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Nucci A, Janaszkiewicz J, Rocha EPC, Rendueles O. Emergence of novel non-aggregative variants under negative frequency-dependent selection in Klebsiella variicola. MICROLIFE 2023; 4:uqad038. [PMID: 37781688 PMCID: PMC10540941 DOI: 10.1093/femsml/uqad038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/05/2023] [Accepted: 09/09/2023] [Indexed: 10/03/2023]
Abstract
Klebsiella variicola is an emergent human pathogen causing diverse infections, some of which in the urinary tract. However, little is known about the evolution and maintenance of genetic diversity in this species, the molecular mechanisms and their population dynamics. Here, we characterized the emergence of a novel rdar-like (rough and dry) morphotype which is contingent both on the genetic background and the environment. We show that mutations in either the nitrogen assimilation control gene (nac) or the type III fimbriae regulator, mrkH, suffice to generate rdar-like colonies. These morphotypes are primarily selected for the reduced inter-cellular aggregation as a result of MrkH loss-of-function which reduces type 3 fimbriae expression. Additionally, these clones also display increased growth rate and reduced biofilm formation. Direct competitions between rdar and wild type clones show that mutations in mrkH provide large fitness advantages. In artificial urine, the morphotype is under strong negative frequency-dependent selection and can socially exploit wild type strains. An exhaustive search for mrkH mutants in public databases revealed that ca 8% of natural isolates analysed had a truncated mrkH gene many of which were due to insertions of IS elements, including a reported clinical isolate with rdar morphology. These strains were rarely hypermucoid and often isolated from human, mostly from urine and blood. The decreased aggregation of these mutants could have important clinical implications as we hypothesize that such clones could better disperse within the host allowing colonisation of other body sites and potentially leading to systemic infections.
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Affiliation(s)
- Amandine Nucci
- Institut Pasteur, Université Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, F-75015, Paris, France
| | - Juliette Janaszkiewicz
- Institut Pasteur, Université Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, F-75015, Paris, France
| | - Eduardo P C Rocha
- Institut Pasteur, Université Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, F-75015, Paris, France
| | - Olaya Rendueles
- Institut Pasteur, Université Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, F-75015, Paris, France
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2
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Vasconcelos MA, da Silva BR, Andrade AL, de Azevedo Pinheiro A, Evaristo FFV, Arruda FVS, Lorenzón EN, Cilli EM, Teixeira EH. Antimicrobial and Antibiofilm Activity of Synthetic Peptide [W7]KR12-KAEK Against Enterococcus faecalis Strains. Curr Microbiol 2023; 80:325. [PMID: 37606794 DOI: 10.1007/s00284-023-03445-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 08/07/2023] [Indexed: 08/23/2023]
Abstract
The emergence of infections caused by microorganisms in the oral cavity and increasing concerns regarding the use of antibiotics have resulted in the development of novel antimicrobial molecules, such as antimicrobial synthetic peptides. The purpose of this study was to evaluate the antimicrobial and antibiofilm activities of the native peptide KR-12 and its derivative, the synthetic peptide [W7]KR12-KAEK, against planktonic and biofilms Enterococcus faecalis strains. The methods used to evaluate the antimicrobial activity in planktonic cultures include minimum inhibitory concentration and minimum bactericidal concentration assays. The effects of [W7]KR12-KAEK on biofilm formation and mature biofilms were evaluated by quantifying biomass (crystal violet staining) and counting colony-forming units. Structural assessments of the biofilms and cellular morphological changes were performed using scanning electron microscopy. Peptide [W7]KR12-KAEK showed potential antimicrobial activity against planktonic cells. Interestingly, the native peptide KR-12 showed no antimicrobial activity. Moreover, it inhibited biofilm formation and disrupted the mature biofilms of E. faecalis strains. These results suggest that [W7]KR12-KAEK may be a potential molecule for the development of auxiliary antimicrobial therapies against oral infections.
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Affiliation(s)
- Mayron Alves Vasconcelos
- Laboratório Integrado de Biomoléculas, Departamento de Patologia e Medicina Legal, Universidade Federal do Ceará, Fortaleza, CE, Brazil
- Universidade do Estado de Minas Gerais, Unidade de Divinópolis, Divinópolis, MG, Brazil
- Faculdade de Educação de Itapipoca (FACEDI), Universidade Estadual do Ceará, Itapipoca, CE, Brazil
| | - Bruno Rocha da Silva
- Laboratório Integrado de Biomoléculas, Departamento de Patologia e Medicina Legal, Universidade Federal do Ceará, Fortaleza, CE, Brazil
- Universidade de Fortaleza (UNIFOR), Fortaleza, CE, Brazil
| | - Alexandre Lopes Andrade
- Laboratório Integrado de Biomoléculas, Departamento de Patologia e Medicina Legal, Universidade Federal do Ceará, Fortaleza, CE, Brazil
| | - Aryane de Azevedo Pinheiro
- Laboratório Integrado de Biomoléculas, Departamento de Patologia e Medicina Legal, Universidade Federal do Ceará, Fortaleza, CE, Brazil
| | | | - Francisco Vassiliepe Sousa Arruda
- Laboratório Integrado de Biomoléculas, Departamento de Patologia e Medicina Legal, Universidade Federal do Ceará, Fortaleza, CE, Brazil
- UNINTA, Sobral, CE, Brazil
| | | | - Eduardo Maffud Cilli
- Instituto de Química, Universidade Estadual Paulista (UNESP), Araraquara, SP, Brazil
| | - Edson Holanda Teixeira
- Laboratório Integrado de Biomoléculas, Departamento de Patologia e Medicina Legal, Universidade Federal do Ceará, Fortaleza, CE, Brazil.
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3
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Kang Y, Wu H, Zhang Y, Wu Q, Guan Q, Lu K, Lin Y. Differential distribution patterns and assembly processes of soil microbial communities under contrasting vegetation types at distinctive altitudes in the Changbai Mountain. Front Microbiol 2023; 14:1152818. [PMID: 37333641 PMCID: PMC10272400 DOI: 10.3389/fmicb.2023.1152818] [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] [Received: 01/28/2023] [Accepted: 03/29/2023] [Indexed: 06/20/2023] Open
Abstract
Diversity patterns and community assembly of soil microorganisms are essential for understanding soil biodiversity and ecosystem processes. Investigating the impacts of environmental factors on microbial community assembly is crucial for comprehending the functions of microbial biodiversity and ecosystem processes. However, these issues remain insufficiently investigated in related studies despite their fundamental significance. The present study aimed to assess the diversity and assembly of soil bacterial and fungal communities to altitude and soil depth variations in mountain ecosystems by using 16S and ITS rRNA gene sequence analyses. In addition, the major roles of environmental factors in determining soil microbial communities and assembly processes were further investigated. The results showed a U-shaped pattern of the soil bacterial diversity at 0-10 cm soil depth along altitudes, reaching a minimum value at 1800 m, while the fungal diversity exhibited a monotonically decreasing trend with increasing altitude. At 10-20 cm soil depth, the soil bacterial diversity showed no apparent changes along altitudinal gradients, while the fungal Chao1 and phylogenetic diversity (PD) indices exhibited hump-shaped patterns with increasing altitude, reaching a maximum value at 1200 m. Soil bacterial and fungal communities were distinctively distributed with altitude at the same depth of soil, and the spatial turnover rates in fungi was greater than in bacteria. Mantel tests suggested soil physiochemical and climate variables significantly correlated with the β diversity of microbial community at two soil depths, suggesting both soil and climate heterogeneity contributed to the variation of bacterial and fungal community. Correspondingly, a novel phylogenetic null model analysis demonstrated that the community assembly of soil bacterial and fungal communities were dominated by deterministic and stochastic processes, respectively. The assembly processes of bacterial community were significantly related to the soil DOC and C:N ratio, while the fungal community assembly processes were significantly related to the soil C:N ratio. Our results provide a new perspective to assess the responses of soil microbial communities to variations with altitude and soil depth.
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Affiliation(s)
- Yujuan Kang
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Haitao Wu
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Yifan Zhang
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- College of Tourism and Geography Sciences, Jilin Normal University, Siping, China
| | - Qiong Wu
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- College of Tourism and Geography Sciences, Jilin Normal University, Siping, China
| | - Qiang Guan
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Kangle Lu
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Yiling Lin
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
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Liu H, Li FY, Liu J, Shi C, Tang K, Yang Q, Liu Y, Fu Q, Gao X, Wang N, Guo W. The reciprocal changes in dominant species with complete metabolic functions explain the decoupling phenomenon of microbial taxonomic and functional composition in a grassland. Front Microbiol 2023; 14:1113157. [PMID: 37007478 PMCID: PMC10060659 DOI: 10.3389/fmicb.2023.1113157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 02/22/2023] [Indexed: 03/18/2023] Open
Abstract
The decoupling of microbial functional and taxonomic components refers to the phenomenon that a drastic change in microbial taxonomic composition leads to no or only a gentle change in functional composition. Although many studies have identified this phenomenon, the mechanisms underlying it are still unclear. Here we demonstrate, using metagenomics data from a steppe grassland soil under different grazing and phosphorus addition treatments, that there is no “decoupling” in the variation of taxonomic and metabolic functional composition of the microbial community within functional groups at species level. In contrast, the high consistency and complementarity between the abundance and functional gene diversity of two dominant species made metabolic functions unaffected by grazing and phosphorus addition. This complementarity between the two dominant species shapes a bistability pattern that differs from functional redundancy in that only two species cannot form observable redundancy in a large microbial community. In other words, the “monopoly” of metabolic functions by the two most abundant species leads to the disappearance of functional redundancy. Our findings imply that for soil microbial communities, the impact of species identity on metabolic functions is much greater than that of species diversity, and it is more important to monitor the dynamics of key dominant microorganisms for accurately predicting the changes in the metabolic functions of the ecosystems.
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Affiliation(s)
- Huaiqiang Liu
- Ministry of Education Key Laboratory of Ecology and Resource Use on the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Frank Yonghong Li
- Ministry of Education Key Laboratory of Ecology and Resource Use on the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
- Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education of China, Hohhot, China
- *Correspondence: Frank Yonghong Li,
| | - Jiayue Liu
- Ministry of Education Key Laboratory of Ecology and Resource Use on the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Chunjun Shi
- Ministry of Education Key Laboratory of Ecology and Resource Use on the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Kuanyan Tang
- Ministry of Education Key Laboratory of Ecology and Resource Use on the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Qianhui Yang
- Ministry of Education Key Laboratory of Ecology and Resource Use on the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Yu Liu
- Ministry of Education Key Laboratory of Ecology and Resource Use on the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Qiang Fu
- Ministry of Education Key Laboratory of Ecology and Resource Use on the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Xiaotian Gao
- Ministry of Education Key Laboratory of Ecology and Resource Use on the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Ning Wang
- Ministry of Education Key Laboratory of Ecology and Resource Use on the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Wei Guo
- Ministry of Education Key Laboratory of Ecology and Resource Use on the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
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5
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Chen Y, Lyu Y, Zhang J, Li Q, Lyu L, Zhou Y, Kong J, Zeng X, Zhang S, Li J. Riddles of Lost City: Chemotrophic Prokaryotes Drives Carbon, Sulfur, and Nitrogen Cycling at an Extinct Cold Seep, South China Sea. Microbiol Spectr 2023; 11:e0333822. [PMID: 36511717 PMCID: PMC9927161 DOI: 10.1128/spectrum.03338-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 11/21/2022] [Indexed: 12/15/2022] Open
Abstract
Deep-sea cold seeps are one of the most productive ecosystems that sustained by hydrocarbons carried by the fluid. Once the seep fluid ceases, the thriving autotrophic communities die out, terming as the extinct seep. But heterotrophic fauna can still survive even for thousands of years. The critical role of prokaryotes in active seeps are well defined, but their functions in extinct seeps are poorly understood to date. Here, we clarified the diversity, taxonomic specificity, interspecies correlation, and metabolic profiles of sediment prokaryotes at an extinct seep site of Haima cold seep, South China Sea. Alpha diversity of archaea significantly increased, while that of bacteria remained unchanged in extinct seep compared to active seep. However, archaea composition did not differ significantly at extinct seep from active or nonseep sites based on weighted-unifrac dissimilarity, while bacteria composition exhibited significant difference. Distribution of archaea and bacteria showed clear specificity to extinct seeps, indicating the unique life strategies here. Prokaryotes might live chemolithoautotrophically on cycling of inorganic carbon, sulfur, and nitrogen, or chemoorganotrophically on recycling of hydrocarbons. Notably, many of the extinct seep specific species and networked keystone lineages are classified as Proteobacteria. Regarding the functional diversity and metabolic flexibility of this clade, Proteobacteria is supposed to integrate the geochemical cycles and play a critical role in energy and resource supplement for microbiome in extinct seep. Collectively, our findings shed lights on the microbial ecology and functional diversity in extinct seeps, providing new understanding of biogeochemical cycling after fluid cessation. IMPORTANCE This research paper uncovered the potential mechanisms for microbiota mediated geochemical cycling in extinct cold seep, advancing our understanding in deep sea microbiology ecology.
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Affiliation(s)
- Yu Chen
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong, People’s Republic of China
| | - Yuanjiao Lyu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, People’s Republic of China
| | - Jian Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, People’s Republic of China
| | - Qiqi Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, People’s Republic of China
| | - Lina Lyu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, People’s Republic of China
| | - Yingli Zhou
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong, People’s Republic of China
| | - Jie Kong
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong, People’s Republic of China
| | - Xinyang Zeng
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong, People’s Republic of China
| | - Si Zhang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong, People’s Republic of China
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, People’s Republic of China
| | - Jie Li
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong, People’s Republic of China
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, People’s Republic of China
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6
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Response of Intestinal Microbiota of Tiger Puffer ( Takifugu rubripes) to the Fish Oil Finishing Strategy. Microorganisms 2023; 11:microorganisms11010208. [PMID: 36677500 PMCID: PMC9862291 DOI: 10.3390/microorganisms11010208] [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] [Received: 12/01/2022] [Revised: 01/03/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
The fish oil finishing (FOF) strategy, that is, re-feeding fish with fish oil (FO)-based diet after a certain period of feeding with alternative lipid source-based diets. On tiger puffer, the present study investigated the response of intestinal microbiota to FOF. Fish were fed four diets based on FO, soybean oil, palm oil and beef tallow as lipid sources, respectively, firstly for 50 days (growing-out period), and then fed the FO-based diet for 30 more days (FOF period). The results showed that dietary terrestrially sourced oils impaired the intestinal function in the growing-out period. However, the activities of amylase, trypsin and anti-oxidative enzymes (SOD, CAT, T-AOC), as well as gene expression of inflammatory cytokines (IL-1β, TNF-α, TGF-β) and tight junction protein (Claudin4, Claudin7, Claudin18, JAM, ZO-1) in the intestine were significantly recovered by FOF. The 16S rDNA sequencing analysis showed that FOF improved the similarity of bacterial community among the groups. The MetaStat analysis confirmed that FOF regulated the abundance of butyric acid-producing bacteria (Lachnospiraceae, Eubacterium, Butyricicoccus, Clostridium and Roseburia) and bacteria related to digestion and absorption (Sphingomonas, Romboutsia and Brevibacillus). In conclusion, FOF can recover the intestine function. The intestinal microbiota probably participated in and played a key role in the recovery process.
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7
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Lin Y, Xu X, Maróti G, Strube ML, Kovács ÁT. Adaptation and phenotypic diversification of Bacillus thuringiensis biofilm are accompanied by fuzzy spreader morphotypes. NPJ Biofilms Microbiomes 2022; 8:27. [PMID: 35418164 PMCID: PMC9007996 DOI: 10.1038/s41522-022-00292-1] [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: 09/03/2021] [Accepted: 03/19/2022] [Indexed: 11/12/2022] Open
Abstract
Bacillus cereus group (Bacillus cereus sensu lato) has a diverse ecology, including various species that produce biofilms on abiotic and biotic surfaces. While genetic and morphological diversification enables the adaptation of multicellular communities, this area remains largely unknown in the Bacillus cereus group. In this work, we dissected the experimental evolution of Bacillus thuringiensis 407 Cry- during continuous recolonization of plastic beads. We observed the evolution of a distinct colony morphotype that we named fuzzy spreader (FS) variant. Most multicellular traits of the FS variant displayed higher competitive ability versus the ancestral strain, suggesting an important role for diversification in the adaptation of B. thuringiensis to the biofilm lifestyle. Further genetic characterization of FS variant revealed the disruption of a guanylyltransferase gene by an insertion sequence (IS) element, which could be similarly observed in the genome of a natural isolate. The evolved FS and the deletion mutant in the guanylyltransferase gene (Bt407ΔrfbM) displayed similarly altered aggregation and hydrophobicity compared to the ancestor strain, suggesting that the adaptation process highly depends on the physical adhesive forces.
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Affiliation(s)
- Yicen Lin
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Xinming Xu
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Gergely Maróti
- Institute of Plant Biology, Biological Research Center, ELKH, 6726, Szeged, Hungary
| | - Mikael Lenz Strube
- Bacterial Ecophysiology and Biotechnology Group, DTU Bioengineering, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, 2800, Lyngby, Denmark.
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8
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Sathiyamoorthi E, Faleye OS, Lee JH, Raj V, Lee J. Antibacterial and Antibiofilm Activities of Chloroindoles Against Vibrio parahaemolyticus. Front Microbiol 2021; 12:714371. [PMID: 34408739 PMCID: PMC8365150 DOI: 10.3389/fmicb.2021.714371] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 07/13/2021] [Indexed: 01/05/2023] Open
Abstract
Vibrio parahaemolyticus is a food-borne pathogen recognized as the prominent cause of seafood-borne gastroenteritis globally, necessitating novel therapeutic strategies. This study examined the antimicrobial and antivirulence properties of indole and 16 halogenated indoles on V. parahaemolyticus. Among them, 4-chloroindole, 7-chloroindole, 4-iodoindole, and 7-iodoindole effectively inhibited planktonic cell growth, biofilm formation, bacterial motility, fimbrial activity, hydrophobicity, protease activity, and indole production. Specifically, 4-chloroindole at 20 μg/mL inhibited more than 80% of biofilm formation with a minimum inhibitory concentration (MIC) of 50 μg/mL against V. parahaemolyticus and Vibrio harveyi. In contrast, 7-chloroindole inhibited biofilm formation without affecting planktonic cell growth with a MIC of 200 μg/mL. Both chlorinated indoles caused visible damage to the cell membrane, and 4-chloroindole at 100 μg/mL had a bactericidal effect on V. parahaemolyticus within 30 min treatment, which is superior to the effect of tetracycline at the same dose. The quantitative structure-activity relationship (QSAR) analyses revealed that chloro and bromo at positions 4 or 5 of the indole are essential for eradicating the growth of V. parahaemolyticus. These results suggest that halogenated indoles have potential use in antimicrobial and antivirulence strategies against Vibrio species.
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Affiliation(s)
| | | | | | | | - Jintae Lee
- School of Chemical Engineering, Yeungnam University, Gyeongsan, South Korea
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9
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Melkonian C, Fillinger L, Atashgahi S, da Rocha UN, Kuiper E, Olivier B, Braster M, Gottstein W, Helmus R, Parsons JR, Smidt H, van der Waals M, Gerritse J, Brandt BW, Röling WFM, Molenaar D, van Spanning RJM. High biodiversity in a benzene-degrading nitrate-reducing culture is sustained by a few primary consumers. Commun Biol 2021; 4:530. [PMID: 33953314 PMCID: PMC8099898 DOI: 10.1038/s42003-021-01948-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 03/03/2021] [Indexed: 01/04/2023] Open
Abstract
A key question in microbial ecology is what the driving forces behind the persistence of large biodiversity in natural environments are. We studied a microbial community with more than 100 different types of species which evolved in a 15-years old bioreactor with benzene as the main carbon and energy source and nitrate as the electron acceptor. Using genome-centric metagenomics plus metatranscriptomics, we demonstrate that most of the community members likely feed on metabolic left-overs or on necromass while only a few of them, from families Rhodocyclaceae and Peptococcaceae, are candidates to degrade benzene. We verify with an additional succession experiment using metabolomics and metabarcoding that these few community members are the actual drivers of benzene degradation. As such, we hypothesize that high species richness is maintained and the complexity of a natural community is stabilized in a controlled environment by the interdependencies between the few benzene degraders and the rest of the community members, ultimately resulting in a food web with different trophic levels.
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Affiliation(s)
- Chrats Melkonian
- Department of Molecular Cell Biology, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
| | - Lucas Fillinger
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Ulisses Nunes da Rocha
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Esther Kuiper
- Department of Molecular Cell Biology, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Brett Olivier
- Department of Molecular Cell Biology, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Martin Braster
- Department of Molecular Cell Biology, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Willi Gottstein
- Department of Molecular Cell Biology, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Rick Helmus
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - John R Parsons
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | | | - Jan Gerritse
- Unit Subsurface and Groundwater Systems, Deltares, Utrecht, The Netherlands
| | - Bernd W Brandt
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam, University of Amsterdam and Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Wilfred F M Röling
- Department of Molecular Cell Biology, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Douwe Molenaar
- Department of Molecular Cell Biology, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Rob J M van Spanning
- Department of Molecular Cell Biology, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
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10
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Zlatkov N, Nadeem A, Uhlin BE, Wai SN. Eco-evolutionary feedbacks mediated by bacterial membrane vesicles. FEMS Microbiol Rev 2021; 45:fuaa047. [PMID: 32926132 PMCID: PMC7968517 DOI: 10.1093/femsre/fuaa047] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 09/11/2020] [Indexed: 12/27/2022] Open
Abstract
Bacterial membrane vesicles (BMVs) are spherical extracellular organelles whose cargo is enclosed by a biological membrane. The cargo can be delivered to distant parts of a given habitat in a protected and concentrated manner. This review presents current knowledge about BMVs in the context of bacterial eco-evolutionary dynamics among different environments and hosts. BMVs may play an important role in establishing and stabilizing bacterial communities in such environments; for example, bacterial populations may benefit from BMVs to delay the negative effect of certain evolutionary trade-offs that can result in deleterious phenotypes. BMVs can also perform ecosystem engineering by serving as detergents, mediators in biochemical cycles, components of different biofilms, substrates for cross-feeding, defense systems against different dangers and enzyme-delivery mechanisms that can change substrate availability. BMVs further contribute to bacteria as mediators in different interactions, with either other bacterial species or their hosts. In short, BMVs extend and deliver phenotypic traits that can have ecological and evolutionary value to both their producers and the ecosystem as a whole.
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Affiliation(s)
- Nikola Zlatkov
- Department of Molecular Biology and The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, SE-90187 Umeå, Sweden
| | - Aftab Nadeem
- Department of Molecular Biology and The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, SE-90187 Umeå, Sweden
| | - Bernt Eric Uhlin
- Department of Molecular Biology and The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, SE-90187 Umeå, Sweden
| | - Sun Nyunt Wai
- Department of Molecular Biology and The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, SE-90187 Umeå, Sweden
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11
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Ahmed MN, Abdelsamad A, Wassermann T, Porse A, Becker J, Sommer MOA, Høiby N, Ciofu O. The evolutionary trajectories of P. aeruginosa in biofilm and planktonic growth modes exposed to ciprofloxacin: beyond selection of antibiotic resistance. NPJ Biofilms Microbiomes 2020; 6:28. [PMID: 32709907 PMCID: PMC7381665 DOI: 10.1038/s41522-020-00138-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 07/06/2020] [Indexed: 12/22/2022] Open
Abstract
Ciprofloxacin (CIP) is used to treat Pseudomonas aeruginosa biofilm infections. We showed that the pathways of CIP-resistance development during exposure of biofilms and planktonic P. aeruginosa populations to subinhibitory levels of CIP depend on the mode of growth. In the present study, we analyzed CIP-resistant isolates obtained from previous evolution experiments, and we report a variety of evolved phenotypic and genotypic changes that occurred in parallel with the evolution of CIP-resistance. Cross-resistance to beta-lactam antibiotics was associated with mutations in genes involved in cell-wall recycling (ftsZ, murG); and could also be explained by mutations in the TCA cycle (sdhA) genes and in genes involved in arginine catabolism. We found that CIP-exposed isolates that lacked mutations in quorum-sensing genes and acquired mutations in type IV pili genes maintained swarming motility and lost twitching motility, respectively. Evolved CIP-resistant isolates showed high fitness cost in planktonic competition experiments, yet persisted in the biofilm under control conditions, compared with ancestor isolates and had an advantage when exposed to CIP. Their persistence in biofilm competition experiments in spite of their fitness cost in planktonic growth could be explained by their prolonged lag-phase. Interestingly, the set of mutated genes that we identified in these in vitro-evolved CIP-resistant colonies, overlap with a large number of patho-adaptive genes previously reported in P. aeruginosa isolates from cystic fibrosis (CF) patients. This suggests that the antibiotic stress is contributing to the bacterial evolution in vivo, and that adaptive laboratory evolution can be used to predict the in vivo evolutionary trajectories.
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Affiliation(s)
- Marwa N Ahmed
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark.,Department of Microbiology, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Ahmed Abdelsamad
- Department of Genetics, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Tina Wassermann
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
| | - Andreas Porse
- Novo Nordisk Foundation Center for Sustainability, Technical University of Denmark, Lyngby, Denmark
| | - Janna Becker
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Morten O A Sommer
- Novo Nordisk Foundation Center for Sustainability, Technical University of Denmark, Lyngby, Denmark
| | - Niels Høiby
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark.,Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
| | - Oana Ciofu
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark.
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12
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Nghe P, de Vos MGJ, Kingma E, Kogenaru M, Poelwijk FJ, Laan L, Tans SJ. Predicting Evolution Using Regulatory Architecture. Annu Rev Biophys 2020; 49:181-197. [PMID: 32040932 DOI: 10.1146/annurev-biophys-070317-032939] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The limits of evolution have long fascinated biologists. However, the causes of evolutionary constraint have remained elusive due to a poor mechanistic understanding of studied phenotypes. Recently, a range of innovative approaches have leveraged mechanistic information on regulatory networks and cellular biology. These methods combine systems biology models with population and single-cell quantification and with new genetic tools, and they have been applied to a range of complex cellular functions and engineered networks. In this article, we review these developments, which are revealing the mechanistic causes of epistasis at different levels of biological organization-in molecular recognition, within a single regulatory network, and between different networks-providing first indications of predictable features of evolutionary constraint.
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Affiliation(s)
- Philippe Nghe
- Laboratoire de Biochimie, UMR CBI 8231, ESPCI Paris, PSL Research University, 75005 Paris, France
| | - Marjon G J de Vos
- University of Groningen, GELIFES, 9747 AG Groningen, The Netherlands
| | - Enzo Kingma
- Bionanoscience Department, Delft University of Technology, 2629HZ Delft, The Netherlands
| | - Manjunatha Kogenaru
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Frank J Poelwijk
- cBio Center, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Liedewij Laan
- Bionanoscience Department, Delft University of Technology, 2629HZ Delft, The Netherlands
| | - Sander J Tans
- Bionanoscience Department, Delft University of Technology, 2629HZ Delft, The Netherlands.,AMOLF, 1098 XG Amsterdam, The Netherlands;
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13
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Clarke L, Pelin A, Phan M, Wong A. The effect of environmental heterogeneity on the fitness of antibiotic resistance mutations in Escherichia coli. Evol Ecol 2020. [DOI: 10.1007/s10682-019-10027-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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14
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Mojica KDA, Carlson CA, Behrenfeld MJ. Regulation of Low and High Nucleic Acid Fluorescent Heterotrophic Prokaryote Subpopulations and Links to Viral-Induced Mortality Within Natural Prokaryote-Virus Communities. MICROBIAL ECOLOGY 2020; 79:213-230. [PMID: 31161232 DOI: 10.1007/s00248-019-01393-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 05/27/2019] [Indexed: 06/09/2023]
Abstract
Flow cytometric analysis of marine prokaryotes routinely reveals two distinct clusters of heterotrophic cells referred to as high nucleic acid fluorescent (HNA) and low nucleic acid fluorescent (LNA) populations. Evidence suggests that these may represent physiologically and ecologically distinct prokaryote populations. According to the "kill the winner" hypothesis, viral lysis reduces the efficiency of the microbial loop by decreasing the biomass and activity of the most abundant and active members of a population (i.e., competition specialist). Thus, viral-induced mortality may vary according to the physiology of HNA and LNA cells, with implications for the marine carbon cycle. Here, the abundance and production of heterotrophic prokaryotic populations were assessed in the North Atlantic during two phases of the annual plankton cycle and related to bottom-up (i.e., organic carbon variability) and top-down processes (i.e., viral abundance and lytic production). Our results demonstrate that the relative abundance of HNA and LNA heterotrophic cells and heterotrophic prokaryote production vary according to organic carbon variability in the water column, which can be strongly influenced by the physical eddy field (i.e., type of eddy: cyclonic, anticyclonic, or no eddy). In addition, the abundance and lytic production of virus subpopulations were correlated with the cellular production and abundance of heterotrophic HNA and LNA prokaryote communities. Our data suggest group- and activity-specific linkages between hosts and viruses (i.e., HNA-V1 and LNA-V2). Specifically, V1 had a greater contribution to total viral production (i.e., 2.6-fold higher than V2 viruses), similar to their putative host. Finally, we explore potential implications of group- and activity-specific linkages between host and virus groups on the flux of carbon through the microbial food web.
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Affiliation(s)
- Kristina D A Mojica
- Department of Botany and Plant Pathology, Cordley Hall 2082, Oregon State University, Corvallis, OR, 97331-29052, USA.
| | - Craig A Carlson
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA, 93106-6250, USA
| | - Mike J Behrenfeld
- Department of Botany and Plant Pathology, Cordley Hall 2082, Oregon State University, Corvallis, OR, 97331-29052, USA
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15
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Ou W, Hu H, Yang P, Dai J, Ai Q, Zhang W, Zhang Y, Mai K. Dietary daidzein improved intestinal health of juvenile turbot in terms of intestinal mucosal barrier function and intestinal microbiota. FISH & SHELLFISH IMMUNOLOGY 2019; 94:132-141. [PMID: 31461659 DOI: 10.1016/j.fsi.2019.08.059] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 08/20/2019] [Accepted: 08/24/2019] [Indexed: 06/10/2023]
Abstract
A 12-week feeding trial was conducted to investigate the effect of dietary daidzein on the intestinal mucosal barrier function and the intestinal microbiota profile of juvenile turbot (Scophthalmus maximus L.). Three isonitrogenous and isolipidic experimental diets were formulated to contain 0 (FM), 40 (D.40) and 400 (D.400) mg kg-1 daidzein, respectively. Fish fed D.400 had significantly lower growth performance than fish fed D.40. Dietary daidzein significantly increased the feed efficiency, while significantly decreased the feed intake. Daidzein supplementation increased the activity of total anti-oxidative capacity and the gene expression of anti-inflammatory cytokine transforming growth factor-β1, Mucin-2 and tight junction proteins (Tricellulin, Zonula occludens-1 transcript variant 1, Zonula occludens-1 transcript variant 2 and Claudin-like and Occludin), and down-regulated the gene expression of pro-inflammatory cytokines interleukin-1β and tumor necrosis factor-α in the intestine of turbot. Dietary daidzein increased intestinal microbial diversities, the abundance of several short chain fatty acids producers, and decreased the abundance of some potential pathogenic bacteria. However, D.400 had dual effects on lactic acid bacteria and increased the abundance of potential harmful bacterium Prevotella copri. Collectively, dietary daidzein at the levels of 40 and 400 mg kg-1 could enhance the intestinal mucosal barrier function and alter the intestinal microbiota of turbot. However, high dose of daidzein must be treated with caution for its unclear effects on intestinal microbiota of turbot in the present study.
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Affiliation(s)
- Weihao Ou
- The Key Laboratory of Aquaculture Nutrition and Feed (Ministry of Agriculture) & the Key Laboratory of Mariculture (Ministry of Education), Ocean University of China, Qingdao, 266003, PR China
| | - Haibin Hu
- The Key Laboratory of Aquaculture Nutrition and Feed (Ministry of Agriculture) & the Key Laboratory of Mariculture (Ministry of Education), Ocean University of China, Qingdao, 266003, PR China
| | - Pei Yang
- The Key Laboratory of Aquaculture Nutrition and Feed (Ministry of Agriculture) & the Key Laboratory of Mariculture (Ministry of Education), Ocean University of China, Qingdao, 266003, PR China
| | - Jihong Dai
- The Key Laboratory of Aquaculture Nutrition and Feed (Ministry of Agriculture) & the Key Laboratory of Mariculture (Ministry of Education), Ocean University of China, Qingdao, 266003, PR China
| | - Qinghui Ai
- The Key Laboratory of Aquaculture Nutrition and Feed (Ministry of Agriculture) & the Key Laboratory of Mariculture (Ministry of Education), Ocean University of China, Qingdao, 266003, PR China
| | - Wenbing Zhang
- The Key Laboratory of Aquaculture Nutrition and Feed (Ministry of Agriculture) & the Key Laboratory of Mariculture (Ministry of Education), Ocean University of China, Qingdao, 266003, PR China
| | - Yanjiao Zhang
- The Key Laboratory of Aquaculture Nutrition and Feed (Ministry of Agriculture) & the Key Laboratory of Mariculture (Ministry of Education), Ocean University of China, Qingdao, 266003, PR China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, PR China.
| | - Kangsen Mai
- The Key Laboratory of Aquaculture Nutrition and Feed (Ministry of Agriculture) & the Key Laboratory of Mariculture (Ministry of Education), Ocean University of China, Qingdao, 266003, PR China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, PR China
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16
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Das S, Smith K, Sarker S, Peters A, Adriaanse K, Eden P, Ghorashi SA, Forwood JK, Raidal SR. Assessing circovirus gene flow in multiple spill-over events. Virus Genes 2019; 55:802-814. [PMID: 31463770 DOI: 10.1007/s11262-019-01702-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 08/19/2019] [Indexed: 11/29/2022]
Abstract
The establishment of viral pathogens in new host environments following spillover events probably requires adaptive changes within both the new host and pathogen. After many generations, signals for ancient cross-species transmission may become lost and a strictly host-adapted phylogeny may mimic true co-divergence while the virus may retain an inherent ability to jump host species. The mechanistic basis for such processes remains poorly understood. To study the dynamics of virus-host co-divergence and the arbitrary chances of spillover in various reservoir hosts with equal ecological opportunity, we examined structural constraints of capsid protein in extant populations of Beak and feather disease virus (BFDV) during known spillover events. By assessing reservoir-based genotype stratification, we identified co-divergence defying signatures in the evolution BFDV which highlighted primordial processes of cryptic host adaptation and competing forces of host co-divergence and cross-species transmission. We demonstrate that, despite extensive surface plasticity gathered over a longer span of evolution, structural constraints of the capsid protein allow opportunistic host switching in host-adapted populations. This study provides new insights into how small populations of endangered psittacine species may face multidirectional forces of infection from reservoirs with apparently co-diverging genotypes.
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Affiliation(s)
- Shubhagata Das
- School of Animal and Veterinary Sciences, Charles Sturt University, Boorooma Street, Wagga Wagga, NSW, 2650, Australia
| | - Kate Smith
- School of Biomedical Sciences, Charles Sturt University, Boorooma Street, Wagga Wagga, NSW, 2650, Australia
| | - Subir Sarker
- Department of Physiology, Anatomy and Microbiology, School of Life Sciences, La Trobe University, Melbourne, 3086, Australia
| | - Andrew Peters
- School of Animal and Veterinary Sciences, Charles Sturt University, Boorooma Street, Wagga Wagga, NSW, 2650, Australia
| | - Katherine Adriaanse
- Healesville Sanctuary, Zoos Victoria, Badger Creek Road, Healesville, VIC, 3777, Australia
| | - Paul Eden
- Healesville Sanctuary, Zoos Victoria, Badger Creek Road, Healesville, VIC, 3777, Australia
| | - Seyed A Ghorashi
- School of Animal and Veterinary Sciences, Charles Sturt University, Boorooma Street, Wagga Wagga, NSW, 2650, Australia
| | - Jade K Forwood
- School of Biomedical Sciences, Charles Sturt University, Boorooma Street, Wagga Wagga, NSW, 2650, Australia
| | - Shane R Raidal
- School of Animal and Veterinary Sciences, Charles Sturt University, Boorooma Street, Wagga Wagga, NSW, 2650, Australia.
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17
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Ciofu O, Tolker-Nielsen T. Tolerance and Resistance of Pseudomonas aeruginosa Biofilms to Antimicrobial Agents-How P. aeruginosa Can Escape Antibiotics. Front Microbiol 2019; 10:913. [PMID: 31130925 PMCID: PMC6509751 DOI: 10.3389/fmicb.2019.00913] [Citation(s) in RCA: 383] [Impact Index Per Article: 76.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 04/10/2019] [Indexed: 11/24/2022] Open
Abstract
Pseudomonas aeruginosa is one of the six bacterial pathogens, Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp., which are commonly associated with antimicrobial resistance, and denoted by their acronym ESKAPE. P. aeruginosa is also recognized as an important cause of chronic infections due to its ability to form biofilms, where the bacteria are present in aggregates encased in a self-produced extracellular matrix and are difficult or impossible to eradicate with antibiotic treatment. P. aeruginosa causes chronic infections in the lungs of patients with cystic fibrosis and chronic obstructive lung disease, as well as chronic urinary tract infections in patients with permanent bladder catheter, and ventilator-associated pneumonia in intubated patients, and is also an important pathogen in chronic wounds. Antibiotic treatment cannot eradicate these biofilm infections due to their intrinsic antibiotic tolerance and the development of mutational antibiotic resistance. The tolerance of biofilms to antibiotics is multifactorial involving physical, physiological, and genetic determinants, whereas the antibiotic resistance of bacteria in biofilms is caused by mutations and driven by the repeated exposure of the bacteria to high levels of antibiotics. In this review, both the antimicrobial tolerance and the development of resistance to antibiotics in P. aeruginosa biofilms are discussed. Possible therapeutic approaches based on the understanding of the mechanisms involved in the tolerance and resistances of biofilms to antibiotics are also addressed.
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Affiliation(s)
- Oana Ciofu
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, Costerton Biofilm Center, University of Copenhagen, Copenhagen, Denmark
| | - Tim Tolker-Nielsen
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, Costerton Biofilm Center, University of Copenhagen, Copenhagen, Denmark
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18
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Gajigan AP, Yñiguez AT, Villanoy CL, San Diego-McGlone ML, Jacinto GS, Conaco C. Diversity and community structure of marine microbes around the Benham Rise underwater plateau, northeastern Philippines. PeerJ 2018; 6:e4781. [PMID: 29785352 PMCID: PMC5960264 DOI: 10.7717/peerj.4781] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 04/26/2018] [Indexed: 12/30/2022] Open
Abstract
Microbes are central to the structuring and functioning of marine ecosystems. Given the remarkable diversity of the ocean microbiome, uncovering marine microbial taxa remains a fundamental challenge in microbial ecology. However, there has been little effort, thus far, to describe the diversity of marine microorganisms in the region of high marine biodiversity around the Philippines. Here, we present data on the taxonomic diversity of bacteria and archaea in Benham Rise, Philippines, Western Pacific Ocean, using 16S V4 rRNA gene sequencing. The major bacterial and archaeal phyla identified in the Benham Rise are Proteobacteria, Cyanobacteria, Actinobacteria, Bacteroidetes, Marinimicrobia, Thaumarchaeota and, Euryarchaeota. The upper mesopelagic layer exhibited greater microbial diversity and richness compared to surface waters. Vertical zonation of the microbial community is evident and may be attributed to physical stratification of the water column acting as a dispersal barrier. Canonical Correspondence Analysis (CCA) recapitulated previously known associations of taxa and physicochemical parameters in the environment, such as the association of oligotrophic clades with low nutrient surface water and deep water clades that have the capacity to oxidize ammonia or nitrite at the upper mesopelagic layer. These findings provide foundational information on the diversity of marine microbes in Philippine waters. Further studies are warranted to gain a more comprehensive picture of microbial diversity within the region.
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Affiliation(s)
- Andrian P Gajigan
- Marine Science Institute, University of the Philippines Diliman, Quezon City, Philippines.,Current affiliation: Department of Oceanography, University of Hawaii at Manoa, USA
| | - Aletta T Yñiguez
- Marine Science Institute, University of the Philippines Diliman, Quezon City, Philippines
| | - Cesar L Villanoy
- Marine Science Institute, University of the Philippines Diliman, Quezon City, Philippines
| | | | - Gil S Jacinto
- Marine Science Institute, University of the Philippines Diliman, Quezon City, Philippines
| | - Cecilia Conaco
- Marine Science Institute, University of the Philippines Diliman, Quezon City, Philippines
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19
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.Rainey PB, Remigi P, Farr AD, Lind PA. Darwin was right: where now for experimental evolution? Curr Opin Genet Dev 2017; 47:102-109. [DOI: 10.1016/j.gde.2017.09.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 09/13/2017] [Accepted: 09/14/2017] [Indexed: 01/02/2023]
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20
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Vetsigian K. Diverse modes of eco-evolutionary dynamics in communities of antibiotic-producing microorganisms. Nat Ecol Evol 2017. [DOI: 10.1038/s41559-017-0189] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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21
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Martínez-García R, Tarnita CE. Seasonality can induce coexistence of multiple bet-hedging strategies in Dictyostelium discoideum via storage effect. J Theor Biol 2017; 426:104-116. [PMID: 28536035 DOI: 10.1016/j.jtbi.2017.05.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Revised: 05/05/2017] [Accepted: 05/17/2017] [Indexed: 02/06/2023]
Abstract
The social amoeba Dictyostelium discoideum has been recently suggested as an example of bet-hedging in microbes. In the presence of resources, amoebae reproduce as unicellular organisms. Resource depletion, however, leads to a starvation phase in which the population splits between aggregators, which form a fruiting body made of a stalk and resistant spores, and non-aggregators, which remain as vegetative cells. Spores are favored when starvation periods are long, but vegetative cells can exploit resources in environments where food replenishes quickly. The investment in aggregators versus non-aggregators can therefore be understood as a bet-hedging strategy that evolves in response to stochastic starvation times. A genotype (or strategy) is defined by the balance between each type of cells. In this framework, if the ecological conditions on a patch are defined in terms of the mean starvation time (i.e. time between the onset of starvation and the arrival of a new food pulse), a single genotype dominates each environment, which is inconsistent with the huge genetic diversity observed in nature. Here we investigate whether seasonality, represented by a periodic, wet-dry alternation in the mean starvation times, allows the coexistence of several strategies in a single patch. We study this question in a non-spatial (well-mixed) setting in which different strains compete for a common pool of resources over a sequence of growth-starvation cycles. We find that seasonality induces a temporal storage effect that can promote the stable coexistence of multiple genotypes. Two conditions need to be met in our model. First, there has to be a temporal niche partitioning (two well-differentiated habitats within the year), which requires not only different mean starvation times between seasons but also low variance within each season. Second, each season's well-adapted strain has to grow and create a large enough population that permits its survival during the subsequent unfavorable season, which requires the number of growth-starvation cycles within each season to be sufficiently large. These conditions allow the coexistence of two bet-hedging strategies. Additional tradeoffs among life-history traits can expand the range of coexistence and increase the number of coexisting strategies, contributing toward explaining the genetic diversity observed in D. discoideum. Although focused on this cellular slime mold, our results are general and may be easily extended to other microbes.
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Affiliation(s)
- Ricardo Martínez-García
- Department of Ecology and Evolutionary Biology, Princeton University. Princeton NJ 08544, USA
| | - Corina E Tarnita
- Department of Ecology and Evolutionary Biology, Princeton University. Princeton NJ 08544, USA.
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22
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Kraemer SA, Soucy JPR, Kassen R. Antagonistic interactions of soil pseudomonads are structured in time. FEMS Microbiol Ecol 2017; 93:3106319. [DOI: 10.1093/femsec/fix046] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 04/05/2017] [Indexed: 12/15/2022] Open
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23
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Gonçalves AT, Gallardo-Escárate C. Microbiome dynamic modulation through functional diets based on pre- and probiotics (mannan-oligosaccharides and Saccharomyces cerevisiae) in juvenile rainbow trout (Oncorhynchus mykiss). J Appl Microbiol 2017; 122:1333-1347. [PMID: 28256031 DOI: 10.1111/jam.13437] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 02/06/2017] [Accepted: 02/25/2017] [Indexed: 12/26/2022]
Abstract
AIMS This study used high-throughput sequencing to evaluate the intestinal microbiome dynamics in rainbow trout (Oncorhynchus mykiss) fed commercial diets supplemented with either pre- or probiotics (0·6% mannan-oligosaccharides and 0·5% Saccharomyces cerevisiae respectively) or the mixture of both. METHODS AND RESULTS A total of 57 fish whole intestinal mucosa and contents bacterial communities were characterized by high-throughput sequencing and analysis of the V3-V4 region of the 16S rRNA gene, as well as the relationship between plasma biochemical health indicators and microbiome diversity. This was performed at 7, 14 and 30 days after start feeding functional diets, and microbiome diversity increased when fish fed functional diets after 7 days and it was positively correlated with plasma cholesterol levels. Dominant phyla were, in descending order, Proteobacteria, Firmicutes, Actinobacteria, Acidobacteria, Bacteroidetes and Fusobacteria. However, functional diets reduced the abundance of Gammaproteobacteria to favour abundances of organisms from Firmicutes and Fusobacteria, two phyla with members that confer beneficial effects. A dynamic shift of the microbiome composition was observed with changes after 7 days of feeding and the modulation by functional diets tend to cluster the corresponding groups apart from CTRL group. The core microbiome showed an overall stability with functional diets, except genus such as Escherichia-Shigella that suffered severe reductions on their abundances when feeding any of the functional diets. CONCLUSIONS Functional diets based on pre- or probiotics dynamically modulate intestinal microbiota of juvenile trout engaging taxonomical abundance shifts that might impact fish physiological performance. SIGNIFICANCE AND IMPACT OF THE STUDY This study shows for the first time the microbiome modulation dynamics by functional diets based on mannan-oligosaccharides and S. cerevisiae and their synergy using culture independent high-throughput sequencing technology, revealing the complexity behind the dietary modulation with functional feeds in aquatic organisms.
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Affiliation(s)
- A T Gonçalves
- Laboratory of Biotechnology and Aquatic Genomics, Interdisciplinary Center for Aquaculture Research (INCAR), Universidad de Concepción, Concepción, Chile
| | - C Gallardo-Escárate
- Laboratory of Biotechnology and Aquatic Genomics, Interdisciplinary Center for Aquaculture Research (INCAR), Universidad de Concepción, Concepción, Chile
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24
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Coloma SE, Dienstbier A, Bamford DH, Sivonen K, Roine E, Hiltunen T. Newly isolatedNodulariaphage influences cyanobacterial community dynamics. Environ Microbiol 2017; 19:273-286. [DOI: 10.1111/1462-2920.13601] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 10/25/2016] [Accepted: 11/16/2016] [Indexed: 12/18/2022]
Affiliation(s)
- S. E. Coloma
- Department of Food and Environmental SciencesViikinkaari 9, 00014 University of HelsinkiHelsinki Finland
| | - A. Dienstbier
- Department of BiosciencesViikinkaari 9, 00014 University of HelsinkiHelsinki Finland
| | - D. H. Bamford
- Department of BiosciencesViikinkaari 9, 00014 University of HelsinkiHelsinki Finland
- Institute of BiotechnologyViikinkaari 9, 00014 University of HelsinkiHelsinki Finland
| | - K. Sivonen
- Department of Food and Environmental SciencesViikinkaari 9, 00014 University of HelsinkiHelsinki Finland
| | - E. Roine
- Department of BiosciencesViikinkaari 9, 00014 University of HelsinkiHelsinki Finland
- Institute of BiotechnologyViikinkaari 9, 00014 University of HelsinkiHelsinki Finland
| | - T. Hiltunen
- Department of Food and Environmental SciencesViikinkaari 9, 00014 University of HelsinkiHelsinki Finland
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Evolution of Ecological Diversity in Biofilms of Pseudomonas aeruginosa by Altered Cyclic Diguanylate Signaling. J Bacteriol 2016; 198:2608-18. [PMID: 27021563 PMCID: PMC5019052 DOI: 10.1128/jb.00048-16] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 03/22/2016] [Indexed: 11/29/2022] Open
Abstract
The ecological and evolutionary forces that promote and maintain diversity in biofilms are not well understood. To quantify these forces, three Pseudomonas aeruginosa populations were experimentally evolved from strain PA14 in a daily cycle of attachment, assembly, and dispersal for 600 generations. Each biofilm population evolved diverse colony morphologies and mutator genotypes defective in DNA mismatch repair. This diversity enhanced population fitness and biofilm output, owing partly to rare, early colonizing mutants that enhanced attachment of others. Evolved mutants exhibited various levels of the intracellular signal cyclic-di-GMP, which associated with their timing of adherence. Manipulating cyclic-di-GMP levels within individual mutants revealed a network of interactions in the population that depended on various attachment strategies related to this signal. Diversification in biofilms may therefore arise and be reinforced by initial colonists that enable community assembly.
IMPORTANCE How biofilm diversity assembles, evolves, and contributes to community function is largely unknown. This presents a major challenge for understanding evolution during chronic infections and during the growth of all surface-associated microbes. We used experimental evolution to probe these dynamics and found that diversity, partly related to altered cyclic-di-GMP levels, arose and persisted due to the emergence of ecological interdependencies related to attachment patterns. Clonal isolates failed to capture population attributes, which points to the need to account for diversity in infections. More broadly, this study offers an experimental framework for linking phenotypic variation to distinct ecological strategies in biofilms and for studying eco-evolutionary interactions.
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Dudaniec RY, Tesson SVM. Applying landscape genetics to the microbial world. Mol Ecol 2016; 25:3266-75. [PMID: 27146426 DOI: 10.1111/mec.13691] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Revised: 04/07/2016] [Accepted: 05/03/2016] [Indexed: 12/31/2022]
Abstract
Landscape genetics, which explicitly quantifies landscape effects on gene flow and adaptation, has largely focused on macroorganisms, with little attention given to microorganisms. This is despite overwhelming evidence that microorganisms exhibit spatial genetic structuring in relation to environmental variables. The increasing accessibility of genomic data has opened up the opportunity for landscape genetics to embrace the world of microorganisms, which may be thought of as 'the invisible regulators' of the macroecological world. Recent developments in bioinformatics and increased data accessibility have accelerated our ability to identify microbial taxa and characterize their genetic diversity. However, the influence of the landscape matrix and dynamic environmental factors on microorganism genetic dispersal and adaptation has been little explored. Also, because many microorganisms coinhabit or codisperse with macroorganisms, landscape genomic approaches may improve insights into how micro- and macroorganisms reciprocally interact to create spatial genetic structure. Conducting landscape genetic analyses on microorganisms requires that we accommodate shifts in spatial and temporal scales, presenting new conceptual and methodological challenges not yet explored in 'macro'-landscape genetics. We argue that there is much value to be gained for microbial ecologists from embracing landscape genetic approaches. We provide a case for integrating landscape genetic methods into microecological studies and discuss specific considerations associated with the novel challenges this brings. We anticipate that microorganism landscape genetic studies will provide new insights into both micro- and macroecological processes and expand our knowledge of species' distributions, adaptive mechanisms and species' interactions in changing environments.
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Affiliation(s)
- Rachael Y Dudaniec
- Department of Biological Sciences, Macquarie University, Sydney, NSW, 2109, Australia
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Presloid JB, Mohammad TF, Lauring AS, Novella IS. Antigenic diversification is correlated with increased thermostability in a mammalian virus. Virology 2016; 496:203-214. [PMID: 27344137 DOI: 10.1016/j.virol.2016.06.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 06/10/2016] [Accepted: 06/14/2016] [Indexed: 10/21/2022]
Abstract
The theory of plastogenetic congruence posits that ultimately, the pressure to maintain function in the face of biomolecular destabilization produces robustness. As temperature goes up so does destabilization. Thus, genetic robustness, defined as phenotypic constancy despite mutation, should correlate with survival during thermal challenge. We tested this hypothesis using vesicular stomatitis virus (VSV). We produced two sets of evolved strains after selection for higher thermostability by either preincubation at 37°C or by incubation at 40°C during infection. These VSV populations became more thermostable and also more fit in the absence of thermal selection, demonstrating an absence of tradeoffs. Eleven out of 12 evolved populations had a fixed, nonsynonymous substitution in the nucleocapsid (N) open reading frame. There was a partial correlation between thermostability and mutational robustness that was observed when the former was measured at 42°C, but not at 37°C. These results are consistent with our earlier work and suggest that the relationship between robustness and thermostability is complex. Surprisingly, many of the thermostable strains also showed increased resistance to monoclonal antibody and polyclonal sera, including sera from natural hosts. These data suggest that evolved thermostability may lead to antigenic diversification and an increased ability to escape immune surveillance in febrile hosts, and potentially to an improved robustness. These relationships have important implications not only in terms of viral pathogenesis, but also for the development of vaccine vectors and oncolytic agents.
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Affiliation(s)
- John B Presloid
- Department of Medical Microbiology and Immunology, College of Medicine and Life Sciences, The University of Toledo, 3055 Arlington Avenue, Toledo OH 43614, USA
| | - Tasneem F Mohammad
- Department of Medical Microbiology and Immunology, College of Medicine and Life Sciences, The University of Toledo, 3055 Arlington Avenue, Toledo OH 43614, USA
| | - Adam S Lauring
- Department of Internal Medicine, Division of Infectious Diseases and Department of Microbiology & Immunology. University of Michigan, Ann Arbor, MI 41809, USA.
| | - Isabel S Novella
- Department of Medical Microbiology and Immunology, College of Medicine and Life Sciences, The University of Toledo, 3055 Arlington Avenue, Toledo OH 43614, USA.
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Braker G, Conrad R. Diversity, structure, and size of N(2)O-producing microbial communities in soils--what matters for their functioning? ADVANCES IN APPLIED MICROBIOLOGY 2016; 75:33-70. [PMID: 21807245 DOI: 10.1016/b978-0-12-387046-9.00002-5] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Nitrous oxide (N(2)O) is mainly generated via nitrification and denitrification processes in soils and subsequently emitted into the atmosphere where it causes well-known radiative effects. How nitrification and denitrification are affected by proximal and distal controls has been studied extensively in the past. The importance of the underlying microbial communities, however, has been acknowledged only recently. Particularly, the application of molecular methods to study nitrifiers and denitrifiers directly in their habitats enabled addressing how environmental factors influence the diversity, community composition, and size of these functional groups in soils and whether this is of relevance for their functioning and N(2)O production. In this review, we summarize the current knowledge on community-function interrelationships. Aerobic nitrification (ammonia oxidation) and anaerobic denitrification are clearly under different controls. While N(2)O is an obligatory intermediate in denitrification, its production during ammonia oxidation depends on whether nitrite, the end product, is further reduced. Moreover, individual strains vary strongly in their responses to environmental cues, and so does N(2)O production. We therefore conclude that size and structure of both functional groups are relevant with regard to production and emission of N(2)O from soils. Diversity affects on function, however, are much more difficult to assess, as it is not resolved as yet how individual nitrification or denitrification genotypes are related to N(2)O production. More research is needed for further insights into the relation of microbial communities to ecosystem functions, for instance, how the actively nitrifying or denitrifying part of the community may be related to N(2)O emission.
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Affiliation(s)
- Gesche Braker
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, Marburg, Germany.
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Wright ES, Vetsigian KH. Inhibitory interactions promote frequent bistability among competing bacteria. Nat Commun 2016; 7:11274. [PMID: 27097658 PMCID: PMC4844671 DOI: 10.1038/ncomms11274] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 03/09/2016] [Indexed: 02/06/2023] Open
Abstract
It is largely unknown how the process of microbial community assembly is affected by the order of species arrival, initial species abundances and interactions between species. A minimal way of capturing competitive abilities in a frequency-dependent manner is with an invasibility network specifying whether a species at low abundance can increase in frequency in an environment dominated by another species. Here, using a panel of prolific small-molecule producers and a habitat with feast-and-famine cycles, we show that the most abundant strain can often exclude other strains—resulting in bistability between pairs of strains. Instead of a single winner, the empirically determined invasibility network is ruled by multiple strains that cannot invade each other, and does not contain loops of cyclic dominance. Antibiotic inhibition contributes to bistability by helping producers resist invasions while at high abundance and by reducing producers' ability to invade when at low abundance. We know little about the effect of relationships between species on the assembly of microbial communities. Here the authors map pairwise invasion relations between bacteria and find that instead of one strain dominating, inhibitory interactions mean that often neither strain can invade the other.
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Affiliation(s)
- Erik S Wright
- Department of Bacteriology, Wisconsin Institute for Discovery, University of Wisconsin-Madison, 330 N. Orchard Street, Madison, Wisconsin 53715, USA
| | - Kalin H Vetsigian
- Department of Bacteriology, Wisconsin Institute for Discovery, University of Wisconsin-Madison, 330 N. Orchard Street, Madison, Wisconsin 53715, USA
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Steenackers HP, Parijs I, Dubey A, Foster KR, Vanderleyden J. Experimental evolution in biofilm populations. FEMS Microbiol Rev 2016; 40:373-97. [PMID: 26895713 PMCID: PMC4852284 DOI: 10.1093/femsre/fuw002] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/21/2016] [Indexed: 12/19/2022] Open
Abstract
Biofilms are a major form of microbial life in which cells form dense surface associated communities that can persist for many generations. The long-life of biofilm communities means that they can be strongly shaped by evolutionary processes. Here, we review the experimental study of evolution in biofilm communities. We first provide an overview of the different experimental models used to study biofilm evolution and their associated advantages and disadvantages. We then illustrate the vast amount of diversification observed during biofilm evolution, and we discuss (i) potential ecological and evolutionary processes behind the observed diversification, (ii) recent insights into the genetics of adaptive diversification, (iii) the striking degree of parallelism between evolution experiments and real-life biofilms and (iv) potential consequences of diversification. In the second part, we discuss the insights provided by evolution experiments in how biofilm growth and structure can promote cooperative phenotypes. Overall, our analysis points to an important role of biofilm diversification and cooperation in bacterial survival and productivity. Deeper understanding of both processes is of key importance to design improved antimicrobial strategies and diagnostic techniques. This review paper provides an overview of (i) the different experimental models used to study biofilm evolution, (ii) the vast amount of diversification observed during biofilm evolution (including potential causes and consequences) and (iii) recent insights in how growth in biofilms can lead to the evolution of cooperative phenotypes.
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Affiliation(s)
- Hans P Steenackers
- Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics, KU Leuven, Leuven 3001, Belgium
| | - Ilse Parijs
- Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics, KU Leuven, Leuven 3001, Belgium
| | | | - Kevin R Foster
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK Oxford Centre for Integrative Systems Biology, University of Oxford, Oxford OX1 3QU, UK
| | - Jozef Vanderleyden
- Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics, KU Leuven, Leuven 3001, Belgium
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31
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Louca S, Doebeli M. Calibration and analysis of genome-based models for microbial ecology. eLife 2015; 4:e08208. [PMID: 26473972 PMCID: PMC4608356 DOI: 10.7554/elife.08208] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2015] [Accepted: 09/17/2015] [Indexed: 12/11/2022] Open
Abstract
Microbial ecosystem modeling is complicated by the large number of unknown parameters and the lack of appropriate calibration tools. Here we present a novel computational framework for modeling microbial ecosystems, which combines genome-based model construction with statistical analysis and calibration to experimental data. Using this framework, we examined the dynamics of a community of Escherichia coli strains that emerged in laboratory evolution experiments, during which an ancestral strain diversified into two coexisting ecotypes. We constructed a microbial community model comprising the ancestral and the evolved strains, which we calibrated using separate monoculture experiments. Simulations reproduced the successional dynamics in the evolution experiments, and pathway activation patterns observed in microarray transcript profiles. Our approach yielded detailed insights into the metabolic processes that drove bacterial diversification, involving acetate cross-feeding and competition for organic carbon and oxygen. Our framework provides a missing link towards a data-driven mechanistic microbial ecology.
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Affiliation(s)
- Stilianos Louca
- Institute of Applied Mathematics, University of British Columbia, Vancouver, Canada
| | - Michael Doebeli
- Department of Zoology, University of British Columbia, Vancouver, Canada
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32
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Frenkel EM, McDonald MJ, Van Dyken JD, Kosheleva K, Lang GI, Desai MM. Crowded growth leads to the spontaneous evolution of semistable coexistence in laboratory yeast populations. Proc Natl Acad Sci U S A 2015; 112:11306-11. [PMID: 26240355 PMCID: PMC4568650 DOI: 10.1073/pnas.1506184112] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Identifying the mechanisms that create and maintain biodiversity is a central challenge in biology. Stable diversification of microbial populations often requires the evolution of differences in resource utilization. Alternatively, coexistence can be maintained by specialization to exploit spatial heterogeneity in the environment. Here, we report spontaneous diversification maintained by a related but distinct mechanism: crowding avoidance. During experimental evolution of laboratory Saccharomyces cerevisiae populations, we observed the repeated appearance of "adherent" (A) lineages able to grow as a dispersed film, in contrast to their crowded "bottom-dweller" (B) ancestors. These two types stably coexist because dispersal reduces interference competition for nutrients among kin, at the cost of a slower maximum growth rate. This tradeoff causes the frequencies of the two types to oscillate around equilibrium over the course of repeated cycles of growth, crowding, and dispersal. However, further coevolution of the A and B types can perturb and eventually destroy their coexistence over longer time scales. We introduce a simple mathematical model of this "semistable" coexistence, which explains the interplay between ecological and evolutionary dynamics. Because crowded growth generally limits nutrient access in biofilms, the mechanism we report here may be broadly important in maintaining diversity in these natural environments.
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Affiliation(s)
- Evgeni M Frenkel
- Department of Organismic and Evolutionary Biology, Department of Physics, and Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, MA 02138; Program in Biophysics, Harvard University, Boston, MA 02115
| | - Michael J McDonald
- Department of Organismic and Evolutionary Biology, Department of Physics, and Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, MA 02138
| | | | - Katya Kosheleva
- Department of Organismic and Evolutionary Biology, Department of Physics, and Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, MA 02138
| | - Gregory I Lang
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015
| | - Michael M Desai
- Department of Organismic and Evolutionary Biology, Department of Physics, and Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, MA 02138;
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O'Malley MA, Travisano M, Velicer GJ, Bolker JA. How Do Microbial Populations and Communities Function as Model Systems? QUARTERLY REVIEW OF BIOLOGY 2015; 90:269-93. [DOI: 10.1086/682588] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Esteban DJ, Hysa B, Bartow-McKenney C. Temporal and Spatial Distribution of the Microbial Community of Winogradsky Columns. PLoS One 2015; 10:e0134588. [PMID: 26248298 PMCID: PMC4527761 DOI: 10.1371/journal.pone.0134588] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 07/10/2015] [Indexed: 01/03/2023] Open
Abstract
Winogradsky columns are model microbial ecosystems prepared by adding pond sediment to a clear cylinder with additional supplements and incubated with light. Environmental gradients develop within the column creating diverse niches that allow enrichment of specific bacteria. The enrichment culture can be used to study soil and sediment microbial community structure and function. In this study we used a 16S rRNA gene survey to characterize the microbial community dynamics during Winogradsky column development to determine the rate and extent of change from the source sediment community. Over a period of 60 days, the microbial community changed from the founding pond sediment population: Cyanobacteria, Chloroflexi, Nitrospirae, and Planctomycetes increased in relative abundance over time, while most Proteobacteria decreased in relative abundance. A unique, light-dependent surface biofilm community formed by 60 days that was less diverse and dominated by a few highly abundant bacteria. 67–72% of the surface community was comprised of highly enriched taxa that were rare in the source pond sediment, including the Cyanobacteria Anabaena, a member of the Gemmatimonadetes phylum, and a member of the Chloroflexi class Anaerolinea. This indicates that rare taxa can become abundant under appropriate environmental conditions and supports the hypothesis that rare taxa serve as a microbial seed bank. We also present preliminary findings that suggest that bacteriophages may be active in the Winogradsky community. The dynamics of certain taxa, most notably the Cyanobacteria, showed a bloom-and-decline pattern, consistent with bacteriophage predation as predicted in the kill-the-winner hypothesis. Time-lapse photography also supported the possibility of bacteriophage activity, revealing a pattern of colony clearance similar to formation of viral plaques. The Winogradsky column, a technique developed early in the history of microbial ecology to enrich soil microbes, may therefore be a useful model system to investigate both microbial and viral ecology.
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Affiliation(s)
- David J Esteban
- Department of Biology, Vassar College, Poughkeepsie, New York, United States of America
- * E-mail:
| | - Bledi Hysa
- Department of Biology, Vassar College, Poughkeepsie, New York, United States of America
| | - Casey Bartow-McKenney
- Department of Biology, Vassar College, Poughkeepsie, New York, United States of America
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35
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36
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Marvig RL, Sommer LM, Jelsbak L, Molin S, Johansen HK. Evolutionary insight from whole-genome sequencing of Pseudomonas aeruginosa from cystic fibrosis patients. Future Microbiol 2015; 10:599-611. [DOI: 10.2217/fmb.15.3] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
ABSTRACT The opportunistic pathogen Pseudomonas aeruginosa causes chronic airway infections in patients with cystic fibrosis (CF), and it is directly associated with the morbidity and mortality connected with this disease. The ability of P. aeruginosa to establish chronic infections in CF patients is suggested to be due to the large genetic repertoire of P. aeruginosa and its ability to genetically adapt to the host environment. Here, we review the recent work that has applied whole-genome sequencing to understand P. aeruginosa population genomics, within-host microevolution and diversity, mutational mechanisms, genetic adaptation and transmission events. Finally, we summarize the advances in relation to medical applications and laboratory evolution experiments.
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Affiliation(s)
| | - Lea M Sommer
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Lars Jelsbak
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Søren Molin
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Helle Krogh Johansen
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
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Lambert G, Kussell E. Quantifying selective pressures driving bacterial evolution using lineage analysis. PHYSICAL REVIEW. X 2015; 5:011016. [PMID: 26213639 PMCID: PMC4511495 DOI: 10.1103/physrevx.5.011016] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Organisms use a variety of strategies to adapt to their environments and maximize long-term growth potential, but quantitative characterization of the benefits conferred by the use of such strategies, as well as their impact on the whole population's rate of growth, remains challenging. Here, we use a path-integral framework that describes how selection acts on lineages -i.e. the life-histories of individuals and their ancestors- to demonstrate that lineage-based measurements can be used to quantify the selective pressures acting on a population. We apply this analysis to E. coli bacteria exposed to cyclical treatments of carbenicillin, an antibiotic that interferes with cell-wall synthesis and affects cells in an age-dependent manner. While the extensive characterization of the life-history of thousands of cells is necessary to accurately extract the age-dependent selective pressures caused by carbenicillin, the same measurement can be recapitulated using lineage-based statistics of a single surviving cell. Population-wide evolutionary pressures can be extracted from the properties of the surviving lineages within a population, providing an alternative and efficient procedure to quantify the evolutionary forces acting on a population. Importantly, this approach is not limited to age-dependent selection, and the framework can be generalized to detect signatures of other trait-specific selection using lineage-based measurements. Our results establish a powerful way to study the evolutionary dynamics of life under selection, and may be broadly useful in elucidating selective pressures driving the emergence of antibiotic resistance and the evolution of survival strategies in biological systems.
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Affiliation(s)
- Guillaume Lambert
- The Institute of Genomics and Systems Biology, The University of Chicago
| | - Edo Kussell
- Department of Biology and Center for Genomics and Systems Biology, New York University and Department of Physics, New York University
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Puentes-Téllez PE, van Elsas JD. Sympatric metabolic diversification of experimentally evolved Escherichia coli in a complex environment. Antonie van Leeuwenhoek 2014; 106:565-76. [DOI: 10.1007/s10482-014-0228-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 06/26/2014] [Indexed: 11/24/2022]
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Cole JK, Hutchison JR, Renslow RS, Kim YM, Chrisler WB, Engelmann HE, Dohnalkova AC, Hu D, Metz TO, Fredrickson JK, Lindemann SR. Phototrophic biofilm assembly in microbial-mat-derived unicyanobacterial consortia: model systems for the study of autotroph-heterotroph interactions. Front Microbiol 2014; 5:109. [PMID: 24778628 PMCID: PMC3985010 DOI: 10.3389/fmicb.2014.00109] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2013] [Accepted: 03/04/2014] [Indexed: 11/24/2022] Open
Abstract
Microbial autotroph-heterotroph interactions influence biogeochemical cycles on a global scale, but the diversity and complexity of natural systems and their intractability to in situ manipulation make it challenging to elucidate the principles governing these interactions. The study of assembling phototrophic biofilm communities provides a robust means to identify such interactions and evaluate their contributions to the recruitment and maintenance of phylogenetic and functional diversity over time. To examine primary succession in phototrophic communities, we isolated two unicyanobacterial consortia from the microbial mat in Hot Lake, Washington, characterizing the membership and metabolic function of each consortium. We then analyzed the spatial structures and quantified the community compositions of their assembling biofilms. The consortia retained the same suite of heterotrophic species, identified as abundant members of the mat and assigned to Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes. Autotroph growth rates dominated early in assembly, yielding to increasing heterotroph growth rates late in succession. The two consortia exhibited similar assembly patterns, with increasing relative abundances of members from Bacteroidetes and Alphaproteobacteria concurrent with decreasing relative abundances of those from Gammaproteobacteria. Despite these similarities at higher taxonomic levels, the relative abundances of individual heterotrophic species were substantially different in the developing consortial biofilms. This suggests that, although similar niches are created by the cyanobacterial metabolisms, the resulting webs of autotroph-heterotroph and heterotroph-heterotroph interactions are specific to each primary producer. The relative simplicity and tractability of the Hot Lake unicyanobacterial consortia make them useful model systems for deciphering interspecies interactions and assembly principles relevant to natural microbial communities.
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Affiliation(s)
- Jessica K Cole
- Biological Sciences Division, Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory Richland, WA, USA
| | - Janine R Hutchison
- Chemical, Biological, and Physical Sciences Division, National Security Directorate, Pacific Northwest National Laboratory Richland, WA, USA
| | - Ryan S Renslow
- Scientific Resources Division, William R. Wiley Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory Richland, WA, USA
| | - Young-Mo Kim
- Biological Sciences Division, Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory Richland, WA, USA
| | - William B Chrisler
- Biological Sciences Division, Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory Richland, WA, USA
| | - Heather E Engelmann
- Chemical, Biological, and Physical Sciences Division, National Security Directorate, Pacific Northwest National Laboratory Richland, WA, USA
| | - Alice C Dohnalkova
- Scientific Resources Division, William R. Wiley Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory Richland, WA, USA
| | - Dehong Hu
- Scientific Resources Division, William R. Wiley Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory Richland, WA, USA
| | - Thomas O Metz
- Biological Sciences Division, Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory Richland, WA, USA
| | - Jim K Fredrickson
- Biological Sciences Division, Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory Richland, WA, USA
| | - Stephen R Lindemann
- Biological Sciences Division, Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory Richland, WA, USA
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40
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Kraemer SA, Velicer GJ. Social complementation and growth advantages promote socially defective bacterial isolates. Proc Biol Sci 2014; 281:20140036. [PMID: 24573856 DOI: 10.1098/rspb.2014.0036] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Social interactions among diverse individuals that encounter one another in nature have often been studied among animals but rarely among microbes. For example, the evolutionary forces that determine natural frequencies of bacteria that express cooperative behaviours at low levels remain poorly understood. Natural isolates of the soil bacterium Myxococcus xanthus sampled from the same fruiting body often vary in social phenotypes, such as group swarming and multicellular development. Here, we tested whether genotypes highly proficient at swarming or development might promote the persistence of less socially proficient genotypes from the same fruiting body. Fast-swarming strains complemented slower isolates, allowing the latter to keep pace with faster strains in mixed groups. During development, one low-sporulating strain was antagonized by high sporulators, whereas others with severe developmental defects had those defects partially complemented by high-sporulating strains. Despite declining in frequency overall during competition experiments spanning multiple cycles of development, developmentally defective strains exhibited advantages during the growth phases of competitions. These results suggest that microbes with low-sociality phenotypes often benefit from interacting with more socially proficient strains. Such complementation may combine with advantages at other traits to increase equilibrium frequencies of low-sociality genotypes in natural populations.
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Affiliation(s)
- Susanne A Kraemer
- Centre for Advanced Research in Environmental Genomics, Department of Biology, University of Ottawa, , 30 Marie Curie Private, Ottawa, Ontario, Canada , K2P 6N5, Institute for Integrative Biology, ETH Zürich, , Universitaetsstrasse 16, Zürich 8092, Switzerland, Department of Biology, Indiana University, , Bloomington, IN, USA
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41
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Herrera CM. Population growth of the floricolous yeast Metschnikowia reukaufii: effects of nectar host, yeast genotype, and host × genotype interaction. FEMS Microbiol Ecol 2014; 88:250-7. [PMID: 24512559 DOI: 10.1111/1574-6941.12284] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2013] [Revised: 12/24/2013] [Accepted: 01/13/2014] [Indexed: 11/30/2022] Open
Abstract
Genetic diversity and genotypic diversity of wild populations of the floricolous yeast Metschnikowia reukaufii exhibit a strong host-mediated component, with genotypes being nonrandomly distributed among flowers of different plant species. To unravel the causal mechanism of this pattern of host-mediated genetic diversity, this paper examines experimentally whether floral nectars of different host plants differ in their quality as a growing substrate for M. reukaufii and also whether genetically distinct yeast strains differ in their relative ability to thrive in nectars of different species (host × genotype interaction). Genetically distinct M. reukaufii strains were grown in natural nectar of different hosts under controlled conditions. Population growth varied widely among nectar hosts, revealing that different host plants provided microhabitats of different quality for M. reukaufii. Different M. reukaufii strains responded in different ways to interspecific nectar variation, and variable growth responses were significantly associated with genetic differences between strains, thus leading to a significant host × genotype interaction. Results of this study provide support for the diversifying selection hypothesis as the underlying mechanism preserving high genetic diversity in wild M. reukaufii populations and also suggest that consequences of functional plant-pollinator diversity may surpass the domain of the mutualistic organisms to implicate associated microorganisms.
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David-Palma M, Libkind D, Sampaio JP. Global distribution, diversity hot spots and niche transitions of an astaxanthin-producing eukaryotic microbe. Mol Ecol 2014; 23:921-32. [DOI: 10.1111/mec.12642] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Revised: 12/05/2013] [Accepted: 12/13/2013] [Indexed: 01/20/2023]
Affiliation(s)
- Márcia David-Palma
- Departamento de Ciências da Vida; Faculdade de Ciências e Tecnologia; Centro de Recursos Microbiológicos (CREM); Universidade Nova de Lisboa; 2829-516 Caparica Portugal
| | - Diego Libkind
- Laboratorio de Microbiología Aplicada y Biotecnología; Instituto de Investigaciones en Biodiversidad y Medioambiente (INIBIOMA); CONICET - UNComahue; Quintral 1250 (8400), Bariloche Argentina
| | - José Paulo Sampaio
- Departamento de Ciências da Vida; Faculdade de Ciências e Tecnologia; Centro de Recursos Microbiológicos (CREM); Universidade Nova de Lisboa; 2829-516 Caparica Portugal
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Herrera CM, Pozo MI, Bazaga P. Nonrandom genotype distribution among floral hosts contributes to local and regional genetic diversity in the nectar-living yeastMetschnikowia reukaufii. FEMS Microbiol Ecol 2013; 87:568-75. [DOI: 10.1111/1574-6941.12245] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Revised: 11/03/2013] [Accepted: 11/04/2013] [Indexed: 11/29/2022] Open
Affiliation(s)
| | - María I. Pozo
- Estación Biológica de Doñana; CSIC; Sevilla Spain
- Laboratory of Plant Ecology; University of Leuven; Heverlee Belgium
| | - Pilar Bazaga
- Estación Biológica de Doñana; CSIC; Sevilla Spain
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Bowen JL, Byrnes JEK, Weisman D, Colaneri C. Functional gene pyrosequencing and network analysis: an approach to examine the response of denitrifying bacteria to increased nitrogen supply in salt marsh sediments. Front Microbiol 2013; 4:342. [PMID: 24348464 PMCID: PMC3841915 DOI: 10.3389/fmicb.2013.00342] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 10/29/2013] [Indexed: 11/13/2022] Open
Abstract
Functional gene pyrosequencing is emerging as a useful tool to examine the diversity and abundance of microbes that facilitate key biogeochemical processes. One such process, denitrification, is of particular importance because it converts fixed nitrate (NO(-) 3) to N2 gas, which returns to the atmosphere. In nitrogen limited salt marshes, removal of NO(-) 3 prior to entering adjacent waters helps prevent eutrophication. Understanding the dynamics of salt marsh microbial denitrification is thus imperative for the maintenance of healthy coastal ecosystems. We used pyrosequencing of the nirS gene to examine the denitrifying community response to fertilization in experimentally enriched marsh plots. A key challenge in the analysis of sequence data derived from pyrosequencing is understanding whether small differences in gene sequences are ecologically meaningful. We applied a novel approach from information theory to determine that the optimal similarity level for clustering DNA sequences into OTUs, while still capturing the ecological complexity of the system, was 88%. With this clustering, phylogenetic analysis yielded 6 dominant clades of denitrifiers, the largest of which, accounting for more than half of all the sequences collected, had no close cultured representatives. Of the 638 OTUs identified, only 11 were present in all plots and no single OTU was dominant. We did, however, find a large number of specialist OTUs that were present only in a single plot. The high degree of endemic OTUs, while accounting for a large proportion of the nirS diversity in the plots, were found in lower abundance than the generalist taxa. The proportion of specialist taxa increased with increasing supply of nutrients, suggesting that addition of fertilizer may create conditions that expand the niche space for denitrifying organisms and may enhance the genetic capacity for denitrification.
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Affiliation(s)
- Jennifer L Bowen
- Department of Biology, University of Massachusetts Boston Boston, MA, USA
| | - Jarrett E K Byrnes
- Department of Biology, University of Massachusetts Boston Boston, MA, USA
| | - David Weisman
- Department of Biology, University of Massachusetts Boston Boston, MA, USA
| | - Cory Colaneri
- Department of Biology, University of Massachusetts Boston Boston, MA, USA
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Abstract
Mutant lineages may cause cancer-like overgrowths in microbial populations. Theory predicts that microbial regulatory controls may be designed to limit the origin and competitive potential of rogue lineages. A new study shows how a Salmonella species protects itself against overgrowths.
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Schlatter DC, DavelosBaines AL, Xiao K, Kinkel LL. Resource use of soilborne Streptomyces varies with location, phylogeny, and nitrogen amendment. MICROBIAL ECOLOGY 2013; 66:961-971. [PMID: 23959115 DOI: 10.1007/s00248-013-0280-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 08/06/2013] [Indexed: 06/02/2023]
Abstract
In this study, we explore variation in resource use among Streptomyces in prairie soils. Resource use patterns were highly variable among Streptomyces isolates and were significantly related to location, phylogeny, and nitrogen (N) amendment history. Streptomyces populations from soils less than 1 m apart differed significantly in their ability to use resources, indicating that drivers of resource use phenotypes in soil are highly localized. Variation in resource use within Streptomyces genetic groups was significantly associated with the location from which Streptomyces were isolated, suggesting that resource use is adapted to local environments. Streptomyces from soils under long-term N amendment used fewer resources and grew less efficiently than those from non-amended soils, demonstrating that N amendment selects for Streptomyces with more limited catabolic capacities. Finally, resource use among Streptomyces populations was correlated with soil carbon content and Streptomyces population densities. We hypothesize that variation in resource use among Streptomyces reflects adaptation to local resource availability and competitive species interactions in soil and that N amendments alter selection for resource use phenotypes.
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Álvarez-Pérez S, de Vega C, Herrera CM. Multilocus sequence analysis of nectar pseudomonads reveals high genetic diversity and contrasting recombination patterns. PLoS One 2013; 8:e75797. [PMID: 24116076 PMCID: PMC3792982 DOI: 10.1371/journal.pone.0075797] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 08/20/2013] [Indexed: 12/11/2022] Open
Abstract
The genetic and evolutionary relationships among floral nectar-dwelling Pseudomonas 'sensu stricto' isolates associated to South African and Mediterranean plants were investigated by multilocus sequence analysis (MLSA) of four core housekeeping genes (rrs, gyrB, rpoB and rpoD). A total of 35 different sequence types were found for the 38 nectar bacterial isolates characterised. Phylogenetic analyses resulted in the identification of three main clades [nectar groups (NGs) 1, 2 and 3] of nectar pseudomonads, which were closely related to five intrageneric groups: Pseudomonas oryzihabitans (NG 1); P. fluorescens, P. lutea and P. syringae (NG 2); and P. rhizosphaerae (NG 3). Linkage disequilibrium analysis pointed to a mostly clonal population structure, even when the analysis was restricted to isolates from the same floristic region or belonging to the same NG. Nevertheless, signatures of recombination were observed for NG 3, which exclusively included isolates retrieved from the floral nectar of insect-pollinated Mediterranean plants. In contrast, the other two NGs comprised both South African and Mediterranean isolates. Analyses relating diversification to floristic region and pollinator type revealed that there has been more unique evolution of the nectar pseudomonads within the Mediterranean region than would be expected by chance. This is the first work analysing the sequence of multiple loci to reveal geno- and ecotypes of nectar bacteria.
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Affiliation(s)
- Sergio Álvarez-Pérez
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
- * E-mail:
| | - Clara de Vega
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
| | - Carlos M. Herrera
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
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McCann HC, Rikkerink EHA, Bertels F, Fiers M, Lu A, Rees-George J, Andersen MT, Gleave AP, Haubold B, Wohlers MW, Guttman DS, Wang PW, Straub C, Vanneste J, Rainey PB, Templeton MD. Genomic analysis of the Kiwifruit pathogen Pseudomonas syringae pv. actinidiae provides insight into the origins of an emergent plant disease. PLoS Pathog 2013; 9:e1003503. [PMID: 23935484 PMCID: PMC3723570 DOI: 10.1371/journal.ppat.1003503] [Citation(s) in RCA: 185] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2013] [Accepted: 05/28/2013] [Indexed: 11/19/2022] Open
Abstract
The origins of crop diseases are linked to domestication of plants. Most crops were domesticated centuries--even millennia--ago, thus limiting opportunity to understand the concomitant emergence of disease. Kiwifruit (Actinidia spp.) is an exception: domestication began in the 1930s with outbreaks of canker disease caused by P. syringae pv. actinidiae (Psa) first recorded in the 1980s. Based on SNP analyses of two circularized and 34 draft genomes, we show that Psa is comprised of distinct clades exhibiting negligible within-clade diversity, consistent with disease arising by independent samplings from a source population. Three clades correspond to their geographical source of isolation; a fourth, encompassing the Psa-V lineage responsible for the 2008 outbreak, is now globally distributed. Psa has an overall clonal population structure, however, genomes carry a marked signature of within-pathovar recombination. SNP analysis of Psa-V reveals hundreds of polymorphisms; however, most reside within PPHGI-1-like conjugative elements whose evolution is unlinked to the core genome. Removal of SNPs due to recombination yields an uninformative (star-like) phylogeny consistent with diversification of Psa-V from a single clone within the last ten years. Growth assays provide evidence of cultivar specificity, with rapid systemic movement of Psa-V in Actinidia chinensis. Genomic comparisons show a dynamic genome with evidence of positive selection on type III effectors and other candidate virulence genes. Each clade has highly varied complements of accessory genes encoding effectors and toxins with evidence of gain and loss via multiple genetic routes. Genes with orthologs in vascular pathogens were found exclusively within Psa-V. Our analyses capture a pathogen in the early stages of emergence from a predicted source population associated with wild Actinidia species. In addition to candidate genes as targets for resistance breeding programs, our findings highlight the importance of the source population as a reservoir of new disease.
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Affiliation(s)
- Honour C. McCann
- New Zealand Institute for Advanced Study and Allan Wilson Centre, Massey University, Auckland, New Zealand
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Canada
| | - Erik H. A. Rikkerink
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Frederic Bertels
- New Zealand Institute for Advanced Study and Allan Wilson Centre, Massey University, Auckland, New Zealand
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Mark Fiers
- The New Zealand Institute for Plant and Food Research Limited, Lincoln, New Zealand
| | - Ashley Lu
- The New Zealand Institute for Plant and Food Research Limited, Lincoln, New Zealand
| | - Jonathan Rees-George
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Mark T. Andersen
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Andrew P. Gleave
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | | | - Mark W. Wohlers
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - David S. Guttman
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Canada
| | - Pauline W. Wang
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Canada
| | - Christina Straub
- New Zealand Institute for Advanced Study and Allan Wilson Centre, Massey University, Auckland, New Zealand
| | - Joel Vanneste
- The New Zealand Institute for Plant and Food Research Limited, Ruakura, Hamilton, New Zealand
| | - Paul B. Rainey
- New Zealand Institute for Advanced Study and Allan Wilson Centre, Massey University, Auckland, New Zealand
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Matthew D. Templeton
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
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Vasileiadis S, Puglisi E, Arena M, Cappa F, van Veen JA, Cocconcelli PS, Trevisan M. Soil microbial diversity patterns of a lowland spring environment. FEMS Microbiol Ecol 2013; 86:172-84. [DOI: 10.1111/1574-6941.12150] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Revised: 05/09/2013] [Accepted: 05/21/2013] [Indexed: 11/30/2022] Open
Affiliation(s)
- Sotirios Vasileiadis
- Institute of Agricultural and Environmental Chemistry; Universitá Cattolica del Sacro Cuore; Piacenza; Italy
| | - Edoardo Puglisi
- Institute of Microbiology; Università Cattolica del Sacro Cuore; Piacenza; Italy
| | - Maria Arena
- Institute of Agricultural and Environmental Chemistry; Universitá Cattolica del Sacro Cuore; Piacenza; Italy
| | - Fabrizio Cappa
- Institute of Microbiology; Università Cattolica del Sacro Cuore; Piacenza; Italy
| | | | - Pier S. Cocconcelli
- Institute of Microbiology; Università Cattolica del Sacro Cuore; Piacenza; Italy
| | - Marco Trevisan
- Institute of Agricultural and Environmental Chemistry; Universitá Cattolica del Sacro Cuore; Piacenza; Italy
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Microbial community structure of three traditional zambian fermented products: mabisi, chibwantu and munkoyo. PLoS One 2013; 8:e63948. [PMID: 23691123 PMCID: PMC3653860 DOI: 10.1371/journal.pone.0063948] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Accepted: 04/11/2013] [Indexed: 11/19/2022] Open
Abstract
Around the world, raw materials are converted into fermented food products through microbial and enzymatic activity. Products are typically produced using a process known as batch culture, where small volumes of an old culture are used to initiate a fresh culture. Repeated over many years, and provided samples are not shared among producers, batch culture techniques allow for the natural evolution of independent microbial ecosystems. While these products form an important part of the diets of many people because of their nutritional, organoleptic and food safety properties, for many traditional African fermented products the microbial communities responsible for fermentation are largely unknown. Here we describe the microbial composition of three traditional fermented non-alcoholic beverages that are widely consumed across Zambia: the milk based product Mabisi and the cereal based products Munkoyo and Chibwantu. Using culture and non-culture based techniques, we found that six to eight lactic acid bacteria predominate in all products. We then used this data to investigate in more detail the factors affecting community structure. We found that products made from similar raw materials do not harbor microbial communities that are more similar to each other than those made from different raw materials. We also found that samples from the same product taken at the same location were as different from each other in terms of microbial community structure and composition, as those from geographically very distant locations. These results suggest that microbial community structure in these products is neither a simple consequence of the raw materials used, nor the particular suite of microbes available in the environment but that anthropogenic variables (e.g., competition among sellers or organoleptic preferences by different tribes) are important in shaping the microbial community structures.
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