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Mukhopadhyay S, Bishayi R, Shaji A, Lee AH, Gupta R, Mohajeri M, Katiyar A, McKee B, Schmitz IR, Shin R, Lele TP, Lele PP. Dynamic Adaptation in Extant Porins Facilitates Antibiotic Tolerance in Energetic Escherichia coli. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.07.583920. [PMID: 38496420 PMCID: PMC10942424 DOI: 10.1101/2024.03.07.583920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Bacteria can tolerate antibiotics despite lacking the genetic components for resistance. The prevailing notion is that tolerance results from depleted cellular energy or cell dormancy. In contrast to this view, many cells in the tolerant population of Escherichia coli can exhibit motility - a phenomenon that requires cellular energy, specifically, the proton-motive force (PMF). As these motile-tolerant cells are challenging to isolate from the heterogeneous tolerant population, their survival mechanism is unknown. Here, we discovered that motile bacteria segregate themselves from the tolerant population under micro-confinement, owing to their unique ability to penetrate micron-sized channels. Single-cell measurements on the motile-tolerant population showed that the cells retained a high PMF, but they did not survive through active efflux alone. By utilizing growth assays, single-cell fluorescence studies, and chemotaxis assays, we showed that the cells survived by dynamically inhibiting the function of existing porins in the outer membrane. A drug transport model for porin-mediated intake and efflux pump-mediated expulsion suggested that energetic tolerant cells withstand antibiotics by constricting their porins. The novel porin adaptation we have uncovered is independent of gene expression changes and may involve electrostatic modifications within individual porins to prevent extracellular ligand entry.
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2
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Kiørboe T. Predation in a Microbial World: Mechanisms and Trade-Offs of Flagellate Foraging. ANNUAL REVIEW OF MARINE SCIENCE 2024; 16:361-381. [PMID: 37368955 DOI: 10.1146/annurev-marine-020123-102001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
Heterotrophic nanoflagellates are the main consumers of bacteria and picophytoplankton in the ocean and thus play a key role in ocean biogeochemistry. They are found in all major branches of the eukaryotic tree of life but are united by all being equipped with one or a few flagella that they use to generate a feeding current. These microbial predators are faced with the challenges that viscosity at this small scale impedes predator-prey contact and that their foraging activity disturbs the ambient water and thus attracts their own flow-sensing predators. Here, I describe some of the diverse adaptations of the flagellum to produce sufficient force to overcome viscosity and of the flagellar arrangement to minimize fluid disturbances, and thus of the various solutions to optimize the foraging-predation risk trade-off. I demonstrate how insights into this trade-off can be used to develop robust trait-based models of microbial food webs.
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Affiliation(s)
- Thomas Kiørboe
- Centre for Ocean Life, DTU Aqua, Technical University of Denmark, Kongens Lyngby, Denmark;
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3
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Ramoneda J, Fan K, Lucas JM, Chu H, Bissett A, Strickland MS, Fierer N. Ecological relevance of flagellar motility in soil bacterial communities. THE ISME JOURNAL 2024; 18:wrae067. [PMID: 38648266 PMCID: PMC11095265 DOI: 10.1093/ismejo/wrae067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/27/2024] [Accepted: 04/18/2024] [Indexed: 04/25/2024]
Abstract
Flagellar motility is a key bacterial trait as it allows bacteria to navigate their immediate surroundings. Not all bacteria are capable of flagellar motility, and the distribution of this trait, its ecological associations, and the life history strategies of flagellated taxa remain poorly characterized. We developed and validated a genome-based approach to infer the potential for flagellar motility across 12 bacterial phyla (26 192 unique genomes). The capacity for flagellar motility was associated with a higher prevalence of genes for carbohydrate metabolism and higher maximum potential growth rates, suggesting that flagellar motility is more prevalent in environments with higher carbon availability. To test this hypothesis, we applied a method to infer the prevalence of flagellar motility in whole bacterial communities from metagenomic data and quantified the prevalence of flagellar motility across four independent field studies that each captured putative gradients in soil carbon availability (148 metagenomes). We observed a positive relationship between the prevalence of bacterial flagellar motility and soil carbon availability in all datasets. Since soil carbon availability is often correlated with other factors that could influence the prevalence of flagellar motility, we validated these observations using metagenomic data from a soil incubation experiment where carbon availability was directly manipulated with glucose amendments. This confirmed that the prevalence of bacterial flagellar motility is consistently associated with soil carbon availability over other potential confounding factors. This work highlights the value of combining predictive genomic and metagenomic approaches to expand our understanding of microbial phenotypic traits and reveal their general environmental associations.
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Affiliation(s)
- Josep Ramoneda
- Cooperative Institute for Research in Environmental Sciences (CIRES), University of Colorado, 80309 Boulder, CO, United States
- Spanish Research Council (CSIC), Center for Advanced Studies of Blanes (CEAB), 17300 Blanes, Spain
| | - Kunkun Fan
- Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 210008 Nanjing, China
| | - Jane M Lucas
- Cary Institute of Ecosystem Studies, 12545 Millbrook, NY, United States
| | - Haiyan Chu
- Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 210008 Nanjing, China
- University of Chinese Academy of Sciences, 101408 Beijing, China
| | | | - Michael S Strickland
- Department of Soil and Water Systems, University of Idaho, 83843 Moscow, ID, United States
| | - Noah Fierer
- Cooperative Institute for Research in Environmental Sciences (CIRES), University of Colorado, 80309 Boulder, CO, United States
- Department of Ecology and Evolutionary Biology, University of Colorado, 80309 Boulder, CO, United States
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4
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Xu 徐伟青 LWQ, Bryan JS, Kilic Z, Pressé S. Two-state swimming: Strategy and survival of a model bacterial predator in response to environmental cues. Biophys J 2023; 122:3060-3068. [PMID: 37330639 PMCID: PMC10432179 DOI: 10.1016/j.bpj.2023.06.008] [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: 11/18/2022] [Revised: 04/03/2023] [Accepted: 06/13/2023] [Indexed: 06/19/2023] Open
Abstract
Bdellovibrio bacteriovorus is a predatory bacterium preying upon Gram-negative bacteria. As such, B. bacteriovorus has the potential to control antibiotic-resistant pathogens and biofilm populations. To survive and reproduce, B. bacteriovorus must locate and infect a host cell. However, in the temporary absence of prey, it is largely unknown how B. bacteriovorus modulate their motility patterns in response to physical or chemical environmental cues to optimize their energy expenditure. To investigate B. bacteriovorus' predation strategy, we track and quantify their motion by measuring speed distributions as a function of starvation time. While an initial unimodal speed distribution relaxing to one for pure diffusion at long times may be expected, instead we observe a bimodal speed distribution with one mode centered around that expected from diffusion and the other centered at higher speeds. What is more, for an increasing amount of time over which B. bacteriovorus is starved, we observe a progressive reweighting from the active swimming state to an apparent diffusive state in the speed distribution. Distributions of trajectory-averaged speeds for B. bacteriovorus are largely unimodal, indicating switching between a faster swim speed and an apparent diffusive state within individual observed trajectories rather than there being distinct active swimming and apparent diffusive populations. We also find that B. bacteriovorus' apparent diffusive state is not merely caused by the diffusion of inviable bacteria as subsequent spiking experiments show that bacteria can be resuscitated and bimodality restored. Indeed, starved B. bacteriovorus may modulate the frequency and duration of active swimming as a means of balancing energy consumption and procurement. Our results thus point to a reweighting of the swimming frequency on a trajectory basis rather than a population level basis.
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Affiliation(s)
- Lance W Q Xu 徐伟青
- Department of Physics, Arizona State University, Tempe, Arizona; Center for Biological Physics, Arizona State University, Tempe, Arizona
| | - J Shepard Bryan
- Department of Physics, Arizona State University, Tempe, Arizona; Center for Biological Physics, Arizona State University, Tempe, Arizona
| | - Zeliha Kilic
- Single-Molecule Imaging Center, Saint Jude's Children Hospital, Memphis, Tennessee
| | - Steve Pressé
- Department of Physics, Arizona State University, Tempe, Arizona; Center for Biological Physics, Arizona State University, Tempe, Arizona; School of Molecular Sciences, Arizona State University, Tempe, Arizona.
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5
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Ramasamy KP, Brugel S, Eriksson K, Andersson A. Pseudomonas ability to utilize different carbon substrates and adaptation influenced by protozoan grazing. ENVIRONMENTAL RESEARCH 2023:116419. [PMID: 37321339 DOI: 10.1016/j.envres.2023.116419] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 06/09/2023] [Accepted: 06/12/2023] [Indexed: 06/17/2023]
Abstract
Bacteria are major utilizers of dissolved organic matter in aquatic systems. In coastal areas bacteria are supplied with a mixture of food sources, spanning from refractive terrestrial dissolved organic matter to labile marine autochthonous organic matter. Modelling scenarios indicate that in northern coastal areas, the inflow of terrestrial organic matter will increase, and autochthonous production will decrease, thus bacteria will experience a change in the food source composition. How bacteria will cope with such changes is not known. Here, we tested the ability of an isolated bacterium from the northern Baltic Sea coast, Pseudomonas sp., to adapt to varying substrates. We performed a 7-months chemostat experiment, where three different substrates were provided: glucose, representing labile autochthonous organic carbon, sodium benzoate representing refractive organic matter, and acetate - a labile but low energy food source. Growth rate has been pointed out as a key factor for fast adaptation, and since protozoan grazers speed-up the growth rate we added a ciliate to half of the incubations. The results show that the isolated Pseudomonas is adapted to utilize both labile and ring-structured refractive substrates. The growth rate was the highest on the benzoate substrate, and the production increased over time indicating that adaptation did occur. Further, our findings indicate that predation can cause Pseudomonas to change their phenotype to resist and promote survival in various carbon substrates. Genome sequencing reveals different mutations in the genome of adapted populations compared to the native populations, suggesting the adaptation of Pseudomonas sp. To changing environment.
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Affiliation(s)
- Kesava Priyan Ramasamy
- Department of Ecology and Environmental Science, Umeå University, Sweden; Umeå Marine Sciences Centre, Umeå University, Hörnefors, Sweden.
| | - Sonia Brugel
- Department of Ecology and Environmental Science, Umeå University, Sweden; Umeå Marine Sciences Centre, Umeå University, Hörnefors, Sweden
| | - Karolina Eriksson
- Department of Ecology and Environmental Science, Umeå University, Sweden; Umeå Marine Sciences Centre, Umeå University, Hörnefors, Sweden
| | - Agneta Andersson
- Department of Ecology and Environmental Science, Umeå University, Sweden; Umeå Marine Sciences Centre, Umeå University, Hörnefors, Sweden
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6
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Smith WPJ, Wucher BR, Nadell CD, Foster KR. Bacterial defences: mechanisms, evolution and antimicrobial resistance. Nat Rev Microbiol 2023:10.1038/s41579-023-00877-3. [PMID: 37095190 DOI: 10.1038/s41579-023-00877-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2023] [Indexed: 04/26/2023]
Abstract
Throughout their evolutionary history, bacteria have faced diverse threats from other microorganisms, including competing bacteria, bacteriophages and predators. In response to these threats, they have evolved sophisticated defence mechanisms that today also protect bacteria against antibiotics and other therapies. In this Review, we explore the protective strategies of bacteria, including the mechanisms, evolution and clinical implications of these ancient defences. We also review the countermeasures that attackers have evolved to overcome bacterial defences. We argue that understanding how bacteria defend themselves in nature is important for the development of new therapies and for minimizing resistance evolution.
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Affiliation(s)
- William P J Smith
- Division of Genomics, Infection and Evolution, University of Manchester, Manchester, UK.
- Department of Biology, University of Oxford, Oxford, UK.
- Department of Biochemistry, University of Oxford, Oxford, UK.
| | - Benjamin R Wucher
- Department of Biological sciences, Dartmouth College, Hanover, NH, USA
| | - Carey D Nadell
- Department of Biological sciences, Dartmouth College, Hanover, NH, USA
| | - Kevin R Foster
- Department of Biology, University of Oxford, Oxford, UK.
- Department of Biochemistry, University of Oxford, Oxford, UK.
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7
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Wisnoski NI, Lennon JT. Scaling up and down: movement ecology for microorganisms. Trends Microbiol 2023; 31:242-253. [PMID: 36280521 DOI: 10.1016/j.tim.2022.09.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 09/28/2022] [Accepted: 09/30/2022] [Indexed: 11/06/2022]
Abstract
Movement is critical for the fitness of organisms, both large and small. It dictates how individuals acquire resources, evade predators, exchange genetic material, and respond to stressful environments. Movement also influences ecological and evolutionary dynamics at higher organizational levels, such as populations and communities. However, the links between individual motility and the processes that generate and maintain microbial diversity are poorly understood. Movement ecology is a framework linking the physiological and behavioral properties of individuals to movement patterns across scales of space, time, and biological organization. By synthesizing insights from cell biology, ecology, and evolution, we expand theory from movement ecology to predict the causes and consequences of microbial movements.
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Affiliation(s)
- Nathan I Wisnoski
- Wyoming Geographic Information Science Center, University of Wyoming, Laramie, WY 82071, USA; Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA.
| | - Jay T Lennon
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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8
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Afridi MS, Fakhar A, Kumar A, Ali S, Medeiros FHV, Muneer MA, Ali H, Saleem M. Harnessing microbial multitrophic interactions for rhizosphere microbiome engineering. Microbiol Res 2022; 265:127199. [PMID: 36137486 DOI: 10.1016/j.micres.2022.127199] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 07/02/2022] [Accepted: 09/13/2022] [Indexed: 10/14/2022]
Abstract
The rhizosphere is a narrow and dynamic region of plant root-soil interfaces, and it's considered one of the most intricate and functionally active ecosystems on the Earth, which boosts plant health and alleviates the impact of biotic and abiotic stresses. Improving the key functions of the microbiome via engineering the rhizosphere microbiome is an emerging tool for improving plant growth, resilience, and soil-borne diseases. Recently, the advent of omics tools, gene-editing techniques, and sequencing technology has allowed us to unravel the entangled webs of plant-microbes interactions, enhancing plant fitness and tolerance to biotic and abiotic challenges. Plants secrete signaling compounds with low molecular weight into the rhizosphere, that engage various species to generate a massive deep complex array. The underlying principle governing the multitrophic interactions of the rhizosphere microbiome is yet unknown, however, some efforts have been made for disease management and agricultural sustainability. This review discussed the intra- and inter- microbe-microbe and microbe-animal interactions and their multifunctional roles in rhizosphere microbiome engineering for plant health and soil-borne disease management. Simultaneously, it investigates the significant impact of immunity utilizing PGPR and cover crop strategy in increasing rhizosphere microbiome functions for plant development and protection using omics techniques. The ecological engineering of rhizosphere plant interactions could be used as a potential alternative technology for plant growth improvement, sustainable disease control management, and increased production of economically significant crops.
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Affiliation(s)
- Muhammad Siddique Afridi
- Department of Plant Pathology, Federal University of Lavras, CP3037, 37200-900 Lavras, MG, Brazil.
| | - Ali Fakhar
- Division of Applied Science, Gyeongsang National University, South Korea
| | - Ashwani Kumar
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University (A Central University), Sagar 470003, MP, India
| | - Sher Ali
- NMR Lab, Department of Chemistry, Federal University of Paraná, Curitiba 81530-900, PR, Brazil
| | - Flavio H V Medeiros
- Department of Plant Pathology, Federal University of Lavras, CP3037, 37200-900 Lavras, MG, Brazil
| | - Muhammad Atif Muneer
- International Magnesium Institute, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hina Ali
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Muhammad Saleem
- Department of Biological Sciences, Alabama State University, Montgomery, AL 36104, USA
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9
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Random encounters and amoeba locomotion drive the predation of Listeria monocytogenes by Acanthamoeba castellanii. Proc Natl Acad Sci U S A 2022; 119:e2122659119. [PMID: 35914149 PMCID: PMC9371647 DOI: 10.1073/pnas.2122659119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Predatory protozoa play an essential role in shaping microbial populations. Among these protozoa, Acanthamoeba are ubiquitous in the soil and aqueous environments inhabited by Listeria monocytogenes. Observations of predator-prey interactions between these two microorganisms revealed a predation strategy in which Acanthamoeba castellanii assemble L. monocytogenes in aggregates, termed backpacks, on their posterior. The rapid formation and specific location of backpacks led to the assumption that A. castellanii may recruit L. monocytogenes by releasing an attractant. However, this hypothesis has not been validated, and the mechanisms driving this process remained unknown. Here, we combined video microscopy, microfluidics, single-cell image analyses, and theoretical modeling to characterize predator-prey interactions of A. castellanii and L. monocytogenes and determined whether bacterial chemotaxis contributes to the backpack formation. Our results indicate that L. monocytogenes captures are not driven by chemotaxis. Instead, random encounters of bacteria with amoebae initialize bacterial capture and aggregation. This is supported by the strong correlation between experimentally derived capture rates and theoretical encounter models at the single-cell level. Observations of the spatial rearrangement of L. monocytogenes trapped by A. castellanii revealed that bacterial aggregation into backpacks is mainly driven by amoeboid locomotion. Overall, we show that two nonspecific, independent mechanisms, namely random encounters enhanced by bacterial motility and predator surface-bound locomotion, drive backpack formation, resulting in a bacterial aggregate on the amoeba ready for phagocytosis. Due to the prevalence of these two processes in the environment, we expect this strategy to be widespread among amoebae, contributing to their effectiveness as predators.
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10
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Wei J, Li X, Xu X, Xu W, Chen Y, Zhang L, Yang Z, Huang Y. Elevated temperature mitigates the prolonged effect of high nitrogen on Microcystis aeruginosa removal through mixotrophic Ochromonas gloeopara grazing. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 820:153267. [PMID: 35074368 DOI: 10.1016/j.scitotenv.2022.153267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/14/2022] [Accepted: 01/15/2022] [Indexed: 06/14/2023]
Abstract
Cyanobacterial blooms are increasingly threatening the aquatic ecosystem functioning as a result of the global warming and eutrophication. The "top-down" control of cyanobacteria from consumers like the protozoans shows great potential because of the effectiveness and environment-friendliness. To reveal how the nutrition availability and elevated temperature affect the cyanobacteria removal through protozoans grazing, we grew the toxic Microcystis aeruginosa and the mixotrophic Ochromonas gloeopara in monocultures and cocultures at environmentally relevant nitrogen levels (0.5-8.0 mg L-1) under 25 °C and 30 °C, respectively. The growth of M. aeruginosa in monocultures was significantly enhanced as nitrogen concentration and temperature rose, partially benefitting from the promoted photosynthesis. By contrast, nitrogen availability affected neither the photoautotrophic growth nor the feeding on Microcystis of the mixotrophic O. gloeopara, but high temperature induced the mixotroph to be more heterotrophic as evidenced by the suppressed photosynthesis but strengthened feeding activity. Accordingly, the M. aeruginosa removal through O. gloeopara grazing in cocultures was delayed with increasing nitrogen, which, however, was sharply accelerated by elevated temperature. Based on the Gaussian models fitting, the theoretical time that the Microcystis was removed at 25 °C was prolonged from about 7.5 days to 10 days with increased nitrogen, but it was reduced to less than 4.6 days in all groups at 30 °C. While the intensity of Microcystis blooms is strongly positively correlated to the nutrition availability and temperature, the present study provided references for the practical application of Microcystis removal through grazing outdoors.
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Affiliation(s)
- Junjun Wei
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China
| | - Xianxian Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China
| | - Xiaoqing Xu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China
| | - Wenjie Xu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China
| | - Yitong Chen
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China
| | - Lu Zhang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China
| | - Zhou Yang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China
| | - Yuan Huang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China.
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11
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Custer GF, Bresciani L, Dini-Andreote F. Ecological and Evolutionary Implications of Microbial Dispersal. Front Microbiol 2022; 13:855859. [PMID: 35464980 PMCID: PMC9019484 DOI: 10.3389/fmicb.2022.855859] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 03/14/2022] [Indexed: 12/04/2022] Open
Abstract
Dispersal is simply defined as the movement of species across space and time. Despite this terse definition, dispersal is an essential process with direct ecological and evolutionary implications that modulate community assembly and turnover. Seminal ecological studies have shown that environmental context (e.g., local edaphic properties, resident community), dispersal timing and frequency, and species traits, collectively account for patterns of species distribution resulting in either their persistence or unsuccessful establishment within local communities. Despite the key importance of this process, relatively little is known about how dispersal operates in microbiomes across divergent systems and community types. Here, we discuss parallels of macro- and micro-organismal ecology with a focus on idiosyncrasies that may lead to novel mechanisms by which dispersal affects the structure and function of microbiomes. Within the context of ecological implications, we revise the importance of short- and long-distance microbial dispersal through active and passive mechanisms, species traits, and community coalescence, and how these align with recent advances in metacommunity theory. Conversely, we enumerate how microbial dispersal can affect diversification rates of species by promoting gene influxes within local communities and/or shifting genes and allele frequencies via migration or de novo changes (e.g., horizontal gene transfer). Finally, we synthesize how observed microbial assemblages are the dynamic outcome of both successful and unsuccessful dispersal events of taxa and discuss these concepts in line with the literature, thus enabling a richer appreciation of this process in microbiome research.
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Affiliation(s)
- Gordon F Custer
- Department of Plant Science and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, United States
| | - Luana Bresciani
- Department of Plant Science and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, United States
| | - Francisco Dini-Andreote
- Department of Plant Science and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, United States
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12
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Keegstra JM, Carrara F, Stocker R. The ecological roles of bacterial chemotaxis. Nat Rev Microbiol 2022; 20:491-504. [PMID: 35292761 DOI: 10.1038/s41579-022-00709-w] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2022] [Indexed: 02/08/2023]
Abstract
How bacterial chemotaxis is performed is much better understood than why. Traditionally, chemotaxis has been understood as a foraging strategy by which bacteria enhance their uptake of nutrients and energy, yet it has remained puzzling why certain less nutritious compounds are strong chemoattractants and vice versa. Recently, we have gained increased understanding of alternative ecological roles of chemotaxis, such as navigational guidance in colony expansion, localization of hosts or symbiotic partners and contribution to microbial diversity by the generation of spatial segregation in bacterial communities. Although bacterial chemotaxis has been observed in a wide range of environmental settings, insights into the phenomenon are mostly based on laboratory studies of model organisms. In this Review, we highlight how observing individual and collective migratory behaviour of bacteria in different settings informs the quantification of trade-offs, including between chemotaxis and growth. We argue that systematically mapping when and where bacteria are motile, in particular by transgenerational bacterial tracking in dynamic environments and in situ approaches from guts to oceans, will open the door to understanding the rich interplay between metabolism and growth and the contribution of chemotaxis to microbial life.
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Affiliation(s)
| | - Francesco Carrara
- Institute for Environmental Engineering, ETH Zurich, Zurich, Switzerland
| | - Roman Stocker
- Institute for Environmental Engineering, ETH Zurich, Zurich, Switzerland.
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13
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Hoque MM, Noorian P, Espinoza-Vergara G, Manuneedhi Cholan P, Kim M, Rahman MH, Labbate M, Rice SA, Pernice M, Oehlers SH, McDougald D. Adaptation to an amoeba host drives selection of virulence-associated traits in Vibrio cholerae. THE ISME JOURNAL 2022; 16:856-867. [PMID: 34654895 PMCID: PMC8857207 DOI: 10.1038/s41396-021-01134-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 09/20/2021] [Accepted: 09/29/2021] [Indexed: 12/02/2022]
Abstract
Predation by heterotrophic protists drives the emergence of adaptive traits in bacteria, and often these traits lead to altered interactions with hosts and persistence in the environment. Here we studied adaptation of the cholera pathogen, Vibrio cholerae during long-term co-incubation with the protist host, Acanthamoeba castellanii. We determined phenotypic and genotypic changes associated with long-term intra-amoebal host adaptation and how this impacts pathogen survival and fitness. We showed that adaptation to the amoeba host leads to temporal changes in multiple phenotypic traits in V. cholerae that facilitate increased survival and competitive fitness in amoeba. Genome sequencing and mutational analysis revealed that these altered lifestyles were linked to non-synonymous mutations in conserved regions of the flagellar transcriptional regulator, flrA. Additionally, the mutations resulted in enhanced colonisation in zebrafish, establishing a link between adaptation of V. cholerae to amoeba predation and enhanced environmental persistence. Our results show that pressure imposed by amoeba on V. cholerae selects for flrA mutations that serves as a key driver for adaptation. Importantly, this study provides evidence that adaptive traits that evolve in pathogens in response to environmental predatory pressure impact the colonisation of eukaryotic organisms by these pathogens.
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Affiliation(s)
- M. Mozammel Hoque
- grid.117476.20000 0004 1936 7611The iThree Institute, University of Technology Sydney, Sydney, NSW Australia
| | - Parisa Noorian
- grid.117476.20000 0004 1936 7611The iThree Institute, University of Technology Sydney, Sydney, NSW Australia
| | - Gustavo Espinoza-Vergara
- grid.117476.20000 0004 1936 7611The iThree Institute, University of Technology Sydney, Sydney, NSW Australia
| | - Pradeep Manuneedhi Cholan
- grid.1013.30000 0004 1936 834XTuberculosis Research Program at the Centenary Institute, The University of Sydney, Camperdown, NSW Australia ,grid.1013.30000 0004 1936 834XFaculty of Medicine and Health & Marie Bashir Institute, The University of Sydney, Camperdown, NSW Australia
| | - Mikael Kim
- grid.117476.20000 0004 1936 7611Climate Change Cluster, University of Technology Sydney, Sydney, NSW Australia
| | - Md Hafizur Rahman
- grid.117476.20000 0004 1936 7611School of Life Sciences, Faculty of Science, University of Technology Sydney, Sydney, NSW Australia
| | - Maurizio Labbate
- grid.117476.20000 0004 1936 7611School of Life Sciences, Faculty of Science, University of Technology Sydney, Sydney, NSW Australia
| | - Scott A. Rice
- grid.117476.20000 0004 1936 7611The iThree Institute, University of Technology Sydney, Sydney, NSW Australia ,grid.59025.3b0000 0001 2224 0361Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Mathieu Pernice
- grid.117476.20000 0004 1936 7611Climate Change Cluster, University of Technology Sydney, Sydney, NSW Australia
| | - Stefan H. Oehlers
- grid.1013.30000 0004 1936 834XTuberculosis Research Program at the Centenary Institute, The University of Sydney, Camperdown, NSW Australia ,grid.1013.30000 0004 1936 834XFaculty of Medicine and Health & Marie Bashir Institute, The University of Sydney, Camperdown, NSW Australia
| | - Diane McDougald
- grid.117476.20000 0004 1936 7611The iThree Institute, University of Technology Sydney, Sydney, NSW Australia ,grid.59025.3b0000 0001 2224 0361Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
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14
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Shteindel N, Gerchman Y. Pseudomonas aeruginosa Mobbing-Like Behavior against Acanthamoeba castellanii Bacterivore and Its Rapid Control by Quorum Sensing and Environmental Cues. Microbiol Spectr 2021; 9:e0064221. [PMID: 34851177 PMCID: PMC8635135 DOI: 10.1128/spectrum.00642-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 10/26/2021] [Indexed: 01/20/2023] Open
Abstract
Mobbing, group attack of prey on predator, is a behavior seen in many animal species in which prey animals use numbers and coordination to counter individually superior predators. We studied attack behavior of Pseudomonas aeruginosa toward the bacterivore Acanthamoeba castellanii. This behavior consists of directed motility toward and specific adhesion to the predator cells, enacted in seconds and responding to both prey and predator population densities. Attack coordination relies on remote sensing of the predator and the use of the Pseudomonas quinolone signal (PQS), a P. aeruginosa species-specific quorum sensing molecule. Mutants unable to produce the PQS show unspecific adhesion and reduced survival, and a corresponding increase in predator population occurs as a result of predation. The addition of an external PQS restored some predator-specific adherence within seconds, suggesting a novel response mechanism to this quorum sensing (QS) signal. Fast behavioral response of P. aeruginosa to PQS is also supported by the rate of signal accumulation in the culture, reaching relevant concentrations within minutes, enabling bacteria response to self population density in these short timescales. These results portray a well-regulated group attack of the bacteria against their predator, reacting within seconds to environmental cues and species-specific signaling, which is analogous in many ways to animal mobbing behavior. IMPORTANCE Pseudomonas aeruginosa was shown previously to attack amoebae and other predators by adhering to them and injecting them with virulent substances. In this work, we show that an active, coordinated group behavior is enacted by the bacteria to utilize these molecular components, responding to both predator and bacterial population density. In addition to their ecological significance, immediate behavioral changes observed in response to PQS suggest the existence of a fast QS signal cascade, which is different from canonical QS that relies on slow-to-respond gene regulation. Similar regulatory circuits may drive other bacterial adaptations and pathogenicity mechanisms and may have important clinical implications.
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Affiliation(s)
- Nimrod Shteindel
- Department of Environmental and Evolutionary Biology, Faculty of Natural Science, University of Haifa, Haifa, Israel
| | - Yoram Gerchman
- Department of Environmental and Evolutionary Biology, Faculty of Natural Science, University of Haifa, Haifa, Israel
- Department of Biology, Oranim College, Kiryat Tivon, Israel
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15
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Ooi MC, Goulden EF, Smith GG, Bridle AR. Predatory bacteria in the haemolymph of the cultured spiny lobster Panulirus ornatus. MICROBIOLOGY (READING, ENGLAND) 2021; 167. [PMID: 34846286 PMCID: PMC8743626 DOI: 10.1099/mic.0.001113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Bdellovibrio and like organisms (BALOs) are Gram-negative obligate predators of other bacteria in a range of environments. The recent discovery of BALOs in the circulatory system of cultured spiny lobster P. ornatus warrants more investigation. We used a combination of co-culture agar and broth assays and transmission electron microscopy to show a Halobacteriovorax sp. strain Hbv preyed upon the model prey bacterium Vibrio sp. strain Vib. The haemolymph microbiome of juvenile P. ornatus was characterised following injection of phosphate buffered saline (control) or prey and/or predator bacteria for 3 d. The predator Hbv had no effect on survival compared to the control after 3 d. However, when compared to the prey only treatment group, lobsters injected with both prey and predator showed significantly lower abundance of genus Vibrio in the haemolymph bacterial community composition. This study indicates that predatory bacteria are not pathogenic and may assist in controlling microbial population growth in the haemolymph of lobsters.
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Affiliation(s)
- Mei C. Ooi
- Institute for Marine and Antarctic Studies, University of Tasmania, TAS, Australia
- *Correspondence: Mei C. Ooi,
| | - Evan F. Goulden
- Institute for Marine and Antarctic Studies, University of Tasmania, TAS, Australia
- Bribie Island Research Centre, Department of Agriculture and Fisheries, QLD, Australia
| | - Gregory G. Smith
- Institute for Marine and Antarctic Studies, University of Tasmania, TAS, Australia
| | - Andrew R. Bridle
- Institute for Marine and Antarctic Studies, University of Tasmania, TAS, Australia
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16
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Shu L, He Z, Guan X, Yang X, Tian Y, Zhang S, Wu C, He Z, Yan Q, Wang C, Shi Y. A dormant amoeba species can selectively sense and predate on different soil bacteria. Funct Ecol 2021. [DOI: 10.1111/1365-2435.13824] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Longfei Shu
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)Sun Yat‐sen University Guangzhou China
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology Sun Yat‐Sen University Guangzhou China
| | - Zhenzhen He
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)Sun Yat‐sen University Guangzhou China
| | - Xiaotong Guan
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)Sun Yat‐sen University Guangzhou China
| | - Xueqin Yang
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)Sun Yat‐sen University Guangzhou China
| | - Yuehui Tian
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)Sun Yat‐sen University Guangzhou China
| | - Siyi Zhang
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)Sun Yat‐sen University Guangzhou China
| | - Chenyuan Wu
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)Sun Yat‐sen University Guangzhou China
| | - Zhili He
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)Sun Yat‐sen University Guangzhou China
| | - Qingyun Yan
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)Sun Yat‐sen University Guangzhou China
| | - Cheng Wang
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)Sun Yat‐sen University Guangzhou China
| | - Yijing Shi
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology Sun Yat‐Sen University Guangzhou China
- School of Environment Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment SCNU Environmental Research InstituteSouth China Normal University Guangzhou China
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17
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Amacker N, Gao Z, Agaras BC, Latz E, Kowalchuk GA, Valverde CF, Jousset A, Weidner S. Biocontrol Traits Correlate With Resistance to Predation by Protists in Soil Pseudomonads. Front Microbiol 2020; 11:614194. [PMID: 33384680 PMCID: PMC7769776 DOI: 10.3389/fmicb.2020.614194] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 11/19/2020] [Indexed: 12/11/2022] Open
Abstract
Root-colonizing bacteria can support plant growth and help fend off pathogens. It is clear that such bacteria benefit from plant-derived carbon, but it remains ambiguous why they invest in plant-beneficial traits. We suggest that selection via protist predation contributes to recruitment of plant-beneficial traits in rhizosphere bacteria. To this end, we examined the extent to which bacterial traits associated with pathogen inhibition coincide with resistance to protist predation. We investigated the resistance to predation of a collection of Pseudomonas spp. against a range of representative soil protists covering three eukaryotic supergroups. We then examined whether patterns of resistance to predation could be explained by functional traits related to plant growth promotion, disease suppression and root colonization success. We observed a strong correlation between resistance to predation and phytopathogen inhibition. In addition, our analysis highlighted an important contribution of lytic enzymes and motility traits to resist predation by protists. We conclude that the widespread occurrence of plant-protective traits in the rhizosphere microbiome may be driven by the evolutionary pressure for resistance against predation by protists. Protists may therefore act as microbiome regulators promoting native bacteria involved in plant protection against diseases.
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Affiliation(s)
- Nathalie Amacker
- Ecology and Biodiversity Group, Institute of Environmental Biology, University of Utrecht, Utrecht, Netherlands
| | - Zhilei Gao
- Ecology and Biodiversity Group, Institute of Environmental Biology, University of Utrecht, Utrecht, Netherlands
| | - Betina C. Agaras
- Laboratorio de Fisiología y Genética de Bacterias Beneficiosas para Plantas, Departamento de Ciencia y Tecnología, Centro de Bioquímica y Microbiología del Suelo, Universidad Nacional de Quilmes, Buenos Aires, Argentina
| | - Ellen Latz
- German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Leipzig, Germany
| | - George A. Kowalchuk
- Ecology and Biodiversity Group, Institute of Environmental Biology, University of Utrecht, Utrecht, Netherlands
| | - Claudio F. Valverde
- Laboratorio de Fisiología y Genética de Bacterias Beneficiosas para Plantas, Departamento de Ciencia y Tecnología, Centro de Bioquímica y Microbiología del Suelo, Universidad Nacional de Quilmes, Buenos Aires, Argentina
| | - Alexandre Jousset
- Ecology and Biodiversity Group, Institute of Environmental Biology, University of Utrecht, Utrecht, Netherlands
| | - Simone Weidner
- Ecology and Biodiversity Group, Institute of Environmental Biology, University of Utrecht, Utrecht, Netherlands
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands
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18
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Guillonneau R, Baraquet C, Molmeret M. Marine Bacteria Display Different Escape Mechanisms When Facing Their Protozoan Predators. Microorganisms 2020; 8:microorganisms8121982. [PMID: 33322808 PMCID: PMC7763514 DOI: 10.3390/microorganisms8121982] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/24/2020] [Accepted: 12/10/2020] [Indexed: 12/20/2022] Open
Abstract
Free-living amoeba are members of microbial communities such as biofilms in terrestrial, fresh, and marine habitats. Although they are known to live in close association with bacteria in many ecosystems such as biofilms, they are considered to be major bacterial predators in many ecosystems. Little is known on the relationship between protozoa and marine bacteria in microbial communities, more precisely on how bacteria are able survive in environmental niches where these bacterial grazers also live. The objective of this work is to study the interaction between the axenized ubiquitous amoeba Acanthamoeba castellanii and four marine bacteria isolated from immersed biofilm, in order to evaluate if they would be all grazed upon by amoeba or if they would be able to survive in the presence of their predator. At a low bacteria-to-amoeba ratio, we show that each bacterium is phagocytized and follows a singular intracellular path within this host cell, which appears to delay or to prevent bacterial digestion. In particular, one of the bacteria was found in the amoeba nucleolar compartment whereas another strain was expelled from the amoeba in vesicles. We then looked at the fate of the bacteria grown in a higher bacteria-to-amoeba ratio, as a preformed mono- or multi-species biofilm in the presence of A. castellanii. We show that all biofilms were subjected to detachment from the surface in the presence of the amoeba or its supernatant. Overall, these results show that bacteria, when facing the same predator, exhibit a variety of escape mechanisms at the cellular and population level, when we could have expected a simple bacterial grazing. Therefore, this study unravels new insights into the survival of environmental bacteria when facing predators that they could encounter in the same microbial communities.
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Affiliation(s)
- Richard Guillonneau
- Laboratoire MAPIEM, EA4323, Université de Toulon, 83130 La Garde, France; (R.G.); (C.B.)
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Claudine Baraquet
- Laboratoire MAPIEM, EA4323, Université de Toulon, 83130 La Garde, France; (R.G.); (C.B.)
| | - Maëlle Molmeret
- Laboratoire MAPIEM, EA4323, Université de Toulon, 83130 La Garde, France; (R.G.); (C.B.)
- Correspondence:
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19
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Cairns J, Moerman F, Fronhofer EA, Altermatt F, Hiltunen T. Evolution in interacting species alters predator life-history traits, behaviour and morphology in experimental microbial communities. Proc Biol Sci 2020; 287:20200652. [PMID: 32486984 DOI: 10.1098/rspb.2020.0652] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Predator-prey interactions heavily influence the dynamics of many ecosystems. An increasing body of evidence suggests that rapid evolution and coevolution can alter these interactions, with important ecological implications, by acting on traits determining fitness, including reproduction, anti-predatory defence and foraging efficiency. However, most studies to date have focused only on evolution in the prey species, and the predator traits in (co)evolving systems remain poorly understood. Here, we investigated changes in predator traits after approximately 600 generations in a predator-prey (ciliate-bacteria) evolutionary experiment. Predators independently evolved on seven different prey species, allowing generalization of the predator's evolutionary response. We used highly resolved automated image analysis to quantify changes in predator life history, morphology and behaviour. Consistent with previous studies, we found that prey evolution impaired growth of the predator, although the effect depended on the prey species. By contrast, predator evolution did not cause a clear increase in predator growth when feeding on ancestral prey. However, predator evolution affected morphology and behaviour, increasing size, speed and directionality of movement, which have all been linked to higher prey search efficiency. These results show that in (co)evolving systems, predator adaptation can occur in traits relevant to foraging efficiency without translating into an increased ability of the predator to grow on the ancestral prey type.
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Affiliation(s)
- Johannes Cairns
- Wellcome Sanger Institute, Cambridge CB10 1SA, UK.,Organismal and Evolutionary Biology Research Programme, Department of Computer Science, University of Helsinki, 00014 Helsinki, Finland.,Department of Microbiology, University of Helsinki, PO Box 56, 00014 Helsinki, Finland
| | - Felix Moerman
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600 Dübendorf, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland.,ISEM, University of Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | | | - Florian Altermatt
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600 Dübendorf, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Teppo Hiltunen
- Department of Microbiology, University of Helsinki, PO Box 56, 00014 Helsinki, Finland.,Department of Biology, University of Turku, 20014 Turku, Finland
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20
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Koehl MAR. Selective factors in the evolution of multicellularity in choanoflagellates. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2020; 336:315-326. [PMID: 32198827 DOI: 10.1002/jez.b.22941] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 02/12/2020] [Accepted: 02/17/2020] [Indexed: 11/10/2022]
Abstract
Choanoflagellates, unicellular eukaryotes that can form multicellular colonies by cell division and that share a common ancestor with animals, are used as a model system to study functional consequences of being unicellular versus colonial. This review examines performance differences between unicellular and multicellular choanoflagellates in swimming, feeding, and avoiding predation, to provide insights about possible selective advantages of being multicellular for the protozoan ancestors of animals. Each choanoflagellate cell propels water by beating a single flagellum and captures bacterial prey on a collar of microvilli around the flagellum. Formation of multicellular colonies does not improve the swimming performance, but the flux of prey-bearing water to the collars of some of the cells in colonies of certain configurations can be greater than for single cells. Colony geometry appears to affect whether cells in colonies catch more prey per cell per time than do unicellular choanoflagellates. Although multicellular choanoflagellates show chemokinetic behavior in response to oxygen, only the unicellular dispersal stage (fast swimmers without collars) use pH signals to aggregate in locations where bacterial prey might be abundant. Colonies produce larger hydrodynamic signals than do single cells, and raptorial protozoan predators capture colonies while ignoring single cells. In contrast, ciliate predators entrain both single cells and colonies in their feeding currents, but reject larger colonies, whereas passive heliozoan predators show no preference. Thus, the ability of choanoflagellate cells to differentiate into different morphotypes, including multicellular forms, in response to variable aquatic environments might have provided a selective advantage to the ancestors of animals.
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Affiliation(s)
- M A R Koehl
- Department of Integrative Biology, University of California, Berkeley, California
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21
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Nguyen BAT, Chen QL, He JZ, Hu HW. Microbial regulation of natural antibiotic resistance: Understanding the protist-bacteria interactions for evolution of soil resistome. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 705:135882. [PMID: 31818598 DOI: 10.1016/j.scitotenv.2019.135882] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 11/26/2019] [Accepted: 11/30/2019] [Indexed: 06/10/2023]
Abstract
The emergence, evolution and spread of antibiotic resistance genes (ARGs) in the environment represent a global threat to human health. Our knowledge of antibiotic resistance in human-impacted ecosystems is rapidly growing with antibiotic use, organic fertilization and wastewater irrigation identified as key selection pressures. However, the importance of biological interactions, especially predation and competition, as a potential driver of antibiotic resistance in the natural environment with limited anthropogenic disturbance remains largely overlooked. Stress-affected bacteria develop resistance to maximize competition and survival, and similarly bacteria may develop resistance to fight stress under the predation pressure of protists, an essential component of the soil microbiome. In this article, we summarized the major findings for the prevalence of natural ARGs on our planet and discussed the potential selection pressures driving the evolution and development of antibiotic resistance in natural settings. This is the first article that reviewed the potential links between protists and the antibiotic resistance of bacteria, and highlighted the importance of predation by protists as a crucial selection pressure of antibiotic resistance in the absence of anthropogenic disturbance. We conclude that an improved ecological understanding of the protists-bacteria interactions and other biological relationships would greatly expand our ability to predict and mitigate the environmental antibiotic resistance under the context of global change.
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Affiliation(s)
- Bao-Anh Thi Nguyen
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Qing-Lin Chen
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Ji-Zheng He
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Hang-Wei Hu
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia.
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22
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De Corte D, Paredes G, Yokokawa T, Sintes E, Herndl GJ. Differential Response of Cafeteria roenbergensis to Different Bacterial and Archaeal Prey Characteristics. MICROBIAL ECOLOGY 2019; 78:1-5. [PMID: 30448922 DOI: 10.1007/s00248-018-1293-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 11/09/2018] [Indexed: 06/09/2023]
Abstract
In the marine environment, the abundance of Bacteria and Archaea is either controlled bottom-up via nutrient availability or top-down via grazing. Heterotrophic nanoflagellates (HNF) are mainly responsible for prokaryotic grazing losses besides viral lysis. However, the grazing specificity of HNF on specific bacterial and archaeal taxa is under debate. Bacteria and Archaea might have different nutritive values and surface properties affecting the growth rates of HNF. In this study, we offered different bacterial and archaeal strains with different morphologic and physiologic characteristics to Cafeteria roenbergensis, one of the most abundant and ubiquitous species of HNF in the ocean. Two Nitrosopumilus maritimus-related strains isolated from the northern Adriatic Sea (Nitrosopumilus adriaticus, Nitrosopumilus piranensis), two Nitrosococcus strains, and two fast growing marine Bacteria (Pseudoalteromonas sp. and Marinobacter sp.) were fed to Cafeteria cultures. Cafeteria roenbergensis exhibited high growth rates when feeding on Pseudoalteromonas sp., Marinobacter sp., and Nitrosopumilus adriaticus, while the addition of the other strains resulted in minimal growth. Taken together, our data suggest that the differences in growth of Cafeteria roenbergensis associated to grazing on different thaumarchaeal and bacterial strains are likely due to the subtle metabolic, cell size, and physiological differences between different bacterial and thaumarchaeal taxa. Moreover, Nitrosopumilus adriaticus experienced a similar grazing pressure by Cafeteria roenbergensis as compared to the other strains, suggesting that other HNF may also prey on Archaea which might have important consequences on the global biogeochemical cycles.
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Affiliation(s)
- Daniele De Corte
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria.
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natushima 2-15, Yokosuka, Kanagawa, 237-0061, Japan.
| | - Gabriela Paredes
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Taichi Yokokawa
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natushima 2-15, Yokosuka, Kanagawa, 237-0061, Japan
| | - Eva Sintes
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Gerhard J Herndl
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, PO Box 59, 1790 AB, Den Burg, The Netherlands
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23
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Dong Y, Geng J, Liu J, Pang M, Awan F, Lu C, Liu Y. Roles of three TonB systems in the iron utilization and virulence of the Aeromonas hydrophila Chinese epidemic strain NJ-35. Appl Microbiol Biotechnol 2019; 103:4203-4215. [PMID: 30972460 DOI: 10.1007/s00253-019-09757-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 03/08/2019] [Indexed: 12/19/2022]
Abstract
The TonB system functions in iron transport and has been identified in certain Gram-negative bacteria. Recently, we reported three TonB systems in the Aeromonas hydrophila Chinese epidemic strain NJ-35, but the functions of these systems have not been thoroughly elucidated to date. In this study, we investigated the role of these TonB systems in A. hydrophila iron utilization and virulence. We found that tonB1 and tonB2 were preferentially transcribed in iron-chelated conditions, where gene expression levels were approximately 8- and 68-fold higher compared with iron-rich conditions, respectively; tonB3 was consistently transcribed at a low level under iron-repleted and iron-depleted conditions. Only the TonB2 system was required to utilize iron-binding proteins. The tonB123 mutant showed increased susceptibility to erythromycin and roxithromycin. In addition, all three tonB genes were involved in A. hydrophila virulence in zebrafish, and various phenotypes associated with environmental survival were changed with varying degrees in each tonB mutant. TonB2 plays a relatively major role in adhesion, motility, and biofilm formation, while TonB3 is more involved in the anti-phagocytosis of A. hydrophila. In each observed phenotype, no significant difference was found between the single- and double-deletion mutants, whereas the triple-deletion mutant exhibited the most serious defects, indicating that all three TonB systems of A. hydrophila coordinately complement one another. In conclusion, this study elucidates the importance of TonB in iron acquisition and virulence of A. hydrophila, which lays the foundation for future studies regarding the survival mechanisms of this bacterium in iron-restricted environments.
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Affiliation(s)
- Yuhao Dong
- Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Jinzhu Geng
- Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Jin Liu
- Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Maoda Pang
- Key Lab of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, Jiangsu, China
| | - Furqan Awan
- Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Chengping Lu
- Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Yongjie Liu
- Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
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24
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Chiellini C, Pasqualetti C, Lanzoni O, Fagorzi C, Bazzocchi C, Fani R, Petroni G, Modeo L. Harmful Effect of Rheinheimera sp. EpRS3 ( Gammaproteobacteria) Against the Protist Euplotes aediculatus (Ciliophora, Spirotrichea): Insights Into the Ecological Role of Antimicrobial Compounds From Environmental Bacterial Strains. Front Microbiol 2019; 10:510. [PMID: 31001206 PMCID: PMC6457097 DOI: 10.3389/fmicb.2019.00510] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 02/27/2019] [Indexed: 01/24/2023] Open
Abstract
Rheinheimera sp. strain EpRS3, isolated from the rhizosphere of Echinacea purpurea, is already known for its ability to produce antibacterial compounds. By use of culture experiments, we verified and demonstrated its harmful effect against the ciliated protist Euplotes aediculatus (strain EASCc1), which by FISH experiments resulted to harbor in its cytoplasm the obligate bacterial endosymbiont Polynucleobacter necessarius (Betaproteobacteria) and the secondary endosymbiont "Candidatus Nebulobacter yamunensis" (Gammaproteobacteria). In culture experiments, the number of ciliates treated both with liquid broth bacteria-free (Supernatant treatment) and bacteria plus medium (Tq treatment), decreases with respect to control cells, with complete disappearance of ciliates within 6 h after Tq treatment. Results suggest that Rheinheimera sp. EpRS3 produces and releases in liquid culture one or more bioactive molecules affecting E. aediculatus survival. TEM analysis of control (not treated) ciliates allowed to morphologically characterize both kind of E. aediculatus endosymbionts. In treated ciliates, collected soon after the arising of cell suffering leading to death, TEM observations revealed some ultrastructural damages, indicating that P. necessarius endosymbionts went into degradation and vacuolization after both Supernatant and Tq treatments. Additionally, TEM investigation showed that when the ciliate culture was inoculated with Tq treatment, both a notable decrease of P. necessarius number and an increase of damaged and degraded mitochondria occur. FISH experiments performed on treated ciliates confirmed TEM results and, by means of the specific probe herein designed, disclosed the presence of Rheinheimera sp. EpRS3 both inside phagosomes and free in cytoplasm in ciliates after Tq treatment. This finding suggests a putative ability of Rheinheimera sp. EpRS3 to reintroduce itself in the environment avoiding ciliate digestion.
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Affiliation(s)
| | | | | | - Camilla Fagorzi
- Department of Biology, University of Florence, Florence, Italy
| | - Chiara Bazzocchi
- Department of Veterinary Medicine, University of Milan, Milan, Italy
| | - Renato Fani
- Department of Biology, University of Florence, Florence, Italy
| | | | - Letizia Modeo
- Department of Biology, University of Pisa, Pisa, Italy
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25
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Andac T, Weigmann P, Velu SKP, Pinçe E, Volpe G, Volpe G, Callegari A. Active matter alters the growth dynamics of coffee rings. SOFT MATTER 2019; 15:1488-1496. [PMID: 30570633 DOI: 10.1039/c8sm01350k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
How particles are deposited at the edge of evaporating droplets, i.e. the coffee ring effect, plays a crucial role in phenomena as diverse as thin-film deposition, self-assembly, and biofilm formation. Recently, microorganisms have been shown to passively exploit and alter these deposition dynamics to increase their survival chances under harshening conditions. Here, we show that, as the droplet evaporation rate slows down, bacterial mobility starts playing a major role in determining the growth dynamics of the edge of drying droplets. Such motility-induced dynamics can influence several biophysical phenomena, from the formation of biofilms to the spreading of pathogens in humid environments and on surfaces subject to periodic drying. Analogous dynamics in other active matter systems can be exploited for technological applications in printing, coating, and self-assembly, where the standard coffee-ring effect is often a nuisance.
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Affiliation(s)
- Tugba Andac
- Soft Matter Lab, Department of Physics, Bilkent University, Ankara, Turkey.
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26
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Gao Z, Karlsson I, Geisen S, Kowalchuk G, Jousset A. Protists: Puppet Masters of the Rhizosphere Microbiome. TRENDS IN PLANT SCIENCE 2019; 24:165-176. [PMID: 30446306 DOI: 10.1016/j.tplants.2018.10.011] [Citation(s) in RCA: 116] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 10/15/2018] [Accepted: 10/18/2018] [Indexed: 05/18/2023]
Abstract
The rhizosphere microbiome is a central determinant of plant performance. Microbiome assembly has traditionally been investigated from a bottom-up perspective, assessing how resources such as root exudates drive microbiome assembly. However, the importance of predation as a driver of microbiome structure has to date largely remained overlooked. Here we review the importance of protists, a paraphyletic group of unicellular eukaryotes, as a key regulator of microbiome assembly. Protists can promote plant-beneficial functions within the microbiome, accelerate nutrient cycling, and remove pathogens. We conclude that protists form an essential component of the rhizosphere microbiome and that accounting for predator-prey interactions would greatly improve our ability to predict and manage microbiome function at the service of plant growth and health.
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Affiliation(s)
- Zhilei Gao
- Institute of Environmental Biology, Ecology & Biodiversity, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; These authors contributed equally
| | - Ida Karlsson
- Institute of Environmental Biology, Ecology & Biodiversity, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; Dept. of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, 75007 Uppsala, Sweden; These authors contributed equally
| | - Stefan Geisen
- Department of Terrestrial Ecology, Netherlands Institute of Ecology, 6708 PB Wageningen, The Netherlands
| | - George Kowalchuk
- Institute of Environmental Biology, Ecology & Biodiversity, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Alexandre Jousset
- Institute of Environmental Biology, Ecology & Biodiversity, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
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27
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Lancaster CE, Ho CY, Hipolito VEB, Botelho RJ, Terebiznik MR. Phagocytosis: what's on the menu? 1. Biochem Cell Biol 2018; 97:21-29. [PMID: 29791809 DOI: 10.1139/bcb-2018-0008] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Phagocytosis is an evolutionarily conserved process. In Protozoa, phagocytosis fulfills a feeding mechanism, while in Metazoa, phagocytosis diversified to play multiple organismal roles, including immune defence, tissue homeostasis, and remodeling. Accordingly, phagocytes display a high level of plasticity in their capacity to recognize, engulf, and process targets that differ in composition and morphology. Here, we review how phagocytosis adapts to its multiple roles and discuss in particular the effect of target morphology in phagocytic uptake and phagosome maturation.
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Affiliation(s)
- Charlene E Lancaster
- a Department of Biological Sciences, University of Toronto at Scarborough, Toronto, ON M1C 1A4, Canada.,b Department of Cell and System Biology, University of Toronto at Scarborough, Toronto, ON M1C 1A4, Canada
| | - Cheuk Y Ho
- a Department of Biological Sciences, University of Toronto at Scarborough, Toronto, ON M1C 1A4, Canada
| | - Victoria E B Hipolito
- c Molecular Science Graduate Program, Ryerson University, Toronto, ON M5B 2K3, Canada.,d Department of Chemistry and Biology, Ryerson University, Toronto, ON M5B 2K3, Canada
| | - Roberto J Botelho
- c Molecular Science Graduate Program, Ryerson University, Toronto, ON M5B 2K3, Canada.,d Department of Chemistry and Biology, Ryerson University, Toronto, ON M5B 2K3, Canada
| | - Mauricio R Terebiznik
- a Department of Biological Sciences, University of Toronto at Scarborough, Toronto, ON M1C 1A4, Canada.,b Department of Cell and System Biology, University of Toronto at Scarborough, Toronto, ON M1C 1A4, Canada
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28
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Dann LM, McKerral JC, Smith RJ, Tobe SS, Paterson JS, Seymour JR, Oliver RL, Mitchell JG. Microbial micropatches within microbial hotspots. PLoS One 2018; 13:e0197224. [PMID: 29787564 PMCID: PMC5963804 DOI: 10.1371/journal.pone.0197224] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 04/28/2018] [Indexed: 11/19/2022] Open
Abstract
The spatial distributions of organism abundance and diversity are often heterogeneous. This includes the sub-centimetre distributions of microbes, which have 'hotspots' of high abundance, and 'coldspots' of low abundance. Previously we showed that 300 μl abundance hotspots, coldspots and background regions were distinct at all taxonomic levels. Here we build on these results by showing taxonomic micropatches within these 300 μl microscale hotspots, coldspots and background regions at the 1 μl scale. This heterogeneity among 1 μl subsamples was driven by heightened abundance of specific genera. The micropatches were most pronounced within hotspots. Micropatches were dominated by Pseudomonas, Bacteroides, Parasporobacterium and Lachnospiraceae incertae sedis, with Pseudomonas and Bacteroides being responsible for a shift in the most dominant genera in individual hotspot subsamples, representing up to 80.6% and 47.3% average abundance, respectively. The presence of these micropatches implies the ability these groups have to create, establish themselves in, or exploit heterogeneous microenvironments. These genera are often particle-associated, from which we infer that these micropatches are evidence for sub-millimetre aggregates and the aquatic polymer matrix. These findings support the emerging paradigm that the microscale distributions of planktonic microbes are numerically and taxonomically heterogeneous at scales of millimetres and less. We show that microscale microbial hotspots have internal structure within which specific local nutrient exchanges and cellular interactions might occur.
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Affiliation(s)
- Lisa M. Dann
- College of Science and Engineering at Flinders University, Adelaide, South Australia, Australia
- * E-mail:
| | - Jody C. McKerral
- School of Computer Science, Engineering and Mathematics at Flinders University, Adelaide, South Australia, Australia
| | - Renee J. Smith
- College of Science and Engineering at Flinders University, Adelaide, South Australia, Australia
| | - Shanan S. Tobe
- College of Science and Engineering at Flinders University, Adelaide, South Australia, Australia
| | - James S. Paterson
- College of Science and Engineering at Flinders University, Adelaide, South Australia, Australia
| | - Justin R. Seymour
- Plant Functional Biology and Climate Change Cluster (C3) at University of Technology Sydney, Sydney, New South Wales, Australia
| | - Rod L. Oliver
- CSIRO Land and Water Waite Research Institute, Adelaide, South Australia, Australia
| | - James G. Mitchell
- College of Science and Engineering at Flinders University, Adelaide, South Australia, Australia
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Liu J, Dong Y, Wang N, Li S, Yang Y, Wang Y, Awan F, Lu C, Liu Y. Tetrahymena thermophila Predation Enhances Environmental Adaptation of the Carp Pathogenic Strain Aeromonas hydrophila NJ-35. Front Cell Infect Microbiol 2018; 8:76. [PMID: 29594069 PMCID: PMC5861188 DOI: 10.3389/fcimb.2018.00076] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 02/27/2018] [Indexed: 01/21/2023] Open
Abstract
Persistence of Aeromonas hydrophila in aquatic environments is the principle cause of fish hemorrhagic septicemia. Protistan predation has been considered to be a strong driving force for the evolution of bacterial defense strategies. In this study, we investigated the adaptive traits of A. hydrophila NJ-35, a carp pathogenic strain, in response to Tetrahymena thermophila predation. After subculturing with Tetrahymena, over 70% of A. hydrophila colonies were small colony variants (SCVs). The SCVs displayed enhanced biofilm formation, adhesion, fitness, and resistance to bacteriophage infection and oxidative stress as compared to the non-Tetrahymena-exposed strains. In contrast, the SCVs exhibited decreased intracellular bacterial number in RAW264.7 macrophages and were highly attenuated for virulence in zebrafish. Considering the outer membrane proteins (OMPs) are directly involved in bacterial interaction with the external surroundings, we investigated the roles of OMPs in the antipredator fitness behaviors of A. hydrophila. A total of 38 differentially expressed proteins were identified in the SCVs by quantitative proteomics. Among them, three lipoproteins including SurA, Slp, and LpoB, and a serine/threonine protein kinase (Stpk) were evidenced to be associated with environmental adaptation of the SCVs. Also, the three lipoproteins were involved in attenuated virulence of SCVs through the proinflammatory immune response mediated by TLR2. This study provides an important contribution to the understanding of the defensive traits of A. hydrophila against protistan predators.
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Affiliation(s)
- Jin Liu
- Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Yuhao Dong
- Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Nannan Wang
- Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Shougang Li
- Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Yuanyuan Yang
- Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Yao Wang
- Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Furqan Awan
- Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Chengping Lu
- Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Yongjie Liu
- Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
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30
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Raghupathi PK, Liu W, Sabbe K, Houf K, Burmølle M, Sørensen SJ. Synergistic Interactions within a Multispecies Biofilm Enhance Individual Species Protection against Grazing by a Pelagic Protozoan. Front Microbiol 2018; 8:2649. [PMID: 29375516 PMCID: PMC5767253 DOI: 10.3389/fmicb.2017.02649] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 12/19/2017] [Indexed: 01/02/2023] Open
Abstract
Biofilm formation has been shown to confer protection against grazing, but little information is available on the effect of grazing on biofilm formation and protection in multispecies consortia. With most biofilms in nature being composed of multiple bacterial species, the interactions and dynamics of a multispecies bacterial biofilm subject to grazing by a pelagic protozoan predator were investigated. To this end, a mono and multispecies biofilms of four bacterial soil isolates, namely Xanthomonas retroflexus, Stenotrophomonas rhizophila, Microbacterium oxydans and Paenibacillus amylolyticus, were constructed and subjected to grazing by the ciliate Tetrahymena pyriformis. In monocultures, grazing strongly reduced planktonic cell numbers in P. amylolyticus and S. rhizophila and also X. retroflexus. At the same time, cell numbers in the underlying biofilms increased in S. rhizophila and X. retroflexus, but not in P. amylolyticus. This may be due to the fact that while grazing enhanced biofilm formation in the former two species, no biofilm was formed by P. amylolyticus in monoculture, either with or without grazing. In four-species biofilms, biofilm formation was higher than in the best monoculture, a strong biodiversity effect that was even more pronounced in the presence of grazing. While cell numbers of X. retroflexus, S. rhizophila, and P. amylolyticus in the planktonic fraction were greatly reduced in the presence of grazers, cell numbers of all three species strongly increased in the biofilm. Our results show that synergistic interactions between the four-species were important to induce biofilm formation, and suggest that bacterial members that produce more biofilm when exposed to the grazer not only protect themselves but also supported other members which are sensitive to grazing, thereby providing a "shared grazing protection" within the four-species biofilm model. Hence, complex interactions shape the dynamics of the biofilm and enhance overall community fitness under stressful conditions such as grazing. These emerging inter- and intra-species interactions could play a vital role in biofilm dynamics in natural environments like soil or aquatic systems.
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Affiliation(s)
- Prem K. Raghupathi
- Laboratory of Microbiology, Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Ghent, Belgium
- Section for Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Wenzheng Liu
- Section for Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Koen Sabbe
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Kurt Houf
- Laboratory of Microbiology, Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Ghent, Belgium
| | - Mette Burmølle
- Section for Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Søren J. Sørensen
- Section for Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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31
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Johnke J, Boenigk J, Harms H, Chatzinotas A. Killing the killer: predation between protists and predatory bacteria. FEMS Microbiol Lett 2017; 364:3746136. [PMID: 28444379 DOI: 10.1093/femsle/fnx089] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 04/20/2017] [Indexed: 02/05/2023] Open
Abstract
Predation by microbes is one of the main drivers of bacterial mortality in the environment. In most ecosystems multiple micropredators compete at least partially for the same bacterial resource. Predatory interactions between these micropredators might lead to shifts within microbial communities. Integrating these interactions is therefore crucial for the understanding of ecosystem functioning. In this study, we investigated the predation between two groups of micropredators, i.e. phagotrophic protists and Bdellovibrio and like organisms (BALOs). BALOs are obligate predators of Gram-negative bacteria. We hypothesised that protists can prey upon BALOs despite the small size and high swimming speed of the latter, which makes them potentially hard to capture. Predation experiments including three protists, i.e. one filter feeder and two interception feeder, showed that BALOs are a relevant prey for these protists. The growth rate on BALOs differed for the respective protists. The filter feeding ciliate was growing equally well on the BALOs and on Escherichia coli, whereas the two flagellate species grew less well on the BALOs compared to E. coli. However, BALOs might not be a favourable food source in resource-rich environments as they are not enabling all protists to grow as much as on bacteria of bigger volume.
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Affiliation(s)
- Julia Johnke
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany
| | - Jens Boenigk
- Biodiversity Department and Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, 45117 Essen, Germany
| | - Hauke Harms
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
| | - Antonis Chatzinotas
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
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32
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Seiler C, van Velzen E, Neu TR, Gaedke U, Berendonk TU, Weitere M. Grazing resistance of bacterial biofilms: a matter of predators’ feeding trait. FEMS Microbiol Ecol 2017; 93:4107106. [DOI: 10.1093/femsec/fix112] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 09/05/2017] [Indexed: 11/12/2022] Open
Affiliation(s)
- Claudia Seiler
- Helmholtz Centre for Environmental Research – UFZ, Department of River Ecology, 39114 Magdeburg, Germany
| | - Ellen van Velzen
- Department of Ecology and Ecosystem Modelling, University of Potsdam, 14469 Potsdam, Germany
| | - Thomas R. Neu
- Helmholtz Centre for Environmental Research – UFZ, Department of River Ecology, 39114 Magdeburg, Germany
| | - Ursula Gaedke
- Department of Ecology and Ecosystem Modelling, University of Potsdam, 14469 Potsdam, Germany
| | - Thomas U. Berendonk
- Technische Universität Dresden, Institute of Hydrobiology, 01062 Dresden, Germany
| | - Markus Weitere
- Helmholtz Centre for Environmental Research – UFZ, Department of River Ecology, 39114 Magdeburg, Germany
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33
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Cobo-Simón M, Tamames J. Relating genomic characteristics to environmental preferences and ubiquity in different microbial taxa. BMC Genomics 2017; 18:499. [PMID: 28662636 PMCID: PMC5492924 DOI: 10.1186/s12864-017-3888-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 06/21/2017] [Indexed: 11/10/2022] Open
Abstract
Background Despite the important role that microorganisms play in environmental processes, the low percentage of cultured microbes (5%) has limited, until now, our knowledge of their ecological strategies. However, the development of high-throughput sequencing has generated a huge amount of genomic and metagenomic data without the need of culturing that can be used to study ecological questions. This study aims to estimate the functional capabilities, genomic sizes and 16S copy number of different taxa in relation to their ubiquity and their environmental preferences. Results To achieve this goal, we compiled data regarding the presence of each prokaryotic genera in diverse environments. Then, genomic characteristics such as genome size, 16S rRNA gene copy number, and functional content of the genomes were related to their ubiquity and different environmental preferences of the corresponding taxa. The results showed clear correlations between genomic characteristics and environmental conditions. Conclusions Ubiquity and adaptation were linked to genome size, while 16S copy number was not directly related to ubiquity. We observed that different combinations of these two characteristics delineate the different environments. Besides, the analysis of functional classes showed some clear signatures linked to particular environments. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3888-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marta Cobo-Simón
- Systems Biology Programme, Centro Nacional de Biotecnología (CNB-CSIC), C/Darwin 3, 28049, Madrid, Spain
| | - Javier Tamames
- Systems Biology Programme, Centro Nacional de Biotecnología (CNB-CSIC), C/Darwin 3, 28049, Madrid, Spain.
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34
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Pernthaler J. Competition and niche separation of pelagic bacteria in freshwater habitats. Environ Microbiol 2017; 19:2133-2150. [PMID: 28370850 DOI: 10.1111/1462-2920.13742] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 03/19/2017] [Accepted: 03/23/2017] [Indexed: 11/29/2022]
Abstract
Freshwater bacterioplankton assemblages are composed of sympatric populations that can be delineated, for example, by ribosomal RNA gene relatedness and that differ in key ecophysiological properties. They may be free-living or attached, specialized for particular concentrations or subsets of substrates, or invest a variable amount of their resources in defence traits against protistan predators and viruses. Some may be motile and tactic whereas others are not, with far-reaching implications for their respective life styles and niche partitioning. The co-occurrence of competitors with overlapping growth requirements has profound consequences for the stability of community functions; it can to some extent be explained by habitat factors such as the microscale complexity and spatiotemporal variability of the lacustrine environments. On the other hand, the composition and diversity of freshwater microbial assemblages also reflects non-equilibrium states, dispersal and the stochasticity of community assembly processes. This review synoptically discusses the competition and niche separation of heterotrophic bacterial populations (defined at various levels of phylogenetic resolution) in the pelagic zone of inland surface waters from a variety of angles, focusing on habitat heterogeneity and the resulting biogeographic distribution patterns, the ecophysiological adaptations to the substrate field and the interactions of prokaryotes with predators and viruses.
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Affiliation(s)
- Jakob Pernthaler
- Limnological Station Kilchberg, Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
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35
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de Souza TK, Soares SS, Benitez LB, Rott MB. Interaction Between Methicillin-Resistant Staphylococcus aureus (MRSA) and Acanthamoeba polyphaga. Curr Microbiol 2017; 74:541-549. [DOI: 10.1007/s00284-017-1196-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 01/06/2017] [Indexed: 11/30/2022]
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36
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Nadeau J, Lindensmith C, Deming JW, Fernandez VI, Stocker R. Microbial Morphology and Motility as Biosignatures for Outer Planet Missions. ASTROBIOLOGY 2016; 16:755-774. [PMID: 27552160 PMCID: PMC5069736 DOI: 10.1089/ast.2015.1376] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 06/13/2016] [Indexed: 05/23/2023]
Abstract
Meaningful motion is an unambiguous biosignature, but because life in the Solar System is most likely to be microbial, the question is whether such motion may be detected effectively on the micrometer scale. Recent results on microbial motility in various Earth environments have provided insight into the physics and biology that determine whether and how microorganisms as small as bacteria and archaea swim, under which conditions, and at which speeds. These discoveries have not yet been reviewed in an astrobiological context. This paper discusses these findings in the context of Earth analog environments and environments expected to be encountered in the outer Solar System, particularly the jovian and saturnian moons. We also review the imaging technologies capable of recording motility of submicrometer-sized organisms and discuss how an instrument would interface with several types of sample-collection strategies. Key Words: In situ measurement-Biosignatures-Microbiology-Europa-Ice. Astrobiology 16, 755-774.
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Affiliation(s)
- Jay Nadeau
- 1 GALCIT, California Institute of Technology , Pasadena, California
| | - Chris Lindensmith
- 2 Jet Propulsion Laboratory, California Institute of Technology , Pasadena, California
| | - Jody W Deming
- 3 Department of Biological Oceanography, University of Washington , Seattle, Washington
| | - Vicente I Fernandez
- 4 Department of Civil and Environmental Engineering, Massachusetts Institute of Technology , Cambridge, Massachusetts
| | - Roman Stocker
- 4 Department of Civil and Environmental Engineering, Massachusetts Institute of Technology , Cambridge, Massachusetts
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37
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Callieri C, Amalfitano S, Corno G, Bertoni R. Grazing-induced Synechococcus microcolony formation: experimental insights from two freshwater phylotypes. FEMS Microbiol Ecol 2016; 92:fiw154. [PMID: 27411979 DOI: 10.1093/femsec/fiw154] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/07/2016] [Indexed: 11/13/2022] Open
Abstract
Freshwater cyanobacteria of the genus Synechococcus are ubiquitous and organized either as single cells of diverse morphology or as microcolonies of different size. We studied the formation of microcolonies induced by the mixotrophic nanoflagellate Poterioochromonas sp. grazing on two Synechococcus strains belonging to phylotypes with different content of phycobiliproteins (PE: phycoerythrin-rich cells, L.Albano Group A; PC: phycocyanin-rich cells, MW101C3 Group I). The quantitative variations in cell abundance, morphological and physiological conditions were assessed on short-term incubations in semi-continuous cultures, single culture (PE, PC) and co-culture (PE+PC), with and without predators, by flow cytometry, and PhytoPAM. Under grazing pressure, we observed that (i) the abundance of PE single cells decreased over time with a concomitant formation of PE microcolonies; (ii) in PC single cultures, no significant variation in single cells was found and microcolonies did not form; (iii) both PE and PC formed monoclonal microcolonies in co-culture; (iv) PC cells increased the photosynthetic efficiency of the PSII (higher Fv/Fm) in co-culture. In the aftermath of microcolony formation as a predation-induced adaptation, our findings indicated a different response of Synechococcus phylotypes potentially co-existing in natural environment and the importance of their interaction.
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Affiliation(s)
| | | | - Gianluca Corno
- Institute of Ecosystem Study, CNR-ISE, 28922 Verbania, Italy
| | - Roberto Bertoni
- Institute of Ecosystem Study, CNR-ISE, 28922 Verbania, Italy
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Sunagawa S, Coelho LP, Chaffron S, Kultima JR, Labadie K, Salazar G, Djahanschiri B, Zeller G, Mende DR, Alberti A, Cornejo-Castillo FM, Costea PI, Cruaud C, d'Ovidio F, Engelen S, Ferrera I, Gasol JM, Guidi L, Hildebrand F, Kokoszka F, Lepoivre C, Lima-Mendez G, Poulain J, Poulos BT, Royo-Llonch M, Sarmento H, Vieira-Silva S, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Bowler C, de Vargas C, Gorsky G, Grimsley N, Hingamp P, Iudicone D, Jaillon O, Not F, Ogata H, Pesant S, Speich S, Stemmann L, Sullivan MB, Weissenbach J, Wincker P, Karsenti E, Raes J, Acinas SG, Bork P. Ocean plankton. Structure and function of the global ocean microbiome. Science 2015; 348:1261359. [PMID: 25999513 DOI: 10.1126/science.1261359] [Citation(s) in RCA: 1381] [Impact Index Per Article: 153.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Microbes are dominant drivers of biogeochemical processes, yet drawing a global picture of functional diversity, microbial community structure, and their ecological determinants remains a grand challenge. We analyzed 7.2 terabases of metagenomic data from 243 Tara Oceans samples from 68 locations in epipelagic and mesopelagic waters across the globe to generate an ocean microbial reference gene catalog with >40 million nonredundant, mostly novel sequences from viruses, prokaryotes, and picoeukaryotes. Using 139 prokaryote-enriched samples, containing >35,000 species, we show vertical stratification with epipelagic community composition mostly driven by temperature rather than other environmental factors or geography. We identify ocean microbial core functionality and reveal that >73% of its abundance is shared with the human gut microbiome despite the physicochemical differences between these two ecosystems.
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Affiliation(s)
- Shinichi Sunagawa
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
| | - Luis Pedro Coelho
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Samuel Chaffron
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, 3000 Leuven, Belgium. Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium. Department of Applied Biological Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Jens Roat Kultima
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Karine Labadie
- CEA-Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Guillem Salazar
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain
| | - Bardya Djahanschiri
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Georg Zeller
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Daniel R Mende
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Adriana Alberti
- CEA-Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Francisco M Cornejo-Castillo
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain
| | - Paul I Costea
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Corinne Cruaud
- CEA-Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Francesco d'Ovidio
- Sorbonne Universités, UPMC, Université Paris 06, CNRS-IRD-MNHN, LOCEAN Laboratory, 4 Place Jussieu, 75005 Paris France
| | - Stefan Engelen
- CEA-Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Isabel Ferrera
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain
| | - Josep M Gasol
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain
| | - Lionel Guidi
- CNRS, UMR 7093, Laboratoire d'Océanographie de Villefranche-sur-Mer, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France. Sorbonne Universités, UPMC Université Paris 06, UMR 7093, LOV, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France
| | - Falk Hildebrand
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Florian Kokoszka
- Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, F-75005 Paris, France. Laboratoire de Physique des Océans UBO-IUEM, Place Copernic 29820 Plouzané, France
| | - Cyrille Lepoivre
- Aix Marseille Université CNRS IGS UMR 7256, 13288 Marseille, France
| | - Gipsi Lima-Mendez
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, 3000 Leuven, Belgium. Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium. Department of Applied Biological Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Julie Poulain
- CEA-Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Bonnie T Poulos
- Department of Ecology and Evolutionary Biology, University of Arizona, 1007 East Lowell Street, Tucson, AZ 85721, USA
| | - Marta Royo-Llonch
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain
| | - Hugo Sarmento
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain. Department of Hydrobiology, Federal University of São Carlos (UFSCar), Rodovia Washington Luiz, 13565-905 São Carlos, São Paulo, Brazil
| | - Sara Vieira-Silva
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, 3000 Leuven, Belgium. Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium. Department of Applied Biological Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Céline Dimier
- Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, F-75005 Paris, France. CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universités, UPMC Université Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Marc Picheral
- CNRS, UMR 7093, Laboratoire d'Océanographie de Villefranche-sur-Mer, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France. Sorbonne Universités, UPMC Université Paris 06, UMR 7093, LOV, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France
| | - Sarah Searson
- CNRS, UMR 7093, Laboratoire d'Océanographie de Villefranche-sur-Mer, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France. Sorbonne Universités, UPMC Université Paris 06, UMR 7093, LOV, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France
| | - Stefanie Kandels-Lewis
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany. Directors' Research, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | | | - Chris Bowler
- Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, F-75005 Paris, France
| | - Colomban de Vargas
- CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universités, UPMC Université Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Gabriel Gorsky
- CNRS, UMR 7093, Laboratoire d'Océanographie de Villefranche-sur-Mer, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France. Sorbonne Universités, UPMC Université Paris 06, UMR 7093, LOV, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France
| | - Nigel Grimsley
- CNRS UMR 7232, BIOM, Avenue du Fontaulé, 66650 Banyuls-sur-Mer, France. Sorbonne Universités Paris 06, OOB UPMC, Avenue du Fontaulé, 66650 Banyuls-sur-Mer, France
| | - Pascal Hingamp
- Aix Marseille Université CNRS IGS UMR 7256, 13288 Marseille, France
| | - Daniele Iudicone
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Olivier Jaillon
- CEA-Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France. CNRS, UMR 8030, CP5706, Evry, France. Université d'Evry, UMR 8030, CP5706, Evry, France
| | - Fabrice Not
- CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universités, UPMC Université Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-001, Japan
| | - Stephane Pesant
- PANGAEA, Data Publisher for Earth and Environmental Science, University of Bremen, Bremen, Germany. MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Sabrina Speich
- Department of Geosciences, Laboratoire de Météorologie Dynamique (LMD), Ecole Normale Supérieure, 24 rue Lhomond, 75231 Paris Cedex 05, France. Laboratoire de Physique des Océans UBO-IUEM, Place Copernic, 29820 Plouzané, France
| | - Lars Stemmann
- CNRS, UMR 7093, Laboratoire d'Océanographie de Villefranche-sur-Mer, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France. Sorbonne Universités, UPMC Université Paris 06, UMR 7093, LOV, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France
| | - Matthew B Sullivan
- Department of Ecology and Evolutionary Biology, University of Arizona, 1007 East Lowell Street, Tucson, AZ 85721, USA
| | - Jean Weissenbach
- CEA-Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France. CNRS, UMR 8030, CP5706, Evry, France. Université d'Evry, UMR 8030, CP5706, Evry, France
| | - Patrick Wincker
- CEA-Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France. CNRS, UMR 8030, CP5706, Evry, France. Université d'Evry, UMR 8030, CP5706, Evry, France
| | - Eric Karsenti
- Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, F-75005 Paris, France. Directors' Research, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
| | - Jeroen Raes
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, 3000 Leuven, Belgium. Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium. Department of Applied Biological Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium.
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain.
| | - Peer Bork
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany. Max-Delbrück-Centre for Molecular Medicine, 13092 Berlin, Germany.
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Song C, Mazzola M, Cheng X, Oetjen J, Alexandrov T, Dorrestein P, Watrous J, van der Voort M, Raaijmakers JM. Molecular and chemical dialogues in bacteria-protozoa interactions. Sci Rep 2015; 5:12837. [PMID: 26246193 PMCID: PMC4542665 DOI: 10.1038/srep12837] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 07/10/2015] [Indexed: 12/23/2022] Open
Abstract
Protozoan predation of bacteria can significantly affect soil microbial community composition and ecosystem functioning. Bacteria possess diverse defense strategies to resist or evade protozoan predation. For soil-dwelling Pseudomonas species, several secondary metabolites were proposed to provide protection against different protozoan genera. By combining whole-genome transcriptome analyses with (live) imaging mass spectrometry (IMS), we observed multiple changes in the molecular and chemical dialogues between Pseudomonas fluorescens and the protist Naegleria americana. Lipopeptide (LP) biosynthesis was induced in Pseudomonas upon protozoan grazing and LP accumulation transitioned from homogeneous distributions across bacterial colonies to site-specific accumulation at the bacteria-protist interface. Also putrescine biosynthesis was upregulated in P. fluorescens upon predation. We demonstrated that putrescine induces protozoan trophozoite encystment and adversely affects cyst viability. This multifaceted study provides new insights in common and strain-specific responses in bacteria-protozoa interactions, including responses that contribute to bacterial survival in highly competitive soil and rhizosphere environments.
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Affiliation(s)
- Chunxu Song
- 1] Laboratory of Phytopathology, Wageningen University, 6708 PB Wageningen, the Netherlands [2] Microbial Ecology Department, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, the Netherlands
| | - Mark Mazzola
- USDA-ARS, 1104 N. Western Ave., Wenatchee, Washington 98801
| | - Xu Cheng
- Laboratory of Phytopathology, Wageningen University, 6708 PB Wageningen, the Netherlands
| | - Janina Oetjen
- Center for Industrial Mathematics, University of Bremen, 28359 Bremen, Germany
| | - Theodore Alexandrov
- 1] MALDI Imaging Lab, University of Bremen, 28359 Bremen, Germany [2] Center for Industrial Mathematics, University of Bremen, 28359 Bremen, Germany [3] SCiLS GmbH, 28359 Bremen, Germany [4] Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego , San Diego, California 92093, United States [5] Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Pieter Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego , San Diego, California 92093, United States
| | - Jeramie Watrous
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego , San Diego, California 92093, United States
| | - Menno van der Voort
- Laboratory of Phytopathology, Wageningen University, 6708 PB Wageningen, the Netherlands
| | - Jos M Raaijmakers
- 1] Laboratory of Phytopathology, Wageningen University, 6708 PB Wageningen, the Netherlands [2] Microbial Ecology Department, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, the Netherlands
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Spychała M, Sowińska A, Starzyk J, Masłowski A. Protozoa and metazoa relations to technological conditions of non-woven textile filters for wastewater treatment. ENVIRONMENTAL TECHNOLOGY 2015; 36:1865-1875. [PMID: 25704123 DOI: 10.1080/09593330.2015.1014863] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The objective of this study was a preliminary identification of basic groups of micro-organisms in the cross-sectional profile of geotextile filters for septic tank effluent (STE) treatment and their relations to technological conditions. Reactors with textile filters treating wastewater were investigated on a semi-technical scale. Filters were vertically situated and STE was filtered through them under hydrostatic pressure at a wastewater surface height of 7-20 cm. Filters were made of four layers of non-woven TS 20 geotextile of 0.9 mm thickness. Various groups of organisms were observed; the most abundant group comprised free-swimming and crawling ciliates, less abundant were stalked ciliates and the least numerous were nematodes. The individual counts of all groups of micro-organisms investigated during the study were variable according to time and space. The high abundance of Opercularia, a commonly observed genus of stalked ciliates, was related to the high efficiency of wastewater treatment and dissolved oxygen concentration of about 1.0 g/m3. Numbers of free-swimming and crawling ciliates had a tendency to decrease in relation to the depth of filter cross-sectional profile. The variability in counts of particular groups of organisms could be related to the local stress conditions. No correlation between identified organism count and total mass concentration in the cross-sectional filter profile was found.
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Affiliation(s)
- Marcin Spychała
- a Department of Hydraulic and Sanitary Engineering , Poznan University of Life Sciences , Piątkowska St. 94A, Poznań 60-649 , Poland
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Rocke E, Pachiadaki MG, Cobban A, Kujawinski EB, Edgcomb VP. Protist Community Grazing on Prokaryotic Prey in Deep Ocean Water Masses. PLoS One 2015; 10:e0124505. [PMID: 25894547 PMCID: PMC4404134 DOI: 10.1371/journal.pone.0124505] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 03/03/2015] [Indexed: 11/19/2022] Open
Abstract
Oceanic protist grazing at mesopelagic and bathypelagic depths, and their subsequent effects on trophic links between eukaryotes and prokaryotes, are not well constrained. Recent studies show evidence of higher than expected grazing activity by protists down to mesopelagic depths. This study provides the first exploration of protist grazing in the bathypelagic North Atlantic Deep Water (NADW). Grazing was measured throughout the water column at three stations in the South Atlantic using fluorescently-labeled prey analogues. Grazing in the deep Antarctic Intermediate water (AAIW) and NADW at all three stations removed 3.79% ± 1.72% to 31.14% ± 8.24% of the standing prokaryote stock. These results imply that protist grazing may be a significant source of labile organic carbon at certain meso- and bathypelagic depths.
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Affiliation(s)
- Emma Rocke
- Life Science Department, Hong Kong University of Science and Technology, Hong Kong SAR
| | - Maria G. Pachiadaki
- Geology and Geophysics Department, Woods Hole Oceanographic Institution, Woods Hole, MA, United States of America
| | - Alec Cobban
- Geology and Geophysics Department, Woods Hole Oceanographic Institution, Woods Hole, MA, United States of America
- Falmouth Academy Internship Program, Falmouth Academy, Falmouth, MA, United States of America
| | - Elizabeth B. Kujawinski
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, United States of America
| | - Virginia P. Edgcomb
- Geology and Geophysics Department, Woods Hole Oceanographic Institution, Woods Hole, MA, United States of America
- * E-mail:
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Lambrecht E, Baré J, Claeys M, Chavatte N, Bert W, Sabbe K, Houf K. Transmission electron microscopy sample preparation protocols for the ultrastructural study of cysts of free-living protozoa. Biotechniques 2015; 58:181-8. [PMID: 25861930 DOI: 10.2144/000114274] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 01/05/2015] [Indexed: 11/23/2022] Open
Abstract
Cysts of free-living protozoa have an impact on the ecology and epidemiology of bacteria because they may act as a transmission vector or shelter the bacteria against hash environmental conditions. Detection and localization of intracystic bacteria and examination of the en- and excystment dynamics is a major challenge because no detailed protocols for ultrastructural analysis of cysts are currently available. Transmission electron microscopy (TEM) is ideally suited for those analyses; however, conventional TEM protocols are not satisfactory for cysts of free-living protozoa. Here we report on the design and testing of four protocols for TEM sample preparation of cysts. Two protocols, one based on chemical fixation in coated well plates and one on high-pressure freezing, were selected as the most effective for TEM-based ultrastructural studies of cysts. Our protocols will enable improved analysis of cyst structure and a better understanding of bacterial survival mechanisms in cysts.
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Affiliation(s)
- Ellen Lambrecht
- Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Julie Baré
- Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium.,Unit of Coordination in Veterinary Diagnostics-Epidemiology and Risk Assessment, CODA-CERVA, Ukkel, Belgium
| | - Myriam Claeys
- Nematology Research Unit, Department of Biology, Ghent University, Ghent, Belgium
| | - Natascha Chavatte
- Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Wim Bert
- Nematology Research Unit, Department of Biology, Ghent University, Ghent, Belgium
| | - Koen Sabbe
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Ghent, Belgium
| | - Kurt Houf
- Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
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Wanjugi P, Harwood VJ. Protozoan predation is differentially affected by motility of enteric pathogens in water vs. sediments. MICROBIAL ECOLOGY 2014; 68:751-760. [PMID: 24952019 DOI: 10.1007/s00248-014-0444-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 06/05/2014] [Indexed: 06/03/2023]
Abstract
Survival of enteric bacteria in aquatic habitats varies depending upon species, strain, and environmental pressures, but the mechanisms governing their fate are poorly understood. Although predation by protozoa is a known, top-down control mechanism on bacterial populations, its influence on the survival of fecal-derived pathogens has not been systematically studied. We hypothesized that motility, a variable trait among pathogens, can influence predation rates and bacterial survival. We compared the survival of two motile pathogens of fecal origin by culturing Escherichia coli O157 and Salmonella enterica Typhimurium. Each species had a motile and non-motile counterpart and was cultured in outdoor microcosms with protozoan predators (Tetrahymena pyriformis) present or absent. Motility had a significant, positive effect on S. enterica levels in water and sediment in the presence or absence of predators. In contrast, motility had a significant negative effect on E. coli O157 levels in sediment, but did not affect water column levels. The presence/absence of protozoa consistently accounted for a greater proportion of the variability in bacterial levels (>95 %) than in bacterial motility (<4 %) in the water column. In sediments, however, motility was more important than predation for both bacteria. Calculations of total CFU/microcosm showed decreasing bacterial concentrations over time under all conditions except for S. enterica in the absence of predation, which increased ∼0.5-1.0 log over 5 days. These findings underscore the complexity of predicting the survival of enteric microorganisms in aquatic habitats, which has implications for the accuracy of risk assessment and modeling of water quality.
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Affiliation(s)
- Pauline Wanjugi
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, SCA 110, Tampa, FL, 33620, USA
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Fieseler L, Doyscher D, Loessner MJ, Schuppler M. Acanthamoeba release compounds which promote growth of Listeria monocytogenes and other bacteria. Appl Microbiol Biotechnol 2014; 98:3091-7. [DOI: 10.1007/s00253-014-5534-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Revised: 01/07/2014] [Accepted: 01/09/2014] [Indexed: 11/30/2022]
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Schuppler M. How the interaction of Listeria monocytogenes and Acanthamoeba spp. affects growth and distribution of the food borne pathogen. Appl Microbiol Biotechnol 2014; 98:2907-16. [PMID: 24557567 DOI: 10.1007/s00253-014-5546-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Revised: 01/10/2014] [Accepted: 01/13/2014] [Indexed: 10/25/2022]
Abstract
Listeria monocytogenes is a foodborne opportunistic pathogen capable to switch from an environmental saprophyte to a potentially fatal human pathogen. The fact that the pathogen maintains the genes suitable for an elaborate infectious process indicates that these genes are required to survive in the environment. However, no environmental host reservoir for L. monocytogenes has been identified so far. The similarity of free-living, bacteria-scavenging amoebae to macrophages led to the hypothesis that protozoa may represent the missing link in the ecology and pathology of L. monocytogenes. Consequently, numerous studies have been published reporting on the potential of Acanthamoeba spp. to serve as host for a variety of pathogenic bacteria. However, the data on the interaction of L. monocytogenes with Acanthamoeba spp. are inconsistent and relatively little information on the impact of this interaction on growth and distribution of the foodborne pathogen is currently available. Hence, this review focuses on the interaction of L. monocytogenes and Acanthamoeba spp. affecting survival and growth of the foodborne pathogen in natural and man-made environments, in order to highlight the potential impact of this interplay on food safety and human health.
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Affiliation(s)
- Markus Schuppler
- Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092, Zurich, Switzerland,
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Biology of the Marine Heterotrophic Dinoflagellate Oxyrrhis marina: Current Status and Future Directions. Microorganisms 2013; 1:33-57. [PMID: 27694763 PMCID: PMC5029500 DOI: 10.3390/microorganisms1010033] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Revised: 09/02/2013] [Accepted: 10/08/2013] [Indexed: 11/17/2022] Open
Abstract
Heterotrophic dinoflagellates are prevalent protists in marine environments, which play an important role in the carbon cycling and energy flow in the marine planktonic community. Oxyrrhismarina (Dinophyceae), a widespread heterotrophic dinoflagellate, is a model species used for a broad range of ecological, biogeographic, and evolutionary studies. Despite the increasing research effort on this species, there lacks a synthesis of the existing data and a coherent picture of this organism. Here we reviewed the literature to provide an overview of what is known regarding the biology of O. marina, and identify areas where further studies are needed. As an early branch of the dinoflagellate lineage, O. marina shares similarity with typical dinoflagellates in permanent condensed chromosomes, less abundant nucleosome proteins compared to other eukaryotes, multiple gene copies, the occurrence of trans-splicing in nucleus-encoded mRNAs, highly fragmented mitochondrial genome, and disuse of ATG as a start codon for mitochondrial genes. On the other hand, O. marina also exhibits some distinct cytological features (e.g., different flagellar structure, absence of girdle and sulcus or pustules, use of intranuclear spindle in mitosis, presence of nuclear plaque, and absence of birefringent periodic banded chromosomal structure) and genetic features (e.g., a single histone-like DNA-associated protein, cob-cox3 gene fusion, 5' oligo-U cap in the mitochondrial transcripts of protein-coding genes, the absence of mRNA editing, the presence of stop codon in the fused cob-cox3 mRNA produced by post-transcriptional oligoadenylation, and vestigial plastid genes). The best-studied biology of this dinoflagellate is probably the prey and predators types, which include a wide range of organisms. On the other hand, the abundance of this species in the natural waters and its controlling factors, genome organization and gene expression regulation that underlie the unusual cytological and ecological characteristics are among the areas that urgently need study.
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A physical explanation of the temperature dependence of physiological processes mediated by cilia and flagella. Proc Natl Acad Sci U S A 2013; 110:14693-8. [PMID: 23959901 DOI: 10.1073/pnas.1300891110] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The majority of biological rates are known to exhibit temperature dependence. Here I reveal a direct link between temperature and ecologically relevant rates such as swimming speeds in Archaea, Bacteria, and Eukaryotes as well as fluid-pumping and filtration rates in many metazoans, and show that this relationship is driven by movement rates of cilia and flagella. I develop models of the temperature dependence of cilial and flagellar movement rates and evaluate these with an extensive compilation of data from the literature. The model captures the temperature dependence of viscosity and provides a mechanistic and biologically interpretable explanation for the temperature dependence of a range of ecologically relevant processes; it also reveals a clear dependence on both reaction rate-like processes and the physics of the environment. The incorporation of viscosity allows further insight into the effects of environmental temperature variation and of processes, such as disease, that affect the viscosity of blood or other body fluids.
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Sonowal R, Nandimath K, Kulkarni SS, Koushika SP, Nanjundiah V, Mahadevan S. Hydrolysis of aromatic β-glucosides by non-pathogenic bacteria confers a chemical weapon against predators. Proc Biol Sci 2013; 280:20130721. [PMID: 23677347 PMCID: PMC3673059 DOI: 10.1098/rspb.2013.0721] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Accepted: 04/18/2013] [Indexed: 11/12/2022] Open
Abstract
Bacteria present in natural environments such as soil have evolved multiple strategies to escape predation. We report that natural isolates of Enterobacteriaceae that actively hydrolyze plant-derived aromatic β-glucosides such as salicin, arbutin and esculin, are able to avoid predation by the bacteriovorous amoeba Dictyostelium discoideum and nematodes of multiple genera belonging to the family Rhabditidae. This advantage can be observed under laboratory culture conditions as well as in the soil environment. The aglycone moiety released by the hydrolysis of β-glucosides is toxic to predators and acts via the dopaminergic receptor Dop-1 in the case of Caenorhabditis elegans. While soil isolates of nematodes belonging to the family Rhabditidae are repelled by the aglycone, laboratory strains and natural isolates of Caenorhabditis sp. are attracted to the compound, mediated by receptors that are independent of Dop-1, leading to their death. The β-glucosides-positive (Bgl(+)) bacteria that are otherwise non-pathogenic can obtain additional nutrients from the dead predators, thereby switching their role from prey to predator. This study also offers an evolutionary explanation for the retention by bacteria of 'cryptic' or 'silent' genetic systems such as the bgl operon.
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Affiliation(s)
- Robert Sonowal
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore 560 012, India
| | - Krithi Nandimath
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore 560 012, India
| | | | - Sandhya P. Koushika
- National Centre for Biological Sciences, Bangalore 560065, India
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Vidyanand Nanjundiah
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore 560 012, India
| | - S. Mahadevan
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore 560 012, India
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Corno G, Villiger J, Pernthaler J. Coaggregation in a microbial predator–prey system affects competition and trophic transfer efficiency. Ecology 2013. [DOI: 10.1890/12-1652.1] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Abstract
Bacteria play an indispensable role in marine biogeochemistry by recycling dissolved organic matter. Motile species can exploit small, ephemeral solute patches through chemotaxis and thereby gain a fitness advantage over nonmotile competitors. This competition occurs in a turbulent environment, yet turbulence is generally considered inconsequential for bacterial uptake. In contrast, we show that turbulence affects uptake by stirring nutrient patches into networks of thin filaments that motile bacteria can readily exploit. We find that chemotactic motility is subject to a trade-off between the uptake benefit due to chemotaxis and the cost of locomotion, resulting in an optimal swimming speed. A second trade-off results from the competing effects of stirring and mixing and leads to the prediction that chemotaxis is optimally favored at intermediate turbulence intensities.
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Affiliation(s)
- John R Taylor
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Wilberforce Road, Cambridge CB3 0WA, UK
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