, Proteobacteria and Firmicutes, comprised >5% of the OTUs abundance and accounted for 99% of the total reads. OTUs pertaining to the top families (Chitinophagaceae, Caulobacteraceae, Sphingomonadaceae, Bradyrhizobiaceae, Halomonadaceae) held >90% of reads. The abundance of Actinobacteria was less (0.7%), whereas members of other phyla (Deinococcus-Thermus, Cyanobacteria/Chloroplast, Fusobacteria, and Acidobacteria) constituted a minor fraction of reads. The bacterial community in the studied ancient alluvium differs from other permafrost sediments, mainly by predominance of Bacteroidetes (>52%). The diversity of this preserved bacterial community has the potential to cause effects unknown if prompted to thaw and spread with changing climate. Therefore, this study elicits further reason to study how reintroduction of these ancient bacteria could affect the surrounding ecosystem, including current bacterial species.
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Affiliation(s)
- Anatoli Brouchkov
- Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia; Tyumen State University, Volodarskogo 6, Tyumen 625003, Russia
| | - Marsel Kabilov
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Lavrentiev Avenue 8, Novosibirsk 630090, Russia
| | - Svetlana Filippova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Avenue 33, bld. 2, Moscow 119071, Russia
| | - Olga Baturina
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Lavrentiev Avenue 8, Novosibirsk 630090, Russia
| | - Victor Rogov
- Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia
| | - Valery Galchenko
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Avenue 33, bld. 2, Moscow 119071, Russia
| | - Andrey Mulyukin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Avenue 33, bld. 2, Moscow 119071, Russia
| | - Oksana Fursova
- Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia
| | - Gennady Pogorelko
- NI Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia; Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, USA.
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64
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Wang S, Yang F, Yang B. Global effect of CsrA on gene expression in enterohemorrhagic Escherichia coli O157:H7. Res Microbiol 2017; 168:700-709. [PMID: 28870757 DOI: 10.1016/j.resmic.2017.08.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 08/21/2017] [Accepted: 08/23/2017] [Indexed: 01/25/2023]
Abstract
The post-transcriptional regulator CsrA regulates multiple unrelated processes such as central carbon metabolism, motility, biofilm formation and bacterial virulence in different bacteria. However, regulation by CsrA in enterohemorrhagic Escherichia coli (EHEC) O157:H7 is still largely unknown. In this study, we performed a detailed analysis of gene expression differences between the EHEC O157:H7 wild-type strain and a corresponding csrA::kan mutant using RNA-seq technology. Genes whose expression was affected by CsrA were identified and grouped into different clusters of orthologous group categories. Genes located in the locus of enterocyte effacement (LEE) pathogenicity island were significantly upregulated, whereas expression of flagella-related genes was significantly reduced in the csrA::kan mutant. Subsequent bacterial adherence and motility assays showed that inactivation of CsrA in EHEC O157:H7 resulted in a significant increase in bacterial adherence to host epithelial cells, with a concomitant loss of swimming motility on semi-solid agar plates. Furthermore, we also found that CsrA regulates genes not previously identified in other bacterial species, including genes encoding cytochrome oxidases and those required for nitrogen metabolism. Our results provide essential insight into the regulatory function of CsrA.
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Affiliation(s)
- Shaomeng Wang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin 300457, PR China.
| | - Fan Yang
- Department of Neurosurgery, Tianjin First Central Hospital, Tianjin 300192, PR China.
| | - Bin Yang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin 300457, PR China.
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65
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Griko YV, Rask JC, Raychev R. Advantage of Animal Models with Metabolic Flexibility for Space Research Beyond Low Earth Orbit. ACTA ACUST UNITED AC 2017. [DOI: 10.1089/space.2016.0024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Yuri V. Griko
- Space Biosciences Division, NASA-Ames Research Center, Moffett Field, California
| | - Jon C. Rask
- Space Biosciences Division, NASA-Ames Research Center, Moffett Field, California
- KBRwyle, Moffett Field, California
| | - Raycho Raychev
- Space Challenges Program, EnduroSat, Inc., Sofia, Bulgaria
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66
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Emerson JB, Adams RI, Román CMB, Brooks B, Coil DA, Dahlhausen K, Ganz HH, Hartmann EM, Hsu T, Justice NB, Paulino-Lima IG, Luongo JC, Lymperopoulou DS, Gomez-Silvan C, Rothschild-Mancinelli B, Balk M, Huttenhower C, Nocker A, Vaishampayan P, Rothschild LJ. Schrödinger's microbes: Tools for distinguishing the living from the dead in microbial ecosystems. MICROBIOME 2017; 5:86. [PMID: 28810907 PMCID: PMC5558654 DOI: 10.1186/s40168-017-0285-3] [Citation(s) in RCA: 236] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 06/05/2017] [Indexed: 05/16/2023]
Abstract
While often obvious for macroscopic organisms, determining whether a microbe is dead or alive is fraught with complications. Fields such as microbial ecology, environmental health, and medical microbiology each determine how best to assess which members of the microbial community are alive, according to their respective scientific and/or regulatory needs. Many of these fields have gone from studying communities on a bulk level to the fine-scale resolution of microbial populations within consortia. For example, advances in nucleic acid sequencing technologies and downstream bioinformatic analyses have allowed for high-resolution insight into microbial community composition and metabolic potential, yet we know very little about whether such community DNA sequences represent viable microorganisms. In this review, we describe a number of techniques, from microscopy- to molecular-based, that have been used to test for viability (live/dead determination) and/or activity in various contexts, including newer techniques that are compatible with or complementary to downstream nucleic acid sequencing. We describe the compatibility of these viability assessments with high-throughput quantification techniques, including flow cytometry and quantitative PCR (qPCR). Although bacterial viability-linked community characterizations are now feasible in many environments and thus are the focus of this critical review, further methods development is needed for complex environmental samples and to more fully capture the diversity of microbes (e.g., eukaryotic microbes and viruses) and metabolic states (e.g., spores) of microbes in natural environments.
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Affiliation(s)
- Joanne B. Emerson
- Department of Microbiology, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210 USA
- Current Address: Department of Plant Pathology, University of California, Davis, CA USA
| | - Rachel I. Adams
- Department of Plant & Microbial Biology, University of California, Berkeley, 111 Koshland Hall, Berkeley, CA 94720 USA
| | - Clarisse M. Betancourt Román
- Biology and the Built Environment Center, Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403 USA
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403 USA
| | - Brandon Brooks
- Department of Plant & Microbial Biology, University of California, Berkeley, 111 Koshland Hall, Berkeley, CA 94720 USA
- Department of Earth and Planetary Sciences, University of California, Berkeley, Berkeley, CA 94720 USA
| | - David A. Coil
- Genome Center, University of California Davis, 451 Health Sciences Drive, Davis, CA 95616 USA
| | - Katherine Dahlhausen
- Genome Center, University of California Davis, 451 Health Sciences Drive, Davis, CA 95616 USA
| | - Holly H. Ganz
- Genome Center, University of California Davis, 451 Health Sciences Drive, Davis, CA 95616 USA
| | - Erica M. Hartmann
- Biology and the Built Environment Center, Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403 USA
- Department of Civil and Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208 USA
| | - Tiffany Hsu
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 665 Huntington Avenue, Boston, MA 02115 USA
- The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Nicholas B. Justice
- Lawrence Berkeley National Lab, 1 Cyclotron Road, 955-512L, Berkeley, CA 94720 USA
| | - Ivan G. Paulino-Lima
- Universities Space Research Association, NASA Ames Research Center, Mail Stop 239-20, Building 239, room 377, Moffett Field, CA 94035-1000 USA
| | - Julia C. Luongo
- Department of Mechanical Engineering, University of Colorado at Boulder, 1111 Engineering Drive, 427 UCB, Boulder, CO 80309 USA
| | - Despoina S. Lymperopoulou
- Department of Plant & Microbial Biology, University of California, Berkeley, 111 Koshland Hall, Berkeley, CA 94720 USA
| | - Cinta Gomez-Silvan
- Lawrence Berkeley National Lab, 1 Cyclotron Road, 955-512L, Berkeley, CA 94720 USA
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94702 USA
| | | | - Melike Balk
- Department of Earth Sciences – Petrology, Faculty of Geosciences, Utrecht University, P.O. Box 80.021, 3508 TA Utrecht, The Netherlands
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 665 Huntington Avenue, Boston, MA 02115 USA
- The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Andreas Nocker
- IWW Water Centre, Moritzstrasse 26, 45476 Mülheim an der Ruhr, Germany
| | - Parag Vaishampayan
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA USA
| | - Lynn J. Rothschild
- Planetary Sciences and Astrobiology, NASA Ames Research Center, Mail Stop 239-20, Building 239, room 361, Moffett Field, CA 94035-1000 USA
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67
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Ou F, McGoverin C, Swift S, Vanholsbeeck F. Absolute bacterial cell enumeration using flow cytometry. J Appl Microbiol 2017; 123:464-477. [DOI: 10.1111/jam.13508] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 05/18/2017] [Accepted: 06/04/2017] [Indexed: 11/29/2022]
Affiliation(s)
- F. Ou
- Department of Physics; The Dodd-Walls Centre for Photonic and Quantum Technologies; The University of Auckland; Auckland New Zealand
| | - C. McGoverin
- Department of Physics; The Dodd-Walls Centre for Photonic and Quantum Technologies; The University of Auckland; Auckland New Zealand
| | - S. Swift
- School of Medical Sciences; The University of Auckland; Auckland New Zealand
| | - F. Vanholsbeeck
- Department of Physics; The Dodd-Walls Centre for Photonic and Quantum Technologies; The University of Auckland; Auckland New Zealand
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68
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Abstract
Unrelated spore-forming bacteria share unique characteristics stemming from the presence of highly resistant endospores, leading to similar challenges in health and disease. These characteristics are related to the presence of these highly transmissible spores, which are commonly spread within the environment and are implicated in host-to-host transmission. In humans, spore-forming bacteria contribute to a variety of pathological processes that share similar characteristics, including persistence, chronicity, relapses and the maintenance of the resistome. We first outline the necessity of characterizing the totality of the spore-forming bacteria as the sporobiota based on their unique common characteristics. We further propose that the collection of all genes of spore-forming bacteria be known as the sporobiome. Such differentiation is critical for exploring the cross-talk between the sporobiota and other members of the gut microbiota, and will allow for a better understanding of the implications of the sporobiota and sporobiome in a variety of pathologies and the spread of antibiotic resistance.
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Affiliation(s)
- George Tetz
- Human Microbiology Institute, 423 West 127 Street, New York, NY 10027 USA
| | - Victor Tetz
- Human Microbiology Institute, 423 West 127 Street, New York, NY 10027 USA
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69
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Crespo D, Grilo TF, Baptista J, Coelho JP, Lillebø AI, Cássio F, Fernandes I, Pascoal C, Pardal MÂ, Dolbeth M. New climatic targets against global warming: will the maximum 2 °C temperature rise affect estuarine benthic communities? Sci Rep 2017; 7:3918. [PMID: 28634416 PMCID: PMC5478632 DOI: 10.1038/s41598-017-04309-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 05/12/2017] [Indexed: 11/09/2022] Open
Abstract
The Paris Agreement signed by 195 countries in 2015 sets out a global action plan to avoid dangerous climate change by limiting global warming to remain below 2 °C. Under that premise, in situ experiments were run to test the effects of 2 °C temperature increase on the benthic communities in a seagrass bed and adjacent bare sediment, from a temperate European estuary. Temperature was artificially increased in situ and diversity and ecosystem functioning components measured after 10 and 30 days. Despite some warmness effects on the analysed components, significant impacts were not verified on macro and microfauna structure, bioturbation or in the fluxes of nutrients. The effect of site/habitat seemed more important than the effects of the warmness, with the seagrass habitat providing more homogenous results and being less impacted by warmness than the adjacent bare sediment. The results reinforce that most ecological responses to global changes are context dependent and that ecosystem stability depends not only on biological diversity but also on the availability of different habitats and niches, highlighting the role of coastal wetlands. In the context of the Paris Agreement it seems that estuarine benthic ecosystems will be able to cope if global warming remains below 2 °C.
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Affiliation(s)
- Daniel Crespo
- Centre for Functional Ecology - CFE, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal.
| | - Tiago Fernandes Grilo
- MARE - Marine and Environmental Sciences Centre, Laboratório Marítimo da Guia - Faculdade de Ciências da Universidade de Lisboa, Av. Nossa Senhora do Cabo, 939, 2750-374, Cascais, Portugal
| | - Joana Baptista
- Centre for Functional Ecology - CFE, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal
| | - João Pedro Coelho
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, Novo Edifício do Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos s/n, 4450-208, Matosinhos, Portugal
- Department of Chemistry & CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Ana Isabel Lillebø
- Department of Biology & CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Fernanda Cássio
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- Institute of Science and Innovation for Bio-sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Isabel Fernandes
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- Institute of Science and Innovation for Bio-sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Cláudia Pascoal
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- Institute of Science and Innovation for Bio-sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Miguel Ângelo Pardal
- Centre for Functional Ecology - CFE, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal
| | - Marina Dolbeth
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, Novo Edifício do Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos s/n, 4450-208, Matosinhos, Portugal
- Department of Biology & CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
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70
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Liang K, Richardson JJ, Doonan CJ, Mulet X, Ju Y, Cui J, Caruso F, Falcaro P. An Enzyme-Coated Metal-Organic Framework Shell for Synthetically Adaptive Cell Survival. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201704120] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Kang Liang
- School of Chemical Engineering; The University of New South Wales; Sydney NSW 2052 Australia
- Graduate School of Biomedical Engineering; The University of New South Wales; Sydney NSW 2052 Australia
- CSIRO Manufacturing, CSIRO; Private Bag 10 Clayton South Victoria 3169 Australia
| | - Joseph J. Richardson
- CSIRO Manufacturing, CSIRO; Private Bag 10 Clayton South Victoria 3169 Australia
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, and the Department of Chemical and Biomolecular Engineering; The University of Melbourne; Parkville Victoria 3010 Australia
| | - Christian J. Doonan
- School of Chemistry and Physics; The University of Adelaide; Adelaide South Australia 5005 Australia
| | - Xavier Mulet
- CSIRO Manufacturing, CSIRO; Private Bag 10 Clayton South Victoria 3169 Australia
| | - Yi Ju
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, and the Department of Chemical and Biomolecular Engineering; The University of Melbourne; Parkville Victoria 3010 Australia
| | - Jiwei Cui
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, and the Department of Chemical and Biomolecular Engineering; The University of Melbourne; Parkville Victoria 3010 Australia
- Key Laboratory of Colloid and Interface Chemistry of Ministry of Education, and the; School of Chemistry and Chemical Engineering; Shandong University; Jinan 250100 China
| | - Frank Caruso
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, and the Department of Chemical and Biomolecular Engineering; The University of Melbourne; Parkville Victoria 3010 Australia
| | - Paolo Falcaro
- Institute of Physical and Theoretical Chemistry; Graz University of Technology; Stremayrgasse 9 Graz 8010 Austria
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71
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Liang K, Richardson JJ, Doonan CJ, Mulet X, Ju Y, Cui J, Caruso F, Falcaro P. An Enzyme-Coated Metal-Organic Framework Shell for Synthetically Adaptive Cell Survival. Angew Chem Int Ed Engl 2017; 56:8510-8515. [DOI: 10.1002/anie.201704120] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Indexed: 01/07/2023]
Affiliation(s)
- Kang Liang
- School of Chemical Engineering; The University of New South Wales; Sydney NSW 2052 Australia
- Graduate School of Biomedical Engineering; The University of New South Wales; Sydney NSW 2052 Australia
- CSIRO Manufacturing, CSIRO; Private Bag 10 Clayton South Victoria 3169 Australia
| | - Joseph J. Richardson
- CSIRO Manufacturing, CSIRO; Private Bag 10 Clayton South Victoria 3169 Australia
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, and the Department of Chemical and Biomolecular Engineering; The University of Melbourne; Parkville Victoria 3010 Australia
| | - Christian J. Doonan
- School of Chemistry and Physics; The University of Adelaide; Adelaide South Australia 5005 Australia
| | - Xavier Mulet
- CSIRO Manufacturing, CSIRO; Private Bag 10 Clayton South Victoria 3169 Australia
| | - Yi Ju
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, and the Department of Chemical and Biomolecular Engineering; The University of Melbourne; Parkville Victoria 3010 Australia
| | - Jiwei Cui
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, and the Department of Chemical and Biomolecular Engineering; The University of Melbourne; Parkville Victoria 3010 Australia
- Key Laboratory of Colloid and Interface Chemistry of Ministry of Education, and the; School of Chemistry and Chemical Engineering; Shandong University; Jinan 250100 China
| | - Frank Caruso
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, and the Department of Chemical and Biomolecular Engineering; The University of Melbourne; Parkville Victoria 3010 Australia
| | - Paolo Falcaro
- Institute of Physical and Theoretical Chemistry; Graz University of Technology; Stremayrgasse 9 Graz 8010 Austria
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72
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Abstract
Most cells in nature are not actively dividing, yet are able to return to the cell cycle given the appropriate environmental signals. There is now ample evidence that quiescent G0 cells are not shut-down but still metabolically and transcriptionally active. Quiescent cells must maintain a basal transcriptional capacity to maintain transcripts and proteins necessary for survival. This implies a tight control over RNA polymerases: RNA pol II for mRNA transcription during G0, but especially RNA pol I and RNA pol III to maintain an appropriate level of structural RNAs, raising the possibility that specific transcriptional control mechanisms evolved in quiescent cells. In accordance with this, we recently discovered that RNA interference is necessary to control RNA polymerase I transcription during G0. While this mini-review focuses on yeast model organisms (Saccharomyces cerevisiae and Schizosaccharomyces pombe), parallels are drawn to other eukaryotes and mammalian systems, in particular stem cells.
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Affiliation(s)
- Benjamin Roche
- a Cold Spring Harbor Laboratory , Cold Spring Harbor , NY , USA
| | - Benoit Arcangioli
- b Genome Dynamics Unit , UMR 3525 CNRS, Institut Pasteur, 25-28 rue du Docteur Roux , Paris , France
| | - Robert Martienssen
- a Cold Spring Harbor Laboratory , Cold Spring Harbor , NY , USA.,c Howard Hughes Medical Institute-Gordon and Betty Moore Foundation (HHMI-GBM) Investigator , NY , USA
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73
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Çetiner U, Rowe I, Schams A, Mayhew C, Rubin D, Anishkin A, Sukharev S. Tension-activated channels in the mechanism of osmotic fitness in Pseudomonas aeruginosa. J Gen Physiol 2017; 149:595-609. [PMID: 28424229 PMCID: PMC5412531 DOI: 10.1085/jgp.201611699] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 01/16/2017] [Accepted: 03/20/2017] [Indexed: 12/14/2022] Open
Abstract
Pseudomonas aeruginosa is resistant to drastic osmotic changes because of its ability to quickly jettison small osmolytes through osmotic release channels. Çetiner et al. reveal that it uses one MscL-like and at least two types of MscS-like channels during its osmotic response. Pseudomonas aeruginosa (PA) is an opportunistic pathogen with an exceptional ability to adapt to a range of environments. Part of its adaptive potential is the ability to survive drastic osmolarity changes. Upon a sudden dilution of external medium, such as during exposure to rain, bacteria evade mechanical rupture by engaging tension-activated channels that act as osmolyte release valves. In this study, we compare fast osmotic permeability responses in suspensions of wild-type PA and Escherichia coli (EC) strains in stopped-flow experiments and provide electrophysiological descriptions of osmotic-release channels in PA. Using osmotic dilution experiments, we first show that PA tolerates a broader range of shocks than EC. We record the kinetics of cell equilibration reported by light scattering responses to osmotic up- and down-shocks. PA exhibits a lower water permeability and faster osmolyte release rates during large osmotic dilutions than EC, which correlates with better survival. To directly characterize the PA tension-activated channels, we generate giant spheroplasts from this microorganism and record current responses in excised patches. Unlike EC, which relies primarily on two types of channels, EcMscS and EcMscL, to generate a distinctive two-wave pressure ramp response, PA exhibits a more gradual response that is dominated by MscL-type channels. Genome analysis, cloning, and expression reveal that PA possesses one MscL-type (PaMscL) and two MscS-type (PaMscS-1 and 2) proteins. In EC spheroplasts, both PaMscS channels exhibit a slightly earlier activation by pressure compared with EcMscS. Unitary currents reveal that PaMscS-2 has a smaller conductance, higher anionic preference, stronger inactivation, and slower recovery compared with PaMscS-1. We conclude that PA relies on MscL as the major valve defining a high rate of osmolyte release sufficient to curb osmotic swelling under extreme shocks, but it still requires MscS-type channels with a strong propensity to inactivation to properly terminate massive permeability response.
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Affiliation(s)
- Uğur Çetiner
- Department of Biology, University of Maryland, College Park, MD 20742.,Institute of Physical Science and Technology, University of Maryland, College Park, MD 20742.,Maryland Biophysics Program, University of Maryland, College Park, MD 20742
| | - Ian Rowe
- Department of Biology, University of Maryland, College Park, MD 20742.,Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742
| | - Anthony Schams
- Department of Biology, University of Maryland, College Park, MD 20742
| | - Christina Mayhew
- Department of Biology, University of Maryland, College Park, MD 20742
| | - Deanna Rubin
- Department of Biology, University of Maryland, College Park, MD 20742
| | - Andriy Anishkin
- Department of Biology, University of Maryland, College Park, MD 20742
| | - Sergei Sukharev
- Department of Biology, University of Maryland, College Park, MD 20742 .,Institute of Physical Science and Technology, University of Maryland, College Park, MD 20742.,Maryland Biophysics Program, University of Maryland, College Park, MD 20742
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74
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Yu X, Li Y, Cui Y, Liu R, Li Y, Chen Q, Gu Y, Zhao K, Xiang Q, Xu K, Zhang X. An indoleacetic acid-producing Ochrobactrum sp. MGJ11 counteracts cadmium effect on soybean by promoting plant growth. J Appl Microbiol 2017; 122:987-996. [PMID: 27995689 DOI: 10.1111/jam.13379] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 11/16/2016] [Accepted: 12/08/2016] [Indexed: 11/29/2022]
Abstract
AIMS To analyse whether some indoleacetic acid (IAA)-secreting plant growth-promoting bacteria can alleviate cadmium (Cd) stress, the role of an Ochrobactrum sp. MGJ11 from rhizosphere of soybean in promoting plant growth, and to evaluate the counteracting Cd effects on soybean. METHODS AND RESULTS Ochrobactrum sp. MGJ11 produced 121·2 mg l-1 of IAA. MGJ11 increased soybean root length, shoot length and biomass by 30·1, 30·8 and 13·4% respectively. In liquid medium, no IAA production was detected in Cd concentration of 100 mg l-1 . In soil with 20-80 mg kg-1 Cd, MGJ11 promoted soybean root elongation (29·4-161·4%) and increased the shoot length (up to 52·7%) and biomass (up to 87·2%). After growing for 38 days, Cd concentrations in the roots of inoculated soybean were lower than in those of noninoculated plants. Only a little Cd (2·6-16·9 μg g-1 ) was translocated from the root to shoot. CONCLUSIONS Ochrobactrum sp. MGJ11 secretes IAA and shows tolerance against Cd. MGJ11 inoculation improves the root length, shoot length and biomass of soybean in both vermiculite and Cd vermiculite, and decreases Cd concentration of soybean root. The characteristics of MGJ11 suggest that it could be used for promoting soybean growth and lowering bioavailability of soil Cd for soybean root. SIGNIFICANCE AND IMPACT OF THE STUDY In this study, we isolated a plant growth-promoting Ochrobactrum with the activity of mitigating Cd toxicity to plant roots. The Ochrobactrum can be considered as a potential bioaugmentation agent that promotes plant growth, especially in some agricultural systems, or that helps in the phytoremediation of Cd-contaminated soil.
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Affiliation(s)
- X Yu
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Y Li
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Y Cui
- Sichuan Provincial Academy of Natural Resource and Sciences, Chengdu, China
| | - R Liu
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Y Li
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Q Chen
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Y Gu
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - K Zhao
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Q Xiang
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - K Xu
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - X Zhang
- College of Resources, Sichuan Agricultural University, Chengdu, China
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75
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Liu J, Zhou R, Li L, Peters BM, Li B, Lin CW, Chuang TL, Chen D, Zhao X, Xiong Z, Xu Z, Shirtliff ME. Viable but non-culturable state and toxin gene expression of enterohemorrhagic Escherichia coli O157 under cryopreservation. Res Microbiol 2017; 168:188-193. [DOI: 10.1016/j.resmic.2016.11.002] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Revised: 11/08/2016] [Accepted: 11/14/2016] [Indexed: 10/20/2022]
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76
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Ivanova EA, Korvigo IO, Aparin BF, Chirak EL, Pershina EV, Romaschenko NS, Provorov NA, Andronov EE. The preservation of microbial DNA in archived soils of various genetic types. PLoS One 2017; 12:e0173901. [PMID: 28339464 PMCID: PMC5365134 DOI: 10.1371/journal.pone.0173901] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Accepted: 02/28/2017] [Indexed: 02/01/2023] Open
Abstract
This study is a comparative analysis of samples of archived (stored for over 70–90 years) and modern soils of two different genetic types–chernozem and sod-podzolic soils. We revealed a reduction in biodiversity of archived soils relative to their modern state. Particularly, long-term storage in the museum exerted a greater impact on the microbiomes of sod-podzolic soils, while chernozem samples better preserved the native community. Thus, the persistence of microbial DNA in soil is largely determined by the physico-chemical characteristics that differ across soil types. Chernozems create better conditions for the long-term DNA preservation than sod-podzolic soils. This results in supposedly higher levels of biodiversity conservation in the microbiomes of chernozem with preservation of major microbial taxa dominant in the modern (control) soil samples, which makes archived chernozems a promising object for paleosoil studies.
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Affiliation(s)
- Ekaterina A. Ivanova
- Laboratory of Microbiological Monitoring and Bioremediation of Soils, All-Russia Research Institute for Agricultural Microbiology, Saint-Petersburg, Russia
- Laboratory of Biology and Biochemistry of Soils, V.V. Dokuchaev Soil Science Institute, Moscow, Russia
- * E-mail:
| | - Ilia O. Korvigo
- Laboratory of Microbiological Monitoring and Bioremediation of Soils, All-Russia Research Institute for Agricultural Microbiology, Saint-Petersburg, Russia
- Laboratory of Functional Analysis of the Genome, Moscow Institute of Physics and Technology, Moscow, Russia
- ITMO University, Saint-Petersburg, Russia
| | - Boris F. Aparin
- Department of Soil Science and Soil Ecology of Saint-Petersburg State University, Saint-Petersburg, Russia
| | - Evgenii L. Chirak
- Laboratory of Microbiological Monitoring and Bioremediation of Soils, All-Russia Research Institute for Agricultural Microbiology, Saint-Petersburg, Russia
| | - Elizaveta V. Pershina
- Laboratory of Microbiological Monitoring and Bioremediation of Soils, All-Russia Research Institute for Agricultural Microbiology, Saint-Petersburg, Russia
- Department of Microbiology and Genetics of Saint-Petersburg State University, Saint-Petersburg, Russia
| | - Nikolay S. Romaschenko
- Laboratory of Microbiological Monitoring and Bioremediation of Soils, All-Russia Research Institute for Agricultural Microbiology, Saint-Petersburg, Russia
| | - Nikolai A. Provorov
- Laboratory of Microbiological Monitoring and Bioremediation of Soils, All-Russia Research Institute for Agricultural Microbiology, Saint-Petersburg, Russia
| | - Evgeny E. Andronov
- Laboratory of Microbiological Monitoring and Bioremediation of Soils, All-Russia Research Institute for Agricultural Microbiology, Saint-Petersburg, Russia
- Laboratory of Biology and Biochemistry of Soils, V.V. Dokuchaev Soil Science Institute, Moscow, Russia
- Department of Microbiology and Genetics of Saint-Petersburg State University, Saint-Petersburg, Russia
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77
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Hughes E, Head B, Maltman C, Piercey-Normore M, Yurkov V. Aerobic anoxygenic phototrophs in gold mine tailings in Nopiming Provincial Park, Manitoba, Canada. Can J Microbiol 2017; 63:212-218. [PMID: 28194995 DOI: 10.1139/cjm-2016-0448] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A sampling trip to Central Gold Mine, Nopiming Provincial Park, Canada, was taken in September 2011. Abundance, distribution, and physiology of aerobic anoxygenic phototrophs (AAP) from 4 locations were studied. Enumeration revealed 14.6% of culturable microbes were AAP. Five strains (NM4.16, NM4.18, C4, C9, C11) were chosen for analysis. All grow best on complex media without vitamin requirements and with an optimal pH 7.0-8.0, with strain C4 preferring pH 6.0. Strain NM4.18 tolerates the highest pH 11.0. Optimal temperature for all is 28 °C (range of 2-37 °C except NM4.16, which survives 45 °C). Strains C9, C11, and NM4.18 grew in 1.0%, 2.0%, and 5.0% NaCl, respectively, while NM4.16 and C4 grew only without NaCl. Isolates were all highly resistant to toxic metal(oid) oxides: tellurite (1500 μg/mL, all), tellurate (1500 μg/mL, C11), selenite (5000 μg/mL, C9, C11, and NM4.18), selenate (1000 μg/mL, C9 and C11), and orthometavanadate and metavanadate (5000 μg/mL, C11 and NM4.18). They could reduce tellurite to the less toxic elemental tellurium. Full 16S rRNA gene sequencing revealed all strains are Alphaproteobacteria, with C4 and NM4.16 closely related to Porphyrobacter colymbi (99.4% and 99.7% sequence similarity, respectively), C9 to Brevundimonas variabilis (99.1%), C11 to Brevundimonas bacteroides (98.6%), and NM4.18 to Erythromonas ursincola (98.5%).
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Affiliation(s)
- Elizabeth Hughes
- a Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Breanne Head
- a Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Chris Maltman
- a Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | | | - Vladimir Yurkov
- a Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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Orruño M, Kaberdin VR, Arana I. Survival strategies of Escherichia coli and Vibrio spp.: contribution of the viable but nonculturable phenotype to their stress-resistance and persistence in adverse environments. World J Microbiol Biotechnol 2017; 33:45. [PMID: 28161849 DOI: 10.1007/s11274-017-2218-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Accepted: 01/23/2017] [Indexed: 12/11/2022]
Abstract
In their natural ecosystems, bacteria are continuously exposed to changing environmental factors including physicochemical parameters (e.g. temperature, pH, etc.), availability of nutrients as well as interaction(s) with other organisms. To increase their tolerance and survival under adverse conditions, bacteria trigger a number of adaptation mechanisms. One of the well-known adaptation responses of the non-spore-forming bacteria is the acquisition of the viable but non-culturable (VBNC) state. This phenotype is induced by different stress factors (e.g. low temperature) and is characterized by the temporal loss of culturability, which can potentially be restored. Moreover, this response can be combined with the bust and boom strategy, which implies the death of the main population of the stressed cells (or their entry into the VBNC state) upon stress, thus enabling the remaining cells (i.e. residual culturable population) to subsist at the expense of the dead or/and VBNC cells. In this review, we discuss the characteristics of the VBNC state, its biological significance and contribution to bacterial survival.
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Affiliation(s)
- M Orruño
- Department of Immunology, Microbiology and Parasitology, University of the Basque Country (UPV/EHU), Barrio Sarriena S/n, 48940, Leioa, Spain
| | - V R Kaberdin
- Department of Immunology, Microbiology and Parasitology, University of the Basque Country (UPV/EHU), Barrio Sarriena S/n, 48940, Leioa, Spain.,IKERBASQUE, Basque Foundation for Science, María Díaz de Haro 3, 48013, Bilbao, Spain
| | - I Arana
- Department of Immunology, Microbiology and Parasitology, University of the Basque Country (UPV/EHU), Barrio Sarriena S/n, 48940, Leioa, Spain.
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Xia X, Larios-Valencia J, Liu Z, Xiang F, Kan B, Wang H, Zhu J. OxyR-activated expression of Dps is important for Vibrio cholerae oxidative stress resistance and pathogenesis. PLoS One 2017; 12:e0171201. [PMID: 28151956 PMCID: PMC5289545 DOI: 10.1371/journal.pone.0171201] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Accepted: 01/18/2017] [Indexed: 11/19/2022] Open
Abstract
Vibrio cholerae is the causative agent of cholera, a dehydrating diarrheal disease. This Gram-negative pathogen is able to modulate its gene expression in order to combat stresses encountered in both aquatic and host environments, including stress posed by reactive oxygen species (ROS). In order to further the understanding of V. cholerae’s transcriptional response to ROS, we performed an RNA sequencing analysis to determine the transcriptional profile of V. cholerae when exposed to hydrogen hydroperoxide. Of 135 differentially expressed genes, VC0139 was amongst the genes with the largest induction. VC0139 encodes a protein homologous to the DPS (DNA-binding protein from starved cells) protein family, which are widely conserved and are implicated in ROS resistance in other bacteria. Using a promoter reporter assay, we show that during exponential growth, dps is induced by H2O2 in a manner dependent on the ROS-sensing transcriptional regulator, OxyR. Upon entry into stationary phase, the major stationary phase regulator RpoS is required to transcribe dps. Deletion of dps impaired V. cholerae resistance to both inorganic and organic hydroperoxides. Furthermore, we show that Dps is involved in resistance to multiple environmental stresses. Finally, we found that Dps is important for V. cholerae adult mouse colonization, but becomes dispensable in the presence of antioxidants. Taken together, our results suggest that Dps plays vital roles in both V. cholerae stress resistance and pathogenesis.
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Affiliation(s)
- Xiaoyun Xia
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jessie Larios-Valencia
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Zhi Liu
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
- Department of Biotechnology, Huazhong University of Science and Technology, Wuhan, China
| | - Fu Xiang
- College of Life Sciences, Huanggang Normal University, Huanggang, China
| | - Biao Kan
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Hui Wang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
- * E-mail: (HW); (JZ)
| | - Jun Zhu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
- * E-mail: (HW); (JZ)
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80
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Gorr TA. Hypometabolism as the ultimate defence in stress response: how the comparative approach helps understanding of medically relevant questions. Acta Physiol (Oxf) 2017; 219:409-440. [PMID: 27364602 DOI: 10.1111/apha.12747] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 01/28/2016] [Accepted: 06/28/2016] [Indexed: 12/22/2022]
Abstract
First conceptualized from breath-hold diving mammals, later recognized as the ultimate cell autonomous survival strategy in anoxia-tolerant vertebrates and burrowing or hibernating rodents, hypometabolism is typically recruited by resilient organisms to withstand and recover from otherwise life-threatening hazards. Through the coordinated down-regulation of biosynthetic, proliferative and electrogenic expenditures at times when little ATP can be generated, a metabolism turned 'down to the pilot light' allows the re-balancing of energy demand with supply at a greatly suppressed level in response to noxious exogenous stimuli or seasonal endogenous cues. A unifying hallmark of stress-tolerant organisms, the adaptation effectively prevents lethal depletion of ATP, thus delineating a marked contrast with susceptible species. Along with disengaged macromolecular syntheses, attenuated transmembrane ion shuttling and PO2 -conforming respiration rates, the metabolic slowdown in tolerant species usually culminates in a non-cycling, quiescent phenotype. However, such a reprogramming also occurs in leading human pathophysiologies. Ranging from microbial infections through ischaemia-driven infarcts to solid malignancies, cells involved in these disorders may again invoke hypometabolism to endure conditions non-permissive for growth. At the same time, their reduced activities underlie the frequent development of a general resistance to therapeutic interventions. On the other hand, a controlled induction of hypometabolic and/or hypothermic states by pharmacological means has recently stimulated intense research aimed at improved organ preservation and patient survival in situations requiring acutely administered critical care. The current review article therefore presents an up-to-date survey of concepts and applications of a coordinated and reversibly down-regulated metabolic rate as the ultimate defence in stress responses.
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Affiliation(s)
- T. A. Gorr
- Institute of Veterinary Physiology; Vetsuisse Faculty; University of Zurich; Zurich Switzerland
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81
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Lee WB, Fu CY, Chang WH, You HL, Wang CH, Lee MS, Lee GB. A microfluidic device for antimicrobial susceptibility testing based on a broth dilution method. Biosens Bioelectron 2017; 87:669-678. [DOI: 10.1016/j.bios.2016.09.008] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 08/25/2016] [Accepted: 09/01/2016] [Indexed: 10/21/2022]
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Bell T, Tylianakis JM. Microbes in the Anthropocene: spillover of agriculturally selected bacteria and their impact on natural ecosystems. Proc Biol Sci 2016; 283:20160896. [PMID: 27928044 PMCID: PMC5204138 DOI: 10.1098/rspb.2016.0896] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 10/11/2016] [Indexed: 12/13/2022] Open
Abstract
Soil microbial communities are enormously diverse, with at least millions of species and trillions of genes unknown to science or poorly described. Soil microbial communities are key components of agriculture, for example, in provisioning nitrogen and protecting crops from pathogens, providing overall ecosystem services in excess of $1000bn per year. It is important to know how humans are affecting this hidden diversity. Much is known about the negative consequences of agricultural intensification on higher organisms, but almost nothing is known about how alterations to landscapes affect microbial diversity, distributions and processes. We review what is known about spatial flows of microbes and their response to land-use change, and outline nine hypotheses to advance research of microbiomes across landscapes. We hypothesize that intensified agriculture selects for certain taxa and genes, which then 'spill over' into adjacent unmodified areas and generate a halo of genetic differentiation around agricultural fields. Consequently, the spatial configuration and management intensity of different habitats combines with the dispersal ability of individual taxa to determine the extent of spillover, which can impact the functioning of adjacent unmodified habitats. When landscapes are heterogeneous and dispersal rates are high, this will select for large genomes that allow exploitation of multiple habitats, a process that may be accelerated through horizontal gene transfer. Continued expansion of agriculture will increase genotypic similarity, making microbial community functioning increasingly variable in human-dominated landscapes, potentially also impacting the consistent provisioning of ecosystem services. While the resulting economic costs have not been calculated, it is clear that dispersal dynamics of microbes should be taken into consideration to ensure that ecosystem functioning and services are maintained in agri-ecosystem mosaics.
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Affiliation(s)
- Thomas Bell
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, Berkshire SL5 7PY, UK
| | - Jason M Tylianakis
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, Berkshire SL5 7PY, UK
- Centre for Integrative Ecology, School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
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83
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Transcriptomic analysis on the formation of the viable putative non-culturable state of beer-spoilage Lactobacillus acetotolerans. Sci Rep 2016; 6:36753. [PMID: 27819317 PMCID: PMC5098190 DOI: 10.1038/srep36753] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 10/20/2016] [Indexed: 02/08/2023] Open
Abstract
Lactic acid bacteria (LAB) are the most common beer-spoilage bacteria regardless of beer type, and thus pose significant problems for the brewery industry. The aim of this study was to investigate the genetic mechanisms involved in the ability of the hard-to-culture beer-spoilage bacterium Lactobacillus acetotolerans to enter into the viable putative non-culturable (VPNC) state. A genome-wide transcriptional analysis of beer-spoilage L. acetotolerans strains BM-LA14526, BM-LA14527, and BM-LA14528 under normal, mid-term and VPNC states were performed using RNA-sequencing (RNA-seq) and further bioinformatics analyses. GO function, COG category, and KEGG pathway enrichment analysis were conducted to investigate functional and related metabolic pathways of the differentially expressed genes. Functional and pathway enrichment analysis indicated that heightened stress response and reduction in genes associated with transport, metabolic process, and enzyme activity might play important roles in the formation of the VPNC state. This is the first transcriptomic analysis on the formation of the VPNC state of beer spoilage L. acetotolerans.
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84
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Buysschaert B, Byloos B, Leys N, Van Houdt R, Boon N. Reevaluating multicolor flow cytometry to assess microbial viability. Appl Microbiol Biotechnol 2016; 100:9037-9051. [PMID: 27687990 DOI: 10.1007/s00253-016-7837-5] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 08/29/2016] [Accepted: 09/01/2016] [Indexed: 01/14/2023]
Abstract
Flow cytometry is a rapid and quantitative method to determine bacterial viability. Although different stains can be used to establish viability, staining protocols are inconsistent and lack a general optimization approach. Very few "true" multicolor protocols, where dyes are combined in one sample, have been developed for microbiological applications. In this mini-review, the discrepancy between protocols for cell-permeant nucleic acid and functional stains are discussed as well as their use as viability dyes. Furthermore, optimization of staining protocols for a specific setup are described. Original data using the red-excitable SYTO dyes SYTO 59 to 64 and SYTO 17, combined with functional stains, for double and triple staining applications is also included. As each dye and dye combination behaves differently within a certain combination of medium matrix, microorganism, and instrument, protocols need to be tuned to obtain reproducible results. Therefore, single, double, and triple stains are reviewed, including the different parameters that influence staining such as stain kinetics, optimal stain concentration, and the effect of the chelator EDTA as membrane permeabilizer. In the last section, we highlight the need to investigate the stability of multicolor assays to ensure correct results as multiwell autoloaders are now commonly used.
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Affiliation(s)
- Benjamin Buysschaert
- Centre for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Bo Byloos
- Centre for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Ghent, Belgium.,Unit of Microbiology, Belgian Nuclear Research Centre (SCK-CEN), Boeretang 200, 2400, Mol, Belgium
| | - Natalie Leys
- Unit of Microbiology, Belgian Nuclear Research Centre (SCK-CEN), Boeretang 200, 2400, Mol, Belgium
| | - Rob Van Houdt
- Unit of Microbiology, Belgian Nuclear Research Centre (SCK-CEN), Boeretang 200, 2400, Mol, Belgium
| | - Nico Boon
- Centre for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Ghent, Belgium.
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85
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Feyhl-Buska J, Chen Y, Jia C, Wang JX, Zhang CL, Boyd ES. Influence of Growth Phase, pH, and Temperature on the Abundance and Composition of Tetraether Lipids in the Thermoacidophile Picrophilus torridus. Front Microbiol 2016; 7:1323. [PMID: 27625636 PMCID: PMC5003844 DOI: 10.3389/fmicb.2016.01323] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 08/10/2016] [Indexed: 11/13/2022] Open
Abstract
The abundance and composition of glycerol dibiphytanyl glycerol tetraether (GDGT) and glycerol tribiphytanyl glycerol tetraether (GTGT) lipids were determined as a function of growth phase as a proxy for nutrient availability, the pH of growth medium, and incubation temperature in cultures of the thermoacidophile Picrophilus torridus. Regardless of the cultivation condition, the abundance of GDGTs and GTGTs was greater in the polar than core fraction, with a marked decrease in core GDGTs in cultures harvested during log phase growth. These data are consistent with previous suggestions indicating that core GDGTs are re-functionalized during polar lipid synthesis. Under all conditions examined, polar lipids were enriched in a GDGT with 2 cyclopentyl rings (GDGT-2), indicating GDGT-2 is the preferred lipid in this taxon. However, lag or stationary phase grown cells or cells subjected to pH or thermal stress were enriched in GDGTs with 4, 5, or 6 rings and depleted in GDGTs with 1, 2, 3, rings relative to log phase cells grown under optimal conditions. Variation in the composition of polar GDGT lipids in cells harvested during various growth phases tended to be greater than in cells cultivated over a pH range of 0.3–1.1 and a temperature range of 53–63°C. These results suggest that the growth phase, the pH of growth medium, and incubation temperature are all important factors that shape the composition of tetraether lipids in Picrophilus. The similarity in enrichment of GDGTs with more rings in cultures undergoing nutrient, pH, and thermal stress points to GDGT cyclization as a generalized physiological response to stress in this taxon.
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Affiliation(s)
- Jayme Feyhl-Buska
- Department of Microbiology and Immunology, Montana State University Bozeman, MT, USA
| | - Yufei Chen
- State Key Laboratory of Marine Geology, Tongji University Shanghai, China
| | - Chengling Jia
- State Key Laboratory of Marine Geology, Tongji University Shanghai, China
| | - Jin-Xiang Wang
- State Key Laboratory of Marine Geology, Tongji University Shanghai, China
| | - Chuanlun L Zhang
- State Key Laboratory of Marine Geology, Tongji University Shanghai, China
| | - Eric S Boyd
- Department of Microbiology and Immunology, Montana State UniversityBozeman, MT, USA; NASA Astrobiology InstituteMountain View, CA, USA
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86
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Farhana I, Hossain ZZ, Tulsiani SM, Jensen PKM, Begum A. Survival of Vibrio cholerae O1 on fomites. World J Microbiol Biotechnol 2016; 32:146. [DOI: 10.1007/s11274-016-2100-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Accepted: 06/17/2016] [Indexed: 12/11/2022]
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87
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Wu ML, Gengenbacher M, Dick T. Mild Nutrient Starvation Triggers the Development of a Small-Cell Survival Morphotype in Mycobacteria. Front Microbiol 2016; 7:947. [PMID: 27379076 PMCID: PMC4909757 DOI: 10.3389/fmicb.2016.00947] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 06/01/2016] [Indexed: 11/13/2022] Open
Abstract
Mycobacteria, generally believed to be non-sporulating, are well known to survive shock starvation in saline for extended periods of time in a non-replicating state without any apparent morphological changes. Here, we uncover that mycobacteria can undergo cellular differentiation by exposing Mycobacterium smegmatis to mild starvation conditions. Traces of various carbon sources in saline triggered the development of a novel small resting cell (SMRC) morphotype. Development of SMRCs could also be observed for other mycobacteria, suggesting evolutionary conservation of this differentiation pathway. Fluorescence microscopic analyses showed that development of SMRCs progresses via septated, multi-nucleoided cell intermediates, which divide to generate mono-nucleoided SMRCs. Intriguingly, saline shock-starved large resting cells (LARCs), which did not show cell size or surface changes when observed by scanning electron microscopy, remodeled their internal structure to septated, multi-nucleoided cells, similar to the intermediates seen during differentiation to SMRCs. Our results suggest that mycobacteria harbor a starvation-induced differentiation program in which at first septated, multi-nucleoided cells are generated. Under zero-nutrient conditions bacteria terminate development at this stage as LARCs. In the presence of traces of a carbon source, these multi-nucleoided cells continue differentiation into mono-nucleoided SMRCs. Both SMRCs and LARCs exhibited extreme antibiotic tolerance. SMRCs showed increased long-term starvation survival, which was associated with the presence of lipid inclusion bodies.
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Affiliation(s)
- Mu-Lu Wu
- Antibacterial Drug Discovery Laboratory, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore Singapore, Singapore
| | - Martin Gengenbacher
- Tuberculosis Research Laboratory, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore Singapore, Singapore
| | - Thomas Dick
- Antibacterial Drug Discovery Laboratory, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore Singapore, Singapore
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Ruiz P, Poblete-Morales M, Irgang R, Toranzo AE, Avendaño-Herrera R. Survival behaviour and virulence of the fish pathogen Vibrio ordalii in seawater microcosms. DISEASES OF AQUATIC ORGANISMS 2016; 120:27-38. [PMID: 27304868 DOI: 10.3354/dao03005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Vibrio ordalii, the causative agent of atypical vibriosis, is a Gram-negative, motile, rod-shaped bacterium that severely affects the salmonid aquaculture industry. V. ordalii has been biochemically, antigenically and genetically characterized. However, studies on the survival behaviour of this bacterium in aquatic environments are scarce, and there is no information regarding its disease transmission and infectious abilities outside of the fish host or regarding water as a possible reservoir. The present study investigated the survival behaviour of V. ordalii Vo-LM-06 and Vo-LM-18 in sterile and non-sterile seawater microcosms. After a year in sterile seawater without nutrients, 1% of both V. ordalii strains survived (~10(3) colony-forming units ml(-1)), and long-term maintenance did not affect bacterial biochemical or genetic properties. Additionally, V. ordalii maintained for 60 d in sterile seawater remained infective in rainbow trout Oncorhynchus mykiss. However, after 2 d of natural seawater exposure, this bacterium became non-culturable, indicating that autochthonous microbiota may play an important role in survival. Recuperation assays that added fresh medium to non-sterile microcosms did not favour V. ordalii recovery on solid media. Our results contribute towards a better understanding of V. ordalii survival behaviour in seawater ecosystems.
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Affiliation(s)
- Pamela Ruiz
- Laboratorio de Patología de Organismos Acuáticos y Biotecnología Acuícola, Facultad de Ciencias Biológicas, Universidad Andrés Bello, 2520000 Viña del Mar, Chile
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Viswanathan A, Anufrieva O, Sala A, Yli-Harja O, Kandhavelu M. Phase-dependent dynamics of the lac promoter under nutrient stress. Res Microbiol 2016; 167:451-61. [PMID: 27106257 DOI: 10.1016/j.resmic.2016.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Revised: 04/04/2016] [Accepted: 04/04/2016] [Indexed: 11/26/2022]
Abstract
To survive, a bacterial population must sense nutrient availability and adjust its growth phase accordingly. Few studies have quantitatively analyzed the single-cell behavior of stress and growth phase-related transcriptional changes in Escherichia coli. To investigate the dynamic changes in transcription during different growth phases and starvation, we analyzed the single-cell transcriptional dynamics of the E. coli lac promoter. Cells were grown under different starvation conditions, including glucose, magnesium, phosphate and thiamine limitations, and transcription dynamics was quantified using a single RNA detection method at different phases. Differences in gene expression over conditions and phases indicate that stochasticity in transcription dynamics is directly connected to cell phase and availability of nutrients. Except for glucose, the pattern of transcription dynamics under all starvation conditions appears to be similar. Transcriptional bursts were more prominent in lag and stationary phase cells starved for energy sources. Identical behavior was observed in exponential phase cells starved for phosphate and thiamine. Noise measurements under all nutrient exhaustion conditions indicate that intrinsic noise is higher than extrinsic noise. Our results, obtained in a relA1 mutational background, which led to suboptimal production of ppGpp, suggest that the single-cell transcriptional changes we observed were largely ppGpp-independent. Taken together, we propose that, under different starvation conditions, cells are able to decrease the trend in cell-to-cell variability in transcription as a common means of adaptation.
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Affiliation(s)
- Anisha Viswanathan
- Molecular Signaling Lab, Computational Systems Biology Research Group, Department of Signal Processing, Tampere University of Technology, P.O.Box 553, 33101 Tampere, Finland
| | - Olga Anufrieva
- Molecular Signaling Lab, Computational Systems Biology Research Group, Department of Signal Processing, Tampere University of Technology, P.O.Box 553, 33101 Tampere, Finland
| | - Adrien Sala
- Molecular Signaling Lab, Computational Systems Biology Research Group, Department of Signal Processing, Tampere University of Technology, P.O.Box 553, 33101 Tampere, Finland
| | - Olli Yli-Harja
- Molecular Signaling Lab, Computational Systems Biology Research Group, Department of Signal Processing, Tampere University of Technology, P.O.Box 553, 33101 Tampere, Finland; Institute for Systems Biology, 1441N 34th Street, Seattle, WA, 98103-8904, USA
| | - Meenakshisundaram Kandhavelu
- Molecular Signaling Lab, Computational Systems Biology Research Group, Department of Signal Processing, Tampere University of Technology, P.O.Box 553, 33101 Tampere, Finland.
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90
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Kirschner AK. Determination of viable legionellae in engineered water systems: Do we find what we are looking for? WATER RESEARCH 2016; 93:276-288. [PMID: 26928563 PMCID: PMC4913838 DOI: 10.1016/j.watres.2016.02.016] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Revised: 02/06/2016] [Accepted: 02/09/2016] [Indexed: 05/06/2023]
Abstract
In developed countries, legionellae are one of the most important water-based bacterial pathogens caused by management failure of engineered water systems. For routine surveillance of legionellae in engineered water systems and outbreak investigations, cultivation-based standard techniques are currently applied. However, in many cases culture-negative results are obtained despite the presence of viable legionellae, and clinical cases of legionellosis cannot be traced back to their respective contaminated water source. Among the various explanations for these discrepancies, the presence of viable but non-culturable (VBNC) Legionella cells has received increased attention in recent discussions and scientific literature. Alternative culture-independent methods to detect and quantify legionellae have been proposed in order to complement or even substitute the culture method in the future. Such methods should detect VBNC Legionella cells and provide a more comprehensive picture of the presence of legionellae in engineered water systems. However, it is still unclear whether and to what extent these VBNC legionellae are hazardous to human health. Current risk assessment models to predict the risk of legionellosis from Legionella concentrations in the investigated water systems contain many uncertainties and are mainly based on culture-based enumeration. If VBNC legionellae should be considered in future standard analysis, quantitative risk assessment models including VBNC legionellae must be proven to result in better estimates of human health risk than models based on cultivation alone. This review critically evaluates current methods to determine legionellae in the VBNC state, their potential to complement the standard culture-based method in the near future, and summarizes current knowledge on the threat that VBNC legionellae may pose to human health.
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Affiliation(s)
- Alexander K.T. Kirschner
- Medical University Vienna, Institute for Hygiene and Applied Immunology, Water Hygiene, Kinderspitalgasse 15, A-1090 Vienna, Austria
- Interuniversity Cooperation Centre for Water & Health, Austria
- Medical University Vienna, Institute for Hygiene and Applied Immunology, Water Hygiene Kinderspitalgasse 16, A-1090 Vienna, Austria . URL: http://www.waterandhealth.at
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91
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Atzinger A, Butela K, Lawrence JG. The O-antigen mediates differential survival of Salmonella against communities of natural predators. MICROBIOLOGY-SGM 2016; 162:610-621. [PMID: 26888189 DOI: 10.1099/mic.0.000259] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Antigenically distinct members of bacterial species can be differentially distributed in the environment. Predators known to consume antigenically distinct prey with different efficiencies are also differentially distributed. Here we show that antigenically distinct, but otherwise isogenic and physiologically indistinct, strains of Salmonella enterica show differential survival in natural soil, sediment and intestinal environments, where they would face a community of predators. Decline in overall cell numbers is attenuated by factors that inhibit the action of predators, including heat and antiprotozoal and antihelminthic drugs. Moreover, the fitness of strains facing these predators - calculated by comparing survival with and without treatments attenuating predator activity - varies between environments. These results suggest that relative survival in natural environments is arbitrated by communities of natural predators whose feeding preferences, if not species composition, vary between environments. These data support the hypothesis that survival against natural predators may drive the differential distribution of bacteria among microenvironments.
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Affiliation(s)
- Aletheia Atzinger
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Kristen Butela
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Jeffrey G Lawrence
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
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92
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Shinoda S, Imamura D, Mizuno T, Miyoshi SI, Ramamurthy T. International collaborative research on infectious diseases by Japanese universities and institutes in Asia and Africa, with a special emphasis on J-GRID. Biocontrol Sci 2016; 20:77-89. [PMID: 26133505 DOI: 10.4265/bio.20.77] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
In developed countries including Japan, malignant tumor (cancer), heart disease and cerebral apoplexy are major causes of death, but infectious diseases are still responsible for a high number of deaths in developing countries, especially among children aged less than 5 years. World Health Statistics published by WHO reports a high percentage of mortality from infectious diseases in children, and many of these diseases may be subject to transmission across borders and could possibly invade Japan. Given this situation, the Ministry of Education, Culture, Sports, Science and Technology (MEXT) of Japan initiated Phase I of the Program of Founding Research Centers for Emerging and Reemerging Infectious Disease, which ran from FY 2005 to 2009, and involved 8 Japanese universities and 2 research centers. The program was established for the following purposes: 1) creation of a domestic research structure to promote the accumulation of fundamental knowledge about infectious diseases, 2) establishment of 13 overseas research collaboration centers in 8 countries at high risk of emerging and reemerging infections and at which Japanese researchers are stationed and conduct research in partnership with overseas instructors, 3) development of a network among domestic and overseas research centers, and 4) development of human resources. The program was controlled under MEXT and managed by the RIKEN Center of Research Network for Infectious Diseases (Riken CRNID). Phase II of the program was set up as the Japan Initiative for Global Research Network on Infectious Diseases (J-GRID), and has been running in FY 2010-2014. Phase III will start in April 2015, and will be organized by the newly established Japanese governmental organization "Japan Agency for Medical Research and Development (AMED)", the so-called Japanese style NIH. The Collaborative Research Center of Okayama University for Infectious Diseases in India (CRCOUI) was started up in 2007 at the National Institute of Cholera and Enteric Disease, Kolkata, India. Major projects of CRCOUI are concerned with diarrheal diseases such as, 1) active surveillance of diarrheal patients, 2) development of dysentery vaccines, 3) viable but nonculturable (VBNC) Vibrio cholerae, and 4) pathogenic mechanisms of various diarrhogenic microorganisms. This review article outlines project of J-GRID and CRCOUI which the authors carried out collaboratively with NICED staff members.
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Affiliation(s)
- Sumio Shinoda
- Collaborative Research Center of Okayama University for Infectious Disease in India
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93
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McLain JE, Cytryn E, Durso LM, Young S. Culture-based Methods for Detection of Antibiotic Resistance in Agroecosystems: Advantages, Challenges, and Gaps in Knowledge. JOURNAL OF ENVIRONMENTAL QUALITY 2016; 45:432-40. [PMID: 27065389 DOI: 10.2134/jeq2015.06.0317] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Various culture-based methodologies are used in assessment of antibiotic resistance in samples collected in agroecosystems. Culture-based methods commonly involve isolating target bacteria on general or selective media and assessing growth in response to specific concentrations of antibiotics. The advantages of culture-based methods are multifold. In particular, isolation of bacteria is key to understanding phenotypic characteristics of isolates and their resistance patterns, and most national and international antibiotic resistance monitoring projects are isolate based. This review covers current knowledge of bacterial groups and antibiotics commonly targeted in resistance studies using bacterial culture and discusses the range in methods used, data interpretation, and factors supporting and confounding the use of culture-based methods in assessment of antibiotic resistance. Gaps in knowledge related to study design and resistance databases are discussed. Finally, a case is made for the integration of culture-based and molecular methods to better inform our understanding of antibiotic resistance in agroecosystems.
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94
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Vassallo CN, Wall D. Tissue repair in myxobacteria: A cooperative strategy to heal cellular damage. Bioessays 2016; 38:306-15. [PMID: 26898360 DOI: 10.1002/bies.201500132] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Damage repair is a fundamental requirement of all life as organisms find themselves in challenging and fluctuating environments. In particular, damage to the barrier between an organism and its environment (e.g. skin, plasma membrane, bacterial cell envelope) is frequent because these organs/organelles directly interact with the external world. Here, we discuss the general strategies that bacteria use to cope with damage to their cell envelope and their repair limits. We then describe a novel damage-coping mechanism used by multicellular myxobacteria. We propose that cell-cell transfer of membrane material within a population serves as a wound-healing strategy and provide evidence for its utility. We suggest that--similar to how tissues in eukaryotes have evolved cooperative methods of damage repair--so too have some bacteria that live a multicellular lifestyle.
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Affiliation(s)
| | - Daniel Wall
- Department of Molecular Biology, University of Wyoming, Laramie, WY, USA
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95
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Olsen RO, Hoffmann F, Hess-Erga OK, Larsen A, Thuestad G, Hoell IA. Ultraviolet radiation as a ballast water treatment strategy: Inactivation of phytoplankton measured with flow cytometry. MARINE POLLUTION BULLETIN 2016; 103:270-275. [PMID: 26719070 DOI: 10.1016/j.marpolbul.2015.12.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 12/08/2015] [Accepted: 12/10/2015] [Indexed: 06/05/2023]
Abstract
This study investigates different UV doses (mJ/cm(2)) and the effect of dark incubation on the survival of the algae Tetraselmis suecica, to simulate ballast water treatment and subsequent transport. Samples were UV irradiated and analyzed by flow cytometry and standard culturing methods. Doses of ≥400 mJ/cm(2) rendered inactivation after 1 day as measured by all analytical methods, and are recommended for ballast water treatment if immediate impairment is required. Irradiation with lower UV doses (100-200 mJ/cm(2)) gave considerable differences of inactivation between experiments and analytical methods. Nevertheless, inactivation increased with increasing doses and incubation time. We argue that UV doses ≥100 mJ/cm(2) and ≤200 mJ/cm(2) can be sufficient if the water is treated at intake and left in dark ballast tanks. The variable results demonstrate the challenge of giving unambiguous recommendations on duration of dark incubation needed for inactivation when algae are treated with low UV doses.
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Affiliation(s)
| | - Friederike Hoffmann
- University of Bergen, P.O. Box 7800, 5020 Bergen, Norway; Uni Research Environment, Thormoehlensgt. 49b, 5006 Bergen, Norway
| | | | - Aud Larsen
- Uni Research Environment, Thormoehlensgt. 49b, 5006 Bergen, Norway
| | - Gunnar Thuestad
- Stord/Haugesund University College, Klingenbergvegen 8, 5414 Stord, Norway
| | - Ingunn Alne Hoell
- Stord/Haugesund University College, Klingenbergvegen 8, 5414 Stord, Norway.
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96
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The long-term survival of Acinetobacter baumannii ATCC 19606T under nutrient-deprived conditions does not require the entry into the viable but non-culturable state. Arch Microbiol 2016; 198:399-407. [DOI: 10.1007/s00203-016-1200-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 01/26/2016] [Accepted: 01/29/2016] [Indexed: 12/19/2022]
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97
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Hesari N, Alum A, Elzein M, Abbaszadegan M. A biosensor platform for rapid detection of E. coli in drinking water. Enzyme Microb Technol 2016; 83:22-8. [DOI: 10.1016/j.enzmictec.2015.11.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 11/21/2015] [Accepted: 11/21/2015] [Indexed: 11/28/2022]
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98
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Imamura D, Mizuno T, Miyoshi SI, Shinoda S. Stepwise changes in viable but nonculturable Vibrio cholerae cells. Microbiol Immunol 2016; 59:305-10. [PMID: 25664673 DOI: 10.1111/1348-0421.12246] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 02/03/2015] [Accepted: 02/06/2015] [Indexed: 11/26/2022]
Abstract
Many bacterial species are known to become viable but nonculturable (VBNC) under conditions that are unsuitable for growth. In this study, the requirements for resuscitation of VBNC-state Vibrio cholerae cells were found to change over time. Although VBNC cells could initially be converted to culturable by treatment with catalase or HT-29 cell extract, they subsequently entered a state that was not convertible to culturable by these factors. However, fluorescence microscopy revealed the presence of live cells in this state, from which VBNC cells were resuscitated by co-cultivation with HT-29 human colon adenocarcinoma cells. Ultimately, all cells entered a state from which they could not be resuscitated, even by co-cultivation with HT-29. These characteristic changes in VBNC-state cells were a common feature of strains in both V. cholerae O1 and O139 serogroups. Thus, the VBNC state of V. cholerae is not a single property but continues to change over time.
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Affiliation(s)
- Daisuke Imamura
- Collaborative Research Center of Okayama University for Infectious Diseases in India, National Institute of Cholera and Enteric Diseases, First Floor ID Hospital Campus, 57 Dr. S. C. Banerjee Road, Beliaghata, Kolkata, 700010, India
| | - Tamaki Mizuno
- Collaborative Research Center of Okayama University for Infectious Diseases in India, National Institute of Cholera and Enteric Diseases, First Floor ID Hospital Campus, 57 Dr. S. C. Banerjee Road, Beliaghata, Kolkata, 700010, India
| | - Shin-ichi Miyoshi
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama, 700-8530, Japan
| | - Sumio Shinoda
- Collaborative Research Center of Okayama University for Infectious Diseases in India, National Institute of Cholera and Enteric Diseases, First Floor ID Hospital Campus, 57 Dr. S. C. Banerjee Road, Beliaghata, Kolkata, 700010, India
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99
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Yoshioka S, Newell PD. Disruption of de novo purine biosynthesis in Pseudomonas fluorescens Pf0-1 leads to reduced biofilm formation and a reduction in cell size of surface-attached but not planktonic cells. PeerJ 2016; 4:e1543. [PMID: 26788425 PMCID: PMC4715448 DOI: 10.7717/peerj.1543] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 12/07/2015] [Indexed: 01/17/2023] Open
Abstract
Pseudomonas fluorescens Pf0-1 is one of the model organisms for biofilm research. Our previous transposon mutagenesis study suggested a requirement for the de novo purine nucleotide biosynthesis pathway for biofilm formation by this organism. This study was performed to verify that observation and investigate the basis for the defects in biofilm formation shown by purine biosynthesis mutants. Constructing deletion mutations in 8 genes in this pathway, we found that they all showed reductions in biofilm formation that could be partly or completely restored by nucleotide supplementation or genetic complementation. We demonstrated that, despite a reduction in biofilm formation, more viable mutant cells were recovered from the surface-attached population than from the planktonic phase under conditions of purine deprivation. Analyses using scanning electron microscopy revealed that the surface-attached mutant cells were 25 ∼ 30% shorter in length than WT, which partly explains the reduced biomass in the mutant biofilms. The laser diffraction particle analyses confirmed this finding, and further indicated that the WT biofilm cells were smaller than their planktonic counterparts. The defects in biofilm formation and reductions in cell size shown by the mutants were fully recovered upon adenine or hypoxanthine supplementation, indicating that the purine shortages caused reductions in cell size. Our results are consistent with surface attachment serving as a survival strategy during nutrient deprivation, and indicate that changes in the cell size may be a natural response of P. fluorescens to growth on a surface. Finally, cell sizes in WT biofilms became slightly smaller in the presence of exogenous adenine than in its absence. Our findings suggest that purine nucleotides or related metabolites may influence the regulation of cell size in this bacterium.
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Affiliation(s)
- Shiro Yoshioka
- Department of Life and Coordination-Complex Molecular Science, Institute for Molecular Science, National Institutes of Natural Sciences , Okazaki, Aichi , Japan
| | - Peter D Newell
- Department of Biological Sciences, Oswego State University of New York , Oswego, NY , USA
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100
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Ruike W, Higashimori A, Yaguchi J, Li YY. Use of real-time PCR with propidium monoazide for enumeration of viable Escherichia coli in anaerobic digestion. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2016; 74:1243-1254. [PMID: 27642844 DOI: 10.2166/wst.2016.327] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A combination of propidium monoazide (PMA) with real-time quantitative polymerase chain reaction (PMA-qPCR) was optimized to enumerate only viable Escherichia coli in anaerobic digestion processes. Repeating the PMA treatment twice and a final concentration of 100 μM resulted in an effective exclusion of DNA from heat-treated E. coli cells. In three anaerobic digestion processes, real-time PCR, PMA-qPCR, and the most probable number method (MPN) were used to estimate the numbers of total, viable, and culturable E. coli cells, respectively. Culturable concentrations of fecal coliforms were also measured by the membrane filter method. For thermophilic digestion, the reductions in total and viable E. coli cells from the digester influent to the effluent were significantly lower than those in culturable cells and fecal coliforms by two to four orders of magnitude. For mesophilic digestion, the differences in the reductions in E. coli and fecal coliforms counts were less than two orders of magnitude. Based on the measurements of viable E. coli determined by the PMA-qPCR method, the microbial quality of digester effluents was discussed for agricultural application, and pasteurization after anaerobic digestion was suggested for the destruction of viable pathogens.
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Affiliation(s)
- Wataru Ruike
- Department of Civil and Environmental Engineering, Tohoku University, 6-6-06 Aoba, Aramaki, Aobaku, Sendai 980-8579 Japan
| | - Atsushi Higashimori
- Department of Civil and Environmental Engineering, Tohoku University, 6-6-06 Aoba, Aramaki, Aobaku, Sendai 980-8579 Japan
| | - Junichi Yaguchi
- Department of Civil and Environmental Engineering, National Institute of Technology, Hachinohe College, 16-1 Uwanotai, Tamonoki, Hachinohe 039-1192, Japan E-mail:
| | - Yu-You Li
- Department of Civil and Environmental Engineering, Tohoku University, 6-6-06 Aoba, Aramaki, Aobaku, Sendai 980-8579 Japan
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