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Qi S, Wang J, Zhang Y, Naz M, Afzal MR, Du D, Dai Z. Omics Approaches in Invasion Biology: Understanding Mechanisms and Impacts on Ecological Health. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091860. [PMID: 37176919 PMCID: PMC10181282 DOI: 10.3390/plants12091860] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 04/21/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023]
Abstract
Invasive species and rapid climate change are affecting the control of new plant diseases and epidemics. To effectively manage these diseases under changing environmental conditions, a better understanding of pathophysiology with holistic approach is needed. Multiomics approaches can help us to understand the relationship between plants and microbes and construct predictive models for how they respond to environmental stresses. The application of omics methods enables the simultaneous analysis of plant hosts, soil, and microbiota, providing insights into their intricate relationships and the mechanisms underlying plant-microbe interactions. This can help in the development of novel strategies for enhancing plant health and improving soil ecosystem functions. The review proposes the use of omics methods to study the relationship between plant hosts, soil, and microbiota, with the aim of developing a new technique to regulate soil health. This approach can provide a comprehensive understanding of the mechanisms underlying plant-microbe interactions and contribute to the development of effective strategies for managing plant diseases and improving soil ecosystem functions. In conclusion, omics technologies offer an innovative and holistic approach to understanding plant-microbe interactions and their response to changing environmental conditions.
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Affiliation(s)
- Shanshan Qi
- School of Emergency Management, Jiangsu University, Zhenjiang 212013, China
- Key Laboratory of Modern Agricultural Equipment and Technology, Ministry of Education, School of Agricultural Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Jiahao Wang
- Key Laboratory of Modern Agricultural Equipment and Technology, Ministry of Education, School of Agricultural Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Yi Zhang
- Institute of Environment and Ecology, School of the Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China
| | - Misbah Naz
- Institute of Environment and Ecology, School of the Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China
| | - Muhammad Rahil Afzal
- Institute of Environment and Ecology, School of the Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China
| | - Daolin Du
- Institute of Environment and Ecology, School of the Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China
| | - Zhicong Dai
- School of Emergency Management, Jiangsu University, Zhenjiang 212013, China
- Institute of Environment and Ecology, School of the Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China
- Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, China
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2
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Prosdocimi EM, Arioli S, Mapelli F, Zeaiter Z, Fusi M, Daffonchio D, Borin S, Crotti E. Cell phenotype changes and oxidative stress response in Vibrio spp. induced into viable but non-culturable (VBNC) state. ANN MICROBIOL 2023. [DOI: 10.1186/s13213-022-01703-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Abstract
Purpose
Aquatic bacteria of the genus Vibrio include animal and human pathogens. The occurrence of Vibrio-related diseases has been associated with the current climate change-driven increase of sea surface temperature. Vibrio spp. can enter into the viable but non-culturable (VBNC) state, as a consequence of starvation in seawater at low temperatures. In such physiological state, Vibrio cells are no longer culturable on standard media agar plates but can resuscitate if incubated at 30 °C prior to plating, retaining virulence. Since limited information is available on regards to this topic, in this work, we characterized the phenotypic changes of four Vibrio spp. strains (one laboratory strain and three environmental isolates) in cold seawater microcosms, investigating the relationship between resuscitation and a hydrogen peroxide-induced oxidative stress.
Methods
Cell phenotypic changes and the effect of hydrogen peroxide and/or catalase addition to the medium were studied on VBNC and resuscitated cells by flow cytometry in microcosm experiments, paralleled by culturability experiments by plating.
Results
The cells of all the Vibrio strains changed their phenotype upon the induction of the VBNC state resulting in cell dwarfing and decrease in DNA quantity, losing the ability to grow on solid media. These features were partially or totally reverted when the cells were treated for resuscitation. Hydrogen peroxide at concentrations as low as 0.007 mM prevented resuscitation and a prolonged exposure to hydrogen peroxide at concentrations far under those inhibiting the growth of log-phase cells permanently damaged VBNC cells, which could not be resuscitated. However, the potential of culturability of VBNC cells could be preserved, at least for a part of the population, by plating the cells in the presence of catalase. The study also showed that during the resuscitation process, the cells gradually increased their resistance to hydrogen peroxide.
Conclusions
The timing and mode of induction of the VBNC state, as well as cell resuscitation and response to hydrogen peroxide, differed among Vibrio strains, indicating that induction and resuscitation from dormancy could vary in the context of species belonging to a single genus.
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Increased Rate of Yeast Cultivation from Packaged Beer with Environmentally Relevant Anaerobic Handling. Microbiol Spectr 2022; 10:e0265622. [PMID: 36314915 PMCID: PMC9769982 DOI: 10.1128/spectrum.02656-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Beer production necessitates oxygen exclusion for the proper packaging and aging of the beer. Standard operating procedures, including those for quality testing, involve culturing microbes from packaged beer exposed to atmospheric oxygen, despite the generalized fact that packaged beer is an anaerobic environment. Our research goal was to apply an environmentally relevant culturing approach to improve yeast cultivation from bottled beer by attempting to ameliorate transplant shock. This is applicable to uniquely scrutinous quality assurance/control objectives and/or to grand cultivation goals, such as ancient beer samples. Although yeasts have the genetic capacity of oxygen protection, their epigenetic/biochemical states within anaerobic packaging may not adequately protect all cells from reactive oxygen species (ROS) at the moment of opening. Soon after opening, beer yeasts were found to be catalase negative, indicating deficient protection from at least one ROS. The general reduction/inhibition of growth was observed when the beer yeast was exposed to ROS in media, and atmospheric bottle opening was found to expose beer yeast to significantly increased levels of ROS. Our primary finding is that different oxygen handling methodologies (aerobic/microaerophilic/anaerobic) significantly impact the viable Saccharomyces yeast recovery rates of Bamberger's Mahr's Bräu Unfiltered Lager. Immediate anaerobic handling improved cultivation success rates, with significantly higher colony forming units (CFU)/mL being cultured, and reduced the volume of beer required to recover viable yeast. Aerobic standard operating procedures have mainly been developed to harvest yeast on large volumetric samples and/or samples with high viable cell numbers, but these procedures may be suboptimal and may underrepresent potential viable cell numbers. IMPORTANCE Procedures of beer production and packaging exclude oxygen to create a shelf-stable anaerobic environment, within which any viable organisms are stored. However, standard methodologies to cultivate microbes from such environments generally include opening in an oxygenated atmosphere. This study applies environmentally relevant culturing methods and compares the yeast recovery rates of beers handled in various oxygen conditions. When beer bottles were opened in anoxic conditions, higher colony counts were obtained, so a smaller volume of beer was required to recover viable cells. The yeast in beer, stored anaerobically, may not be biochemically prepared to fully protect cells from oxygen at the moment of opening. Negative catalase activity showed beer yeasts' vulnerabilities to reactive oxygen. Atmospheric opening may reduce viability, causing the underreporting of viable cells. Anaerobic opening could increase the odds of successfully detecting/cultivating viable cell(s) that are present, which is pertinent to uniquely stringent quality screens and ambitious culturing attempts from rare samples.
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Yu H, Liu S, Qin H, Zhou Z, Zhao H, Zhang S, Mao J. Artificial intelligence-based approaches for traditional fermented alcoholic beverages' development: review and prospect. Crit Rev Food Sci Nutr 2022; 64:2879-2889. [PMID: 36310425 DOI: 10.1080/10408398.2022.2128034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Traditional fermented alcoholic beverages (TFABs) have gained widespread acceptance and enjoyed great popularity for centuries. COVID-19 pandemics lead to the surge in health demand for diet, thus TFABs once again attract increased focus for the health benefits. Though the production technology is quite mature, food companies and research institutions are looking for transformative innovation in TFABs to make healthy, nutritious offerings that give a competitive advantage in current beverage market. The implementation of intelligent platforms enables companies and researchers to gather, store and analyze data in a more convenient way. The development of data collection methods contributed to the big data environment of TFABs, providing a fresh perspective that helps brewers to observe and improve the production steps. Among data analytical tools, Artificial Intelligence (AI) is considered to be one of the most promising methodological approaches for big data analytics and decision-making of automated production, and machine learning (ML) is an important method to fulfill the goal. This review describes the development trends and challenges of TFABs in big data era and summarize the application of AI-based methods in TFABs. Finally, we provide perspectives on the potential research directions of new frontiers in application of AI approaches in the supply chain of TFABs.
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Affiliation(s)
- Huakun Yu
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, State Key Laboratory of Food Science and Technology, School of Food Science and technology, Jiangnan University, Wuxi, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, China
| | - Shuangping Liu
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, State Key Laboratory of Food Science and Technology, School of Food Science and technology, Jiangnan University, Wuxi, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
- Luzhou Laojiao Group Co. Ltd, Luzhou, China
| | - Hui Qin
- Luzhou Laojiao Group Co. Ltd, Luzhou, China
| | - Zhilei Zhou
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, State Key Laboratory of Food Science and Technology, School of Food Science and technology, Jiangnan University, Wuxi, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
- Shaoxing Key Laboratory of Traditional Fermentation Food and Human Health, Jiangnan University (Shaoxing) Industrial Technology Research Institute, Shaoxing, Zhejiang, China
| | - Hongyuan Zhao
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, State Key Laboratory of Food Science and Technology, School of Food Science and technology, Jiangnan University, Wuxi, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, China
- School of Artificial Intelligence and Computer Science, Jiangnan University, Wuxi, Jiangsu, China
| | - Suyi Zhang
- Luzhou Laojiao Group Co. Ltd, Luzhou, China
| | - Jian Mao
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, State Key Laboratory of Food Science and Technology, School of Food Science and technology, Jiangnan University, Wuxi, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
- Shaoxing Key Laboratory of Traditional Fermentation Food and Human Health, Jiangnan University (Shaoxing) Industrial Technology Research Institute, Shaoxing, Zhejiang, China
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Kapinusova G, Jani K, Smrhova T, Pajer P, Jarosova I, Suman J, Strejcek M, Uhlik O. Culturomics of Bacteria from Radon-Saturated Water of the World's Oldest Radium Mine. Microbiol Spectr 2022; 10:e0199522. [PMID: 36000901 PMCID: PMC9602452 DOI: 10.1128/spectrum.01995-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 08/04/2022] [Indexed: 12/31/2022] Open
Abstract
Balneotherapeutic water springs, such as those with thermal, saline, sulfur, or any other characteristics, have recently been the subject of phylogenetic studies with a closer focus on the description and/or isolation of phylogenetically novel or biotechnologically interesting microorganisms. Generally, however, most such microorganisms are rarely obtained in pure culture or are even, for now, unculturable under laboratory conditions. In this culture-dependent study of radioactive water springs of Jáchymov (Joachimstahl), Czech Republic, we investigated a combination of classical cultivation approaches with those imitating sampling source conditions. Using these environmentally relevant cultivation approaches, over 1,000 pure cultures were successfully isolated from 4 radioactive springs. Subsequent dereplication yielded 121 unique taxonomic units spanning 44 genera and 9 taxonomic classes, ~10% of which were identified as hitherto undescribed taxa. Genomes of the latter were sequenced and analyzed, with a special focus on endogenous defense systems to withstand oxidative stress and aid in radiotolerance. Due to their origin from radioactive waters, we determined the resistance of the isolates to oxidative stress. Most of the isolates were more resistant to menadione than the model strain Deinococcus radiodurans DSM 20539T. Moreover, isolates of the Deinococcacecae, Micrococcaceae, Bacillaceae, Moraxellaceae, and Pseudomonadaceae families even exhibited higher resistance in the presence of hydrogen peroxide. In summary, our culturomic analysis shows that subsurface water springs contain diverse bacterial populations, including as-yet-undescribed taxa and strains with promising biotechnological potential. Furthermore, this study suggests that environmentally relevant cultivation techniques increase the efficiency of cultivation, thus enhancing the chance of isolating hitherto uncultured microorganisms. IMPORTANCE The mine Svornost in Jáchymov (Joachimstahl), Czech Republic is a former silver-uranium mine and the world's first and for a long time only radium mine, nowadays the deepest mine devoted to the extraction of water which is saturated with radon and has therapeutic benefits given its chemical properties. This healing water, which is approximately 13 thousand years old, is used under medical supervision for the treatment of patients with neurological and rheumatic disorders. Our culturomic approach using low concentrations of growth substrates or the environmental matrix itself (i.e., water filtrate) in culturing media combined with prolonged cultivation time resulted in the isolation of a broad spectrum of microorganisms from 4 radioactive springs of Jáchymov which are phylogenetically novel and/or bear various adaptive or coping mechanisms to thrive under selective pressure and can thus provide a wide spectrum of capabilities potentially exploitable in diverse scientific, biotechnological, or medical disciplines.
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Affiliation(s)
- Gabriela Kapinusova
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Kunal Jani
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Tereza Smrhova
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Petr Pajer
- Military Health Institute, Ministry of Defence of the Czech Republic, Prague, Czech Republic
| | - Irena Jarosova
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biotechnology, Prague, Czech Republic
| | - Jachym Suman
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Michal Strejcek
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Ondrej Uhlik
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
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6
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Barbato M, Vacchini V, Engelen AH, Patania G, Mapelli F, Borin S, Crotti E. What lies on macroalgal surface: diversity of polysaccharide degraders in culturable epiphytic bacteria. AMB Express 2022; 12:98. [PMID: 35895126 PMCID: PMC9329506 DOI: 10.1186/s13568-022-01440-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 07/13/2022] [Indexed: 11/10/2022] Open
Abstract
Macroalgal surface constitutes a peculiar ecological niche and an advantageous substratum for microorganisms able to degrade the wide diversity of algal glycans. The degrading enzymatic activities of macroalgal epiphytes are of paramount interest for the industrial by-product sector and biomass resource applications. We characterized the polysaccharide hydrolytic profile of bacterial isolates obtained from three macroalgal species: the red macroalgae Asparagopsis taxiformis and Sphaerococcus coronopifolius (Rhodophyceae) and the brown Halopteris scoparia (Phaeophyceae), sampled in South Portugal. Bacterial enrichment cultures supplemented with chlorinated aliphatic compounds, typically released by marine algae, were established using as inoculum the decaying biomass of the three macroalgae, obtaining a collection of 634 bacterial strains. Although collected from the same site and exposed to the same seawater seeding microbiota, macroalgal cultivable bacterial communities in terms of functional and phylogenetic diversity showed host specificity. Isolates were tested for the hydrolysis of starch, pectin, alginate and agar, exhibiting a different hydrolytic potential according to their host: A. taxiformis showed the highest percentage of active isolates (91%), followed by S. coronopifolius (54%) and H. scoparia (46%). Only 30% of the isolates were able to degrade starch, while the other polymers were degraded by 55-58% of the isolates. Interestingly, several isolates showed promiscuous capacities to hydrolyze more than one polysaccharide. The isolate functional fingerprint was statistically correlated to bacterial phylogeny, host species and enrichment medium. In conclusion, this work depicts macroalgae as holobionts with an associated microbiota of interest for blue biotechnologies, suggesting isolation strategies and bacterial targets for polysaccharidases' discovery.
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Affiliation(s)
- Marta Barbato
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente (DeFENS), Università degli Studi di Milano, via Celoria 2, 20133, Milano, Italy.,Department of Biology, Section for Microbiology, Aarhus University, Ny Munkegade 116, 8000, Aarhus, Denmark
| | - Violetta Vacchini
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente (DeFENS), Università degli Studi di Milano, via Celoria 2, 20133, Milano, Italy
| | - Aschwin H Engelen
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Giovanni Patania
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente (DeFENS), Università degli Studi di Milano, via Celoria 2, 20133, Milano, Italy
| | - Francesca Mapelli
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente (DeFENS), Università degli Studi di Milano, via Celoria 2, 20133, Milano, Italy
| | - Sara Borin
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente (DeFENS), Università degli Studi di Milano, via Celoria 2, 20133, Milano, Italy.
| | - Elena Crotti
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente (DeFENS), Università degli Studi di Milano, via Celoria 2, 20133, Milano, Italy
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7
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Zhang Y, Xiao X, Elhag O, Cai M, Zheng L, Huang F, Jordan HR, Tomberlin JK, Sze SH, Yu Z, Zhang J. Hermetia illucens L. larvae-associated intestinal microbes reduce the transmission risk of zoonotic pathogens in pig manure. Microb Biotechnol 2022; 15:2631-2644. [PMID: 35881487 PMCID: PMC9518977 DOI: 10.1111/1751-7915.14113] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 06/16/2022] [Accepted: 06/18/2022] [Indexed: 12/03/2022] Open
Abstract
Black soldier fly (BSF) larvae are considered a promising biological reactor to convert organic waste and reduce the impact of zoonotic pathogens on the environment. We analysed the effects of BSF larvae on Staphylococcus aureus and Salmonella spp. populations in pig manure (PM), which showed that BSF larvae can significantly reduce the counts of the associated S. aureus and Salmonella spp. Then, using a sterile BSF larval system, we validated the function of BSF larval intestinal microbiota in vivo to suppress pathogens, and lastly, we isolated eight bacterial strains from the BSF larval gut that inhibit S. aureus. Results indicated that functional microbes are essential for BSF larvae to antagonise S. aureus. Moreover, the analysis results of the relationship between the intestinal microbiota and S. aureus and Salmonella spp. showed that Myroides, Tissierella, Oblitimonas, Paenalcalignes, Terrisporobacter, Clostridium, Fastidiosipila, Pseudomonas, Ignatzschineria, Savagea, Moheibacter and Sphingobacterium were negatively correlated with S. aureus and Salmonella. Overall, these results suggested that the potential ability of BSF larvae to inhibit S. aureus and Salmonella spp. present in PM is accomplished primarily by gut‐associated microorganisms.
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Affiliation(s)
- Yuanpu Zhang
- State Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China.,Hubei Hongshan Laboratory, Wuhan, China
| | - Xiaopeng Xiao
- State Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China.,Hubei Hongshan Laboratory, Wuhan, China
| | - Osama Elhag
- State Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China.,Hubei Hongshan Laboratory, Wuhan, China.,Faculty of Science and Technology, Omdurman Islamic University, Khartoum, Sudan
| | - Minmin Cai
- State Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China.,Hubei Hongshan Laboratory, Wuhan, China
| | - Longyu Zheng
- State Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China.,Hubei Hongshan Laboratory, Wuhan, China
| | - Feng Huang
- State Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China.,Hubei Hongshan Laboratory, Wuhan, China
| | - Heather R Jordan
- Department of Biology, Mississippi State University, Mississippi State, Mississippi, USA
| | | | - Sing-Hoi Sze
- Department of Computer Science and Engineering, Texas A&M University, College Station, Texas, USA
| | - Ziniu Yu
- State Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China.,Hubei Hongshan Laboratory, Wuhan, China
| | - Jibin Zhang
- State Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China.,Hubei Hongshan Laboratory, Wuhan, China
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8
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Orozco-Mosqueda MDC, Fadiji AE, Babalola OO, Glick BR, Santoyo G. Rhizobiome engineering: Unveiling complex rhizosphere interactions to enhance plant growth and health. Microbiol Res 2022; 263:127137. [PMID: 35905581 DOI: 10.1016/j.micres.2022.127137] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 06/17/2022] [Accepted: 07/13/2022] [Indexed: 12/13/2022]
Abstract
Crop plants are affected by a series of inhibitory environmental and biotic factors that decrease their growth and production. To counteract these adverse effects, plants work together with the microorganisms that inhabit their rhizosphere, which is part of the soil influenced by root exudates. The rhizosphere is a microecosystem where a series of complex interactions takes place between the resident microorganisms (rhizobiome) and plant roots. Therefore, this study analyzes the dynamics of plant-rhizobiome communication, the role of exudates (diffusible and volatile) as a factor in stimulating a diverse rhizobiome, and the differences between rhizobiomes of domesticated crops and wild plants. The study also analyzes different strategies to decipher the rhizobiome through both classical cultivation techniques and the so-called "omics" sciences. In addition, the rhizosphere engineering concept and the two general strategies to manipulate the rhizobiome, i.e., top down and bottom up engineering have been revisited. In addition, recent studies on the effects on the indigenous rhizobiome of inoculating plants with foreign strains, the impact on the endobiome, and the collateral effects on plant crops are discussed. Finally, understanding of the complex rhizosphere interactions and the biological repercussions of rhizobiome engineering as essential steps for improving plant growth and health is proposed, including under adverse conditions.
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Affiliation(s)
| | - Ayomide Emmanuel Fadiji
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South Africa
| | - Olubukola Oluranti Babalola
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South Africa
| | - Bernard R Glick
- Department of Biology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mich 58030, Mexico.
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9
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Two-Dimensional Cell Separation: a High-Throughput Approach to Enhance the Culturability of Bacterial Cells from Environmental Samples. Microbiol Spectr 2022; 10:e0000722. [PMID: 35467387 PMCID: PMC9248899 DOI: 10.1128/spectrum.00007-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Culture-independent sequence data from various environmental samples have revealed an immense microbial diversity of environmental, clinical, and industrial importance that has not yet been cultured. Cultivation is imperative to validate findings emerging from cultivation-independent molecular data and exploit the isolated organisms for biotechnological purposes. Efforts have been made to boost the cultivability of microbes from environmental samples by use of a range of techniques and instrumentation. The manuscript presents a novel yet simple and innovative approach to improving the cultivability of natural microorganisms without sophisticated instrumentation. By employing gradient centrifugation combined with serial dilution (“two-dimensional cell separation”), significantly higher numbers of genera (>2-fold higher) and species (>3-fold higher) were isolated from environmental samples, including soil, anaerobic sludge, and landfill leachate, than from using serial dilution alone. This simple and robust protocol can be modified for any environment and culture medium and provides access to untapped microbial diversity. IMPORTANCE In the manuscript, we have developed a novel yet simple and innovative approach to improving the cultivability of natural microorganisms without sophisticated instrumentation. The method used gradient centrifugation combined with serial dilution (two-dimensional cell separation) to improve taxum recovery from samples. This simple and robust protocol can be modified for any environment and culture medium and provides access to untapped microbial diversity. This approach can be incorporated with less labor and complexity in laboratories with minimal instrumentation. As cultivation is a workflow that is well suited to lower-resource microbiology labs, we believe improvements in cultivability can increase opportunities for scientific collaborations between low-resource labs and groups focused on high-resource cultivation-independent methodologies.
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10
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Inhibition of Zoonotic Pathogens Naturally Found in Pig Manure by Black Soldier Fly Larvae and Their Intestine Bacteria. INSECTS 2022; 13:insects13010066. [PMID: 35055911 PMCID: PMC8779730 DOI: 10.3390/insects13010066] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 12/16/2022]
Abstract
Simple Summary With the rapid development of the economy and the improvement of people’s living standards, people need to rear a lot of livestock to meet demand for proteins. This also involves an increase in the production of livestock manure. The expanding rate of livestock manure has become a thorny issue, owing to characteristics such as plentiful nitrogen and abundant zoonotic pathogens. The saprophagous larvae of the black soldier fly (BSF) are often associated with animal manure and can significantly reduce the populations of different zoonotic pathogens in livestock manure. However, reports about the mechanisms of this phenomenon are scarce. In this study, we investigated the potential mechanisms of BSF larvae in reducing the zoonotic pathogens naturally found in pig manure. The results clearly showed that zoonotic pathogens in pig manure were significantly decreased after being treated with BSF larvae, and also suggested that the antimicrobial peptides produced by the BSF larvae and gut-associated bacteria are able to antagonize the zoonotic pathogens. This study will contribute to reveal the potential antagonistic mechanisms of BSF larvae against zoonotic pathogens and improve the safety of organic waste conversion by BSF larvae. Abstract Black soldier fly (BSF) larvae are often exposed to organic waste which harbors abundant zoonotic pathogens. We investigated the ability of BSF larvae to inhibit the zoonotic pathogens naturally found in pig manure. The zoonotic pathogens populations were detected by using selective medium during the conversion. Results showed that the viability of the zoonotic pathogens in pig manure was significantly affected. After eight days of conversion, the Coliform populations were undetected, and Staphylococcus aureus and Salmonella spp. decreased significantly on the eighth day. Antimicrobial assays of the purified recombinant defensin-like peptide 4 (DLP4) showed that this peptide exhibits inhibitory activity against S. aureus, Salmonella enterica serovar typhimurium, and Escherichia coli in vitro. Bacteria BSF-CL and BSF-F were isolated from the larvae gut, and both inhibited the growth of S. aureus and E. coli, but Salmonella spp. was sensitive to the BSF-CL strain (but not to the BSF-F strain). The results from our experiments indicate that BSF larvae are capable of functionally inhibiting potential zoonotic pathogens in pig manure through a variety of mechanisms including antimicrobial peptides expression and the gut associate microorganisms. This study provides a theoretical basis for further study on the combined mechanism of BSF larvae immunity and its gut microbes against the zoonotic pathogens in pig manure.
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Liu Y, Xu L, Zhang Z, Huang Z, Fang D, Zheng X, Yang Z, Lu M. Isolation, Identification, and Analysis of Potential Functions of Culturable Bacteria Associated with an Invasive Gall Wasp, Leptocybe invasa. MICROBIAL ECOLOGY 2022; 83:151-166. [PMID: 33758980 DOI: 10.1007/s00248-021-01715-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 02/07/2021] [Indexed: 05/17/2023]
Abstract
Symbioses between invasive insects and bacteria are one of the key drivers of insect invasion success. Gall-inducing insects stimulate host plants to produce galls, which affects the normal growth of plants. Leptocybe invasa Fisher et La Salle, an invasive gall-inducing wasp, mainly damages Eucalyptus plantations in Southern China, but little is known about its associated bacteria. The aim of this study was to assess the diversity of bacterial communities at different developmental stages of L. invasa and to identify possible ecological functions of the associated bacteria. Bacteria associated with L. invasa were isolated using culture-dependent methods and their taxonomic statuses were determined by sequencing the 16S rRNA gene. A total of 88 species belonging to four phyla, 27 families, and 44 genera were identified by phylogenetic analysis. The four phyla were Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes, mainly from the genera Pantoea, Enterobacter, Pseudomonas, Bacillus, Acinetobacter, Curtobacterium, Sphingobium, Klebsiella, and Rhizobium. Among them, 72 species were isolated in the insect gall stage and 46 species were isolated from the adult stage. The most abundant bacterial species were γ-Proteobacteria. We found significant differences in total bacterial counts and community compositions at different developmental stages, and identified possible ecological roles of L. invasa-associated bacteria. This study is the first to systematically investigate the associated bacteria of L. invasa using culture-dependent methods, and provides a reference for other gall-inducing insects and associated bacteria.
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Affiliation(s)
- Yipeng Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Letian Xu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
| | - Zhouqiong Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Zongyou Huang
- Guangxi Key Laboratory of Agric-Environment and Agric-Products Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, China
| | - Dongxue Fang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Xialin Zheng
- Guangxi Key Laboratory of Agric-Environment and Agric-Products Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, China
| | - Zhende Yang
- Guangxi Key Laboratory of Agric-Environment and Agric-Products Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, China
| | - Min Lu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China.
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
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Prakash O, Parmar M, Vaijanapurkar M, Rale V, Shouche YS. Recent trend, biases and limitations of cultivation-based diversity studies of microbes. FEMS Microbiol Lett 2021; 368:6359716. [PMID: 34459476 DOI: 10.1093/femsle/fnab118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 08/27/2021] [Indexed: 12/22/2022] Open
Abstract
The current study attempts to analyze recent trends, biases and limitations of cultivation-based microbial diversity studies based on published, novel species in the past 6 years in the International Journal of Systematic and Evolutionary Microbiology (IJSEM), an official publication of the International Committee on Systematics of Prokaryotes (ICSP) and the Bacteriology and Applied Microbiology (BAM) Division of the International Union of Microbiological Societies (IUMS). IJSEM deals with taxa that have validly published names under the International Code of Nomenclature of Prokaryotes (ICNP). All the relevant publications from the last 6 years were retrieved, sorted and analyzed to get the answers to What is the current rate of novel species description? Which country has contributed substantially and which phyla represented better in culturable diversity studies? What are the current limitations? Published data for the past 6 years indicate that 500-900 novel species are reported annually. China, Korea, Germany, UK, India and the USA are at the forefront while contributions from other nations are meager. Despite the recent development in culturomics tools the dominance of Proteobacteria, Bacteroidetes and Actinobacteria are still prevalent in cultivation, while the representation of archaea, obligate anaerobes, microaerophiles, synergistic symbionts, aerotolerant and other fastidious microbes is poor. Single strain-based taxonomic descriptions prevail and emphasis on objective-based cultivation for biotechnological and environmental significance is not yet conspicuous.
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Affiliation(s)
- Om Prakash
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science (NCCS), Pune 411007, Maharashtra, India
| | - Mrinalini Parmar
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science (NCCS), Pune 411007, Maharashtra, India
| | - Manali Vaijanapurkar
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science (NCCS), Pune 411007, Maharashtra, India.,Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Pune-412115, Maharashtra, India
| | - Vinay Rale
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Pune-412115, Maharashtra, India
| | - Yogesh S Shouche
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science (NCCS), Pune 411007, Maharashtra, India
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Regassa H, Bose D, Mukherjee A. Review of Microorganisms and Their Enzymatic Products for Industrial Bioprocesses. Ind Biotechnol (New Rochelle N Y) 2021. [DOI: 10.1089/ind.2021.0002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Affiliation(s)
- Hailemeleak Regassa
- Faculty of Applied Sciences & Biotechnology, Shoolini University of Biotechnology & Management Sciences, Solan, Himachal Pradesh, India
| | - Debajyoti Bose
- Faculty of Applied Sciences & Biotechnology, Shoolini University of Biotechnology & Management Sciences, Solan, Himachal Pradesh, India
| | - Alivia Mukherjee
- Department of Chemical and Biological Engineering, University of Saskatchewan, Saskatoon, SK, Canada
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Gorrens E, Van Moll L, Frooninckx L, De Smet J, Van Campenhout L. Isolation and Identification of Dominant Bacteria From Black Soldier Fly Larvae ( Hermetia illucens) Envisaging Practical Applications. Front Microbiol 2021; 12:665546. [PMID: 34054771 PMCID: PMC8155639 DOI: 10.3389/fmicb.2021.665546] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 04/15/2021] [Indexed: 11/13/2022] Open
Abstract
This study aimed to establish a representative strain collection of dominant aerobic bacteria from black soldier fly larvae (Hermetia illucens, BSFL). The larvae were fed either chicken feed or fiber-rich substrates to obtain a collection of BSFL-associated microorganisms. Via an approach based on only considering the highest serial dilutions of BSFL extract (to select for the most abundant strains), a total of 172 bacteria were isolated. Identification of these isolates revealed that all bacteria belonged to either the Proteobacteria (66.3%), the Firmicutes (30.2%), the Bacteroidetes (2.9%) or the Actinobacteria (0.6%). Twelve genera were collected, with the most abundantly present ones (i.e., minimally present in at least three rearing cycles) being Enterococcus (29.1%), Escherichia (22.1%), Klebsiella (19.8%), Providencia (11.6%), Enterobacter (7.6%), and Morganella (4.1%). Our collection of dominant bacteria reflects largely the bacterial profiles of BSFL already described in literature with respect to the most important phyla and genera in the gut, but some differences can be noticed depending on substrate, biotic and abiotic factors. Furthermore, this bacterial collection will be the starting point to improve in vitro digestion models for BSFL, to develop mock communities and to find symbionts that can be added during rearing cycles to enhance the larval performances, after functional characterization of the isolates, for instance with respect to enzymatic potential.
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Affiliation(s)
- Ellen Gorrens
- Department of Microbial and Molecular Systems (M2S), Lab4Food, KU Leuven, Geel, Belgium.,Leuven Food Science and Nutrition Research Centre (LFoRCe), KU Leuven, Leuven, Belgium
| | - Laurence Van Moll
- Department of Microbial and Molecular Systems (M2S), Lab4Food, KU Leuven, Geel, Belgium.,Leuven Food Science and Nutrition Research Centre (LFoRCe), KU Leuven, Leuven, Belgium.,Laboratory for Microbiology, Parasitology and Hygiene (LMPH), Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Lotte Frooninckx
- Thomas More University of Applied Sciences, RADIUS, Geel, Belgium
| | - Jeroen De Smet
- Department of Microbial and Molecular Systems (M2S), Lab4Food, KU Leuven, Geel, Belgium.,Leuven Food Science and Nutrition Research Centre (LFoRCe), KU Leuven, Leuven, Belgium
| | - Leen Van Campenhout
- Department of Microbial and Molecular Systems (M2S), Lab4Food, KU Leuven, Geel, Belgium.,Leuven Food Science and Nutrition Research Centre (LFoRCe), KU Leuven, Leuven, Belgium
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Sefrji FO, Marasco R, Michoud G, Seferji KA, Merlino G, Daffonchio D. Kaustia mangrovi gen. nov., sp. nov. isolated from Red Sea mangrove sediments belongs to the recently proposed Parvibaculaceae family within the order Rhizobiales. Int J Syst Evol Microbiol 2021; 71:004806. [PMID: 33999795 PMCID: PMC8289202 DOI: 10.1099/ijsem.0.004806] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 04/09/2021] [Indexed: 12/17/2022] Open
Abstract
We isolated a novel strain, R1DC25T, described as Kaustia mangrovi gen. nov. sp. nov. from the sediments of a mangrove forest on the coast of the Red Sea in Saudi Arabia. This isolate is a moderately halophilic, aerobic/facultatively anaerobic Gram-stain-negative bacterium showing optimum growth at between 30 and 40 °C, at a pH of 8.5 and with 3-5 % NaCl. The genome of R1DC25T comprises a circular chromosome that is 4 630 536 bp in length, with a DNA G+C content of 67.3 mol%. Phylogenetic analyses based on the 16S rRNA gene sequence and whole-genome multilocus sequence analysis of 120 concatenated single-copy genes revealed that R1DC25T represents a distinct lineage within the family Parvibaculaceae in the order Rhizobiales within the class Alphaproteobacteria. R1DC25T showing 95.8, 95.3 and 94.5 % 16S rRNA gene sequence identity with Rhodoligotrophos appendicifer, Rhodoligotrophos jinshengii and Rhodoligotrophos defluvii, respectively. The predominant quinone was Q-10, and the polar lipids were phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, as well as several distinct aminolipids and lipids. The predominant cellular fatty acids were C19 : 0 cyclo ω8c, a combination of C18 : 1ω7c and/or C18 : 1ω6c and C16 : 0. On the basis of the differences in the phenotypic, physiological and biochemical characteristics from its known relatives and the results of our phylogenetic analyses, R1DC25T (=KCTC 72348T;=JCM 33619T;=NCCB 100699T) is proposed to represent a novel species in a novel genus, and we propose the name Kaustia mangrovi gen. nov., sp. nov. (Kaustia, subjective name derived from the abbreviation KAUST for King Abdullah University of Science and Technology; mangrovi, of a mangrove).
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Affiliation(s)
- Fatmah O. Sefrji
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Ramona Marasco
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Grégoire Michoud
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Kholoud A. Seferji
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Giuseppe Merlino
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Daniele Daffonchio
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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Yao Y, Cai X, Fei W, Ren F, Wang F, Luan X, Chen F, Zheng C. Regulating Gut Microbiome: Therapeutic Strategy for Rheumatoid Arthritis During Pregnancy and Lactation. Front Pharmacol 2020; 11:594042. [PMID: 33343364 PMCID: PMC7748111 DOI: 10.3389/fphar.2020.594042] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 10/05/2020] [Indexed: 12/12/2022] Open
Abstract
Rheumatoid arthritis (RA) is an autoimmune disease characterized by synovial inflammation and bone destruction. Microbial infection is considered to be the most important inducement of RA. The pregnancy planning of women in childbearing age is seriously affected by the disease activity of RA. Gut microbiome, related to immunity and inflammatory response of the host. At present, emerging evidence suggested there are significant differences in the diversity and abundance of gut microbiome during pregnancy and lactation, which may be associated with the fluctuation of RA disease activity. Based on these research foundations, we pioneer the idea of regulating gut microbiome for the treatment of RA during pregnancy and lactation. In this review, we mainly introduce the potential treatment strategies for controlling the disease activity of RA based on gut microbiome during pregnancy and lactation. Besides, we also briefly generalize the effects of conventional anti-rheumatic drugs on gut microbiome, the effects of metabolic changes during pregnancy on gut microbiome, alteration of gut microbiome during pregnancy and lactation, and the effects of anti-rheumatic drugs commonly used during pregnancy and lactation on gut microbiome. These will provide a clear knowledge framework for researchers in immune-related diseases during pregnancy. Regulating gut microbiome may be a potential and effective treatment to control the disease activity of RA during pregnancy and lactation.
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Affiliation(s)
- Yao Yao
- Department of Pharmacy, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xiaoyu Cai
- Department of Pharmacy, Hangzhou First People's Hospital, Hangzhou, China
| | - Weidong Fei
- Department of Pharmacy, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Fujia Ren
- Department of Pharmacy, Hangzhou Women's Hospital, Hangzhou, China
| | - Fengmei Wang
- Department of Pharmacy, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xiaofei Luan
- Department of Pharmacy, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Fengying Chen
- Department of Pharmacy, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Caihong Zheng
- Department of Pharmacy, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
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Silva LJ, Crevelin EJ, Souza DT, Lacerda-Júnior GV, de Oliveira VM, Ruiz ALTG, Rosa LH, Moraes LAB, Melo IS. Actinobacteria from Antarctica as a source for anticancer discovery. Sci Rep 2020; 10:13870. [PMID: 32807803 PMCID: PMC7431910 DOI: 10.1038/s41598-020-69786-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 07/03/2020] [Indexed: 01/09/2023] Open
Abstract
Although many advances have been achieved to treat aggressive tumours, cancer remains a leading cause of death and a public health problem worldwide. Among the main approaches for the discovery of new bioactive agents, the prospect of microbial secondary metabolites represents an effective source for the development of drug leads. In this study, we investigated the actinobacterial diversity associated with an endemic Antarctic species, Deschampsia antarctica, by integrated culture-dependent and culture-independent methods and acknowledged this niche as a reservoir of bioactive strains for the production of antitumour compounds. The 16S rRNA-based analysis showed the predominance of the Actinomycetales order, a well-known group of bioactive metabolite producers belonging to the Actinobacteria phylum. Cultivation techniques were applied, and 72 psychrotolerant Actinobacteria strains belonging to the genera Actinoplanes, Arthrobacter, Kribbella, Mycobacterium, Nocardia, Pilimelia, Pseudarthrobacter, Rhodococcus, Streptacidiphilus, Streptomyces and Tsukamurella were identified. The secondary metabolites were screened, and 17 isolates were identified as promising antitumour compound producers. However, the bio-guided assay showed a pronounced antiproliferative activity for the crude extracts of Streptomyces sp. CMAA 1527 and Streptomyces sp. CMAA 1653. The TGI and LC50 values revealed the potential of these natural products to control the proliferation of breast (MCF-7), glioblastoma (U251), lung/non-small (NCI-H460) and kidney (786-0) human cancer cell lines. Cinerubin B and actinomycin V were the predominant compounds identified in Streptomyces sp. CMAA 1527 and Streptomyces sp. CMAA 1653, respectively. Our results suggest that the rhizosphere of D. antarctica represents a prominent reservoir of bioactive actinobacteria strains and reveals it as an important environment for potential antitumour agents.
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Affiliation(s)
- Leonardo Jose Silva
- College of Agriculture "Luiz de Queiroz", University of São Paulo (USP), Piracicaba, SP, Brazil
| | - Eduardo José Crevelin
- Laboratory of Mass Spectrometry Applied To Natural Products Chemistry, Department of Chemistry, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto (FFCLRP), University of São Paulo (USP), Ribeirão Preto, SP, Brazil
| | - Danilo Tosta Souza
- Laboratory of Mass Spectrometry Applied To Natural Products Chemistry, Department of Chemistry, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto (FFCLRP), University of São Paulo (USP), Ribeirão Preto, SP, Brazil
| | - Gileno Vieira Lacerda-Júnior
- Laboratory of Environmental Microbiology, Brazilian Agricultural Research Corporation (EMBRAPA) - Embrapa Environment, Jaguariúna, SP, Brazil
| | - Valeria Maia de Oliveira
- Microbial Resourses Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas (UNICAMP), Campinas, SP, Brazil
| | | | - Luiz Henrique Rosa
- Department of Microbiology, Biological Sciences Institute - Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Luiz Alberto Beraldo Moraes
- Laboratory of Mass Spectrometry Applied To Natural Products Chemistry, Department of Chemistry, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto (FFCLRP), University of São Paulo (USP), Ribeirão Preto, SP, Brazil
| | - Itamar Soares Melo
- Laboratory of Environmental Microbiology, Brazilian Agricultural Research Corporation (EMBRAPA) - Embrapa Environment, Jaguariúna, SP, Brazil.
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Callegari M, Jucker C, Fusi M, Leonardi MG, Daffonchio D, Borin S, Savoldelli S, Crotti E. Hydrolytic Profile of the Culturable Gut Bacterial Community Associated With Hermetia illucens. Front Microbiol 2020; 11:1965. [PMID: 32903451 PMCID: PMC7434986 DOI: 10.3389/fmicb.2020.01965] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 07/24/2020] [Indexed: 12/22/2022] Open
Abstract
Larvae of the black soldier fly (BSF) Hermetia illucens (L.) convert organic waste into high valuable insect biomass that can be used as alternative protein source for animal nutrition or as feedstock for biodiesel production. Since insect biology and physiology are influenced by the gut microbiome, knowledge about the functional role of BSF-associated microorganisms could be exploited to enhance the insect performance and growth. Although an increasing number of culture-independent studies are unveiling the microbiota structure and composition of the BSF gut microbiota, a knowledge gap remains on the experimental validation of the contribution of the microorganisms to the insect growth and development. We aimed at assessing if BSF gut-associated bacteria potentially involved in the breakdown of diet components are able to improve host nutrition. A total of 193 bacterial strains were obtained from guts of BSF larvae reared on a nutritious diet using selective and enrichment media. Most of the bacterial isolates are typically found in the insect gut, with major representatives belonging to the Gammaproteobacteria and Bacilli classes. The hydrolytic profile of the bacterial collection was assessed on compounds typically present in the diet. Finally, we tested the hypothesis that the addition to a nutritionally poor diet of the two isolates Bacillus licheniformis HI169 and Stenotrophomonas maltophilia HI121, selected for their complementary metabolic activities, could enhance BSF growth. B. licheniformis HI169 positively influenced the larval final weight and growth rate when compared to the control. Conversely, the addition of S. maltophilia HI121 to the nutritionally poor diet did not result in a growth enhancement in terms of larval weight and pupal weight and length in comparison to the control, whereas the combination of the two strains positively affected the larval final weight and the pupal weight and length. In conclusion, we isolated BSF-associated bacterial strains with potential positive properties for the host nutrition and we showed that selected isolates may enhance BSF growth, suggesting the importance to evaluate the effect of the bacterial administration on the insect performance.
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Affiliation(s)
- Matteo Callegari
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l’Ambiente (DeFENS), Università degli Studi di Milano, Milan, Italy
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Costanza Jucker
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l’Ambiente (DeFENS), Università degli Studi di Milano, Milan, Italy
| | - Marco Fusi
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- School of Applied Sciences, Edinburgh Napier University, Edinburgh, United Kingdom
| | - Maria Giovanna Leonardi
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l’Ambiente (DeFENS), Università degli Studi di Milano, Milan, Italy
| | - Daniele Daffonchio
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Sara Borin
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l’Ambiente (DeFENS), Università degli Studi di Milano, Milan, Italy
| | - Sara Savoldelli
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l’Ambiente (DeFENS), Università degli Studi di Milano, Milan, Italy
| | - Elena Crotti
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l’Ambiente (DeFENS), Università degli Studi di Milano, Milan, Italy
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A Recent Overview of Microbes and Microbiome Preservation. Indian J Microbiol 2020; 60:297-309. [PMID: 32655197 DOI: 10.1007/s12088-020-00880-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 05/06/2020] [Indexed: 12/17/2022] Open
Abstract
Microbes are mediators in almost all ecosystem processes and act as a pivotal game changer in various ecological activities, globally. Therefore, understanding of microbial community structure and related functions in different environmental and micro-environmental niches is not only critical, but also a matter of greatest importance. Due to our inability to cultivate and preserve all sorts of microorganisms, we are losing some ecologically and industrially relevant components of microbial community, due to extinction caused by environmental and climatic variations with time. Intact sample and microbiome preservation are crucial for future cultivation as well as to study the effects of ecological and climatic variations on community functionality and shift with time, using OMICS. Although, methods for pure culture preservation are almost optimized, the techniques of microbiome preservation still remain as an unsolved challenge for microbiologists due to technical and physiological constraints. Present article discusses, recent approaches of microbial preservation with special reference to intact sample, mixed culture and microbiome preservation. It also incorporates recent practices used to achieve the highest viability and metabolic activities in long-term preserved microbiome.
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Pathak AP, Rathod MG, Mahabole MP, Khairnar RS. Enhanced catalytic activity of Bacillus aryabhattai P1 protease by modulation with nanoactivator. Heliyon 2020; 6:e04053. [PMID: 32529068 PMCID: PMC7276444 DOI: 10.1016/j.heliyon.2020.e04053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/26/2020] [Accepted: 05/19/2020] [Indexed: 11/24/2022] Open
Abstract
In the developing area of modern nanobiotechnology, the research is being focused on enhancement of catalytic performance in terms of efficiency and stability of enzymes to fulfill the industrial demand. In the context of this interdisciplinary era, we isolated and identified alkaline protease producer Bacillus aryabhattai P1 by polyphasic approach and then followed one variable at a time approach to optimize protease production from P1. The modified components of fermentation medium (g/L) were wheat bran 10, soybean flour 10, yeast extract 5, NaCl 10, KH2PO4 1, K2HPO4 1 and MgSO4·7H2O 0.2 (pH 9). The optimum alkaline protease production from P1 was recorded 75 ± 3 U/mg at 35 °C and pH 9 after 96 h of fermentation period. Molecular weight of partially purified P1 alkaline protease was 26 KDa as revealed by SDS-PAGE. Calcium based nanoceramic material was prepared by wet chemical precipitation method and doped in native P1 protease for catalytic activity enhancement. Catalytic activity of modified P1 protease was attained by nanoactivator mediated modulation was more by 5.58 fold at pH 10 and 30 °C temperature. The nanoceramic material named as nanoactivator, with grain size of 40–60 nm was suitable to redesign the active site of P1 protease. Such types of modified proteases can be used in different nanobiotechnological applications.
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Affiliation(s)
- Anupama P Pathak
- School of Life Sciences (DST-FIST Phase-I & UGC-SAP DRS-II Sponsored School), Swami Ramanand Teerth Marathwada University, Nanded 431606, Maharashtra, India
| | - Mukundraj G Rathod
- Department of Biotechnology & Bioinformatics (U.G. & P.G.), Yeshwant College of Information Technology (BT & BI) Parbhani (affiliated to S.R.T.M. University, Nanded), Maharashtra, India
| | - Megha P Mahabole
- School of Physical Sciences, Swami Ramanand Teerth Marathwada University, Nanded 431606, Maharashtra, India
| | - Rajendra S Khairnar
- School of Physical Sciences, Swami Ramanand Teerth Marathwada University, Nanded 431606, Maharashtra, India
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Gutleben J, Loureiro C, Ramírez Romero LA, Shetty S, Wijffels RH, Smidt H, Sipkema D. Cultivation of Bacteria From Aplysina aerophoba: Effects of Oxygen and Nutrient Gradients. Front Microbiol 2020; 11:175. [PMID: 32140143 PMCID: PMC7042410 DOI: 10.3389/fmicb.2020.00175] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 01/24/2020] [Indexed: 12/22/2022] Open
Abstract
Sponge-associated bacteria possess biotechnologically interesting properties but as yet have largely evaded cultivation. Thus, "omics"-based information on the ecology and functional potential of sponge symbionts is awaiting its integration into the design of innovative cultivation approaches. To cultivate bacteria derived from the marine sponge Aplysina aerophoba, nine novel media formulations were created based on the predicted genomic potential of the prevalent sponge symbiont lineage Poribacteria. In addition, to maintain potential microbial metabolic interactions in vitro, a Liquid-Solid cultivation approach and a Winogradsky-column approach were applied. The vast majority of microorganisms in the inoculum appeared viable after cryopreservation of sponge specimen as determined by selective propidium monoazide DNA modification of membrane-compromised cells, however, only 2% of the initial prokaryotic diversity could be recovered through cultivation. In total, 256 OTUs encompassing seven prokaryotic phyla were cultivated. The diversity of the cultivated community was influenced by the addition of the antibiotic aeroplysinin-1 as well as by medium dilution, rather than carbon source. Furthermore, the Winogradsky-column approach reproducibly enriched distinct communities at different column depths, amongst which were numerous Clostridia and OTUs that could not be assigned to a known phylum. While some bacterial taxa such as Pseudovibrio and Ruegeria were recovered from nearly all applied cultivation conditions, others such as Bacteroidetes were specific to certain medium types. Predominant sponge-associated prokaryotic taxa remained uncultured, nonetheless, alternative cultivation approaches applied here enriched for previously uncultivated microbes.
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Affiliation(s)
- Johanna Gutleben
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Catarina Loureiro
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | | | - Sudarshan Shetty
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - René H. Wijffels
- Bioprocess Engineering, AlgaePARC, Wageningen University, Wageningen, Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
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22
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Aguilar NC, Faria MCS, Pedron T, Batista BL, Mesquita JP, Bomfeti CA, Rodrigues JL. Isolation and characterization of bacteria from a brazilian gold mining area with a capacity of arsenic bioaccumulation. CHEMOSPHERE 2020; 240:124871. [PMID: 31546186 DOI: 10.1016/j.chemosphere.2019.124871] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 07/26/2019] [Accepted: 09/14/2019] [Indexed: 06/10/2023]
Abstract
In Paracatu, a city in Minas Gerais State (Brazil), the gold mineral extraction produces wastes that contribute to environmental contamination by arsenic. This work describes the evaluation of arsenic concentration from soil of a gold mining area in Paracatu and the selection of arsenic resistant bacteria. In the process of culturing enrichment, 38 bacterial strains were isolated and the minimum inhibitory concentration (MIC) was determined in solid medium for each strain. Three bacterial strains named P1C1Ib, P2Ic and P2IIB were resistant to 3000 mg L-1 of arsenite. Analysis of 16S rDNA gene sequences revealed that these bacteria belong to Bacillus cereus and Lysinibacillus boronitolerans species. After cultivation of the strains P1C1Ib, P2Ic and P2IIIb, 69.38%-71.88% of arsenite and 82.39%-85.72% of arsenate concentrations were reduced from the culture medium, suggesting the potential application of theses strains in bioremediation processes.
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Affiliation(s)
- Naidilene C Aguilar
- Instituto de Ciência, Engenharia e Tecnologia (ICET), Universidade Federal dos Vales do Jequitinhonha e Mucuri, Teófilo Otoni, Minas Gerais, 39803-371, Brazil
| | - Márcia C S Faria
- Instituto de Ciência, Engenharia e Tecnologia (ICET), Universidade Federal dos Vales do Jequitinhonha e Mucuri, Teófilo Otoni, Minas Gerais, 39803-371, Brazil
| | - Tatiana Pedron
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, São Paulo, 09210170, Brazil
| | - Bruno L Batista
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, São Paulo, 09210170, Brazil
| | - João P Mesquita
- Faculdade de Ciências Exatas (FACET), Universidade Federal dos Vales do Jequitinhonha e Mucuri, 39100-000, Brazil
| | - Cleide A Bomfeti
- Instituto de Ciência, Engenharia e Tecnologia (ICET), Universidade Federal dos Vales do Jequitinhonha e Mucuri, Teófilo Otoni, Minas Gerais, 39803-371, Brazil
| | - Jairo L Rodrigues
- Instituto de Ciência, Engenharia e Tecnologia (ICET), Universidade Federal dos Vales do Jequitinhonha e Mucuri, Teófilo Otoni, Minas Gerais, 39803-371, Brazil.
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23
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De Vero L, Boniotti MB, Budroni M, Buzzini P, Cassanelli S, Comunian R, Gullo M, Logrieco AF, Mannazzu I, Musumeci R, Perugini I, Perrone G, Pulvirenti A, Romano P, Turchetti B, Varese GC. Preservation, Characterization and Exploitation of Microbial Biodiversity: The Perspective of the Italian Network of Culture Collections. Microorganisms 2019; 7:microorganisms7120685. [PMID: 31842279 PMCID: PMC6956255 DOI: 10.3390/microorganisms7120685] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/09/2019] [Accepted: 12/10/2019] [Indexed: 02/06/2023] Open
Abstract
Microorganisms represent most of the biodiversity of living organisms in every ecological habitat. They have profound effects on the functioning of any ecosystem, and therefore on the health of our planet and of human beings. Moreover, microorganisms are the main protagonists in food, medical and biotech industries, and have several environmental applications. Accordingly, the characterization and preservation of microbial biodiversity are essential not only for the maintenance of natural ecosystems but also for research purposes and biotechnological exploitation. In this context, culture collections (CCs) and microbial biological resource centres (mBRCs) are crucial for the safeguarding and circulation of biological resources, as well as for the progress of life sciences. This review deals with the expertise and services of CCs, in particular concerning preservation and characterization of microbial resources, by pointing to the advanced approaches applied to investigate a huge reservoir of microorganisms. Data sharing and web services as well as the tight interconnection between CCs and the biotechnological industry are highlighted. In addition, guidelines and regulations related to quality management systems (QMSs), biosafety and biosecurity issues are discussed according to the perspectives of CCs and mBRCs.
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Affiliation(s)
- Luciana De Vero
- Unimore Microbial Culture Collection, Department of Life Sciences, University of Modena and Reggio Emilia, via Amendola 2, 42122 Reggio Emilia, Italy; (S.C.); (M.G.); (A.P.)
- Correspondence: ; Tel.: +39-0522-522-057
| | - Maria Beatrice Boniotti
- Biobank of Veterinary Resources, Istituto Zooprofilattico Sperimentale della Lombardia ed Emilia Romagna, via Bianchi 9, 25124 Brescia, Italy;
| | - Marilena Budroni
- Department of Agricultural Science, University of Sassari, viale Italia 39, 07100 Sassari, Italy; (M.B.); (I.M.)
| | - Pietro Buzzini
- Department of Agriculture, Food and Environmental Science, University of Perugia, borgo XX Giugno, 74, I-06121 Perugia, Italy; (P.B.); (B.T.)
| | - Stefano Cassanelli
- Unimore Microbial Culture Collection, Department of Life Sciences, University of Modena and Reggio Emilia, via Amendola 2, 42122 Reggio Emilia, Italy; (S.C.); (M.G.); (A.P.)
| | - Roberta Comunian
- Agris Sardegna, Agenzia regionale per la ricerca in agricoltura, Loc. Bonassai, km 18.600 SS291, 07100 Sassari, Italy;
| | - Maria Gullo
- Unimore Microbial Culture Collection, Department of Life Sciences, University of Modena and Reggio Emilia, via Amendola 2, 42122 Reggio Emilia, Italy; (S.C.); (M.G.); (A.P.)
| | - Antonio F. Logrieco
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Via G. Amendola 122/O, 70126 Bari, Italy; (A.F.L.); (G.P.)
| | - Ilaria Mannazzu
- Department of Agricultural Science, University of Sassari, viale Italia 39, 07100 Sassari, Italy; (M.B.); (I.M.)
| | - Rosario Musumeci
- MicroMiB Culture Collection, Department of Medicine and Surgery, University of Milano-Bicocca, via Cadore 48, 20900 Monza, Italy;
| | - Iolanda Perugini
- Department of Life Sciences and Systems Biology, University of Turin, viale Mattioli, 25, 10125 Torino, Italy; (I.P.); (G.C.V.)
| | - Giancarlo Perrone
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Via G. Amendola 122/O, 70126 Bari, Italy; (A.F.L.); (G.P.)
| | - Andrea Pulvirenti
- Unimore Microbial Culture Collection, Department of Life Sciences, University of Modena and Reggio Emilia, via Amendola 2, 42122 Reggio Emilia, Italy; (S.C.); (M.G.); (A.P.)
| | - Paolo Romano
- Mass Spectrometry and Proteomics, Scientific Direction, IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi 10, 16132 Genova, Italy;
| | - Benedetta Turchetti
- Department of Agriculture, Food and Environmental Science, University of Perugia, borgo XX Giugno, 74, I-06121 Perugia, Italy; (P.B.); (B.T.)
| | - Giovanna Cristina Varese
- Department of Life Sciences and Systems Biology, University of Turin, viale Mattioli, 25, 10125 Torino, Italy; (I.P.); (G.C.V.)
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24
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Becker P, Bosschaerts M, Chaerle P, Daniel HM, Hellemans A, Olbrechts A, Rigouts L, Wilmotte A, Hendrickx M. Public Microbial Resource Centers: Key Hubs for Findable, Accessible, Interoperable, and Reusable (FAIR) Microorganisms and Genetic Materials. Appl Environ Microbiol 2019; 85:e01444-19. [PMID: 31471301 PMCID: PMC6803313 DOI: 10.1128/aem.01444-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
In the context of open science, the availability of research materials is essential for knowledge accumulation and to maximize the impact of scientific research. In microbiology, microbial domain biological resource centers (mBRCs) have long-standing experience in preserving and distributing authenticated microbial strains and genetic materials (e.g., recombinant plasmids and DNA libraries) to support new discoveries and follow-on studies. These culture collections play a central role in the conservation of microbial biodiversity and have expertise in cultivation, characterization, and taxonomy of microorganisms. Information associated with preserved biological resources is recorded in databases and is accessible through online catalogues. Legal expertise developed by mBRCs guarantees end users the traceability and legality of the acquired material, notably with respect to the Nagoya Protocol. However, awareness of the advantages of depositing biological materials in professional repositories remains low, and the necessity of securing strains and genetic resources for future research must be emphasized. This review describes the unique position of mBRCs in microbiology and molecular biology through their history, evolving roles, expertise, services, challenges, and international collaborations. It also calls for an increased deposit of strains and genetic resources, a responsibility shared by scientists, funding agencies, and publishers. Journal policies requesting a deposit during submission of a manuscript represent one of the measures to make more biological materials available to the broader community, hence fully releasing their potential and improving openness and reproducibility in scientific research.
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Affiliation(s)
- P Becker
- BCCM/IHEM Fungi Collection, Mycology and Aerobiology, Sciensano, Brussels, Belgium
| | - M Bosschaerts
- BCCM Coordination Cell, Belgian Science Policy, Brussels, Belgium
| | - P Chaerle
- BCCM/DCG Diatoms Collection, Ghent University, Ghent, Belgium
| | - H-M Daniel
- BCCM/MUCL, Mycothèque de l'Université Catholique de Louvain, Earth and Life Institute, Mycology Laboratory, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - A Hellemans
- BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Faculty of Science, Ghent University, Ghent, Belgium
| | - A Olbrechts
- BCCM/GeneCorner Plasmid Collection, Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - L Rigouts
- BCCM/ITM Mycobacteria Collection, Institute of Tropical Medicine, Antwerp, Belgium
| | - A Wilmotte
- BCCM/ULC Cyanobacteria Collection, InBios-Centre for Protein Engineering, Université de Liège, Liège, Belgium
| | - M Hendrickx
- BCCM/IHEM Fungi Collection, Mycology and Aerobiology, Sciensano, Brussels, Belgium
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25
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Secondary Metabolites of Endophytic Actinomycetes: Isolation, Synthesis, Biosynthesis, and Biological Activities. PROGRESS IN THE CHEMISTRY OF ORGANIC NATURAL PRODUCTS 108 2019; 108:207-296. [DOI: 10.1007/978-3-030-01099-7_3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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26
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Rombouts JL, Mos G, Weissbrodt DG, Kleerebezem R, Van Loosdrecht MCM. Diversity and metabolism of xylose and glucose fermenting microbial communities in sequencing batch or continuous culturing. FEMS Microbiol Ecol 2018; 95:5228722. [DOI: 10.1093/femsec/fiy233] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 11/30/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Julius L Rombouts
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Galvin Mos
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - David G Weissbrodt
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Robbert Kleerebezem
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Mark C M Van Loosdrecht
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
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27
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Baveye PC, Otten W, Kravchenko A, Balseiro-Romero M, Beckers É, Chalhoub M, Darnault C, Eickhorst T, Garnier P, Hapca S, Kiranyaz S, Monga O, Mueller CW, Nunan N, Pot V, Schlüter S, Schmidt H, Vogel HJ. Emergent Properties of Microbial Activity in Heterogeneous Soil Microenvironments: Different Research Approaches Are Slowly Converging, Yet Major Challenges Remain. Front Microbiol 2018; 9:1929. [PMID: 30210462 PMCID: PMC6119716 DOI: 10.3389/fmicb.2018.01929] [Citation(s) in RCA: 125] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 07/30/2018] [Indexed: 01/17/2023] Open
Abstract
Over the last 60 years, soil microbiologists have accumulated a wealth of experimental data showing that the bulk, macroscopic parameters (e.g., granulometry, pH, soil organic matter, and biomass contents) commonly used to characterize soils provide insufficient information to describe quantitatively the activity of soil microorganisms and some of its outcomes, like the emission of greenhouse gasses. Clearly, new, more appropriate macroscopic parameters are needed, which reflect better the spatial heterogeneity of soils at the microscale (i.e., the pore scale) that is commensurate with the habitat of many microorganisms. For a long time, spectroscopic and microscopic tools were lacking to quantify processes at that scale, but major technological advances over the last 15 years have made suitable equipment available to researchers. In this context, the objective of the present article is to review progress achieved to date in the significant research program that has ensued. This program can be rationalized as a sequence of steps, namely the quantification and modeling of the physical-, (bio)chemical-, and microbiological properties of soils, the integration of these different perspectives into a unified theory, its upscaling to the macroscopic scale, and, eventually, the development of new approaches to measure macroscopic soil characteristics. At this stage, significant progress has been achieved on the physical front, and to a lesser extent on the (bio)chemical one as well, both in terms of experiments and modeling. With regard to the microbial aspects, although a lot of work has been devoted to the modeling of bacterial and fungal activity in soils at the pore scale, the appropriateness of model assumptions cannot be readily assessed because of the scarcity of relevant experimental data. For significant progress to be made, it is crucial to make sure that research on the microbial components of soil systems does not keep lagging behind the work on the physical and (bio)chemical characteristics. Concerning the subsequent steps in the program, very little integration of the various disciplinary perspectives has occurred so far, and, as a result, researchers have not yet been able to tackle the scaling up to the macroscopic level. Many challenges, some of them daunting, remain on the path ahead. Fortunately, a number of these challenges may be resolved by brand new measuring equipment that will become commercially available in the very near future.
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Affiliation(s)
- Philippe C. Baveye
- UMR ECOSYS, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, rance
| | - Wilfred Otten
- School of Water, Energy and Environment, Cranfield University, Cranfield, United Kingdom
| | - Alexandra Kravchenko
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | - María Balseiro-Romero
- UMR ECOSYS, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, rance
- Department of Soil Science and Agricultural Chemistry, Centre for Research in Environmental Technologies, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Éléonore Beckers
- Soil–Water–Plant Exchanges, Terra Research Centre, BIOSE, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Maha Chalhoub
- UMR ECOSYS, INRA, Université Paris-Saclay, Thiverval-Grignon, France
| | - Christophe Darnault
- Laboratory of Hydrogeoscience and Biological Engineering, L.G. Rich Environmental Laboratory, Department of Environmental Engineering and Earth Sciences, Clemson University, Clemson, SC, United States
| | - Thilo Eickhorst
- Faculty 2 Biology/Chemistry, University of Bremen, Bremen, Germany
| | - Patricia Garnier
- UMR ECOSYS, INRA, Université Paris-Saclay, Thiverval-Grignon, France
| | - Simona Hapca
- Dundee Epidemiology and Biostatistics Unit, School of Medicine, University of Dundee, Dundee, United Kingdom
| | - Serkan Kiranyaz
- Department of Electrical Engineering, Qatar University, Doha, Qatar
| | - Olivier Monga
- Institut de Recherche pour le Développement, Bondy, France
| | - Carsten W. Mueller
- Lehrstuhl für Bodenkunde, Technical University of Munich, Freising, Germany
| | - Naoise Nunan
- Institute of Ecology and Environmental Sciences – Paris, Sorbonne Universités, CNRS, IRD, INRA, P7, UPEC, Paris, France
| | - Valérie Pot
- UMR ECOSYS, INRA, Université Paris-Saclay, Thiverval-Grignon, France
| | - Steffen Schlüter
- Soil System Science, Helmholtz-Zentrum für Umweltforschung GmbH – UFZ, Leipzig, Germany
| | - Hannes Schmidt
- Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, Research Network ‘Chemistry meets Microbiology’, University of Vienna, Vienna, Austria
| | - Hans-Jörg Vogel
- Soil System Science, Helmholtz-Zentrum für Umweltforschung GmbH – UFZ, Leipzig, Germany
- Institute of Soil Science and Plant Nutrition, Martin Luther University of Halle-Wittenberg, Halle, Germany
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28
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Li X, Li C, Ye H, Wang Z, Wu X, Han Y, Xu B. Changes in the microbial communities in vacuum-packaged smoked bacon during storage. Food Microbiol 2018; 77:26-37. [PMID: 30297053 DOI: 10.1016/j.fm.2018.08.007] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 08/15/2018] [Accepted: 08/16/2018] [Indexed: 12/13/2022]
Abstract
This study aimed to gain deeper insights into the microbiota composition and population dynamics, monitor the dominant bacterial populations and identify the specific spoilage microorganisms (SSOs) of vacuum-packed bacon during refrigerated storage using both culture-independent and dependent methods. High-throughout sequencing (HTS) showed that the microbial composition changed greatly with the prolongation of storage time. The diversity of microbiota was abundant at the initial stage then experienced a continuous decrease. Lactic acid bacteria (LAB) mainly Leuconostoc and Lactobacillus dominated the microbial population after seven days of storage. A total of 26 isolates were identified from different growth media using traditional cultivation isolation and identification method. Leuconostoc mesenteroides and Leuconostoc carnosum were the most prevalent species since day 15, while Lactobacillus sakei and Lactobacillus curvatus were only found on day 45, suggesting that they could be responsible for the spoilage of bacon. Serratia, Rahnella, Fusobacterium and Lactococcus underwent a dramatic increase at some point in individual batchs which may be considered as potential contributors to the spoilage.
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Affiliation(s)
- Xinfu Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; State Key Laboratory of Meat Processing and Quality Control, Yurun Group, Nanjing, 211806, China
| | - Cong Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; State Key Laboratory of Meat Processing and Quality Control, Yurun Group, Nanjing, 211806, China
| | - Hua Ye
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Zhouping Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Xiang Wu
- State Key Laboratory of Meat Processing and Quality Control, Yurun Group, Nanjing, 211806, China
| | - Yanqing Han
- State Key Laboratory of Meat Processing and Quality Control, Yurun Group, Nanjing, 211806, China
| | - Baocai Xu
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; School of Food Science and Engineering, Hefei University of Technology, Hefei, 230009, China; State Key Laboratory of Meat Processing and Quality Control, Yurun Group, Nanjing, 211806, China.
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29
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Bendia AG, Araujo GG, Pulschen AA, Contro B, Duarte RTD, Rodrigues F, Galante D, Pellizari VH. Surviving in hot and cold: psychrophiles and thermophiles from Deception Island volcano, Antarctica. Extremophiles 2018; 22:917-929. [PMID: 30109444 DOI: 10.1007/s00792-018-1048-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 08/08/2018] [Indexed: 12/22/2022]
Abstract
Polar volcanoes harbor unique conditions of extreme temperature gradients capable of selecting different types of extremophiles. Deception Island is a marine stratovolcano located at Maritime Antarctica that is notable for its pronounced temperature gradients over very short distances, reaching values up to 100 °C in the fumaroles, and subzero temperatures next to the glaciers. Due to these characteristics, Deception can be considered an interesting analogue of extraterrestrial environments. Our main goal in this study was to isolate thermophilic and psychrophilic bacteria from sediments associated with fumaroles and glaciers from two geothermal sites in Deception Island, comprising temperatures between 0 and 98 °C, and to evaluate their survivability to desiccation and UV-C radiation. Our results revealed that culturable thermophiles and psychrophiles were recovered among the extreme temperature gradient in Deception volcano, which indicates that these extremophiles remain alive even when the conditions do not comprise their growth range. The viability of culturable psychrophiles in hyperthermophilic environments is still poorly understood and our work showed the importance of future studies about their survival strategies in high temperatures. Finally, the spore-forming thermophilic isolates which we found have displayed good survival to desiccation and UV-C irradiation, which suggests their potential to be further explored in astrobiological studies.
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Affiliation(s)
- Amanda G Bendia
- Departamento de Oceanografia Biológica, Instituto Oceanográfico, Universidade de São Paulo, Praça do Oceanográfico 191, São Paulo, SP, 05508-900, Brazil.
| | - Gabriel G Araujo
- Interunities Graduate Program in Biotechnology, Universidade de São Paulo, São Paulo, Brazil
| | - André A Pulschen
- Institute of Chemistry, Universidade de São Paulo, São Paulo, Brazil
| | - Bruna Contro
- Undergraduate Program in Biology, Universidade Estadual Paulista "Julio de Mesquisa Filho", São Paulo, Brazil
| | - Rubens T D Duarte
- Departamento de Oceanografia Biológica, Instituto Oceanográfico, Universidade de São Paulo, Praça do Oceanográfico 191, São Paulo, SP, 05508-900, Brazil
| | - Fábio Rodrigues
- Institute of Chemistry, Universidade de São Paulo, São Paulo, Brazil
| | - Douglas Galante
- Brazilian Synchrotron Light Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, Brazil
| | - Vivian H Pellizari
- Departamento de Oceanografia Biológica, Instituto Oceanográfico, Universidade de São Paulo, Praça do Oceanográfico 191, São Paulo, SP, 05508-900, Brazil
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Zeaiter Z, Mapelli F, Crotti E, Borin S. Methods for the genetic manipulation of marine bacteria. ELECTRON J BIOTECHN 2018. [DOI: 10.1016/j.ejbt.2018.03.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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Untapped bacterial diversity and metabolic potential within Unkeshwar hot springs, India. Arch Microbiol 2018; 200:753-770. [PMID: 29396619 DOI: 10.1007/s00203-018-1484-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 01/23/2018] [Accepted: 01/24/2018] [Indexed: 01/04/2023]
Abstract
Hot springs support diverse and interesting groups of microorganisms adapted to extreme conditions and gaining attention in biotechnological applications. However, due to limitations of cultivation methods, a majority of such extremophiles remain uncultivated and unexplored. The advent of multiple cultivation conditions and specialized culture media could possibly aid to access the unexplored microbial portion of hot springs. In the present study, different media and isolation strategies were applied to isolate hitherto unexplored bacterial taxa in the water samples collected from Unkeshwar hot springs, India. Molecular, phylogenetic and predictive functional characterization of the isolated bacterial population was done using 16S rRNA sequencing coupled with Tax4Fun tools. Furthermore, representative isolates were screened for important enzymes (cellulase, xylanase, amylase, and protease) and heavy metal tolerance (chromium, arsenic) properties. A total of 454 bacterial isolates obtained were mapped into 57 unique bacterial genera and 4 different bacterial phyla. Interestingly, 37 genera not previously isolated from Indian hot springs, were isolated for the first time in the present study. However, most of these genera (23 out of 37) were reported only in metagenomics studies from Indian and global hot springs. Furthermore, around 14 genera not previously cultivated and not detected in metagenomics studies of hot springs are documented here. The metabolic potential was ascertained by determining the abundance of specific genes using in silico based Tax4Fun tool, which identified around 315 metabolic pathways for metabolism of carbohydrates, synthesis of secondary metabolites and degradation of xenobiotic compounds. Bioprospection study revealed that 33 and 25 bacterial genera were positive for enzyme production and resistance to the heavy metals, respectively. The present study revealed the advantages of cultivation methods using a comprehensive multiple isolation approach for exploring untapped and unique bacterial diversity, and also utilities for various biotechnological and environmental applications.
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Dunivin TK, Miller J, Shade A. Taxonomically-linked growth phenotypes during arsenic stress among arsenic resistant bacteria isolated from soils overlying the Centralia coal seam fire. PLoS One 2018; 13:e0191893. [PMID: 29370270 PMCID: PMC5785013 DOI: 10.1371/journal.pone.0191893] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 01/12/2018] [Indexed: 02/05/2023] Open
Abstract
Arsenic (As), a toxic element, has impacted life since early Earth. Thus, microorganisms have evolved many As resistance and tolerance mechanisms to improve their survival outcomes given As exposure. We isolated As resistant bacteria from Centralia, PA, the site of an underground coal seam fire that has been burning since 1962. From a 57.4°C soil collected from a vent above the fire, we isolated 25 unique aerobic As resistant bacterial strains spanning seven genera. We examined their diversity, resistance gene content, transformation abilities, inhibitory concentrations, and growth phenotypes. Although As concentrations were low at the time of soil collection (2.58 ppm), isolates had high minimum inhibitory concentrations (MICs) of arsenate and arsenite (>300 mM and 20 mM respectively), and most isolates were capable of arsenate reduction. We screened isolates (PCR and sequencing) using 12 published primer sets for six As resistance genes (AsRGs). Genes encoding arsenate reductase (arsC) and arsenite efflux pumps (arsB, ACR3(2)) were present, and phylogenetic incongruence between 16S rRNA genes and AsRGs provided evidence for horizontal gene transfer. A detailed investigation of differences in isolate growth phenotypes across As concentrations (lag time to exponential growth, maximum growth rate, and maximum OD590) showed a relationship with taxonomy, providing information that could help to predict an isolate's performance given As exposure in situ. Our results suggest that microbiological management and remediation of environmental As could be informed by taxonomically-linked As tolerance, potential for resistance gene transferability, and the rare biosphere.
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Affiliation(s)
- Taylor K. Dunivin
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
- Environmental and Integrative Toxicological Sciences Doctoral Program, Michigan State University, East Lansing, Michigan, United States of America
| | - Justine Miller
- Lyman Briggs College, Michigan State University, East Lansing, Michigan, United States of America
| | - Ashley Shade
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
- Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, Michigan, United States of America
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33
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He GQ, Liu TJ, Sadiq FA, Gu JS, Zhang GH. Insights into the microbial diversity and community dynamics of Chinese traditional fermented foods from using high-throughput sequencing approaches. J Zhejiang Univ Sci B 2017; 18:289-302. [PMID: 28378567 DOI: 10.1631/jzus.b1600148] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Chinese traditional fermented foods have a very long history dating back thousands of years and have become an indispensable part of Chinese dietary culture. A plethora of research has been conducted to unravel the composition and dynamics of microbial consortia associated with Chinese traditional fermented foods using culture-dependent as well as culture-independent methods, like different high-throughput sequencing (HTS) techniques. These HTS techniques enable us to understand the relationship between a food product and its microbes to a greater extent than ever before. Considering the importance of Chinese traditional fermented products, the objective of this paper is to review the diversity and dynamics of microbiota in Chinese traditional fermented foods revealed by HTS approaches.
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Affiliation(s)
- Guo-Qing He
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China.,Zhejiang Provincial Key Laboratory of Food Microbiology, Zhejiang University, Hangzhou 310058, China
| | - Tong-Jie Liu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China.,Zhejiang Provincial Key Laboratory of Food Microbiology, Zhejiang University, Hangzhou 310058, China
| | - Faizan A Sadiq
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China.,Zhejiang Provincial Key Laboratory of Food Microbiology, Zhejiang University, Hangzhou 310058, China
| | - Jing-Si Gu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China.,Zhejiang Provincial Key Laboratory of Food Microbiology, Zhejiang University, Hangzhou 310058, China
| | - Guo-Hua Zhang
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China.,Zhejiang Provincial Key Laboratory of Food Microbiology, Zhejiang University, Hangzhou 310058, China
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Rodrigues CJC, Pereira RFS, Fernandes P, Cabral JMS, de Carvalho CCCR. Cultivation-based strategies to find efficient marine biocatalysts. Biotechnol J 2017; 12. [PMID: 28294564 DOI: 10.1002/biot.201700036] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 03/02/2017] [Accepted: 03/10/2017] [Indexed: 11/05/2022]
Abstract
Marine bacteria have evolved to survive in the marine environment by using unique physiological, biochemical and metabolic features and the ability to produce enzymes and compounds which may have commercial value. The Azores archipelago presents several ecosystems with strong volcanic activity where bacteria thrive under e.g. high temperatures. In this study, samples collected in the island of São Miguel were screened for biocatalysts possessing e.g. lipase, esterase, amylase, and inulinase activities. After isolation of several hundred bacterial strains, high throughput screening methods allowed the fast identification of biocatalysts. The first cultivation tests were performed on 24-wells microtiter plates with online oxygen monitoring and bacteria able to grow within 24 h were selected for further process development. Bacteria able to produce the desired enzymes were selected for the first round of tests. Four Bacillus strains presented high inulinase activity. The next step in process development was the determination of key parameters for enzyme activity such as temperature, pH, salinity and substrate concentration. The highest inulinase activity, 2.2 gsugars /gprotein h, was attained when the supernatant of a culture of a Bacillus subtilis strain was used in a magnetically stirred bioreactor. This study demonstrates how bacterial strains from marine environments may be used successfully in biotechnological processes.
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Affiliation(s)
- Carlos J C Rodrigues
- iBB-Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Ricardo F S Pereira
- iBB-Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Pedro Fernandes
- iBB-Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Joaquim M S Cabral
- iBB-Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Carla C C R de Carvalho
- iBB-Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
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Feng NX, Yu J, Zhao HM, Cheng YT, Mo CH, Cai QY, Li YW, Li H, Wong MH. Efficient phytoremediation of organic contaminants in soils using plant-endophyte partnerships. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 583:352-368. [PMID: 28117167 DOI: 10.1016/j.scitotenv.2017.01.075] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 01/11/2017] [Accepted: 01/12/2017] [Indexed: 05/20/2023]
Abstract
Soil pollution with organic contaminants is one of the most intractable environmental problems today, posing serious threats to humans and the environment. Innovative strategies for remediating organic-contaminated soils are critically needed. Phytoremediation, based on the synergistic actions of plants and their associated microorganisms, has been recognized as a powerful in situ approach to soil remediation. Suitable combinations of plants and their associated endophytes can improve plant growth and enhance the biodegradation of organic contaminants in the rhizosphere and/or endosphere, dramatically expediting the removal of organic pollutants from soils. However, for phytoremediation to become a more widely accepted and predictable alternative, a thorough understanding of plant-endophyte interactions is needed. Many studies have recently been conducted on the mechanisms of endophyte-assisted phytoremediation of organic contaminants in soils. In this review, we highlight the superiority of organic pollutant-degrading endophytes for practical applications in phytoremediation, summarize alternative strategies for improving phytoremediation, discuss the fundamental mechanisms of endophyte-assisted phytoremediation, and present updated information regarding the advances, challenges, and new directions in the field of endophyte-assisted phytoremediation technology.
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Affiliation(s)
- Nai-Xian Feng
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, School of Environment, Jinan University, Guangzhou 510632, China
| | - Jiao Yu
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, School of Environment, Jinan University, Guangzhou 510632, China
| | - Hai-Ming Zhao
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, School of Environment, Jinan University, Guangzhou 510632, China
| | - Yu-Ting Cheng
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, School of Environment, Jinan University, Guangzhou 510632, China
| | - Ce-Hui Mo
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, School of Environment, Jinan University, Guangzhou 510632, China.
| | - Quan-Ying Cai
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, School of Environment, Jinan University, Guangzhou 510632, China
| | - Yan-Wen Li
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, School of Environment, Jinan University, Guangzhou 510632, China
| | - Hui Li
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, School of Environment, Jinan University, Guangzhou 510632, China
| | - Ming-Hung Wong
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, School of Environment, Jinan University, Guangzhou 510632, China; Consortium on Health, Environment, Education and Research (CHEER), Department of Science and Environmental Studies, The Education University of Hong Kong, Tai Po, Hong Kong, China
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de Carvalho CCCR. Whole cell biocatalysts: essential workers from Nature to the industry. Microb Biotechnol 2017; 10:250-263. [PMID: 27145540 PMCID: PMC5328830 DOI: 10.1111/1751-7915.12363] [Citation(s) in RCA: 140] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 03/28/2016] [Accepted: 03/31/2016] [Indexed: 11/30/2022] Open
Abstract
Microorganisms have been exposed to a myriad of substrates and environmental conditions throughout evolution resulting in countless metabolites and enzymatic activities. Although mankind have been using these properties for centuries, we have only recently learned to control their production, to develop new biocatalysts with high stability and productivity and to improve their yields under new operational conditions. However, microbial cells still provide the best known environment for enzymes, preventing conformational changes in the protein structure in non-conventional medium and under harsh reaction conditions, while being able to efficiently regenerate necessary cofactors and to carry out cascades of reactions. Besides, a still unknown microbe is probably already producing a compound that will cure cancer, Alzeihmer's disease or kill the most resistant pathogen. In this review, the latest developments in screening desirable activities and improving production yields are discussed.
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Affiliation(s)
- Carla C. C. R. de Carvalho
- iBB‐Institute for Bioengineering and BiosciencesDepartment of BioengineeringInstituto Superior TécnicoUniversidade de LisboaAv. Rovisco PaisLisbon1049‐001Portugal
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McCluskey K. A Review of Living Collections with Special Emphasis on Sustainability and Its Impact on Research Across Multiple Disciplines. Biopreserv Biobank 2016; 15:20-30. [PMID: 27869477 PMCID: PMC5327032 DOI: 10.1089/bio.2016.0066] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Formal living collections have unique characteristics that distinguish them from other types of biorepositories. Comprising diverse resources, microbe culture collections, crop and biodiversity plant germplasm collections, and animal germplasm repositories are commonly allied with specific research communities or stakeholder groups. Among living collections, microbial culture collections have very long and unique life histories, with some being older than 100 years. Regulatory, financial, and technical developments have impacted living collections in many ways. International treaty obligations and restrictions on release of genetically modified organisms complicate the activities of living collections. Funding for living collections is a continuing challenge and threatens to create a two-tier system where medically relevant collections are well funded and all other collections are underfunded and hence understaffed. Molecular, genetic, and whole genome sequence analysis of contents of microbes and other living resource collections bring additional value to living collections.
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Affiliation(s)
- Kevin McCluskey
- Fungal Genetics Stock Center, Department of Plant Pathology, Kansas State University , Manhattan, Kansas
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Boundy-Mills KL, Glantschnig E, Roberts IN, Yurkov A, Casaregola S, Daniel HM, Groenewald M, Turchetti B. Yeast culture collections in the twenty-first century: new opportunities and challenges. Yeast 2016; 33:243-60. [PMID: 27144478 DOI: 10.1002/yea.3171] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Revised: 04/28/2016] [Accepted: 04/28/2016] [Indexed: 11/06/2022] Open
Abstract
The twenty-first century has brought new opportunities and challenges to yeast culture collections, whether they are long-standing or recently established. Basic functions such as archiving, characterizing and distributing yeasts continue, but with expanded responsibilities and emerging opportunities. In addition to a number of well-known, large public repositories, there are dozens of smaller public collections that differ in the range of species and strains preserved, field of emphasis and services offered. Several collections have converted their catalogues to comprehensive databases and synchronize them continuously through public services, making it easier for users worldwide to locate a suitable source for specific yeast strains and the data associated with these yeasts. In-house research such as yeast taxonomy continues to be important at culture collections. Because yeast culture collections preserve a broad diversity of species and strains within a species, they are able to make discoveries in many other areas as well, such as biotechnology, functional, comparative and evolution genomics, bioprocesses and novel products. Due to the implementation of the Convention of Biological Diversity (CBD) and the Nagoya Protocol (NP), there are new requirements for both depositors and users to ensure that yeasts were collected following proper procedures and to guarantee that the country of origin will be considered if benefits arise from a yeast's utilization. Intellectual property rights (IPRs) are extremely relevant to the current access and benefit-sharing (ABS) mechanisms; most research and development involving genetic resources and associated traditional knowledge will be subject to this topic. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Kyria L Boundy-Mills
- Phaff Yeast Culture Collection. Food Science and Technology, University of California, Davis, Davis, CA, USA
| | | | - Ian N Roberts
- National Collection of Yeast Cultures, Institute of Food Research, Norwich Research Park, Norwich, UK
| | - Andrey Yurkov
- Leibniz Institute DSMZ - German Collection of Micro-organisms and Cell Cultures, Braunschweig, Germany
| | - Serge Casaregola
- Micalis Institute INRA, AgroParisTech, CIRM-Levures, Université Paris-Saclay, Jouy-en-Josas, Thiverval-Grignon, France
| | - Heide-Marie Daniel
- Mycothéque de l'Université Catholique de Louvain (BCCM/MUCL), Earth and Life Institute, Applied Microbiology, Laboratory of Mycology, Louvain-la-Neuve, Belgium
| | | | - Benedetta Turchetti
- Department of Agricultural, Food and Environmental Science, Industrial Yeasts Collection DBVPG, University of Perugia, Perugia, Italy
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40
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Thomas P, Sekhar AC. Effects Due to Rhizospheric Soil Application of an Antagonistic Bacterial Endophyte on Native Bacterial Community and Its Survival in Soil: A Case Study with Pseudomonas aeruginosa from Banana. Front Microbiol 2016; 7:493. [PMID: 27199897 PMCID: PMC4844927 DOI: 10.3389/fmicb.2016.00493] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 03/27/2016] [Indexed: 01/31/2023] Open
Abstract
Effective translation of research findings from laboratory to agricultural fields is essential for the success of biocontrol or growth promotion trials employing beneficial microorganisms. The rhizosphere is to be viewed holistically as a dynamic ecological niche comprising of diverse microorganisms including competitors and noxious antagonists to the bio-inoculant. This study was undertaken to assess the effects due to the soil application of an endophytic bacterium with multiple pathogen antagonistic potential on native bacterial community and its sustenance in agricultural soil. Pseudomonas aeruginosa was employed as a model system considering its frequent isolation as an endophyte, wide antagonistic effects reported against different phytopathogens and soil pests, and that the species is a known human pathogen which makes its usage in agriculture precarious. Employing the strain ‘GNS.13.2a’ from banana, its survival in field soil and the effects upon soil inoculation were investigated by monitoring total culturable bacterial fraction as the representative indicator of soil microbial community. Serial dilution plating of uninoculated control versus P. aeruginosa inoculated soil from banana rhizosphere indicated a significant reduction in native bacterial cfu soon after inoculation compared with control soil as assessed on cetrimide- nalidixic acid selective medium against nutrient agar. Sampling on day-4 showed a significant reduction in P. aeruginosa cfu in inoculated soil and a continuous dip thereafter registering >99% reduction within 1 week while the native bacterial population resurged with cfu restoration on par with control. This was validated in contained trials with banana plants. Conversely, P. aeruginosa showed static cfu or proliferation in axenic-soil. Lateral introduction of soil microbiome in P. aeruginosa established soil under axenic conditions or its co-incubation with soil microbiota in suspension indicated significant adverse effects by native microbial community. Direct agar-plate challenge assays with individual environmental bacterial isolates displayed varying interactive or antagonistic effects. In effect, the application of P. aeruginosa in rhizospheric soil did not serve any net benefit in terms of sustained survival. Conversely, it caused a disturbance to the native soil bacterial community. The findings highlight the need for monitoring the bio-inoculant(s) in field-soil and assessing the interactive effects with native microbial community before commercial recommendation. varying interactive or antagonistic effects. In effect, the application of P. aeruginosa in rhizospheric soil did not serve any net benefit in terms of sustained survival. Conversely, it caused a disturbance to the native soil bacterial community. The findings highlight the need for monitoring the bio-inoculant(s) in field-soil and assessing the interactive effects with native microbial community before commercial recommendation.
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Affiliation(s)
- Pious Thomas
- Endophytic and Molecular Microbiology Laboratory, Division of Biotechnology, ICAR-Indian Institute of Horticultural Research Bengaluru, India
| | - Aparna C Sekhar
- Endophytic and Molecular Microbiology Laboratory, Division of Biotechnology, ICAR-Indian Institute of Horticultural Research Bengaluru, India
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Water-related environments: a multistep procedure to assess the diversity and enzymatic properties of cultivable bacteria. World J Microbiol Biotechnol 2016; 32:42. [DOI: 10.1007/s11274-015-1997-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 12/10/2015] [Indexed: 10/22/2022]
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Maddaloni M, Pascual DW. Isolation of oxalotrophic bacteria associated with Varroa destructor mites. Lett Appl Microbiol 2015; 61:411-7. [PMID: 26302038 DOI: 10.1111/lam.12486] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2015] [Revised: 08/16/2015] [Accepted: 08/17/2015] [Indexed: 11/29/2022]
Abstract
UNLABELLED Bacteria associated with varroa mites were cultivated and genotyped by 16S RNA. Under our experimental conditions, the cultivable bacteria were few in number, and most of them proved to be fastidious to grow. Cultivation with seven different media under O2 /CO2 conditions and selection for colony morphology yielded a panel of species belonging to 13 different genera grouped in two different phyla, proteobacteria and actinobacteria. This study identified one species of actinobacteria that is a known commensal of the honey bee. Some isolates are oxalotrophic, a finding that may carry ramifications into the use of oxalic acid to control the number of phoretic mites in the managed colonies of honey bees. SIGNIFICANCE AND IMPACT OF THE STUDY Oxalic acid, legally or brevi manu, is widely used to control phoretic Varroa destructor mites, a major drive of current honey bees' colony losses. Unsubstantiated by sanctioned research are rumours that in certain instances oxalic acid is losing efficacy, forcing beekeepers to increase the frequency of treatments. This investigation fathoms the hypothesis that V. destructor associates with bacteria capable of degrading oxalic acid. The data show that indeed oxalotrophy, a rare trait among bacteria, is common in bacteria that we isolated from V. destructor mites. This finding may have ramifications in the use of oxalic acid as a control agent.
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Affiliation(s)
- M Maddaloni
- Department of Infectious Diseases & Pathology, University of Florida, Gainesville, FL, USA
| | - D W Pascual
- Department of Infectious Diseases & Pathology, University of Florida, Gainesville, FL, USA
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Prakash O, Nimonkar Y, Vaishampayan A, Mishra M, Kumbhare S, Josef N, Shouche YS. Pantoea intestinalis sp. nov., isolated from the human gut. Int J Syst Evol Microbiol 2015; 65:3352-3358. [DOI: 10.1099/ijsem.0.000419] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel bacterial strain, 29Y89BT, was isolated from a faecal sample of a healthy human subject. Cells were Gram-stain-negative, motile, non-spore-forming and rod-shaped. Strain 29Y89BT formed cream-coloured colonies 2 mm in diameter on trypticase soy agar and showed optimum growth at 35 °C. Strain 29Y89BT showed highest 16S rRNA gene sequence similarity to Pantoea gaviniae A18/07T (98.4 %) followed by Pantoea calida 1400/07T (97.2 %). Multi-locus sequence analysis using atpD (ATP synthase β subunit), gyrB (DNA gyrase), infB (initiation translation factor 2) and rpoB (RNA polymerase β subunit) genes also supported the result of 16S rRNA gene sequence based phylogeny. Strain 29Y89BT showed 62 and 40.7 % DNA–DNA relatedness with P. calida DSM 22759T and P. gaviniae DSM 22758T. Strain 29Y89BT contained C17
: 0 cyclo, C19
: 0 cyclo ω8c, C16 : 0, C14 : 0 and C12 : 0 as predominant fatty acids. In addition, strain 29Y89BT showed physiological and phenotypic differences from its closest relatives P. gaviniae DSM 22758T and P. calida DSM 22759T. The polar lipid profile mainly comprised phospholipids. The DNA G+C content was 59.1 mol%. Thus, based on the findings of the current study, strain 29Y89BT showed clear delineations from its closest relatives P. gaviniae DSM 22758T and P. calida DSM 22759T, and is thus considered to represent a novel species of the genus Pantoea, for which the name Pantoea intestinalis sp. nov. is proposed. The type strain is 29Y89BT ( = DSM 28113T = MCC 2554T).
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Affiliation(s)
- Om Prakash
- Microbial Culture Collection, National Centre for Cell Science, Pune, Maharastra 411007, India
| | - Yogesh Nimonkar
- Microbial Culture Collection, National Centre for Cell Science, Pune, Maharastra 411007, India
| | - Ankita Vaishampayan
- Microbial Culture Collection, National Centre for Cell Science, Pune, Maharastra 411007, India
| | - Mrinal Mishra
- Microbial Culture Collection, National Centre for Cell Science, Pune, Maharastra 411007, India
| | - Shreyas Kumbhare
- Microbial Culture Collection, National Centre for Cell Science, Pune, Maharastra 411007, India
| | - Neetha Josef
- Microbial Culture Collection, National Centre for Cell Science, Pune, Maharastra 411007, India
| | - Yogesh S. Shouche
- Microbial Culture Collection, National Centre for Cell Science, Pune, Maharastra 411007, India
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Thomas P, Sekhar AC, Upreti R, Mujawar MM, Pasha SS. Optimization of single plate-serial dilution spotting (SP-SDS) with sample anchoring as an assured method for bacterial and yeast cfu enumeration and single colony isolation from diverse samples. ACTA ACUST UNITED AC 2015; 8:45-55. [PMID: 28352572 PMCID: PMC4980700 DOI: 10.1016/j.btre.2015.08.003] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 07/28/2015] [Accepted: 08/05/2015] [Indexed: 11/28/2022]
Abstract
SP-SDS forms a simple tool for bacterial cfu estimation for samples with unknown cfu. Prime recommendation of anchoring specimens to fixed initial OD or a standard base. Six serial dilutions of 20 μl each applied per 9-cm plate followed by manual counting. Suits pure and mixed bacterial stocks, spores, yeasts and composite samples. Superior to alternate techniques like track-dilution, drop-plating or drop-spotting.
We propose a simple technique for bacterial and yeast cfu estimations from diverse samples with no prior idea of viable counts, designated as single plate-serial dilution spotting (SP-SDS) with the prime recommendation of sample anchoring (100 stocks). For pure cultures, serial dilutions were prepared from 0.1 OD (100) stock and 20 μl aliquots of six dilutions (101–106) were applied as 10–15 micro-drops in six sectors over agar-gelled medium in 9-cm plates. For liquid samples 100–105 dilutions, and for colloidal suspensions and solid samples (10% w/v), 101–106 dilutions were used. Following incubation, at least one dilution level yielded 6–60 cfu per sector comparable to the standard method involving 100 μl samples. Tested on diverse bacteria, composite samples and Saccharomyces cerevisiae, SP-SDS offered wider applicability over alternative methods like drop-plating and track-dilution for cfu estimation, single colony isolation and culture purity testing, particularly suiting low resource settings.
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Key Words
- Agricultural biotechnology
- CNA, cetrimide- nalixic acid- agar
- Environmental biotechnology
- Food microbiology
- NA, nutrient agar
- NB, nutrient broth
- OD, optical density
- PDA, potato dextrose agar
- PP, polypropylene bag
- PS, peptone-salt
- Pour-plating
- SATS, spotting- and- tilt- spreading
- SP-SDS, single plate-serial dilution spotting
- Spread-plating
- cfu Estimation
- cfu, colony forming units
- tmtc, too many to count
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Affiliation(s)
- Pious Thomas
- Division of Biotechnology, Indian Institute of Horticultural Research, Hessaraghatta Lake, Bangalore 560089, India
| | - Aparna C Sekhar
- Division of Biotechnology, Indian Institute of Horticultural Research, Hessaraghatta Lake, Bangalore 560089, India
| | - Reshmi Upreti
- Division of Biotechnology, Indian Institute of Horticultural Research, Hessaraghatta Lake, Bangalore 560089, India
| | - Mohammad M Mujawar
- Division of Biotechnology, Indian Institute of Horticultural Research, Hessaraghatta Lake, Bangalore 560089, India
| | - Sadiq S Pasha
- Division of Biotechnology, Indian Institute of Horticultural Research, Hessaraghatta Lake, Bangalore 560089, India
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45
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Hori T, Aoyagi T, Itoh H, Narihiro T, Oikawa A, Suzuki K, Ogata A, Friedrich MW, Conrad R, Kamagata Y. Isolation of microorganisms involved in reduction of crystalline iron(III) oxides in natural environments. Front Microbiol 2015; 6:386. [PMID: 25999927 PMCID: PMC4419728 DOI: 10.3389/fmicb.2015.00386] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 04/15/2015] [Indexed: 11/13/2022] Open
Abstract
Reduction of crystalline Fe(III) oxides is one of the most important electron sinks for organic compound oxidation in natural environments. Yet the limited number of isolates makes it difficult to understand the physiology and ecological impact of the microorganisms involved. Here, two-stage cultivation was implemented to selectively enrich and isolate crystalline iron(III) oxide reducing microorganisms in soils and sediments. Firstly, iron reducers were enriched and other untargeted eutrophs were depleted by 2-years successive culture on a crystalline ferric iron oxide (i.e., goethite, lepidocrocite, hematite, or magnetite) as electron acceptor. Fifty-eight out of 136 incubation conditions allowed the continued existence of microorganisms as confirmed by PCR amplification. High-throughput Illumina sequencing and clone library analysis based on 16S rRNA genes revealed that the enrichment cultures on each of the ferric iron oxides contained bacteria belonging to the Deltaproteobacteria (mainly Geobacteraceae), followed by Firmicutes and Chloroflexi, which also comprised most of the operational taxonomic units (OTUs) identified. Venn diagrams indicated that the core OTUs enriched with all of the iron oxides were dominant in the Geobacteraceae while each type of iron oxides supplemented selectively enriched specific OTUs in the other phylogenetic groups. Secondly, 38 enrichment cultures including novel microorganisms were transferred to soluble-iron(III) containing media in order to stimulate the proliferation of the enriched iron reducers. Through extinction dilution-culture and single colony isolation, six strains within the Deltaproteobacteria were finally obtained; five strains belonged to the genus Geobacter and one strain to Pelobacter. The 16S rRNA genes of these isolates were 94.8-98.1% identical in sequence to cultured relatives. All the isolates were able to grow on acetate and ferric iron but their physiological characteristics differed considerably in terms of growth rate. Thus, the novel strategy allowed to enrich and isolate novel iron(III) reducers that were able to thrive by reducing crystalline ferric iron oxides.
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Affiliation(s)
- Tomoyuki Hori
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology Tsukuba, Japan
| | - Tomo Aoyagi
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology Tsukuba, Japan
| | - Hideomi Itoh
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology Sapporo, Japan
| | - Takashi Narihiro
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology Tsukuba, Japan
| | - Azusa Oikawa
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology Sapporo, Japan
| | - Kiyofumi Suzuki
- Methane Hydrate Research & Development Division, Japan Oil, Gas and Metals National Corporation Chiba, Japan
| | - Atsushi Ogata
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology Tsukuba, Japan
| | - Michael W Friedrich
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry and MARUM, University of Bremen Bremen, Germany
| | - Ralf Conrad
- Max Planck Institute for Terrestrial Microbiology Marburg, Germany
| | - Yoichi Kamagata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology Tsukuba, Japan
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46
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Richards MA, Cassen V, Heavner BD, Ajami NE, Herrmann A, Simeonidis E, Price ND. MediaDB: a database of microbial growth conditions in defined media. PLoS One 2014; 9:e103548. [PMID: 25098325 PMCID: PMC4123892 DOI: 10.1371/journal.pone.0103548] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 06/30/2014] [Indexed: 01/24/2023] Open
Abstract
Isolating pure microbial cultures and cultivating them in the laboratory on defined media is used to more fully characterize the metabolism and physiology of organisms. However, identifying an appropriate growth medium for a novel isolate remains a challenging task. Even organisms with sequenced and annotated genomes can be difficult to grow, despite our ability to build genome-scale metabolic networks that connect genomic data with metabolic function. The scientific literature is scattered with information about defined growth media used successfully for cultivating a wide variety of organisms, but to date there exists no centralized repository to inform efforts to cultivate less characterized organisms by bridging the gap between genomic data and compound composition for growth media. Here we present MediaDB, a manually curated database of defined media that have been used for cultivating organisms with sequenced genomes, with an emphasis on organisms with metabolic network models. The database is accessible online, can be queried by keyword searches or downloaded in its entirety, and can generate exportable individual media formulation files. The data assembled in MediaDB facilitate comparative studies of organism growth media, serve as a starting point for formulating novel growth media, and contribute to formulating media for in silico investigation of metabolic networks. MediaDB is freely available for public use at https://mediadb.systemsbiology.net.
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Affiliation(s)
- Matthew A. Richards
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Victor Cassen
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Benjamin D. Heavner
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Nassim E. Ajami
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Andrea Herrmann
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Evangelos Simeonidis
- Institute for Systems Biology, Seattle, Washington, United States of America
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Nathan D. Price
- Institute for Systems Biology, Seattle, Washington, United States of America
- * E-mail:
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Niu D, Tian K, Prior BA, Wang M, Wang Z, Lu F, Singh S. Highly efficient L-lactate production using engineered Escherichia coli with dissimilar temperature optima for L-lactate formation and cell growth. Microb Cell Fact 2014; 13:78. [PMID: 24884499 PMCID: PMC4075936 DOI: 10.1186/1475-2859-13-78] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 05/11/2014] [Indexed: 11/10/2022] Open
Abstract
UNLABELLED L-Lactic acid, one of the most important chiral molecules and organic acids, is produced via pyruvate from carbohydrates in diverse microorganisms catalyzed by an NAD+-dependent L-lactate dehydrogenase. Naturally, Escherichia coli does not produce L-lactate in noticeable amounts, but can catabolize it via a dehydrogenation reaction mediated by an FMN-dependent L-lactate dehydrogenase. In aims to make the E. coli strain to produce L-lactate, three L-lactate dehydrogenase genes from different bacteria were cloned and expressed. The L-lactate producing strains, 090B1 (B0013-070, ΔldhA::diflldD::Pldh-ldhLca), 090B2 (B0013-070, ΔldhA::diflldD::Pldh-ldhStrb) and 090B3 (B0013-070, ΔldhA::diflldD::Pldh-ldhBcoa) were developed from a previously developed D-lactate over-producing strain, E. coli strain B0013-070 (ack-ptappspflBdldpoxBadhEfrdA) by: (1) deleting ldhA to block D-lactate formation, (2) deleting lldD to block the conversion of L-lactate to pyruvate, and (3) expressing an L-lactate dehydrogenase (L-LDH) to convert pyruvate to L-lactate under the control of the ldhA promoter. Fermentation tests were carried out in a shaking flask and in a 25-l bioreactor. Strains 090B1, 090B2 or 090B3 were shown to metabolize glucose to L-lactate instead of D-lactate. However, L-lactate yield and cell growth rates were significantly different among the metabolically engineered strains which can be attributed to a variation between temperature optimum for cell growth and temperature optimum for enzymatic activity of individual L-LDH. In a temperature-shifting fermentation process (cells grown at 37°C and L-lactate formed at 42°C), E. coli 090B3 was able to produce 142.2 g/l of L-lactate with no more than 1.2 g/l of by-products (mainly acetate, pyruvate and succinate) accumulated. In conclusion, the production of lactate by E. coli is limited by the competition relationship between cell growth and lactate synthesis. Enzymatic properties, especially the thermodynamics of an L-LDH can be effectively used as a factor to regulate a metabolic pathway and its metabolic flux for efficient L-lactate production. HIGHLIGHTS The enzymatic thermodynamics was used as a tool for metabolic regulation. Minimizing the activity of L-lactate dehydrogenase in growth phase improved biomass accumulation. Maximizing the activity of L-lactate dehydrogenase improved lactate productivity in production phase.
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Affiliation(s)
- Dandan Niu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education & The College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China.
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48
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Prakash O, Munot H, Nimonkar Y, Sharma M, Kumbhare S, Shouche YS. Description of Pelistega indica sp. nov., isolated from human gut. Int J Syst Evol Microbiol 2014; 64:1389-1394. [DOI: 10.1099/ijs.0.059782-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, motile, non-spore-forming, coccoid bacterium was isolated from a stool sample of a healthy human subject and formed cream colour colonies on tryptic soy agar. Almost full-length (1500 bp) small subunit rRNA (16S rRNA) gene sequences were generated and a similarity search was conducted by blast. The results of the similarity search indicated that the bacterium belongs to the class
Betaproteobacteria
, family
Alcaligenaceae
. It showed maximum sequence similarity (96.5 %) with
Pelistega europaea
CCUG 39967T followed by
Advenella mimigardefordensis
DSM 17166T (96.1 %) and
Taylorella asinigenitalis
LMG 19572T (95.3 %). The DNA G+C content of strain HM-7T was 42 mol%. Strain HM-7T contained C14 : 0, C16 : 0, C16 : 0 3-OH and C18 : 0 as the dominant fatty acids. Morphological, physiological and biochemical data also indicated that strain HM-7T represents a member of the genus
Pelistega
, but at the same time distinguished it from
Pelistega europaea
CCUG 39967T, the only species of the genus with a validly published name. Based on polyphasic characterization we conclude that the bacterium represents a novel species of the genus
Pelistega
and propose the name Pelistega indica sp. nov., with strain HM-7T ( = MCC 2185T = DSM 27484T) as the type strain of the species.
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Affiliation(s)
- Om Prakash
- Microbial Culture Collection, National Centre for Cell Science, Pune, Maharastra 411007, India
| | - Hitendra Munot
- Microbial Culture Collection, National Centre for Cell Science, Pune, Maharastra 411007, India
| | - Yogesh Nimonkar
- Microbial Culture Collection, National Centre for Cell Science, Pune, Maharastra 411007, India
| | - Madhu Sharma
- Microbial Culture Collection, National Centre for Cell Science, Pune, Maharastra 411007, India
| | - Shreyas Kumbhare
- Microbial Culture Collection, National Centre for Cell Science, Pune, Maharastra 411007, India
| | - Yogesh S. Shouche
- Microbial Culture Collection, National Centre for Cell Science, Pune, Maharastra 411007, India
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Vaz-Moreira I, Nunes OC, Manaia CM. Bacterial diversity and antibiotic resistance in water habitats: searching the links with the human microbiome. FEMS Microbiol Rev 2014; 38:761-78. [PMID: 24484530 DOI: 10.1111/1574-6976.12062] [Citation(s) in RCA: 190] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 12/31/2013] [Accepted: 01/10/2014] [Indexed: 12/14/2022] Open
Abstract
Water is one of the most important bacterial habitats on Earth. As such, water represents also a major way of dissemination of bacteria between different environmental compartments. Human activities led to the creation of the so-called urban water cycle, comprising different sectors (waste, surface, drinking water), among which bacteria can hypothetically be exchanged. Therefore, bacteria can be mobilized between unclean water habitats (e.g. wastewater) and clean or pristine water environments (e.g. disinfected and spring drinking water) and eventually reach humans. In addition, bacteria can also transfer mobile genetic elements between different water types, other environments (e.g. soil) and humans. These processes may involve antibiotic resistant bacteria and antibiotic resistance genes. In this review, the hypothesis that some bacteria may share different water compartments and be also hosted by humans is discussed based on the comparison of the bacterial diversity in different types of water and with the human-associated microbiome. The role of such bacteria as potential disseminators of antibiotic resistance and the inference that currently only a small fraction of the clinically relevant antibiotic resistome may be known is discussed.
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Affiliation(s)
- Ivone Vaz-Moreira
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa/Porto, Rua Dr. António Bernardino Almeida, Porto, Portugal
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50
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Bringing the gut microbiota into focus through microbial culture: recent progress and future perspective. Curr Opin Microbiol 2013; 16:625-9. [PMID: 24148301 DOI: 10.1016/j.mib.2013.09.008] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 09/26/2013] [Indexed: 02/07/2023]
Abstract
Ever-more-powerful 'omics'-based technologies are allowing us to pry deeper and more clearly into the workings of the human gut microbiota. Culture of the component microbes has fallen somewhat behind these efforts for a number of reasons, not least of which being the perceived difficulty in growing microbial species that have previously eluded all efforts to tame them. However, recent advances in the field are beginning to bring success in this area, allowing holistic study of microbes and microbial communities in defined systems. Innovative approaches to the culture and study of the human microbiota will ultimately guide medical practice, as the importance of a robust gut microbial ecosystem in the maintenance of health is increasingly realized.
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