1
|
Mitchell JH, Freedman AH, Delaney JA, Girguis PR. Co-expression analysis reveals distinct alliances around two carbon fixation pathways in hydrothermal vent symbionts. Nat Microbiol 2024; 9:1526-1539. [PMID: 38839975 DOI: 10.1038/s41564-024-01704-y] [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: 06/18/2023] [Accepted: 04/19/2024] [Indexed: 06/07/2024]
Abstract
Most autotrophic organisms possess a single carbon fixation pathway. The chemoautotrophic symbionts of the hydrothermal vent tubeworm Riftia pachyptila, however, possess two functional pathways: the Calvin-Benson-Bassham (CBB) and the reductive tricarboxylic acid (rTCA) cycles. How these two pathways are coordinated is unknown. Here we measured net carbon fixation rates, transcriptional/metabolic responses and transcriptional co-expression patterns of Riftia pachyptila endosymbionts by incubating tubeworms collected from the East Pacific Rise at environmental pressures, temperature and geochemistry. Results showed that rTCA and CBB transcriptional patterns varied in response to different geochemical regimes and that each pathway is allied to specific metabolic processes; the rTCA is allied to hydrogenases and dissimilatory nitrate reduction, whereas the CBB is allied to sulfide oxidation and assimilatory nitrate reduction, suggesting distinctive yet complementary roles in metabolic function. Furthermore, our network analysis implicates the rTCA and a group 1e hydrogenase as key players in the physiological response to limitation of sulfide and oxygen. Net carbon fixation rates were also exemplary, and accordingly, we propose that co-activity of CBB and rTCA may be an adaptation for maintaining high carbon fixation rates, conferring a fitness advantage in dynamic vent environments.
Collapse
|
2
|
Losa J, Heinemann M. Contribution of different macromolecules to the diffusion of a 40 nm particle in Escherichia coli. Biophys J 2024; 123:1211-1221. [PMID: 38555507 PMCID: PMC11140462 DOI: 10.1016/j.bpj.2024.03.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/20/2024] [Accepted: 03/28/2024] [Indexed: 04/02/2024] Open
Abstract
Due to the high concentration of proteins, nucleic acids, and other macromolecules, the bacterial cytoplasm is typically described as a crowded environment. However, the extent to which each of these macromolecules individually affects the mobility of macromolecular complexes, and how this depends on growth conditions, is presently unclear. In this study, we sought to quantify the crowding experienced by an exogenous 40 nm fluorescent particle in the cytoplasm of E. coli under different growth conditions. By performing single-particle tracking measurements in cells selectively depleted of DNA and/or mRNA, we determined the contribution to crowding of mRNA, DNA, and remaining cellular components, i.e., mostly proteins and ribosomes. To estimate this contribution to crowding, we quantified the difference of the particle's diffusion coefficient in conditions with and without those macromolecules. We found that the contributions of the three classes of components were of comparable magnitude, being largest in the case of proteins and ribosomes. We further found that the contributions of mRNA and DNA to crowding were significantly larger than expected based on their volumetric fractions alone. Finally, we found that the crowding contributions change only slightly with the growth conditions. These results reveal how various cellular components partake in crowding of the cytoplasm and the consequences this has for the mobility of large macromolecular complexes.
Collapse
Affiliation(s)
- José Losa
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Matthias Heinemann
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands.
| |
Collapse
|
3
|
Lindsay MR, D’Angelo T, Munson-McGee JH, Saidi-Mehrabad A, Devlin M, McGonigle J, Goodell E, Herring M, Lubelczyk LC, Mascena C, Brown JM, Gavelis G, Liu J, Yousavich DJ, Hamilton-Brehm SD, Hedlund BP, Lang S, Treude T, Poulton NJ, Stepanauskas R, Moser DP, Emerson D, Orcutt BN. Species-resolved, single-cell respiration rates reveal dominance of sulfate reduction in a deep continental subsurface ecosystem. Proc Natl Acad Sci U S A 2024; 121:e2309636121. [PMID: 38573964 PMCID: PMC11009646 DOI: 10.1073/pnas.2309636121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 02/23/2024] [Indexed: 04/06/2024] Open
Abstract
Rates of microbial processes are fundamental to understanding the significance of microbial impacts on environmental chemical cycling. However, it is often difficult to quantify rates or to link processes to specific taxa or individual cells, especially in environments where there are few cultured representatives with known physiology. Here, we describe the use of the redox-enzyme-sensitive molecular probe RedoxSensor™ Green to measure rates of anaerobic electron transfer physiology (i.e., sulfate reduction and methanogenesis) in individual cells and link those measurements to genomic sequencing of the same single cells. We used this method to investigate microbial activity in hot, anoxic, low-biomass (~103 cells mL-1) groundwater of the Death Valley Regional Flow System, California. Combining this method with electron donor amendment experiments and metatranscriptomics confirmed that the abundant spore formers including Candidatus Desulforudis audaxviator were actively reducing sulfate in this environment, most likely with acetate and hydrogen as electron donors. Using this approach, we measured environmental sulfate reduction rates at 0.14 to 26.9 fmol cell-1 h-1. Scaled to volume, this equates to a bulk environmental rate of ~103 pmol sulfate L-1 d-1, similar to potential rates determined with radiotracer methods. Despite methane in the system, there was no evidence for active microbial methanogenesis at the time of sampling. Overall, this method is a powerful tool for estimating species-resolved, single-cell rates of anaerobic metabolism in low-biomass environments while simultaneously linking genomes to phenomes at the single-cell level. We reveal active elemental cycling conducted by several species, with a large portion attributable to Ca. Desulforudis audaxviator.
Collapse
Affiliation(s)
| | | | | | | | - Molly Devlin
- Division of Hydrologic Sciences, Desert Research Institute, Las Vegas, NV89119
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV89154
| | - Julia McGonigle
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME04544
| | - Elizabeth Goodell
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME04544
- Department of Geology, Oberlin College, Oberlin, OH44074
| | - Melissa Herring
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME04544
- Department of Marine and Environmental Sciences, Northeastern University, Boston, MA02115
| | | | | | - Julia M. Brown
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME04544
| | - Greg Gavelis
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME04544
| | - Jiarui Liu
- Department of Earth, Planetary, and Space Sciences, University of California Los Angeles, Los Angeles, CA90095
| | - D. J. Yousavich
- Department of Earth, Planetary, and Space Sciences, University of California Los Angeles, Los Angeles, CA90095
| | | | - Brian P. Hedlund
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV89154
| | - Susan Lang
- School of the Earth, Ocean and Environment, University of South Carolina, Columbia, SC29208
| | - Tina Treude
- Department of Earth, Planetary, and Space Sciences, University of California Los Angeles, Los Angeles, CA90095
- Department of Atmospheric and Oceanic Sciences, University of California Los Angeles, Los Angeles, CA90095
| | | | | | - Duane P. Moser
- Division of Hydrologic Sciences, Desert Research Institute, Las Vegas, NV89119
| | - David Emerson
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME04544
| | - Beth N. Orcutt
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME04544
| |
Collapse
|
4
|
Stevanovic M, Teuber Carvalho JP, Bittihn P, Schultz D. Dynamical model of antibiotic responses linking expression of resistance genes to metabolism explains emergence of heterogeneity during drug exposures. Phys Biol 2024; 21:036002. [PMID: 38412523 PMCID: PMC10988634 DOI: 10.1088/1478-3975/ad2d64] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 01/25/2024] [Accepted: 02/27/2024] [Indexed: 02/29/2024]
Abstract
Antibiotic responses in bacteria are highly dynamic and heterogeneous, with sudden exposure of bacterial colonies to high drug doses resulting in the coexistence of recovered and arrested cells. The dynamics of the response is determined by regulatory circuits controlling the expression of resistance genes, which are in turn modulated by the drug's action on cell growth and metabolism. Despite advances in understanding gene regulation at the molecular level, we still lack a framework to describe how feedback mechanisms resulting from the interdependence between expression of resistance and cell metabolism can amplify naturally occurring noise and create heterogeneity at the population level. To understand how this interplay affects cell survival upon exposure, we constructed a mathematical model of the dynamics of antibiotic responses that links metabolism and regulation of gene expression, based on the tetracycline resistancetetoperon inE. coli. We use this model to interpret measurements of growth and expression of resistance in microfluidic experiments, both in single cells and in biofilms. We also implemented a stochastic model of the drug response, to show that exposure to high drug levels results in large variations of recovery times and heterogeneity at the population level. We show that stochasticity is important to determine how nutrient quality affects cell survival during exposure to high drug concentrations. A quantitative description of how microbes respond to antibiotics in dynamical environments is crucial to understand population-level behaviors such as biofilms and pathogenesis.
Collapse
Affiliation(s)
- Mirjana Stevanovic
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, United States of America
| | - João Pedro Teuber Carvalho
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, United States of America
| | - Philip Bittihn
- Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany
- Institute for the Dynamics of Complex Systems, University of Göttingen, Göttingen, Germany
| | - Daniel Schultz
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, United States of America
| |
Collapse
|
5
|
León-Sobrino C, Ramond JB, Coclet C, Kapitango RM, Maggs-Kölling G, Cowan D. Temporal dynamics of microbial transcription in wetted hyperarid desert soils. FEMS Microbiol Ecol 2024; 100:fiae009. [PMID: 38299778 PMCID: PMC10913055 DOI: 10.1093/femsec/fiae009] [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: 06/12/2023] [Revised: 12/15/2023] [Accepted: 01/30/2024] [Indexed: 02/02/2024] Open
Abstract
Rainfall is rare in hyperarid deserts but, when it occurs, it triggers large biological responses essential for the long-term maintenance of the ecosystem. In drylands, microbes play major roles in nutrient cycling, but their responses to short-lived opportunity windows are poorly understood. Due to its ephemeral nature, mRNA is ideally suited to study microbiome dynamics upon abrupt changes in the environment. We analyzed microbial community transcriptomes after simulated rainfall in a Namib Desert soil over 7 days. Using total mRNA from dry and watered plots we infer short-term functional responses in the microbiome. A rapid two-phase cycle of activation and return to basal state was completed in a short period. Motility systems activated immediately, whereas competition-toxicity increased in parallel to predator taxa and the drying of soils. Carbon fixation systems were downregulated, and reactivated upon return to a near-dry state. The chaperone HSP20 was markedly regulated by watering across all major bacteria, suggesting a particularly important role in adaptation to desiccated ecosystems. We show that transcriptomes provide consistent and high resolution information on microbiome processes in a low-biomass environment, revealing shared patterns across taxa. We propose a structured dispersal-predation dynamic as a central driver of desert microbial responses to rainfall.
Collapse
Affiliation(s)
- Carlos León-Sobrino
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, 0002 Pretoria, South Africa
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs Lyngby, Denmark
| | - Jean-Baptiste Ramond
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, 0002 Pretoria, South Africa
- Extreme Ecosystem Microbiomics and Ecogenomics (E²ME) Lab., Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Clément Coclet
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, 0002 Pretoria, South Africa
| | | | | | - Don A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, 0002 Pretoria, South Africa
| |
Collapse
|
6
|
Hechler RM, Yates MC, Chain FJJ, Cristescu ME. Environmental transcriptomics under heat stress: Can environmental RNA reveal changes in gene expression of aquatic organisms? Mol Ecol 2023. [PMID: 37792902 DOI: 10.1111/mec.17152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 08/10/2023] [Accepted: 09/20/2023] [Indexed: 10/06/2023]
Abstract
To safeguard biodiversity in a changing climate, taxonomic information about species turnover and insights into the health of organisms are required. Environmental DNA approaches are increasingly used for species identification, but cannot provide functional insights. Transcriptomic methods reveal the physiological states of macroorganisms, but are currently species-specific and require tissue sampling or animal sacrifice, making community-wide assessments challenging. Here, we test whether broad functional information (expression level of the transcribed genes) can be harnessed from environmental RNA (eRNA), which includes extra-organismal RNA from macroorganisms along with whole microorganisms. We exposed Daphnia pulex as well as phytoplankton prey and microorganism colonizers to control (20°C) and heat stress (28°C) conditions for 7 days. We sequenced eRNA from tank water (after complete removal of Daphnia) as well as RNA from Daphnia tissue, enabling comparisons of extra-organismal and organismal RNA-based gene expression profiles. Both RNA types detected similar heat stress responses of Daphnia. Using eRNA, we identified 32 Daphnia genes to be differentially expressed following heat stress. Of these, 17 were also differentially expressed and exhibited similar levels of relative expression in organismal RNA. In addition to the extra-organismal Daphnia response, eRNA detected community-wide heat stress responses consisting of distinct functional profiles and 121 differentially expressed genes across eight taxa. Our study demonstrates that environmental transcriptomics based on extra-organismal eRNA can noninvasively reveal gene expression responses of macroorganisms following environmental changes, with broad potential implications for the biomonitoring of health across the trophic chain.
Collapse
Affiliation(s)
- Robert M Hechler
- Department of Biology, McGill University, Montréal, Québec, Canada
| | - Matthew C Yates
- Département des Sciences Biologiques, Université du Québec à Montréal, Montréal, Québec, Canada
| | - Frédéric J J Chain
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | | |
Collapse
|
7
|
Malard LA, Guisan A. Into the microbial niche. Trends Ecol Evol 2023; 38:936-945. [PMID: 37236880 DOI: 10.1016/j.tree.2023.04.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 04/19/2023] [Accepted: 04/27/2023] [Indexed: 05/28/2023]
Abstract
The environmental niche concept describes the distribution of a taxon in the environment and can be used to understand community dynamics, biological invasions, and the impact of environmental changes. The uses and applications are still restricted in microbial ecology, largely due to the complexity of microbial systems and associated methodological limitations. The development of shotgun metagenomics and metatranscriptomics opens new ways to investigate the microbial niche by focusing on the metabolic niche within the environmental space. Here, we propose the metabolic niche framework, which, by defining the fundamental and realised metabolic niche of microorganisms, has the potential to not only provide novel insights into habitat preferences and the metabolism associated, but also to inform on metabolic plasticity, niche shifts, and microbial invasions.
Collapse
Affiliation(s)
- Lucie A Malard
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.
| | - Antoine Guisan
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland; Institute of Earth Surface Dynamics, University of Lausanne, 1015 Lausanne, Switzerland
| |
Collapse
|
8
|
Stevanovic M, Carvalho JPT, Bittihn P, Schultz D. Dynamical model of antibiotic responses linking expression of resistance to metabolism explains emergence of heterogeneity during drug exposures. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.22.558994. [PMID: 37790326 PMCID: PMC10542528 DOI: 10.1101/2023.09.22.558994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Antibiotic responses in bacteria are highly dynamic and heterogeneous, with sudden exposure of bacterial colonies to high drug doses resulting in the coexistence of recovered and arrested cells. The dynamics of the response is determined by regulatory circuits controlling the expression of resistance genes, which are in turn modulated by the drug's action on cell growth and metabolism. Despite advances in understanding gene regulation at the molecular level, we still lack a framework to describe how feedback mechanisms resulting from the interdependence between expression of resistance and cell metabolism can amplify naturally occurring noise and create heterogeneity at the population level. To understand how this interplay affects cell survival upon exposure, we constructed a mathematical model of the dynamics of antibiotic responses that links metabolism and regulation of gene expression, based on the tetracycline resistance tet operon in E. coli. We use this model to interpret measurements of growth and expression of resistance in microfluidic experiments, both in single cells and in biofilms. We also implemented a stochastic model of the drug response, to show that exposure to high drug levels results in large variations of recovery times and heterogeneity at the population level. We show that stochasticity is important to determine how nutrient quality affects cell survival during exposure to high drug concentrations. A quantitative description of how microbes respond to antibiotics in dynamical environments is crucial to understand population-level behaviors such as biofilms and pathogenesis.
Collapse
Affiliation(s)
- Mirjana Stevanovic
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, United States
| | - João Pedro Teuber Carvalho
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, United States
| | - Philip Bittihn
- Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany
- Institute for the Dynamics of Complex Systems, University of Göttingen, Göttingen, Germany
| | - Daniel Schultz
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, United States
| |
Collapse
|
9
|
Debeljak P, Bayer B, Sun Y, Herndl GJ, Obernosterer I. Seasonal patterns in microbial carbon and iron transporter expression in the Southern Ocean. MICROBIOME 2023; 11:187. [PMID: 37596690 PMCID: PMC10439609 DOI: 10.1186/s40168-023-01600-3] [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: 01/13/2023] [Accepted: 06/16/2023] [Indexed: 08/20/2023]
Abstract
BACKGROUND Heterotrophic microbes in the Southern Ocean are challenged by the double constraint of low concentrations of organic carbon (C) and iron (Fe). These essential elements are tightly coupled in cellular processes; however, the prokaryotic requirements of C and Fe under varying environmental settings remain poorly studied. Here, we used a combination of metatranscriptomics and metaproteomics to identify prokaryotic membrane transporters for organic substrates and Fe in naturally iron-fertilized and high-nutrient, low-chlorophyll waters of the Southern Ocean during spring and late summer. RESULTS Pronounced differences in membrane transporter profiles between seasons were observed at both sites, both at the transcript and protein level. When specific compound classes were considered, the two approaches revealed different patterns. At the transcript level, seasonal patterns were only observed for subsets of genes belonging to each transporter category. At the protein level, membrane transporters of organic compounds were relatively more abundant in spring as compared to summer, while the opposite pattern was observed for Fe transporters. These observations suggest an enhanced requirement for organic C in early spring and for Fe in late summer. Mapping transcripts and proteins to 50 metagenomic-assembled genomes revealed distinct taxon-specific seasonal differences pointing to potentially opportunistic clades, such as Pseudomonadales and Nitrincolaceae, and groups with a more restricted repertoire of expressed transporters, such as Alphaproteobacteria and Flavobacteriaceae. CONCLUSION The combined investigations of C and Fe membrane transporters suggest seasonal changes in the microbial requirements of these elements under different productivity regimes. The taxon-specific acquisition strategies of different forms of C and Fe illustrate how diverse microbes could shape transcript and protein expression profiles at the community level at different seasons. Our results on the C- and Fe-related metabolic capabilities of microbial taxa provide new insights into their potential role in the cycling of C and Fe under varying nutrient regimes in the Southern Ocean. Video Abstract.
Collapse
Affiliation(s)
- Pavla Debeljak
- Laboratoire d'Océanographie Microbienne (LOMIC), CNRS, Sorbonne Université, Banyuls/Mer, F-66650, France.
- Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, Vienna, 1030, Austria.
- SupBiotech, Villejuif, France.
| | - Barbara Bayer
- Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, Vienna, 1030, Austria
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Djerassiplatz 1, Vienna, 1030, Austria
| | - Ying Sun
- Laboratoire d'Océanographie Microbienne (LOMIC), CNRS, Sorbonne Université, Banyuls/Mer, F-66650, France
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Gerhard J Herndl
- Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, Vienna, 1030, Austria
- Department of Marine Microbiology and Biogeochemistry, NIOZ (Royal Netherlands Institute for Sea Research), Den Burg, 1790 AB, The Netherlands
- Vienna Metabolomics Center, University of Vienna, Djerassiplatz 1, Vienna, 1030, Austria
| | - Ingrid Obernosterer
- Laboratoire d'Océanographie Microbienne (LOMIC), CNRS, Sorbonne Université, Banyuls/Mer, F-66650, France
| |
Collapse
|
10
|
Li R, Rozum JC, Quail MM, Qasim MN, Sindi SS, Nobile CJ, Albert R, Hernday AD. Inferring gene regulatory networks using transcriptional profiles as dynamical attractors. PLoS Comput Biol 2023; 19:e1010991. [PMID: 37607190 PMCID: PMC10473541 DOI: 10.1371/journal.pcbi.1010991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 09/01/2023] [Accepted: 07/19/2023] [Indexed: 08/24/2023] Open
Abstract
Genetic regulatory networks (GRNs) regulate the flow of genetic information from the genome to expressed messenger RNAs (mRNAs) and thus are critical to controlling the phenotypic characteristics of cells. Numerous methods exist for profiling mRNA transcript levels and identifying protein-DNA binding interactions at the genome-wide scale. These enable researchers to determine the structure and output of transcriptional regulatory networks, but uncovering the complete structure and regulatory logic of GRNs remains a challenge. The field of GRN inference aims to meet this challenge using computational modeling to derive the structure and logic of GRNs from experimental data and to encode this knowledge in Boolean networks, Bayesian networks, ordinary differential equation (ODE) models, or other modeling frameworks. However, most existing models do not incorporate dynamic transcriptional data since it has historically been less widely available in comparison to "static" transcriptional data. We report the development of an evolutionary algorithm-based ODE modeling approach (named EA) that integrates kinetic transcription data and the theory of attractor matching to infer GRN architecture and regulatory logic. Our method outperformed six leading GRN inference methods, none of which incorporate kinetic transcriptional data, in predicting regulatory connections among TFs when applied to a small-scale engineered synthetic GRN in Saccharomyces cerevisiae. Moreover, we demonstrate the potential of our method to predict unknown transcriptional profiles that would be produced upon genetic perturbation of the GRN governing a two-state cellular phenotypic switch in Candida albicans. We established an iterative refinement strategy to facilitate candidate selection for experimentation; the experimental results in turn provide validation or improvement for the model. In this way, our GRN inference approach can expedite the development of a sophisticated mathematical model that can accurately describe the structure and dynamics of the in vivo GRN.
Collapse
Affiliation(s)
- Ruihao Li
- Quantitative and Systems Biology Graduate Program, University of California, Merced, Merced, California, United States of America
| | - Jordan C. Rozum
- Department of Systems Science and Industrial Engineering, Binghamton University (State University of New York), Binghamton, New York, United States of America
| | - Morgan M. Quail
- Quantitative and Systems Biology Graduate Program, University of California, Merced, Merced, California, United States of America
| | - Mohammad N. Qasim
- Quantitative and Systems Biology Graduate Program, University of California, Merced, Merced, California, United States of America
| | - Suzanne S. Sindi
- Department of Applied Mathematics, University of California, Merced, Merced, California, United States of America
| | - Clarissa J. Nobile
- Department of Molecular Cell Biology, University of California, Merced, Merced, California, United States of America
- Health Sciences Research Institute, University of California, Merced, Merced, California, United States of America
| | - Réka Albert
- Department of Physics, Pennsylvania State University, University Park, University Park, Pennsylvania, United States of America
- Department of Biology, Pennsylvania State University, University Park, University Park, Pennsylvania, United States of America
| | - Aaron D. Hernday
- Department of Molecular Cell Biology, University of California, Merced, Merced, California, United States of America
- Health Sciences Research Institute, University of California, Merced, Merced, California, United States of America
| |
Collapse
|
11
|
Schroer WF, Kepner HE, Uchimiya M, Mejia C, Rodriguez LT, Reisch CR, Moran MA. Functional annotation and importance of marine bacterial transporters of plankton exometabolites. ISME COMMUNICATIONS 2023; 3:37. [PMID: 37185952 PMCID: PMC10130141 DOI: 10.1038/s43705-023-00244-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 04/01/2023] [Accepted: 04/14/2023] [Indexed: 05/17/2023]
Abstract
Metabolite exchange within marine microbial communities transfers carbon and other major elements through global cycles and forms the basis of microbial interactions. Yet lack of gene annotations and concern about the quality of existing ones remain major impediments to revealing currencies of carbon flux. We employed an arrayed mutant library of the marine bacterium Ruegeria pomeroyi DSS-3 to experimentally annotate substrates of organic compound transporter systems, using mutant growth and compound drawdown analyses to link transporters to their cognate substrates. Mutant experiments verified substrates for thirteen R. pomeroyi transporters. Four were previously hypothesized based on gene expression data (taurine, glucose/xylose, isethionate, and cadaverine/putrescine/spermidine); five were previously hypothesized based on homology to experimentally annotated transporters in other bacteria (citrate, glycerol, N-acetylglucosamine, fumarate/malate/succinate, and dimethylsulfoniopropionate); and four had no previous annotations (thymidine, carnitine, cysteate, and 3-hydroxybutyrate). These bring the total number of experimentally-verified organic carbon influx transporters to 18 of 126 in the R. pomeroyi genome. In a longitudinal study of a coastal phytoplankton bloom, expression patterns of the experimentally annotated transporters linked them to different stages of the bloom, and also led to the hypothesis that citrate and 3-hydroxybutyrate were among the most highly available bacterial substrates. Improved functional annotation of the gatekeepers of organic carbon uptake is critical for deciphering carbon flux and fate in microbial ecosystems.
Collapse
Affiliation(s)
- William F Schroer
- Department of Marine Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Hannah E Kepner
- Department of Marine Sciences, University of Georgia, Athens, GA, 30602, USA
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Fairbanks, AK, 99775, USA
| | - Mario Uchimiya
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Catalina Mejia
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA
| | | | - Christopher R Reisch
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA
| | - Mary Ann Moran
- Department of Marine Sciences, University of Georgia, Athens, GA, 30602, USA.
| |
Collapse
|
12
|
Alonso-Sáez L, Palacio AS, Cabello AM, Robaina-Estévez S, González JM, Garczarek L, López-Urrutia Á. Transcriptional Mechanisms of Thermal Acclimation in Prochlorococcus. mBio 2023:e0342522. [PMID: 37052490 DOI: 10.1128/mbio.03425-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023] Open
Abstract
Low temperature limits the growth and the distribution of the key oceanic primary producer Prochlorococcus, which does not proliferate above a latitude of ca. 40°. Yet, the molecular basis of thermal acclimation in this cyanobacterium remains unexplored. We analyzed the transcriptional response of the Prochlorococcus marinus strain MIT9301 in long-term acclimations and in natural Prochlorococcus populations along a temperature range enabling its growth (17 to 30°C). MIT9301 upregulated mechanisms of the global stress response at the temperature minimum (17°C) but maintained the expression levels of genes involved in essential metabolic pathways (e.g., ATP synthesis and carbon fixation) along the whole thermal niche. Notably, the declining growth of MIT9301 from the optimum to the minimum temperature was coincident with a transcriptional suppression of the photosynthetic apparatus and a dampening of its circadian expression patterns, indicating a loss in their regulatory capacity under cold conditions. Under warm conditions, the cellular transcript inventory of MIT9301 was strongly streamlined, which may also induce regulatory imbalances due to stochasticity in gene expression. The daytime transcriptional suppression of photosynthetic genes at low temperature was also observed in metatranscriptomic reads mapping to MIT9301 across the global ocean, implying that this molecular mechanism may be associated with the restricted distribution of Prochlorococcus to temperate zones. IMPORTANCE Prochlorococcus is a major marine primary producer with a global impact on atmospheric CO2 fixation. This cyanobacterium is widely distributed across the temperate ocean, but virtually absent at latitudes above 40° for yet unknown reasons. Temperature has been suggested as a major limiting factor, but the exact mechanisms behind Prochlorococcus thermal growth restriction remain unexplored. This study brings us closer to understanding how Prochlorococcus functions under challenging temperature conditions, by focusing on its transcriptional response after long-term acclimation from its optimum to its thermal thresholds. Our results show that the drop in Prochlorococcus growth rate under cold conditions was paralleled by a transcriptional suppression of the photosynthetic machinery during daytime and a loss in the organism's regulatory capacity to maintain circadian expression patterns. Notably, warm temperature induced a marked shrinkage of the organism's cellular transcript inventory, which may also induce regulatory imbalances in the future functioning of this cyanobacterium.
Collapse
Affiliation(s)
- Laura Alonso-Sáez
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Sukarrieta, Spain
| | - Antonio S Palacio
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Sukarrieta, Spain
| | - Ana M Cabello
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Sukarrieta, Spain
| | | | - José M González
- Department of Microbiology, University of La Laguna, La Laguna, Spain
| | - Laurence Garczarek
- Sorbonne Université, CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment (AD2M), Station Biologique de Roscoff (SBR), Roscoff, France
| | - Ángel López-Urrutia
- Centro Oceanográfico de Gijón, Instituto Español de Oceanografía, IEO-CSIC, Gijón, Asturias, Spain
| |
Collapse
|
13
|
Marshall AJ, Phillips L, Longmore A, Hayden HL, Tang C, Heidelberg KB, Mele P. Using metatranscriptomics to better understand the role of microbial nitrogen cycling in coastal sediment benthic flux denitrification efficiency. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023. [PMID: 36992633 DOI: 10.1111/1758-2229.13148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 01/27/2023] [Indexed: 06/19/2023]
Abstract
Spatial and temporal variability in benthic flux denitrification efficiency occurs across Port Phillip Bay, Australia. Here, we assess the capacity for untargeted metatranscriptomics to resolve spatiotemporal differences in the microbial contribution to benthic nitrogen cycling. The most abundant sediment transcripts assembled were associated with the archaeal nitrifier Nitrosopumilus. In sediments close to external inputs of organic nitrogen, the dominant transcripts were associated with Nitrosopumilus nitric oxide nitrite reduction (nirK). The environmental conditions close to organic nitrogen inputs that select for increased transcription in Nitrosopumilus (amoCAB, nirK, nirS, nmo, hcp) additionally selected for increased transcription of bacterial nitrite reduction (nxrB) and transcripts associated with anammox (hzo) but not denitrification (bacterial nirS/nirk). In sediments that are more isolated from external inputs of organic nitrogen dominant transcripts were associated with nitrous oxide reduction (nosZ) and changes in nosZ transcript abundance were uncoupled from transcriptional profiles associated with archaeal nitrification. Coordinated transcription of coupled community-level nitrification-denitrification was not well supported by metatranscriptomics. In comparison, the abundance of archaeal nirK transcripts were site- and season-specific. This study indicates that the transcription of archaeal nirK in response to changing environmental conditions may be an important and overlooked feature of coastal sediment nitrogen cycling.
Collapse
Affiliation(s)
- Alexis J Marshall
- La Trobe University, AgriBio Centre for AgriBiosciences, Bundoora, Australia
- Department of Jobs, Precincts and Regions, AgriBio, Centre for AgriBiosciences, Bundoora, Australia
| | - Lori Phillips
- Department of Jobs, Precincts and Regions, AgriBio, Centre for AgriBiosciences, Bundoora, Australia
| | - Andrew Longmore
- Centre for Aquatic Pollution Identification and Management, Melbourne University, Parkville, Australia
| | - Helen L Hayden
- Department of Jobs, Precincts and Regions, AgriBio, Centre for AgriBiosciences, Bundoora, Australia
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Caixian Tang
- La Trobe University, AgriBio Centre for AgriBiosciences, Bundoora, Australia
| | - Karla B Heidelberg
- Department of Biology, The University of Southern California, Los Angeles, California, USA
| | - Pauline Mele
- La Trobe University, AgriBio Centre for AgriBiosciences, Bundoora, Australia
- Department of Jobs, Precincts and Regions, AgriBio, Centre for AgriBiosciences, Bundoora, Australia
| |
Collapse
|
14
|
Ecological divergence of syntopic marine bacterial species is shaped by gene content and expression. THE ISME JOURNAL 2023; 17:813-822. [PMID: 36871069 DOI: 10.1038/s41396-023-01390-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 02/15/2023] [Accepted: 02/21/2023] [Indexed: 03/06/2023]
Abstract
Identifying mechanisms by which bacterial species evolve and maintain genomic diversity is particularly challenging for the uncultured lineages that dominate the surface ocean. A longitudinal analysis of bacterial genes, genomes, and transcripts during a coastal phytoplankton bloom revealed two co-occurring, highly related Rhodobacteraceae species from the deeply branching and uncultured NAC11-7 lineage. These have identical 16S rRNA gene amplicon sequences, yet their genome contents assembled from metagenomes and single cells indicate species-level divergence. Moreover, shifts in relative dominance of the species during dynamic bloom conditions over 7 weeks confirmed the syntopic species' divergent responses to the same microenvironment at the same time. Genes unique to each species and genes shared but divergent in per-cell inventories of mRNAs accounted for 5% of the species' pangenome content. These analyses uncover physiological and ecological features that differentiate the species, including capacities for organic carbon utilization, attributes of the cell surface, metal requirements, and vitamin biosynthesis. Such insights into the coexistence of highly related and ecologically similar bacterial species in their shared natural habitat are rare.
Collapse
|
15
|
Ryzowicz C, Yildirim N. Differential roles of transcriptional and translational negative autoregulations in protein dynamics. Mol Omics 2023; 19:60-71. [PMID: 36399028 DOI: 10.1039/d2mo00222a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Cells continuously respond to stimuli to function properly by employing a wide variety of regulatory mechanisms that often involve protein up or down regulations. This study focuses on dynamics of a protein with negative autoregulations in E. coli, and assumes that the input signal up-regulates the protein, and then the protein down-regulates its own production via 2 distinct types of mechanisms. The mathematical models describe the dynamics of mRNA and protein for 3 scenarios: (i) a simplistic model with no regulation, (ii) a model with transcriptional negative autoregulation, and (iii) a model with translational negative autoregulation. Our analysis shows that the negative autoregulation models produce faster responses and quicker return times to the input signals compared to the model with no regulation, while the transcriptional autoregulation model is the only model capable of producing oscillatory dynamics. The stochastic simulations predict that the transcriptional autoregulation model is the noisiest followed by the simplistic model, and the translational autoregulation model has the least noise. The noise level depends on the strength of inhibition. Furthermore, the transcriptional autoregulation model filters out the noise in the input signal for longer periods of time, and this time increases as the strength of the feedback gets stronger.
Collapse
Affiliation(s)
- Christopher Ryzowicz
- Division of Natural Sciences, New College of Florida, 5800 Bayshore Road, Sarasota, FL 34243, USA.
| | - Necmettin Yildirim
- Division of Natural Sciences, New College of Florida, 5800 Bayshore Road, Sarasota, FL 34243, USA.
| |
Collapse
|
16
|
Marshall AJ, Phillips L, Longmore A, Hayden HL, Heidelberg KB, Tang C, Mele P. Temporal profiling resolves the drivers of microbial nitrogen cycling variability in coastal sediments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 856:159057. [PMID: 36174701 DOI: 10.1016/j.scitotenv.2022.159057] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 09/21/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
Here we describe the potential for sediment microbial nitrogen-cycling gene (DNA) and activity (RNA) abundances to spatially resolve coastal areas impacted by seasonal variability in external nutrient inputs. Three sites were chosen within a nitrogen-limited embayment, Port Phillip Bay (PPB), Australia that reflect variability in both proximity to external nutrient inputs and the dominant form of available nitrogen. At three sediment depths (0-1; 1-5; 5-10 cm) across a 2 year study key genes involved in nitrification (archaeal amoA and bacterial β-amoA), nitrite reduction (clade I nirS and cluster I nirK, archaeal nirK-a), anaerobic oxidation of ammonium (anammox 16S rRNA phylogenetic marker) and nitrogen fixation (nifH) were quantified. Sediments impacted by a dominance of organic nitrogen inputs were characterised at all time-points and to sediment depths of 10 cm by the highest transcript abundances of archaeal amoA and archaeal nirk-a. Proximity to a dominance of external nitrate inputs was associated with the highest transcript abundances of nirS which temporally co-varied with seasonal changes in sediment nitrate. Sediments isolated from external inputs displayed the greatest depth-specific decrease in quantifiable transcript abundances. In these isolated sediments bacterial β-amoA transcripts were temporally associated with increased sediment ammonium levels. Across this nitrogen limited system variability in the abundance of bacterial β-amoA, archaeal amoA, archaeal nirk-a or nirS transcripts from the sediment surface (0-1 and 5 cm) demonstrated a capacity to improve our ability to monitor coastal zones impacted by anthropogenic nitrogen inputs. Specifically, the spatial detection sensitivity of bacterial β-amoA transcripts could be developed as a metric to determine spatiotemporal impacts of large external loading events. This temporal study demonstrates a capacity for microbial activity metrics to facilitate coastal management strategies through greater spatial resolution of areas impacted by external nutrient inputs.
Collapse
Affiliation(s)
- Alexis J Marshall
- La Trobe University, AgriBio Centre for AgriBiosciences, 5 Ring Road Bundoora, Australia; Department of Jobs, Precincts and Regions, AgriBio, Centre for AgriBiosciences, 5 Ring Road Bundoora, Australia.
| | - Lori Phillips
- Department of Jobs, Precincts and Regions, AgriBio, Centre for AgriBiosciences, 5 Ring Road Bundoora, Australia
| | - Andrew Longmore
- Centre for Aquatic Pollution Identification and Management, Melbourne University, Parkville, Australia
| | - Helen L Hayden
- Department of Jobs, Precincts and Regions, AgriBio, Centre for AgriBiosciences, 5 Ring Road Bundoora, Australia
| | - Karla B Heidelberg
- The University of Southern California, Department of Biology, Los Angeles, CA 90089, United States of America
| | - Caixian Tang
- La Trobe University, AgriBio Centre for AgriBiosciences, 5 Ring Road Bundoora, Australia
| | - Pauline Mele
- La Trobe University, AgriBio Centre for AgriBiosciences, 5 Ring Road Bundoora, Australia; Department of Jobs, Precincts and Regions, AgriBio, Centre for AgriBiosciences, 5 Ring Road Bundoora, Australia
| |
Collapse
|
17
|
Bot JF, van der Oost J, Geijsen N. The double life of CRISPR-Cas13. Curr Opin Biotechnol 2022; 78:102789. [PMID: 36115160 DOI: 10.1016/j.copbio.2022.102789] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/25/2022] [Accepted: 08/07/2022] [Indexed: 12/14/2022]
Abstract
Since the discovery of RNA-programmable nucleases from the prokaryotic adaptive immune system CRISPR-Cas, these proteins have seen rapid and widespread adoption for biotechnological and clinical research. A recently discovered system, CRISPR-Cas13, uses CRISPR RNA guides to target RNA. Interestingly, RNA targeting by Cas13 results in cleavage of both target RNA and bystander RNA. This feature has been used to develop innovative diagnostic tools for the detection of specific RNAs. Unlike in vitro detection of RNA using collateral RNA cleavage, however, initial studies of mammalian cells only revealed highly specific target RNA-knockdown activity. Although these findings have been confirmed subsequently, several recent publications do report Cas13-mediated toxicity and collateral RNA cleavage when using Cas13 in eukaryotes. Here, we review these conflicting observations and discuss its potential molecular basis.
Collapse
Affiliation(s)
- Jorik F Bot
- Dept. of Anatomy & Embryology, Leiden University Medical Center, Einthovenweg 20, 2300 RC Leiden, the Netherlands; The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden node, the Netherlands
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, the Netherlands
| | - Niels Geijsen
- Dept. of Anatomy & Embryology, Leiden University Medical Center, Einthovenweg 20, 2300 RC Leiden, the Netherlands; The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden node, the Netherlands.
| |
Collapse
|
18
|
Liao M, Xie Y, Shi M, Cui J. Over two decades of research on the marine RNA virosphere. IMETA 2022; 1:e59. [PMID: 38867898 PMCID: PMC10989941 DOI: 10.1002/imt2.59] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 08/30/2022] [Accepted: 09/14/2022] [Indexed: 06/14/2024]
Abstract
RNA viruses (realm: Riboviria), including RNA phages and eukaryote-infecting RNA viruses, are essential components of marine ecosystems. A large number of marine RNA viruses have been discovered in the last two decades because of the rapid development of next-generation sequencing (NGS) technology. Indeed, the combination of NGS and state-of-the-art meta-omics methods (viromics, the study of all viruses in a specific environment) has led to a fundamental understanding of the taxonomy and genetic diversity of RNA viruses in the sea, suggesting the complex ecological roles played by RNA viruses in this complex ecosystem. Furthermore, comparisons of viromes in the context of highly variable marine niches reveal the biogeographic patterns and ecological impact of marine RNA viruses, whose role in global ecology is becoming increasingly clearer. In this review, we summarize the characteristics of the global marine RNA virosphere and outline the taxonomic hierarchy of RNA viruses with a specific focus on their ancient evolutionary history. We also review the development of methodology and the major progress resulting from its applications in RNA viromics. The aim of this review is not only to provide an in-depth understanding of multifaceted aspects of marine RNA viruses, but to offer future perspectives on developing a better methodology for discovery, and exploring the evolutionary origin and major ecological significance of marine RNA virosphere.
Collapse
Affiliation(s)
- Meng‐en Liao
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Center for Biosafety Mega‐ScienceChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yunyi Xie
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Center for Biosafety Mega‐ScienceChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Mang Shi
- School of MedicineSun Yat‐sen UniversityShenzhen Campus of Sun Yat‐sen UniversityShenzhenChina
| | - Jie Cui
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Center for Biosafety Mega‐ScienceChinese Academy of SciencesShanghaiChina
- Laboatory for Marine Biology and BiotechnologyPilot National Laboratory for Marine Science and Technology (Qingdao)QingdaoChina
| |
Collapse
|
19
|
Munson-McGee JH, Lindsay MR, Sintes E, Brown JM, D'Angelo T, Brown J, Lubelczyk LC, Tomko P, Emerson D, Orcutt BN, Poulton NJ, Herndl GJ, Stepanauskas R. Decoupling of respiration rates and abundance in marine prokaryoplankton. Nature 2022; 612:764-770. [PMID: 36477536 PMCID: PMC9771814 DOI: 10.1038/s41586-022-05505-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 11/01/2022] [Indexed: 12/12/2022]
Abstract
The ocean-atmosphere exchange of CO2 largely depends on the balance between marine microbial photosynthesis and respiration. Despite vast taxonomic and metabolic diversity among marine planktonic bacteria and archaea (prokaryoplankton)1-3, their respiration usually is measured in bulk and treated as a 'black box' in global biogeochemical models4; this limits the mechanistic understanding of the global carbon cycle. Here, using a technology for integrated phenotype analyses and genomic sequencing of individual microbial cells, we show that cell-specific respiration rates differ by more than 1,000× among prokaryoplankton genera. The majority of respiration was found to be performed by minority members of prokaryoplankton (including the Roseobacter cluster), whereas cells of the most prevalent lineages (including Pelagibacter and SAR86) had extremely low respiration rates. The decoupling of respiration rates from abundance among lineages, elevated counts of proteorhodopsin transcripts in Pelagibacter and SAR86 cells and elevated respiration of SAR86 at night indicate that proteorhodopsin-based phototrophy3,5-7 probably constitutes an important source of energy to prokaryoplankton and may increase growth efficiency. These findings suggest that the dependence of prokaryoplankton on respiration and remineralization of phytoplankton-derived organic carbon into CO2 for its energy demands and growth may be lower than commonly assumed and variable among lineages.
Collapse
Affiliation(s)
| | | | - Eva Sintes
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Instituto Español de Oceanografía-CSIC, Centro Oceanográfico de Baleares, Palma, Spain
| | - Julia M Brown
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | | | - Joe Brown
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | | | | | - David Emerson
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | - Beth N Orcutt
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | | | - Gerhard J Herndl
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ), Utrecht University, Den Burg, The Netherlands
| | | |
Collapse
|
20
|
Favate JS, Liang S, Cope AL, Yadavalli SS, Shah P. The landscape of transcriptional and translational changes over 22 years of bacterial adaptation. eLife 2022; 11:e81979. [PMID: 36214449 PMCID: PMC9645810 DOI: 10.7554/elife.81979] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 10/07/2022] [Indexed: 12/31/2022] Open
Abstract
Organisms can adapt to an environment by taking multiple mutational paths. This redundancy at the genetic level, where many mutations have similar phenotypic and fitness effects, can make untangling the molecular mechanisms of complex adaptations difficult. Here, we use the Escherichia coli long-term evolution experiment (LTEE) as a model to address this challenge. To understand how different genomic changes could lead to parallel fitness gains, we characterize the landscape of transcriptional and translational changes across 12 replicate populations evolving in parallel for 50,000 generations. By quantifying absolute changes in mRNA abundances, we show that not only do all evolved lines have more mRNAs but that this increase in mRNA abundance scales with cell size. We also find that despite few shared mutations at the genetic level, clones from replicate populations in the LTEE are remarkably similar in their gene expression patterns at both the transcriptional and translational levels. Furthermore, we show that the majority of the expression changes are due to changes at the transcriptional level with very few translational changes. Finally, we show how mutations in transcriptional regulators lead to consistent and parallel changes in the expression levels of downstream genes. These results deepen our understanding of the molecular mechanisms underlying complex adaptations and provide insights into the repeatability of evolution.
Collapse
Affiliation(s)
- John S Favate
- Department of Genetics, Rutgers UniversityPiscatawayUnited States
| | - Shun Liang
- Department of Genetics, Rutgers UniversityPiscatawayUnited States
| | - Alexander L Cope
- Department of Genetics, Rutgers UniversityPiscatawayUnited States
- Robert Wood Johnson Medical School, Rutgers UniversityNew BrunswickUnited States
| | - Srujana S Yadavalli
- Department of Genetics, Rutgers UniversityPiscatawayUnited States
- Waksman Institute, Rutgers UniversityPiscatawayUnited States
| | - Premal Shah
- Department of Genetics, Rutgers UniversityPiscatawayUnited States
- Human Genetics Institute of New Jersey, Rutgers UniversityPiscatawayUnited States
| |
Collapse
|
21
|
Wang H, Meister M, Jensen C, Kuss AW, Urich T. The impact of summer drought on peat soil microbiome structure and function-A multi-proxy-comparison. ISME COMMUNICATIONS 2022; 2:78. [PMID: 37938747 PMCID: PMC9723574 DOI: 10.1038/s43705-022-00164-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 08/12/2022] [Indexed: 06/18/2023]
Abstract
Different proxies for changes in structure and/or function of microbiomes have been developed, allowing assessing microbiome dynamics at multiple levels. However, the lack and differences in understanding the microbiome dynamics are due to the differences in the choice of proxies in different studies and the limitations of proxies themselves. Here, using both amplicon and metatranscriptomic sequencings, we compared four different proxies (16/18S rRNA genes, 16/18S rRNA transcripts, mRNA taxonomy and mRNA function) to reveal the impact of a severe summer drought in 2018 on prokaryotic and eukaryotic microbiome structures and functions in two rewetted fen peatlands in northern Germany. We found that both prokaryotic and eukaryotic microbiome compositions were significantly different between dry and wet months. Interestingly, mRNA proxies showed stronger and more significant impacts of drought for prokaryotes, while 18S rRNA transcript and mRNA taxonomy showed stronger drought impacts for eukaryotes. Accordingly, by comparing the accuracy of microbiome changes in predicting dry and wet months under different proxies, we found that mRNA proxies performed better for prokaryotes, while 18S rRNA transcript and mRNA taxonomy performed better for eukaryotes. In both cases, rRNA gene proxies showed much lower to the lowest accuracy, suggesting the drawback of DNA based approaches. To our knowledge, this is the first study comparing all these proxies to reveal the dynamics of both prokaryotic and eukaryotic microbiomes in soils. This study shows that microbiomes are sensitive to (extreme) weather changes in rewetted fens, and the associated microbial changes might contribute to ecological consequences.
Collapse
Affiliation(s)
- Haitao Wang
- Institute of Microbiology, University of Greifswald, Greifswald, Germany.
| | - Mareike Meister
- Diabetes Competence Centre Karlsburg (KDK), Leibniz Institute for Plasma Science and Technology (INP), Karlsburg, Germany
| | - Corinna Jensen
- Human Molecular Genetics Group, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Andreas W Kuss
- Human Molecular Genetics Group, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Tim Urich
- Institute of Microbiology, University of Greifswald, Greifswald, Germany.
| |
Collapse
|
22
|
Linardi D, She W, Zhang Q, Yu Y, Qian PY, Lam H. Proteomining-Based Elucidation of Natural Product Biosynthetic Pathways in Streptomyces. Front Microbiol 2022; 13:913756. [PMID: 35898901 PMCID: PMC9309509 DOI: 10.3389/fmicb.2022.913756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/30/2022] [Indexed: 11/24/2022] Open
Abstract
The genus Streptomyces is known to harbor numerous biosynthetic gene clusters (BGCs) of potential utility in synthetic biology applications. However, it is often difficult to link uncharacterized BGCs with the secondary metabolites they produce. Proteomining refers to the strategy of identifying active BGCs by correlating changes in protein expression with the production of secondary metabolites of interest. In this study, we devised a shotgun proteomics-based workflow to identify active BGCs during fermentation when a variety of compounds are being produced. Mycelia harvested during the non-producing growth phase served as the background. Proteins that were differentially expressed were clustered based on the proximity of the genes in the genome to highlight active BGCs systematically from label-free quantitative proteomics data. Our software tool is easy-to-use and requires only 1 point of comparison where natural product biosynthesis was significantly different. We tested our proteomining clustering method on three Streptomyces species producing different compounds. In Streptomyces coelicolor A3(2), we detected the BGCs of calcium-dependent antibiotic, actinorhodin, undecylprodigiosin, and coelimycin P1. In Streptomyces chrestomyceticus BCC24770, 7 BGCs were identified. Among them, we independently re-discovered the type II PKS for albofungin production previously identified by genome mining and tedious heterologous expression experiments. In Streptomyces tenebrarius, 5 BGCs were detected, including the known apramycin and tobramycin BGC as well as a newly discovered caerulomycin A BGC in this species. The production of caerulomycin A was confirmed by LC-MS and the inactivation of the caerulomycin A BGC surprisingly had a significant impact on the secondary metabolite regulation of S. tenebrarius. In conclusion, we developed an unbiased, high throughput proteomics-based method to complement genome mining methods for the identification of biosynthetic pathways in Streptomyces sp.
Collapse
Affiliation(s)
- Darwin Linardi
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | - Weiyi She
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Hong Kong, Hong Kong SAR, China
- SZU-HKUST Joint PhD Program in Marine Environmental Science, Shenzhen University, Shenzhen, China
- Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | - Qian Zhang
- Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Disease, Department of Gastroenterology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Yi Yu
- Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Disease, Department of Gastroenterology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Pei-Yuan Qian
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Hong Kong, Hong Kong SAR, China
- Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | - Henry Lam
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
- *Correspondence: Henry Lam,
| |
Collapse
|
23
|
Maki JJ, Lippolis JD, Looft T. Proteomic response of Turicibacter bilis MMM721 to chicken bile and its bile acids. BMC Res Notes 2022; 15:236. [PMID: 35780123 PMCID: PMC9250206 DOI: 10.1186/s13104-022-06127-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 06/21/2022] [Indexed: 11/19/2022] Open
Abstract
Objective Bile and its individual components, mainly bile acids, are important for digestion and drive bacterial community dynamics in the upper gastrointestinal tract of chickens. However, specific responses to bile acids have been characterized in only a few commensal bacteria, and it is unclear how other members of the microbiota respond to biliary stress. Here, we used label-free LC–MS/MS to assess the proteomic response of a common inhabitant of the chicken small intestine, Turicibacter bilis MMM721, to 24 h of growth in anaerobic growth media supplemented with 0.1% whole chicken bile, 0.1% taurochenodeoxycholic acid (TCDCA), or 0.1% taurocholic acid (TCA). Results Seventy, 46, and 10 differentially expressed proteins were identified in Turicibacter bilis MMM721 cultured with supplements of chicken bile, TCDCA, and TCA, respectively, when compared to unsupplemented controls. Many differentially expressed proteins were predicted to be involved in ribosomal processes, post-translational modifications and chaperones, and modifications to the cell surface. Ultimately, the T. bilis MMM721 response to whole bile and bile acids is complex and may relate to adaptations for small intestine colonization, with numerous proteins from a variety of functional categories being impacted. Supplementary Information The online version contains supplementary material available at 10.1186/s13104-022-06127-8.
Collapse
Affiliation(s)
- Joel J Maki
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, 50010, USA.,Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA, 50011, USA
| | - John D Lippolis
- Ruminant Diseases and Immunology Research UnitAgricultural Research ServiceDepartment of Agriculture, National Animal Disease Center, Ames, IA, 50010, USA
| | - Torey Looft
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, 50010, USA.
| |
Collapse
|
24
|
Täumer J, Marhan S, Groß V, Jensen C, Kuss AW, Kolb S, Urich T. Linking transcriptional dynamics of CH 4-cycling grassland soil microbiomes to seasonal gas fluxes. THE ISME JOURNAL 2022; 16:1788-1797. [PMID: 35388141 PMCID: PMC9213473 DOI: 10.1038/s41396-022-01229-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 03/07/2022] [Accepted: 03/21/2022] [Indexed: 11/09/2022]
Abstract
Soil CH4 fluxes are driven by CH4-producing and -consuming microorganisms that determine whether soils are sources or sinks of this potent greenhouse gas. To date, a comprehensive understanding of underlying microbiome dynamics has rarely been obtained in situ. Using quantitative metatranscriptomics, we aimed to link CH4-cycling microbiomes to net surface CH4 fluxes throughout a year in two grassland soils. CH4 fluxes were highly dynamic: both soils were net CH4 sources in autumn and winter and sinks in spring and summer, respectively. Correspondingly, methanogen mRNA abundances per gram soil correlated well with CH4 fluxes. Methanotroph to methanogen mRNA ratios were higher in spring and summer, when the soils acted as net CH4 sinks. CH4 uptake was associated with an increased proportion of USCα and γ pmoA and pmoA2 transcripts. We assume that methanogen transcript abundance may be useful to approximate changes in net surface CH4 emissions from grassland soils. High methanotroph to methanogen ratios would indicate CH4 sink properties. Our study links for the first time the seasonal transcriptional dynamics of CH4-cycling soil microbiomes to gas fluxes in situ. It suggests mRNA transcript abundances as promising indicators of dynamic ecosystem-level processes.
Collapse
Affiliation(s)
- Jana Täumer
- Institute of Microbiology, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, Germany
| | - Sven Marhan
- Institute of Soil Science and Land Evaluation, Soil Biology Department, University of Hohenheim, Stuttgart, Germany
| | - Verena Groß
- Institute of Microbiology, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, Germany
| | - Corinna Jensen
- Human Molecular Genetics Group, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Andreas W Kuss
- Human Molecular Genetics Group, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Steffen Kolb
- RA Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany.,Thaer Institute, Faculty of Life Sciences, Humboldt University of Berlin, Berlin, Germany
| | - Tim Urich
- Institute of Microbiology, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, Germany.
| |
Collapse
|
25
|
Grujcic V, Taylor GT, Foster RA. One Cell at a Time: Advances in Single-Cell Methods and Instrumentation for Discovery in Aquatic Microbiology. Front Microbiol 2022; 13:881018. [PMID: 35677911 PMCID: PMC9169044 DOI: 10.3389/fmicb.2022.881018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 04/26/2022] [Indexed: 11/13/2022] Open
Abstract
Studying microbes from a single-cell perspective has become a major theme and interest within the field of aquatic microbiology. One emerging trend is the unfailing observation of heterogeneity in activity levels within microbial populations. Wherever researchers have looked, intra-population variability in biochemical composition, growth rates, and responses to varying environmental conditions has been evident and probably reflect coexisting genetically distinct strains of the same species. Such observations of heterogeneity require a shift away from bulk analytical approaches and development of new methods or adaptation of existing techniques, many of which were first pioneered in other, unrelated fields, e.g., material, physical, and biomedical sciences. Many co-opted approaches were initially optimized using model organisms. In a field with so few cultivable models, method development has been challenging but has also contributed tremendous insights, breakthroughs, and stimulated curiosity. In this perspective, we present a subset of methods that have been effectively applied to study aquatic microbes at the single-cell level. Opportunities and challenges for innovation are also discussed. We suggest future directions for aquatic microbiological research that will benefit from open access to sophisticated instruments and highly interdisciplinary collaborations.
Collapse
Affiliation(s)
- Vesna Grujcic
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Gordon T Taylor
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, United States
| | - Rachel A Foster
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| |
Collapse
|
26
|
Uchimiya M, Schroer W, Olofsson M, Edison AS, Moran MA. Diel investments in metabolite production and consumption in a model microbial system. THE ISME JOURNAL 2022; 16:1306-1317. [PMID: 34921302 PMCID: PMC9038784 DOI: 10.1038/s41396-021-01172-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 11/27/2021] [Accepted: 12/03/2021] [Indexed: 12/01/2022]
Abstract
Organic carbon transfer between surface ocean photosynthetic and heterotrophic microbes is a central but poorly understood process in the global carbon cycle. In a model community in which diatom extracellular release of organic molecules sustained growth of a co-cultured bacterium, we determined quantitative changes in the diatom endometabolome and the bacterial uptake transcriptome over two diel cycles. Of the nuclear magnetic resonance (NMR) peaks in the diatom endometabolites, 38% had diel patterns with noon or mid-afternoon maxima; the remaining either increased (36%) or decreased (26%) through time. Of the genes in the bacterial uptake transcriptome, 94% had a diel pattern with a noon maximum; the remaining decreased over time (6%). Eight diatom endometabolites identified with high confidence were matched to the bacterial genes mediating their utilization. Modeling of these coupled inventories with only diffusion-based phytoplankton extracellular release could not reproduce all the patterns. Addition of active release mechanisms for physiological balance and bacterial recognition significantly improved model performance. Estimates of phytoplankton extracellular release range from only a few percent to nearly half of annual net primary production. Improved understanding of the factors that influence metabolite release and consumption by surface ocean microbes will better constrain this globally significant carbon flux.
Collapse
Affiliation(s)
- Mario Uchimiya
- Department of Marine Sciences, University of Georgia, Athens, GA, 30602, US
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, US
| | - William Schroer
- Department of Marine Sciences, University of Georgia, Athens, GA, 30602, US
| | - Malin Olofsson
- Department of Marine Sciences, University of Georgia, Athens, GA, 30602, US
- Swedish University of Agricultural Sciences, Department of Aquatic Sciences and Assessment, Uppsala, Sweden
| | - Arthur S Edison
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, US
| | - Mary Ann Moran
- Department of Marine Sciences, University of Georgia, Athens, GA, 30602, US.
| |
Collapse
|
27
|
Tiwari N, Bansal M, Santhiya D, Sharma JG. Insights into microbial diversity on plastisphere by multi-omics. Arch Microbiol 2022; 204:216. [PMID: 35316402 DOI: 10.1007/s00203-022-02806-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 02/13/2022] [Accepted: 02/14/2022] [Indexed: 12/20/2022]
Abstract
Plastic pollution is a major concern in marine environment as it takes many years to degrade and is one of the greatest threats to marine life. Plastic surface, referred to as plastisphere, provides habitat for growth and proliferation of various microorganisms. The discovery of these microbes is necessary to identify significant genes, enzymes and bioactive compounds that could help in bioremediation and other commercial applications. Conventional culture techniques have been successful in identifying few microbes from these habitats, leaving majority of them yet to be explored. As such, to recognize the vivid genetic diversity of microbes residing in plastisphere, their structure and corresponding ecological roles within the ecosystem, an emerging technique, called metagenomics has been explored. The technique is expected to provide hitherto unknown information on microbes from the plastisphere. Metagenomics along with next generation sequencing provides comprehensive knowledge on microbes residing in plastisphere that identifies novel microbes for plastic bioremediation, bioactive compounds and other potential benefits. The following review summarizes the efficiency of metagenomics and next generation sequencing technology over conventionally used methods for culturing microbes. It attempts to illustrate the workflow mechanism of metagenomics to elucidate diverse microbial profiles. Further, importance of integrated multi-omics techniques has been highlighted in discovering microbial ecology residing on plastisphere for wider applications.
Collapse
Affiliation(s)
- Neha Tiwari
- Department of Biotechnology, Delhi Technological University, Delhi, India
| | - Megha Bansal
- Department of Biotechnology, Delhi Technological University, Delhi, India
| | - Deenan Santhiya
- Department of Applied Chemistry, Delhi Technological University, Shahbad Daulatpur, Main Bawana Road, Delhi, 110042, India.
| | - Jai Gopal Sharma
- Department of Biotechnology, Delhi Technological University, Delhi, India
| |
Collapse
|
28
|
Taylor JA, Díez-Vives C, Nielsen S, Wemheuer B, Thomas T. Communality in microbial stress response and differential metabolic interactions revealed by time-series analysis of sponge symbionts. Environ Microbiol 2022; 24:2299-2314. [PMID: 35229422 DOI: 10.1111/1462-2920.15962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 02/13/2022] [Accepted: 02/26/2022] [Indexed: 11/03/2022]
Abstract
The diversity and function of sponge-associated symbionts is now increasingly understood, however, we lack an understanding on how they dynamically behave to ensure holobiont stability in the face of environmental variation. Here we performed a metatransciptomics analysis of three microbial symbionts of the sponge Cymbastela concentrica in situ over 14 months and through differential gene expression and correlation analysis to environmental variables uncovered differences that speak to their metabolic activities and level of symbiotic and environmental interactions. The nitrite-oxidising Ca. Porinitrospira cymbastela maintained a seemingly stable metabolism, with the few differentially expressed genes related only to stress responses. The heterotrophic Ca. Porivivens multivorans displayed differential use of holobiont-derived compounds and respiration modes, while the ammonium-oxidising archaeon Ca. Nitrosopumilus cymbastelus differentially expressed genes related to phosphate metabolism and symbiosis effectors. One striking similarity between the symbionts was their similar variation in expression of stress-related genes. Our timeseries study showed that the microbial community of C. concentrica undertakes dynamic gene expression adjustments in response to the surroundings, tuned to deal with general stress and metabolic interactions between holobiont members. The success of these dynamic adjustments likely underpins the stability of the sponge holobiont and may provide resilience against environmental change. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Jessica A Taylor
- Centre for Marine Science and Innovation, University of New South Wales, Sydney, Australia.,School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Cristina Díez-Vives
- Centre for Marine Science and Innovation, University of New South Wales, Sydney, Australia.,Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, Madrid, Spain
| | - Shaun Nielsen
- Centre for Marine Science and Innovation, University of New South Wales, Sydney, Australia
| | - Bernd Wemheuer
- Centre for Marine Science and Innovation, University of New South Wales, Sydney, Australia.,School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Torsten Thomas
- Centre for Marine Science and Innovation, University of New South Wales, Sydney, Australia.,School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| |
Collapse
|
29
|
Diversity and Evolution of Mamiellophyceae: Early-Diverging Phytoplanktonic Green Algae Containing Many Cosmopolitan Species. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2022. [DOI: 10.3390/jmse10020240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The genomic revolution has bridged a gap in our knowledge about the diversity, biology and evolution of unicellular photosynthetic eukaryotes, which bear very few discriminating morphological features among species from the same genus. The high-quality genome resources available in the class Mamiellophyceae (Chlorophyta) have been paramount to estimate species diversity and screen available metagenomic data to assess the biogeography and ecological niches of different species on a global scale. Here we review the current knowledge about the diversity, ecology and evolution of the Mamiellophyceae and the large double-stranded DNA prasinoviruses infecting them, brought by the combination of genomic and metagenomic analyses, including 26 metabarcoding environmental studies, as well as the pan-oceanic GOS and the Tara Oceans expeditions.
Collapse
|
30
|
Complex marine microbial communities partition metabolism of scarce resources over the diel cycle. Nat Ecol Evol 2022; 6:218-229. [DOI: 10.1038/s41559-021-01606-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/01/2021] [Indexed: 12/20/2022]
|
31
|
Omics-Inferred Partitioning and Expression of Diverse Biogeochemical Functions in a Low-O 2 Cyanobacterial Mat Community. mSystems 2021; 6:e0104221. [PMID: 34874776 PMCID: PMC8651085 DOI: 10.1128/msystems.01042-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cyanobacterial mats profoundly influenced Earth’s biological and geochemical evolution and still play important ecological roles in the modern world. However, the biogeochemical functioning of cyanobacterial mats under persistent low-O2 conditions, which dominated their evolutionary history, is not well understood. To investigate how different metabolic and biogeochemical functions are partitioned among community members, we conducted metagenomics and metatranscriptomics on cyanobacterial mats in the low-O2, sulfidic Middle Island sinkhole (MIS) in Lake Huron. Metagenomic assembly and binning yielded 144 draft metagenome assembled genomes, including 61 of medium quality or better, and the dominant cyanobacteria and numerous Proteobacteria involved in sulfur cycling. Strains of a Phormidium autumnale-like cyanobacterium dominated the metagenome and metatranscriptome. Transcripts for the photosynthetic reaction core genes psaA and psbA were abundant in both day and night. Multiple types of psbA genes were expressed from each cyanobacterium, and the dominant psbA transcripts were from an atypical microaerobic type of D1 protein from Phormidium. Further, cyanobacterial transcripts for photosystem I genes were more abundant than those for photosystem II, and two types of Phormidium sulfide quinone reductase were recovered, consistent with anoxygenic photosynthesis via photosystem I in the presence of sulfide. Transcripts indicate active sulfur oxidation and reduction within the cyanobacterial mat, predominately by Gammaproteobacteria and Deltaproteobacteria, respectively. Overall, these genomic and transcriptomic results link specific microbial groups to metabolic processes that underpin primary production and biogeochemical cycling in a low-O2 cyanobacterial mat and suggest mechanisms for tightly coupled cycling of oxygen and sulfur compounds in the mat ecosystem. IMPORTANCE Cyanobacterial mats are dense communities of microorganisms that contain photosynthetic cyanobacteria along with a host of other bacterial species that play important yet still poorly understood roles in this ecosystem. Although such cyanobacterial mats were critical agents of Earth’s biological and chemical evolution through geological time, little is known about how they function under the low-oxygen conditions that characterized most of their natural history. Here, we performed sequencing of the DNA and RNA of modern cyanobacterial mat communities under low-oxygen and sulfur-rich conditions from the Middle Island sinkhole in Lake Huron. The results reveal the organisms and metabolic pathways that are responsible for both oxygen-producing and non-oxygen-producing photosynthesis as well as interconversions of sulfur that likely shape how much O2 is produced in such ecosystems. These findings indicate tight metabolic reactions between community members that help to explain the limited the amount of O2 produced in cyanobacterial mat ecosystems.
Collapse
|
32
|
Nittami T, Batinovic S. Recent advances in understanding the ecology of the filamentous bacteria responsible for activated sludge bulking. Lett Appl Microbiol 2021; 75:759-775. [PMID: 34919734 DOI: 10.1111/lam.13634] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/26/2021] [Accepted: 12/13/2021] [Indexed: 01/30/2023]
Abstract
Activated sludge bulking caused by filamentous bacteria is still a problem in wastewater treatment plants around the world. Bulking is a microbiological problem, and so its solution on species-specific basis is likely to be reached only after their ecology, physiology and metabolism is better understood. Culture-independent molecular methods have provided much useful information about this group of organisms, and in this review, the methods employed and the information they provide are critically assessed. Their application to understanding bulking caused by the most frequently seen filament in Japan, 'Ca. Kouleothrix', is used here as an example of how these techniques might be used to develop control strategies. Whole genome sequences are now available for some of filamentous bacteria responsible for bulking, and so it is possible to understand why these filaments might thrive in activated sludge plants, and provide clues as to how eventually they might be controlled specifically.
Collapse
Affiliation(s)
- T Nittami
- Division of Materials Science and Chemical Engineering, Faculty of Engineering, Yokohama National University, Yokohama, Japan
| | - S Batinovic
- Department of Physiology, Anatomy, and Microbiology, La Trobe University, Bundoora, Vic., Australia
| |
Collapse
|
33
|
Walworth NG, Saito MA, Lee MD, McIlvin MR, Moran DM, Kellogg RM, Fu FX, Hutchins DA, Webb EA. Why Environmental Biomarkers Work: Transcriptome-Proteome Correlations and Modeling of Multistressor Experiments in the Marine Bacterium Trichodesmium. J Proteome Res 2021; 21:77-89. [PMID: 34855411 DOI: 10.1021/acs.jproteome.1c00517] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ocean microbial communities are important contributors to the global biogeochemical reactions that sustain life on Earth. The factors controlling these communities are being increasingly explored using metatranscriptomic and metaproteomic environmental biomarkers. Using published proteomes and transcriptomes from the abundant colony-forming cyanobacterium Trichodesmium (strain IMS101) grown under varying Fe and/or P limitation in low and high CO2, we observed robust correlations of stress-induced proteins and RNAs (i.e., involved in transport and homeostasis) that yield useful information on the nutrient status under low and/or high CO2. Conversely, transcriptional and translational correlations of many other central metabolism pathways exhibit broad discordance. A cellular RNA and protein production/degradation model demonstrates how biomolecules with small initial inventories, such as environmentally responsive proteins, achieve large increases in fold-change units as opposed to those with a higher basal expression and inventory such as metabolic systems. Microbial cells, due to their immersion in the environment, tend to show large adaptive responses in both RNA and protein that result in transcript-protein correlations. These observations and model results demonstrate multi-omic coherence for environmental biomarkers and provide the underlying mechanism for those observations, supporting the promise for global application in detecting responses to environmental stimuli in a changing ocean.
Collapse
Affiliation(s)
- Nathan G Walworth
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, United States
| | - Mak A Saito
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Michael D Lee
- Blue Marble Space Institute of Science, Seattle, Washington 98104, United States.,Exobiology Branch, NASA Ames Research Center, Moffett Field, California 94035, United States
| | - Matthew R McIlvin
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Dawn M Moran
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Riss M Kellogg
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Fei-Xue Fu
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, United States
| | - David A Hutchins
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, United States
| | - Eric A Webb
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, United States
| |
Collapse
|
34
|
Behera BK, Dehury B, Rout AK, Patra B, Mantri N, Chakraborty HJ, Sarkar DJ, Kaushik NK, Bansal V, Singh I, Das BK, Rao AR, Rai A. Metagenomics study in aquatic resource management: Recent trends, applied methodologies and future needs. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101372] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
|
35
|
McDaniel EA, Wahl SA, Ishii S, Pinto A, Ziels R, Nielsen PH, McMahon KD, Williams RBH. Prospects for multi-omics in the microbial ecology of water engineering. WATER RESEARCH 2021; 205:117608. [PMID: 34555741 DOI: 10.1016/j.watres.2021.117608] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 08/20/2021] [Accepted: 08/23/2021] [Indexed: 06/13/2023]
Abstract
Advances in high-throughput sequencing technologies and bioinformatics approaches over almost the last three decades have substantially increased our ability to explore microorganisms and their functions - including those that have yet to be cultivated in pure isolation. Genome-resolved metagenomic approaches have enabled linking powerful functional predictions to specific taxonomical groups with increasing fidelity. Additionally, related developments in both whole community gene expression surveys and metabolite profiling have permitted for direct surveys of community-scale functions in specific environmental settings. These advances have allowed for a shift in microbiome science away from descriptive studies and towards mechanistic and predictive frameworks for designing and harnessing microbial communities for desired beneficial outcomes. Water engineers, microbiologists, and microbial ecologists studying activated sludge, anaerobic digestion, and drinking water distribution systems have applied various (meta)omics techniques for connecting microbial community dynamics and physiologies to overall process parameters and system performance. However, the rapid pace at which new omics-based approaches are developed can appear daunting to those looking to apply these state-of-the-art practices for the first time. Here, we review how modern genome-resolved metagenomic approaches have been applied to a variety of water engineering applications from lab-scale bioreactors to full-scale systems. We describe integrated omics analysis across engineered water systems and the foundations for pairing these insights with modeling approaches. Lastly, we summarize emerging omics-based technologies that we believe will be powerful tools for water engineering applications. Overall, we provide a framework for microbial ecologists specializing in water engineering to apply cutting-edge omics approaches to their research questions to achieve novel functional insights. Successful adoption of predictive frameworks in engineered water systems could enable more economically and environmentally sustainable bioprocesses as demand for water and energy resources increases.
Collapse
Affiliation(s)
- Elizabeth A McDaniel
- Department of Bacteriology, University of Wisconsin - Madison, Madison, WI, USA.
| | | | - Shun'ichi Ishii
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Yokosuka 237-0061, Japan
| | - Ameet Pinto
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA, USA
| | - Ryan Ziels
- Department of Civil Engineering, The University of British Columbia, Vancouver, BC, Canada
| | | | - Katherine D McMahon
- Department of Bacteriology, University of Wisconsin - Madison, Madison, WI, USA; Department of Civil and Environmental Engineering, University of Wisconsin - Madison, Madison, WI, USA
| | - Rohan B H Williams
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Republic of Singapore.
| |
Collapse
|
36
|
Santiago-Rodriguez TM, Hollister EB. Multi 'omic data integration: A review of concepts, considerations, and approaches. Semin Perinatol 2021; 45:151456. [PMID: 34256961 DOI: 10.1016/j.semperi.2021.151456] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The application of 'omic techniques including, but not limited to genomics/metagenomics, transcriptomics/meta-transcriptomics, proteomics/meta-proteomics, and metabolomics to generate multiple datasets from a single sample have facilitated hypothesis generation leading to the identification of biological, molecular and ecological functions and mechanisms, as well as associations and correlations. Despite their power and promise, a variety of challenges must be considered in the successful design and execution of a multi-omics study. In this review, various 'omic technologies applicable to single- and meta-organisms (i.e., host + microbiome) are described, and considerations for sample collection, storage and processing prior to data generation and analysis, as well as approaches to data storage, dissemination and analysis are discussed. Finally, case studies are included as examples of multi-omic applications providing novel insights and a more holistic understanding of biological processes.
Collapse
Affiliation(s)
| | - Emily B Hollister
- Diversigen, Inc, 3 Greenway Plaza, Suite 1575, Houston, TX 77046, USA.
| |
Collapse
|
37
|
Zhang Y, Thompson KN, Branck T, Yan Yan, Nguyen LH, Franzosa EA, Huttenhower C. Metatranscriptomics for the Human Microbiome and Microbial Community Functional Profiling. Annu Rev Biomed Data Sci 2021; 4:279-311. [PMID: 34465175 DOI: 10.1146/annurev-biodatasci-031121-103035] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Shotgun metatranscriptomics (MTX) is an increasingly practical way to survey microbial community gene function and regulation at scale. This review begins by summarizing the motivations for community transcriptomics and the history of the field. We then explore the principles, best practices, and challenges of contemporary MTX workflows: beginning with laboratory methods for isolation and sequencing of community RNA, followed by informatics methods for quantifying RNA features, and finally statistical methods for detecting differential expression in a community context. In thesecond half of the review, we survey important biological findings from the MTX literature, drawing examples from the human microbiome, other (nonhuman) host-associated microbiomes, and the environment. Across these examples, MTX methods prove invaluable for probing microbe-microbe and host-microbe interactions, the dynamics of energy harvest and chemical cycling, and responses to environmental stresses. We conclude with a review of open challenges in the MTX field, including making assays and analyses more robust, accessible, and adaptable to new technologies; deciphering roles for millions of uncharacterized microbial transcripts; and solving applied problems such as biomarker discovery and development of microbial therapeutics.
Collapse
Affiliation(s)
- Yancong Zhang
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Kelsey N Thompson
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Tobyn Branck
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Department of Systems, Synthetic, and Quantitative Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Yan Yan
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Long H Nguyen
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA.,Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02108, USA
| | - Eric A Franzosa
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Curtis Huttenhower
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA
| |
Collapse
|
38
|
Cerro-Gálvez E, Dachs J, Lundin D, Fernández-Pinos MC, Sebastián M, Vila-Costa M. Responses of Coastal Marine Microbiomes Exposed to Anthropogenic Dissolved Organic Carbon. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:9609-9621. [PMID: 33606522 PMCID: PMC8491159 DOI: 10.1021/acs.est.0c07262] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 02/04/2021] [Accepted: 02/04/2021] [Indexed: 05/23/2023]
Abstract
Coastal seawaters receive thousands of organic pollutants. However, we have little understanding of the response of microbiomes to this pool of anthropogenic dissolved organic carbon (ADOC). In this study, coastal microbial communities were challenged with ADOC at environmentally relevant concentrations. Experiments were performed at two Mediterranean sites with different impact by pollutants and nutrients: off the Barcelona harbor ("BCN"), and at the Blanes Bay ("BL"). ADOC additions stimulated prokaryotic leucine incorporation rates at both sites, indicating the use of ADOC as growth substrate. The percentage of "membrane-compromised" cells increased with increasing ADOC, indicating concurrent toxic effects of ADOC. Metagenomic analysis of the BCN community challenged with ADOC showed a significant growth of Methylophaga and other gammaproteobacterial taxa belonging to the rare biosphere. Gene expression profiles showed a taxon-dependent response, with significantly enrichments of transcripts from SAR11 and Glaciecola spp. in BCN and BL, respectively. Further, the relative abundance of transposon-related genes (in BCN) and transcripts (in BL) correlated with the number of differentially abundant genes (in BCN) and transcripts (in BLA), suggesting that microbial responses to pollution may be related to pre-exposure to pollutants, with transposons playing a role in adaptation to ADOC. Our results point to a taxon-specific response to low concentrations of ADOC that impact the functionality, structure and plasticity of the communities in coastal seawaters. This work contributes to address the influence of pollutants on microbiomes and their perturbation to ecosystem services and ocean health.
Collapse
Affiliation(s)
- Elena Cerro-Gálvez
- Department
of Environmental Chemistry, IDAEA-CSIC, Barcelona, Catalunya 08034, Spain
| | - Jordi Dachs
- Department
of Environmental Chemistry, IDAEA-CSIC, Barcelona, Catalunya 08034, Spain
| | - Daniel Lundin
- Centre
for Ecology and Evolution in Microbial Model Systems, EEMiS, Linnaeus University, Kalmar 35195, Sweden
| | | | - Marta Sebastián
- Department
of Marine Biology and Oceanography, ICM-CSIC, Barcelona, Catalunya 08003, Spain
| | - Maria Vila-Costa
- Department
of Environmental Chemistry, IDAEA-CSIC, Barcelona, Catalunya 08034, Spain
| |
Collapse
|
39
|
Faure E, Ayata SD, Bittner L. Towards omics-based predictions of planktonic functional composition from environmental data. Nat Commun 2021; 12:4361. [PMID: 34272373 PMCID: PMC8285379 DOI: 10.1038/s41467-021-24547-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 05/25/2021] [Indexed: 02/06/2023] Open
Abstract
Marine microbes play a crucial role in climate regulation, biogeochemical cycles, and trophic networks. Unprecedented amounts of data on planktonic communities were recently collected, sparking a need for innovative data-driven methodologies to quantify and predict their ecosystemic functions. We reanalyze 885 marine metagenome-assembled genomes through a network-based approach and detect 233,756 protein functional clusters, from which 15% are functionally unannotated. We investigate all clusters' distributions across the global ocean through machine learning, identifying biogeographical provinces as the best predictors of protein functional clusters' abundance. The abundances of 14,585 clusters are predictable from the environmental context, including 1347 functionally unannotated clusters. We analyze the biogeography of these 14,585 clusters, identifying the Mediterranean Sea as an outlier in terms of protein functional clusters composition. Applicable to any set of sequences, our approach constitutes a step towards quantitative predictions of functional composition from the environmental context.
Collapse
Affiliation(s)
- Emile Faure
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, LOV, Villefranche-sur-Mer, France.
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.
| | - Sakina-Dorothée Ayata
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, LOV, Villefranche-sur-Mer, France
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Lucie Bittner
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
- Institut Universitaire de France, Paris, France
| |
Collapse
|
40
|
Martinez-Varela A, Cerro-Gálvez E, Auladell A, Sharma S, Moran MA, Kiene RP, Piña B, Dachs J, Vila-Costa M. Bacterial responses to background organic pollutants in the northeast subarctic Pacific Ocean. Environ Microbiol 2021; 23:4532-4546. [PMID: 34169620 DOI: 10.1111/1462-2920.15646] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 06/16/2021] [Indexed: 12/13/2022]
Abstract
Thousands of man-made synthetic chemicals are released to oceans and compose the anthropogenic dissolved organic carbon (ADOC). Little is known about the effects of this chronic pollution on marine microbiome activities. In this study, we measured the pollution level at three sites in the Northeast Subarctic Pacific Ocean (NESAP) and investigated how mixtures of three model families of ADOC at different environmentally relevant concentrations affected naturally occurring marine bacterioplankton communities' structure and metabolic functioning. The offshore northernmost site (North) had the lowest concentrations of hydrocarbons, as well as organophosphate ester plasticizers, contrasting with the two other continental shelf sites, the southern coastal site (South) being the most contaminated. At North, ADOC stimulated bacterial growth and promoted an increase in the contribution of some Gammaproteobacteria groups (e.g. Alteromonadales) to the 16 rRNA pool. These groups are described as fast responders after oil spills. In contrast, minor changes in South microbiome activities were observed. Gene expression profiles at Central showed the coexistence of ADOC degradation and stress-response strategies to cope with ADOC toxicities. These results show that marine microbial communities at three distinct domains in NESAP are influenced by background concentrations of ADOC, expanding previous assessments for polar and temperate waters.
Collapse
Affiliation(s)
- Alícia Martinez-Varela
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research, IDAEA-CSIC, Barcelona, Catalunya, Spain
| | - Elena Cerro-Gálvez
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research, IDAEA-CSIC, Barcelona, Catalunya, Spain
| | - Adrià Auladell
- Department of Marine Biology and Oceanography, Marine Science Institute, ICM-CSIC, Barcelona, Catalunya, Spain
| | - Shalabh Sharma
- Department of Marine Sciences, University of Georgia, Marine Sciences Building, Athens, GA, USA
| | - Mary Ann Moran
- Department of Marine Sciences, University of Georgia, Marine Sciences Building, Athens, GA, USA
| | - Ronald P Kiene
- Department of Marine Sciences, University of South Alabama, Mobile, AL, USA
| | - Benjamí Piña
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research, IDAEA-CSIC, Barcelona, Catalunya, Spain
| | - Jordi Dachs
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research, IDAEA-CSIC, Barcelona, Catalunya, Spain
| | - Maria Vila-Costa
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research, IDAEA-CSIC, Barcelona, Catalunya, Spain
| |
Collapse
|
41
|
Sharma AK. Translational autoregulation of RF2 protein in E. coli through programmed frameshifting. Phys Rev E 2021; 103:062412. [PMID: 34271674 DOI: 10.1103/physreve.103.062412] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 06/04/2021] [Indexed: 11/07/2022]
Abstract
Various feedback mechanisms regulate the expression of different genes to ensure the required protein levels inside a cell. In this paper, we develop a kinetic model for one such mechanism that autoregulates RF2 protein synthesis in E. coli through programmed frameshifting. The model finds that the programmed frameshifting autoregulates RF2 protein synthesis by two independent mechanisms. First, it increases the rate of RF2 synthesis from each mRNA transcript at low RF2 concentration. Second, programmed frameshifting can dramatically increase the lifetime of RF2 transcripts when RF2 protein levels are lower than a threshold. This sharp increase in mRNA lifetime is caused by a first-order phase transition from a low to a high ribosome density on an RF2 transcript. The high ribosome density prevents the transcript's degradation by shielding it from nucleases, which increases its average lifetime and hence RF2 protein levels. Our study identifies this quality control mechanism that regulates the cellular protein levels by breaking the hierarchy of processes involved in gene expression.
Collapse
Affiliation(s)
- Ajeet K Sharma
- Department of Physics, Indian Institute of Technology, Jammu 181221, India
| |
Collapse
|
42
|
Störiko A, Pagel H, Mellage A, Cirpka OA. Does It Pay Off to Explicitly Link Functional Gene Expression to Denitrification Rates in Reaction Models? Front Microbiol 2021; 12:684146. [PMID: 34220770 PMCID: PMC8250433 DOI: 10.3389/fmicb.2021.684146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 04/29/2021] [Indexed: 11/13/2022] Open
Abstract
Environmental omics and molecular-biological data have been proposed to yield improved quantitative predictions of biogeochemical processes. The abundances of functional genes and transcripts relate to the number of cells and activity of microorganisms. However, whether molecular-biological data can be quantitatively linked to reaction rates remains an open question. We present an enzyme-based denitrification model that simulates concentrations of transcription factors, functional-gene transcripts, enzymes, and solutes. We calibrated the model using experimental data from a well-controlled batch experiment with the denitrifier Paracoccous denitrificans. The model accurately predicts denitrification rates and measured transcript dynamics. The relationship between simulated transcript concentrations and reaction rates exhibits strong non-linearity and hysteresis related to the faster dynamics of gene transcription and substrate consumption, relative to enzyme production and decay. Hence, assuming a unique relationship between transcript-to-gene ratios and reaction rates, as frequently suggested, may be an erroneous simplification. Comparing model results of our enzyme-based model to those of a classical Monod-type model reveals that both formulations perform equally well with respect to nitrogen species, indicating only a low benefit of integrating molecular-biological data for estimating denitrification rates. Nonetheless, the enzyme-based model is a valuable tool to improve our mechanistic understanding of the relationship between biomolecular quantities and reaction rates. Furthermore, our results highlight that both enzyme kinetics (i.e., substrate limitation and inhibition) and gene expression or enzyme dynamics are important controls on denitrification rates.
Collapse
Affiliation(s)
- Anna Störiko
- Center for Applied Geoscience, University of Tübingen, Tübingen, Germany
| | - Holger Pagel
- Biogeophysics, Institute of Soil Science and Land Evaluation, University of Hohenheim, Stuttgart, Germany
| | - Adrian Mellage
- Center for Applied Geoscience, University of Tübingen, Tübingen, Germany
| | - Olaf A. Cirpka
- Center for Applied Geoscience, University of Tübingen, Tübingen, Germany
| |
Collapse
|
43
|
A distinct growth physiology enhances bacterial growth under rapid nutrient fluctuations. Nat Commun 2021; 12:3662. [PMID: 34135315 PMCID: PMC8209047 DOI: 10.1038/s41467-021-23439-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 04/19/2021] [Indexed: 11/13/2022] Open
Abstract
It has long been known that bacteria coordinate their physiology with their nutrient environment, yet our current understanding offers little intuition for how bacteria respond to the second-to-minute scale fluctuations in nutrient concentration characteristic of many microbial habitats. To investigate the effects of rapid nutrient fluctuations on bacterial growth, we couple custom microfluidics with single-cell microscopy to quantify the growth rate of E. coli experiencing 30 s to 60 min nutrient fluctuations. Compared to steady environments of equal average concentration, fluctuating environments reduce growth rate by up to 50%. However, measured reductions in growth rate are only 38% of the growth loss predicted from single nutrient shifts. This enhancement derives from the distinct growth response of cells grown in environments that fluctuate rather than shift once. We report an unexpected physiology adapted for growth in nutrient fluctuations and implicate nutrient timescale as a critical environmental parameter beyond nutrient identity and concentration. Here the authors use microfluidics and single-cell microscopy to quantify the growth dynamics of individual E. coli cells exposed to nutrient fluctuations with periods as short as 30 seconds, finding that nutrient fluctuations reduce growth rates up to 50% compared to a steady nutrient delivery of equal average concentration, implying that temporal variability is an important parameter in bacterial growth.
Collapse
|
44
|
Vishwanathan AS. Microbial fuel cells: a comprehensive review for beginners. 3 Biotech 2021; 11:248. [PMID: 33968591 PMCID: PMC8088421 DOI: 10.1007/s13205-021-02802-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 04/19/2021] [Indexed: 12/13/2022] Open
Abstract
Microbial fuel cells (MFCs) have shown immense potential as a one-stop solution for three major sustainability issues confronting the world today-energy security, global warming and wastewater management. MFCs represent a cross-disciplinary platform for research at the confluence of the natural and engineering sciences. The diversity of variables influencing performance of MFCs has garnered research interest across varied scientific disciplines since the beginning of this century. The increasing number of research publications has made it necessary to keep track of work being carried out by research groups across the globe and consolidate significant findings on a regular basis. Review articles are often the nodal points for beginners who are required to undertake an exploratory survey of literature to identify a suitable research problem. This 'review of reviews' is a ready-reckoner that directs readers to relevant reviews and research articles reporting significant developments in MFC research in the last two decades. The article also highlights the areas needing research attention which when addressed could take this technology a few more steps closer to practical implementation.
Collapse
Affiliation(s)
- A. S. Vishwanathan
- WATER Laboratory, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Puttaparthi, 515134 Andhra Pradesh India
| |
Collapse
|
45
|
Liu L, Lu L, Li H, Meng Z, Dong T, Peng C, Xu X. Divergence of Phyllosphere Microbial Communities Between Females and Males of the Dioecious Populus cathayana. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:351-361. [PMID: 33290085 DOI: 10.1094/mpmi-07-20-0178-r] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Females and males of dioecious plants have evolved sex-specific characteristics in terms of their morphological and physiological properties. However, the differentiation of phyllosphere microbiota in dioecious plants remains largely unexplored. Here, the diversity and composition of female and male Populus cathayana phyllosphere bacterial and fungal communities were investigated using 16S rRNA/ITS1 gene-based MiSeq sequencing. The divergences of bacterial and fungal community compositions occurred between females and males. Both females and males had their unique phyllosphere bacterial and fungal microbiota, such as bacterial Gemmata spp. (5.41%) and fungal Pringsheimia spp. (0.03%) in females and bacterial Chitinophaga spp. (0.009%) and fungal Phaeococcomyces spp. (0.02%) in males. Significant differences in the relative abundance of phyla Proteobacteria and Planctomycetes bacteria and phyla Ascomycota and Basidiomycota fungi (P < 0.05) were also found between females and males. Some bacterial species of genera Spirosoma and Amnibacterium and fungal genera Venturia, Suillus, and Elmerina spp. were significantly enriched in males (P < 0.05). In contrast, levels of fungal genera Phoma and Aureobasidium spp. were significantly higher in females than in males (P < 0.05). The mineral, inorganic, and organic nutrients content contributed differently to the divergence of female and male phyllosphere microbial communities, with 87.08 and 45.17% of the variations being explained for bacterial and fungal communities, respectively. These results highlight the sexual discrimination of phyllosphere microbes on the dioecious plants and provide hints on the potential host-associated species in phyllosphere environments.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
Collapse
Affiliation(s)
- Liling Liu
- Key Laboratory of Southwest China Wildlife Resources Conservation, College of Life Sciences, China West Normal University, Nanchong 637002, China
- Institute of Ecology, China West Normal University, Nanchong 637009, China
| | - Lu Lu
- Key Laboratory of Southwest China Wildlife Resources Conservation, College of Life Sciences, China West Normal University, Nanchong 637002, China
- College of Environmental Science and Engineering, China West Normal University, Nanchong 637009, China
| | - Huilin Li
- Key Laboratory of Southwest China Wildlife Resources Conservation, College of Life Sciences, China West Normal University, Nanchong 637002, China
| | - Zhensi Meng
- Key Laboratory of Southwest China Wildlife Resources Conservation, College of Life Sciences, China West Normal University, Nanchong 637002, China
| | - Tingfa Dong
- Key Laboratory of Southwest China Wildlife Resources Conservation, College of Life Sciences, China West Normal University, Nanchong 637002, China
| | - Chao Peng
- Key Laboratory of Southwest China Wildlife Resources Conservation, College of Life Sciences, China West Normal University, Nanchong 637002, China
- Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, College of Chemistry and Chemical Engineering, China West Normal University, Nanchong 637002, China
| | - Xiao Xu
- Key Laboratory of Southwest China Wildlife Resources Conservation, College of Life Sciences, China West Normal University, Nanchong 637002, China
- Institute of Ecology, China West Normal University, Nanchong 637009, China
| |
Collapse
|
46
|
Yates MC, Derry AM, Cristescu ME. Environmental RNA: A Revolution in Ecological Resolution? Trends Ecol Evol 2021; 36:601-609. [PMID: 33757695 DOI: 10.1016/j.tree.2021.03.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/26/2021] [Accepted: 03/03/2021] [Indexed: 12/11/2022]
Abstract
Current advancements in environmental RNA (eRNA) exploit its relatively fast turnover rate relative to environmental DNA (eDNA) to assess 'metabolically active' or temporally/spatially recent community diversity. However, this focus significantly underutilizes the trove of potential ecological information encrypted in eRNA. Here, we argue for pushing beyond current species-level eDNA detection capabilities by using eRNA to detect any organisms with unique eRNA profiles, potentially including different life-history stages, sexes, or even specific phenotypes within a species. We also discuss the future of eRNA as a means of assessing the physiological status of organisms and the ecological health of populations and communities, reflecting ecosystem-level conditions. We posit that eRNA has the potential to significantly improve the resolution of organism detection, biological monitoring, and biomonitoring applications in ecology.
Collapse
Affiliation(s)
- Matthew C Yates
- Département des Sciences Biologiques, Université du Québec à Montréal, 141 Avenue Président-Kennedy, Montréal, QC, H2X 1Y4, Canada.
| | - Alison M Derry
- Département des Sciences Biologiques, Université du Québec à Montréal, 141 Avenue Président-Kennedy, Montréal, QC, H2X 1Y4, Canada
| | - Melania E Cristescu
- Department of Biology, McGill University, 1205 Dr Penfield Avenue, Montreal, QC, H3A 1B1, Canada
| |
Collapse
|
47
|
Modulating the Gut Microbiota of Humans by Dietary Intervention with Plant Glycans. Appl Environ Microbiol 2021; 87:AEM.02757-20. [PMID: 33355114 DOI: 10.1128/aem.02757-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The human colon contains a community of microbial species, mostly bacteria, which is often referred to as the gut microbiota. The community is considered essential to human well-being by conferring additional energy-harvesting capacity, niche exclusion of pathogens, and molecular signaling activities that are integrated into human physiological processes. Plant polysaccharides (glycans, dietary fiber) are an important source of carbon and energy that supports the maintenance and functioning of the gut microbiota. Therefore, the daily quantity and quality of plant glycans consumed by the human host have the potential to influence health. Members of the gut microbiota differ in ability to utilize different types of plant glycans. Dietary interventions with specific glycans could modulate the microbiota, counteracting ecological perturbations that disrupt the intricate relationships between microbiota and host (dysbiosis). This review considers prospects and research options for modulation of the gut microbiota by the formulation of diets that, when consumed habitually, would correct dysbiosis by building diverse consortia that boost functional resilience. Traditional "prebiotics" favor bifidobacteria and lactobacilli, whereas dietary mixtures of plant glycans that are varied in chemical complexity would promote high-diversity microbiotas. It is concluded that research should aim at improving knowledge of bacterial consortia that, through shared nourishment, degrade and ferment plant glycans. The consortia may vary in composition from person to person, but functional outputs will be consistent in a given context because of metabolic redundancy among bacteria. Thus, the individuality of gut microbiotas could be encompassed, functional resilience encouraged, and correction of dysbiosis achieved.
Collapse
|
48
|
A metatranscriptomic analysis of changing dynamics in the plankton communities adjacent to aquaculture leases in southern Tasmania, Australia. Mar Genomics 2021; 59:100858. [PMID: 33642199 DOI: 10.1016/j.margen.2021.100858] [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: 08/24/2020] [Revised: 02/08/2021] [Accepted: 02/14/2021] [Indexed: 10/22/2022]
Abstract
Aquaculture releases nitrogen to the marine environment, potentially changing dynamics of local plankton populations and causing adverse impacts. Metatranscriptomics have been used to study planktonic nutrient cycles and community dynamics. We hypothesised that the metatranscriptome could be used to monitor changing phytoplankton physiology near leases. To test this hypothesis, opportunistic samples were collected from one oceanic location in winter and one estuarine location in spring and analysed via RNASeq. Transcriptomes from different locations were found to have little overlap, due to different community compositions in the oceanic and estuarine locations. Transcript function was similar at each location. Proximity to the salmon pen had little influence over the transcriptome at the estuarine location. In the oceanic environment, diatom-based activity decreased near pens and dinoflagellate-based activity increased as demonstrated through the abundance of carbon fixation and nitrogen-acquisition-related transcripts. Our initial results suggest that the use of the metatranscriptome in monitoring is promising.
Collapse
|
49
|
Ikert H, Lynch MDJ, Doxey AC, Giesy JP, Servos MR, Katzenback BA, Craig PM. High Throughput Sequencing of MicroRNA in Rainbow Trout Plasma, Mucus, and Surrounding Water Following Acute Stress. Front Physiol 2021; 11:588313. [PMID: 33519501 PMCID: PMC7838646 DOI: 10.3389/fphys.2020.588313] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 12/21/2020] [Indexed: 12/11/2022] Open
Abstract
Circulating plasma microRNAs (miRNAs) are well established as biomarkers of several diseases in humans and have recently been used as indicators of environmental exposures in fish. However, the role of plasma miRNAs in regulating acute stress responses in fish is largely unknown. Tissue and plasma miRNAs have recently been associated with excreted miRNAs; however, external miRNAs have never been measured in fish. The objective of this study was to identify the altered plasma miRNAs in response to acute stress in rainbow trout (Oncorhynchus mykiss), as well as altered miRNAs in fish epidermal mucus and the surrounding ambient water. Small RNA was extracted and sequenced from plasma, mucus, and water collected from rainbow trout pre- and 1 h-post a 3-min air stressor. Following small RNA-Seq and pathway analysis, we identified differentially expressed plasma miRNAs that targeted biosynthetic, degradation, and metabolic pathways. We successfully isolated miRNA from trout mucus and the surrounding water and detected differences in miRNA expression 1-h post air stress. The expressed miRNA profiles in mucus and water were different from the altered plasma miRNA profile, which indicated that the plasma miRNA response was not associated with or immediately reflected in external samples, which was further validated through qPCR. This research expands understanding of the role of plasma miRNA in the acute stress response of fish and is the first report of successful isolation and profiling of miRNA from fish mucus or samples of ambient water. Measurements of miRNA from plasma, mucus, or water can be further studied and have potential to be applied as non-lethal indicators of acute stress in fish.
Collapse
Affiliation(s)
- Heather Ikert
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | | | - Andrew C. Doxey
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - John P. Giesy
- Department of Veterinary Biomedical Sciences, Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
- Department of Environmental Science, Baylor University, Waco, TX, United States
| | - Mark R. Servos
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | | | - Paul M. Craig
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| |
Collapse
|
50
|
Nguyen J, Lara-Gutiérrez J, Stocker R. Environmental fluctuations and their effects on microbial communities, populations and individuals. FEMS Microbiol Rev 2020; 45:6041721. [PMID: 33338228 PMCID: PMC8371271 DOI: 10.1093/femsre/fuaa068] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 12/05/2020] [Indexed: 12/20/2022] Open
Abstract
From the homeostasis of human health to the cycling of Earth's elements, microbial activities underlie environmental, medical and industrial processes. These activities occur in chemical and physical landscapes that are highly dynamic and experienced by bacteria as fluctuations. In this review, we first discuss how bacteria can experience both spatial and temporal heterogeneity in their environments as temporal fluctuations of various timescales (seconds to seasons) and types (nutrient, sunlight, fluid flow, etc.). We then focus primarily on nutrient fluctuations to discuss how bacterial communities, populations and single cells respond to environmental fluctuations. Overall, we find that environmental fluctuations are ubiquitous and diverse, and strongly shape microbial behavior, ecology and evolution when compared with environments in which conditions remain constant over time. We hope this review may serve as a guide toward understanding the significance of environmental fluctuations in microbial life, such that their contributions and implications can be better assessed and exploited.
Collapse
Affiliation(s)
- Jen Nguyen
- Institute for Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zürich, 8093 Zürich, Switzerland.,Microbiology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Juanita Lara-Gutiérrez
- Institute for Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zürich, 8093 Zürich, Switzerland
| | - Roman Stocker
- Institute for Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zürich, 8093 Zürich, Switzerland
| |
Collapse
|