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Rain-Franco A, Peter H, Pavan de Moraes G, Beier S. The cost of adaptability: resource availability constrains functional stability under pulsed disturbances. mSphere 2024; 9:e0072723. [PMID: 38206053 PMCID: PMC10900906 DOI: 10.1128/msphere.00727-23] [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: 11/27/2023] [Accepted: 12/06/2023] [Indexed: 01/12/2024] Open
Abstract
Global change exposes ecosystems to changes in the frequency, magnitude, and concomitancy of disturbances, which impact the composition and functioning of these systems. Here, we experimentally evaluate the effects of salinity disturbances and eutrophication on bacterial communities from coastal ecosystems. The functional stability of these communities is critically important for maintaining water quality, productivity, and ecosystem services, such as fishery yields. Microbial functional stability can be maintained via resistance and resilience, which are reflected in genomic traits such as genome size and codon usage bias and may be linked to metabolic costs. However, little is known about the mechanisms that select these traits under varying nutrient regimes. To study the impact of pulsed disturbances on community assembly and functioning depending on metabolic costs, we performed a 41-day pulse disturbance experiment across two levels of resource availability. Our setup triggered stochastic community re-assembly processes in all treatments. In contrast, we observed consistent and resource availability-dependent patterns of superordinate community functioning and structural patterns, such as functional resistance in response to disturbances, genomic trait distributions, and species diversity. Predicted genomic traits reflected the selection for taxa possessing resistant- and resilience-related traits, particularly under high nutrient availability. Our findings are a step toward unraveling the compositional and genomic underpinnings of functional resistance in microbial communities after exposure to consecutive pulse disturbances. Our work demonstrates how resource availability alleviates metabolic constraints on resistance and resilience, and this has important consequences for predicting water quality and ecosystem productivity of environments exposed to global change. IMPORTANCE Understanding the communities' responses to disturbances is a prerequisite to predicting ecosystem dynamics and, thus, highly relevant considering global change. Microbial communities play key roles in numerous ecosystem functions and services, and the large diversity, rapid growth, and phenotypic plasticity of microorganisms are thought to allow high resistance and resilience. While potential metabolic costs associated with adaptations to fluctuating environments have been debated, little evidence supports trade-offs between resource availability, resistance, and resilience. Here, we experimentally assessed the compositional and functional responses of an aquatic microbial model community to disturbances and systematically manipulated resource availability. Our results demonstrate that the capacity to tolerate environmental fluctuations is constrained by resource availability and reflected in the selection of genomic traits.
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Affiliation(s)
- Angel Rain-Franco
- UMR 7621 Laboratoire d’Océanographie Microbienne, Observatoire Océanologique de Banyuls-sur-Mer, Sorbonne Université, Banyuls-sur-Mer, France
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde, Rostock, Germany
| | - Hannes Peter
- River Ecosystems Laboratory, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
| | - Guilherme Pavan de Moraes
- UMR 7621 Laboratoire d’Océanographie Microbienne, Observatoire Océanologique de Banyuls-sur-Mer, Sorbonne Université, Banyuls-sur-Mer, France
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde, Rostock, Germany
- Department of Botany, Graduate Program in Ecology and Natural Resources (PPGERN), Laboratory of Phycology, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Sara Beier
- UMR 7621 Laboratoire d’Océanographie Microbienne, Observatoire Océanologique de Banyuls-sur-Mer, Sorbonne Université, Banyuls-sur-Mer, France
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde, Rostock, Germany
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2
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Aliperti L, Aptekmann AA, Farfañuk G, Couso LL, Soler-Bistué A, Sánchez IE. r/K selection of GC content in prokaryotes. Environ Microbiol 2023; 25:3255-3268. [PMID: 37813828 DOI: 10.1111/1462-2920.16511] [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: 02/27/2023] [Accepted: 09/16/2023] [Indexed: 10/11/2023]
Abstract
The guanine/cytosine (GC) content of prokaryotic genomes is species-specific, taking values from 16% to 77%. This diversity of selection for GC content remains contentious. We analyse the correlations between GC content and a range of phenotypic and genotypic data in thousands of prokaryotes. GC content integrates well with these traits into r/K selection theory when phenotypic plasticity is considered. High GC-content prokaryotes are r-strategists with cheaper descendants thanks to a lower average amino acid metabolic cost, colonize unstable environments thanks to flagella and a bacillus form and are generalists in terms of resource opportunism and their defence mechanisms. Low GC content prokaryotes are K-strategists specialized for stable environments that maintain homeostasis via a high-cost outer cell membrane and endospore formation as a response to nutrient deprivation, and attain a higher nutrient-to-biomass yield. The lower proteome cost of high GC content prokaryotes is driven by the association between GC-rich codons and cheaper amino acids in the genetic code, while the correlation between GC content and genome size may be partly due to functional diversity driven by r/K selection. In all, molecular diversity in the GC content of prokaryotes may be a consequence of ecological r/K selection.
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Affiliation(s)
- Lucio Aliperti
- Facultad de Ciencias Exactas y Naturales. Laboratorio de Fisiología de Proteínas, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Ariel A Aptekmann
- Marine and Coastal Sciences Department, Rutgers University, New Brunswick, New Jersey, USA
| | - Gonzalo Farfañuk
- Facultad de Ciencias Exactas y Naturales. Laboratorio de Fisiología de Proteínas, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Luciana L Couso
- Facultad de Agronomía, Cátedra de Genética, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Alfonso Soler-Bistué
- Instituto de Investigaciones Biotecnológicas Dr. Rodolfo A. Ugalde, CONICET, Universidad Nacional de San Martín, San Martin, Argentina
| | - Ignacio E Sánchez
- Facultad de Ciencias Exactas y Naturales. Laboratorio de Fisiología de Proteínas, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Buenos Aires, Argentina
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3
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Wang C, Yu QY, Ji NN, Zheng Y, Taylor JW, Guo LD, Gao C. Bacterial genome size and gene functional diversity negatively correlate with taxonomic diversity along a pH gradient. Nat Commun 2023; 14:7437. [PMID: 37978289 PMCID: PMC10656551 DOI: 10.1038/s41467-023-43297-w] [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: 06/06/2023] [Accepted: 11/06/2023] [Indexed: 11/19/2023] Open
Abstract
Bacterial gene repertoires reflect adaptive strategies, contribute to ecosystem functioning and are limited by genome size. However, gene functional diversity does not necessarily correlate with taxonomic diversity because average genome size may vary by community. Here, we analyse gene functional diversity (by shotgun metagenomics) and taxonomic diversity (by 16S rRNA gene amplicon sequencing) to investigate soil bacterial communities along a natural pH gradient in 12 tropical, subtropical, and temperate forests. We find that bacterial average genome size and gene functional diversity decrease, whereas taxonomic diversity increases, as soil pH rises from acid to neutral; as a result, bacterial taxonomic and functional diversity are negatively correlated. The gene repertoire of acid-adapted oligotrophs is enriched in functions of signal transduction, cell motility, secretion system, and degradation of complex compounds, while that of neutral pH-adapted copiotrophs is enriched in functions of energy metabolism and membrane transport. Our results indicate that a mismatch between taxonomic and functional diversity can arise when environmental factors (such as pH) select for adaptive strategies that affect genome size distributions.
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Affiliation(s)
- Cong Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Qing-Yi Yu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Niu-Niu Ji
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
- Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Yong Zheng
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
- School of Geographical Sciences, Fujian Normal University, 350007, Fuzhou, China
| | - John W Taylor
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Liang-Dong Guo
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China.
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China.
| | - Cheng Gao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China.
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China.
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4
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Sheridan PO, Meng Y, Williams TA, Gubry-Rangin C. Genomics of soil depth niche partitioning in the Thaumarchaeota family Gagatemarchaeaceae. Nat Commun 2023; 14:7305. [PMID: 37951938 PMCID: PMC10640624 DOI: 10.1038/s41467-023-43196-0] [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: 02/23/2023] [Accepted: 11/03/2023] [Indexed: 11/14/2023] Open
Abstract
Knowledge of deeply-rooted non-ammonia oxidising Thaumarchaeota lineages from terrestrial environments is scarce, despite their abundance in acidic soils. Here, 15 new deeply-rooted thaumarchaeotal genomes were assembled from acidic topsoils (0-15 cm) and subsoils (30-60 cm), corresponding to two genera of terrestrially prevalent Gagatemarchaeaceae (previously known as thaumarchaeotal Group I.1c) and to a novel genus of heterotrophic terrestrial Thaumarchaeota. Unlike previous predictions, metabolic annotations suggest Gagatemarchaeaceae perform aerobic respiration and use various organic carbon sources. Evolutionary divergence between topsoil and subsoil lineages happened early in Gagatemarchaeaceae history, with significant metabolic and genomic trait differences. Reconstruction of the evolutionary mechanisms showed that the genome expansion in topsoil Gagatemarchaeaceae resulted from extensive early lateral gene acquisition, followed by progressive gene duplication throughout evolutionary history. Ancestral trait reconstruction using the expanded genomic diversity also did not support the previous hypothesis of a thermophilic last common ancestor of the ammonia-oxidising archaea. Ultimately, this study provides a good model for studying mechanisms driving niche partitioning between spatially related ecosystems.
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Affiliation(s)
- Paul O Sheridan
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
- School of Biological and Chemical Sciences, University of Galway, Galway, Ireland
| | - Yiyu Meng
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, Bristol, UK
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5
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Li XD, Lin YC, Yang RS, Kang X, Xin WG, Wang F, Zhang QL, Zhang WP, Lin LB. Genomic and in-vitro characteristics of a novel strain Lacticaseibacillus chiayiensis AACE3 isolated from fermented blueberry. Front Microbiol 2023; 14:1168378. [PMID: 37275148 PMCID: PMC10235500 DOI: 10.3389/fmicb.2023.1168378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 05/04/2023] [Indexed: 06/07/2023] Open
Abstract
Numerous different species of LAB are used in different fields due to their unique characteristics. However, Lacticaseibacillus chiayiensis, a newly established species in 2018, has limited microorganism resources, and lacks comprehensive evaluations of its properties. In this study, L. chiayiensis AACE3, isolated from fermented blueberry, was evaluated by genomic analysis and in vitro assays of the properties. The genome identified genes associated with biofilm formation (luxS, ccpA, brpA), resistance to oxidative stress (tpx, trxA, trxB, hslO), tolerance to acidic conditions (dltA, dltC), resistance to unfavorable osmotic pressure (opuBB, gbuA, gbuB, gbuC), and adhesion (luxS, dltA, dltC). The AACE3 showed 112 unique genes, relative to the other three L. chiayiensis strains. Among them, the presence of genes such as clpP, pepO, and feoA suggests a possible advantage of AACE3 over other L. chiayiensis in terms of environmental adaptation. In vitro evaluation of the properties revealed that AACE3 had robust antibacterial activity against eight common pathogens: Streptococcus agalactiae, Staphylococcus aureus, Escherichia coli, Salmonella enteritidis, Salmonella choleraesuis, Shigella flexneri, Pseudomonas aeruginosa, and Klebsiella pneumoniae. In addition, AACE3 showed more than 80% survival rate in all tests simulating gastrointestinal fluid, and it exhibited high antioxidant capacity. Interestingly, the cell culture supernatant was superior to intact organisms and ultrasonically crushed bacterial extracts in all tests of antioxidant capacity. These results suggested that the antioxidant capacity may originate from certain metabolites and extracellular enzymes produced by AACE3. Moreover, AACE3 was a moderate biofilm producer due to the self-agglomeration effect. Taken together, L. chiayiensis AACE3 appears to be a candidate strain for combating the growing incidence of pathogen infections and antioxidant production.
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Affiliation(s)
- Xin-Dong Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
- Engineering Research Center for Replacement Technology of Feed Antibiotics of Yunnan College, Kunming, Yunnan, China
| | - Yi-Cen Lin
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
- Engineering Research Center for Replacement Technology of Feed Antibiotics of Yunnan College, Kunming, Yunnan, China
| | - Rui-Si Yang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
- Engineering Research Center for Replacement Technology of Feed Antibiotics of Yunnan College, Kunming, Yunnan, China
| | - Xin Kang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
- Engineering Research Center for Replacement Technology of Feed Antibiotics of Yunnan College, Kunming, Yunnan, China
| | - Wei-Gang Xin
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
- Engineering Research Center for Replacement Technology of Feed Antibiotics of Yunnan College, Kunming, Yunnan, China
| | - Feng Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
- Engineering Research Center for Replacement Technology of Feed Antibiotics of Yunnan College, Kunming, Yunnan, China
| | - Qi-Lin Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
- Engineering Research Center for Replacement Technology of Feed Antibiotics of Yunnan College, Kunming, Yunnan, China
| | - Wen-Ping Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
- Engineering Research Center for Replacement Technology of Feed Antibiotics of Yunnan College, Kunming, Yunnan, China
| | - Lian-Bing Lin
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
- Engineering Research Center for Replacement Technology of Feed Antibiotics of Yunnan College, Kunming, Yunnan, China
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6
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von Meijenfeldt FAB, Hogeweg P, Dutilh BE. A social niche breadth score reveals niche range strategies of generalists and specialists. Nat Ecol Evol 2023; 7:768-781. [PMID: 37012375 PMCID: PMC10172124 DOI: 10.1038/s41559-023-02027-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 02/27/2023] [Indexed: 04/05/2023]
Abstract
Generalists can survive in many environments, whereas specialists are restricted to a single environment. Although a classical concept in ecology, niche breadth has remained challenging to quantify for microorganisms because it depends on an objective definition of the environment. Here, by defining the environment of a microorganism as the community it resides in, we integrated information from over 22,000 environmental sequencing samples to derive a quantitative measure of the niche, which we call social niche breadth. At the level of genera, we explored niche range strategies throughout the prokaryotic tree of life. We found that social generalists include opportunists that stochastically dominate local communities, whereas social specialists are stable but low in abundance. Social generalists have a more diverse and open pan-genome than social specialists, but we found no global correlation between social niche breadth and genome size. Instead, we observed two distinct evolutionary strategies, whereby specialists have relatively small genomes in habitats with low local diversity, but relatively large genomes in habitats with high local diversity. Together, our analysis shines data-driven light on microbial niche range strategies.
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Affiliation(s)
- F A Bastiaan von Meijenfeldt
- Theoretical Biology and Bioinformatics, Department of Biology, Science for Life, Utrecht University, Utrecht, the Netherlands
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Texel, the Netherlands
| | - Paulien Hogeweg
- Theoretical Biology and Bioinformatics, Department of Biology, Science for Life, Utrecht University, Utrecht, the Netherlands
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Department of Biology, Science for Life, Utrecht University, Utrecht, the Netherlands.
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany.
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7
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Roxo G, Brilhante M, Moura M, de Sequeira MM, Silva L, Costa JC, Vasconcelos R, Talhinhas P, Romeiras MM. Genome size variation within Crithmum maritimum: Clues on the colonization of insular environments. Ecol Evol 2023; 13:e10009. [PMID: 37091572 PMCID: PMC10116024 DOI: 10.1002/ece3.10009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 03/20/2023] [Accepted: 03/31/2023] [Indexed: 04/25/2023] Open
Abstract
Angiosperms present an astonishing diversity of genome sizes that can vary intra- or interspecifically. The remarkable new cytogenomic data shed some light on our understanding of evolution, but few studies were performed with insular and mainland populations to test possible correlations with dispersal, speciation, and adaptations to insular environments. Here, patterns of cytogenomic diversity were assessed among geographic samples (ca. 114) of Crithmum maritimum (Apiaceae), collected across the Azores and Madeira archipelagos, as well as in adjacent continental areas of Portugal. Using flow cytometry, the results indicated a significant intraspecific genome size variation, spanning from reduced sizes in the insular populations to larger ones in the mainland populations. Moreover, there was a tendency for an increase in genome size along the mainland populations, associated with lower temperatures, higher precipitation, and lower precipitation seasonality. However, this gradient might be the result of historic phylogeographical events associated with previous dispersal and extinction of local populations. Overall, our findings provided evidence that smaller genome sizes might play a critical role in the colonization of islands, corroborating other studies that argue that organisms with smaller genomes use fewer resources, having a selective advantage under insular environments. Although further studies are needed to improve our understanding of the mechanisms underlying genome size evolution on islands, conservation strategies must be promoted to protect the rich cytogenomic diversity found among C. maritimum populations, which occur in coastal areas that are particularly threatened by human activity, pollution, invasive species, and climate changes.
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Affiliation(s)
- Guilherme Roxo
- Linking Landscape, Environment, Agriculture and Food (LEAF), Associated Laboratory TERRA, Instituto Superior de Agronomia (ISA)Universidade de Lisboa, Tapada da AjudaLisbonPortugal
- CIBIO‐Azores, Departamento de BiologiaUniversidade dos AçoresPonta DelgadaPortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land PlanningCIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus de VairãoVairãoPortugal
| | - Miguel Brilhante
- Linking Landscape, Environment, Agriculture and Food (LEAF), Associated Laboratory TERRA, Instituto Superior de Agronomia (ISA)Universidade de Lisboa, Tapada da AjudaLisbonPortugal
| | - Mónica Moura
- CIBIO‐Azores, Departamento de BiologiaUniversidade dos AçoresPonta DelgadaPortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land PlanningCIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus de VairãoVairãoPortugal
| | | | - Luís Silva
- CIBIO‐Azores, Departamento de BiologiaUniversidade dos AçoresPonta DelgadaPortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land PlanningCIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus de VairãoVairãoPortugal
| | - José Carlos Costa
- Linking Landscape, Environment, Agriculture and Food (LEAF), Associated Laboratory TERRA, Instituto Superior de Agronomia (ISA)Universidade de Lisboa, Tapada da AjudaLisbonPortugal
| | - Raquel Vasconcelos
- BIOPOLIS Program in Genomics, Biodiversity and Land PlanningCIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus de VairãoVairãoPortugal
| | - Pedro Talhinhas
- Linking Landscape, Environment, Agriculture and Food (LEAF), Associated Laboratory TERRA, Instituto Superior de Agronomia (ISA)Universidade de Lisboa, Tapada da AjudaLisbonPortugal
| | - Maria M. Romeiras
- Linking Landscape, Environment, Agriculture and Food (LEAF), Associated Laboratory TERRA, Instituto Superior de Agronomia (ISA)Universidade de Lisboa, Tapada da AjudaLisbonPortugal
- Centre for Ecology, Evolution and Environmental Changes (cE3c) & CHANGE—Global Change and Sustainability Institute, Faculdade de CiênciasUniversidade de LisboaLisbonPortugal
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8
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Ngugi DK, Acinas SG, Sánchez P, Gasol JM, Agusti S, Karl DM, Duarte CM. Abiotic selection of microbial genome size in the global ocean. Nat Commun 2023; 14:1384. [PMID: 36914646 PMCID: PMC10011403 DOI: 10.1038/s41467-023-36988-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 02/27/2023] [Indexed: 03/14/2023] Open
Abstract
Strong purifying selection is considered a major evolutionary force behind small microbial genomes in the resource-poor photic ocean. However, very little is currently known about how the size of prokaryotic genomes evolves in the global ocean and whether patterns reflect shifts in resource availability in the epipelagic and relatively stable deep-sea environmental conditions. Using 364 marine microbial metagenomes, we investigate how the average genome size of uncultured planktonic prokaryotes varies across the tropical and polar oceans to the hadal realm. We find that genome size is highest in the perennially cold polar ocean, reflecting elongation of coding genes and gene dosage effects due to duplications in the interior ocean microbiome. Moreover, the rate of change in genome size due to temperature is 16-fold higher than with depth up to 200 m. Our results demonstrate how environmental factors can influence marine microbial genome size selection and ecological strategies of the microbiome.
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Affiliation(s)
- David K Ngugi
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, CSIC, Barcelona, Spain
| | - Pablo Sánchez
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, CSIC, Barcelona, Spain
| | - Josep M Gasol
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, CSIC, Barcelona, Spain
| | - Susana Agusti
- King Abdullah University of Science and Technology, Red Sea Research Center, Thuwal, Saudi Arabia
| | - David M Karl
- Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawaií at Mãnoa, Honolulu, USA
| | - Carlos M Duarte
- King Abdullah University of Science and Technology, Red Sea Research Center, Thuwal, Saudi Arabia
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9
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Cooper RE, Finck J, Chan C, Küsel K. Mixotrophy broadens the ecological niche range of the iron oxidizer Sideroxydans sp. CL21 isolated from an iron-rich peatland. FEMS Microbiol Ecol 2023; 99:6979798. [PMID: 36623865 PMCID: PMC9925335 DOI: 10.1093/femsec/fiac156] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 11/17/2022] [Accepted: 01/06/2023] [Indexed: 01/11/2023] Open
Abstract
Sideroxydans sp. CL21 is a microaerobic, acid-tolerant Fe(II)-oxidizer, isolated from the Schlöppnerbrunnen fen. Since the genome size of Sideroxydans sp. CL21 is 21% larger than that of the neutrophilic Sideroxydans lithotrophicus ES-1, we hypothesized that strain CL21 contains additional metabolic traits to thrive in the fen. The common genomic content of both strains contains homologs of the putative Fe(II) oxidation genes, mtoAB and cyc2. A large part of the accessory genome in strain CL21 contains genes linked to utilization of alternative electron donors, including NiFe uptake hydrogenases, and genes encoding lactate uptake and utilization proteins, motility and biofilm formation, transposable elements, and pH homeostasis mechanisms. Next, we incubated the strain in different combinations of electron donors and characterized the fen microbial communities. Sideroxydans spp. comprised 3.33% and 3.94% of the total relative abundance in the peatland soil and peatland water, respectively. Incubation results indicate Sideroxydans sp. CL21 uses H2 and thiosulfate, while lactate only enhances growth when combined with Fe, H2, or thiosulfate. Rates of H2 utilization were highest in combination with other substrates. Thus, Sideroxydans sp. CL21 is a mixotroph, growing best by simultaneously using substrate combinations, which helps to thrive in dynamic and complex habitats.
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Affiliation(s)
- Rebecca E Cooper
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Jessica Finck
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Clara Chan
- School of Marine Science and Policy, University of Delaware, Newark, DE 19716, United States,Delaware Biotechnology Institute, University of Delaware, Newark, DE 19713, United States,Department of Earth Sciences, University of Delaware, Newark, DE 19716, United States
| | - Kirsten Küsel
- Corresponding author. Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Str. 159, 07743 Jena, Germany. Tel: +49 3641 949461; Fax: +49 3641 949462; E-mail:
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10
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Hackl T, Laurenceau R, Ankenbrand MJ, Bliem C, Cariani Z, Thomas E, Dooley KD, Arellano AA, Hogle SL, Berube P, Leventhal GE, Luo E, Eppley JM, Zayed AA, Beaulaurier J, Stepanauskas R, Sullivan MB, DeLong EF, Biller SJ, Chisholm SW. Novel integrative elements and genomic plasticity in ocean ecosystems. Cell 2023; 186:47-62.e16. [PMID: 36608657 DOI: 10.1016/j.cell.2022.12.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 09/16/2022] [Accepted: 12/05/2022] [Indexed: 01/07/2023]
Abstract
Horizontal gene transfer accelerates microbial evolution. The marine picocyanobacterium Prochlorococcus exhibits high genomic plasticity, yet the underlying mechanisms are elusive. Here, we report a novel family of DNA transposons-"tycheposons"-some of which are viral satellites while others carry cargo, such as nutrient-acquisition genes, which shape the genetic variability in this globally abundant genus. Tycheposons share distinctive mobile-lifecycle-linked hallmark genes, including a deep-branching site-specific tyrosine recombinase. Their excision and integration at tRNA genes appear to drive the remodeling of genomic islands-key reservoirs for flexible genes in bacteria. In a selection experiment, tycheposons harboring a nitrate assimilation cassette were dynamically gained and lost, thereby promoting chromosomal rearrangements and host adaptation. Vesicles and phage particles harvested from seawater are enriched in tycheposons, providing a means for their dispersal in the wild. Similar elements are found in microbes co-occurring with Prochlorococcus, suggesting a common mechanism for microbial diversification in the vast oligotrophic oceans.
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Affiliation(s)
- Thomas Hackl
- Massachusetts Institute of Technology, Department of Civil and Environmental Engineering, Cambridge, MA 02139, USA; Groningen Institute for Evolutionary Life Sciences, University of Groningen, 9700CC Groningen, the Netherlands.
| | - Raphaël Laurenceau
- Massachusetts Institute of Technology, Department of Civil and Environmental Engineering, Cambridge, MA 02139, USA
| | - Markus J Ankenbrand
- Massachusetts Institute of Technology, Department of Civil and Environmental Engineering, Cambridge, MA 02139, USA; University of Würzburg, Center for Computational and Theoretical Biology, 97070 Würzburg, Germany
| | - Christina Bliem
- Massachusetts Institute of Technology, Department of Civil and Environmental Engineering, Cambridge, MA 02139, USA
| | - Zev Cariani
- Massachusetts Institute of Technology, Department of Civil and Environmental Engineering, Cambridge, MA 02139, USA
| | - Elaina Thomas
- Massachusetts Institute of Technology, Department of Civil and Environmental Engineering, Cambridge, MA 02139, USA
| | - Keven D Dooley
- Massachusetts Institute of Technology, Department of Civil and Environmental Engineering, Cambridge, MA 02139, USA
| | - Aldo A Arellano
- Massachusetts Institute of Technology, Department of Civil and Environmental Engineering, Cambridge, MA 02139, USA
| | - Shane L Hogle
- Massachusetts Institute of Technology, Department of Civil and Environmental Engineering, Cambridge, MA 02139, USA
| | - Paul Berube
- Massachusetts Institute of Technology, Department of Civil and Environmental Engineering, Cambridge, MA 02139, USA
| | - Gabriel E Leventhal
- Massachusetts Institute of Technology, Department of Civil and Environmental Engineering, Cambridge, MA 02139, USA
| | - Elaine Luo
- Daniel K. Inouye Center for Microbial Oceanography, Research and Education, University of Hawai'i Manoa, Honolulu, HI 96822, USA
| | - John M Eppley
- Daniel K. Inouye Center for Microbial Oceanography, Research and Education, University of Hawai'i Manoa, Honolulu, HI 96822, USA
| | - Ahmed A Zayed
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA; Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | | | | | - Matthew B Sullivan
- Department of Microbiology & Department of Civil, Environmental, and Geodetic Engineering, Ohio State University, Columbus, OH 43210, USA; EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA; Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Edward F DeLong
- Daniel K. Inouye Center for Microbial Oceanography, Research and Education, University of Hawai'i Manoa, Honolulu, HI 96822, USA
| | - Steven J Biller
- Wellesley College, Department of Biological Sciences, Wellesley, MA 02481, USA
| | - Sallie W Chisholm
- Massachusetts Institute of Technology, Department of Civil and Environmental Engineering, Cambridge, MA 02139, USA; Massachusetts Institute of Technology, Department of Biology, Cambridge, MA 02139, USA.
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11
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Hackl T, Laurenceau R, Ankenbrand MJ, Bliem C, Cariani Z, Thomas E, Dooley KD, Arellano AA, Hogle SL, Berube P, Leventhal GE, Luo E, Eppley JM, Zayed AA, Beaulaurier J, Stepanauskas R, Sullivan MB, DeLong EF, Biller SJ, Chisholm SW. Novel integrative elements and genomic plasticity in ocean ecosystems. Cell 2023. [DOI: doi.org/10.1016/j.cell.2022.12.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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12
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Beier S, Werner J, Bouvier T, Mouquet N, Violle C. Trait-trait relationships and tradeoffs vary with genome size in prokaryotes. Front Microbiol 2022; 13:985216. [PMID: 36338105 PMCID: PMC9634001 DOI: 10.3389/fmicb.2022.985216] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 09/20/2022] [Indexed: 11/21/2022] Open
Abstract
We report genomic traits that have been associated with the life history of prokaryotes and highlight conflicting findings concerning earlier observed trait correlations and tradeoffs. In order to address possible explanations for these contradictions we examined trait–trait variations of 11 genomic traits from ~18,000 sequenced genomes. The studied trait–trait variations suggested: (i) the predominance of two resistance and resilience-related orthogonal axes and (ii) at least in free living species with large effective population sizes whose evolution is little affected by genetic drift an overlap between a resilience axis and an oligotrophic-copiotrophic axis. These findings imply that resistance associated traits of prokaryotes are globally decoupled from resilience related traits and in the case of free-living communities also from traits associated with resource availability. However, further inspection of pairwise scatterplots showed that resistance and resilience traits tended to be positively related for genomes up to roughly five million base pairs and negatively for larger genomes. Genome size distributions differ across habitats and our findings therefore point to habitat dependent tradeoffs between resistance and resilience. This in turn may preclude a globally consistent assignment of prokaryote genomic traits to the competitor - stress-tolerator - ruderal (CSR) schema that sorts species depending on their location along disturbance and productivity gradients into three ecological strategies and may serve as an explanation for conflicting findings from earlier studies. All reviewed genomic traits featured significant phylogenetic signals and we propose that our trait table can be applied to extrapolate genomic traits from taxonomic marker genes. This will enable to empirically evaluate the assembly of these genomic traits in prokaryotic communities from different habitats and under different productivity and disturbance scenarios as predicted via the resistance-resilience framework formulated here.
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Affiliation(s)
- Sara Beier
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Rostock, Germany
- UMR 7621 Laboratoire d’Océanographie Microbienne, Observatoire Océanologique de Banyuls-sur-Mer, Sorbonne Université, Banyuls-sur-Mer, France
- *Correspondence: Sara Beier,
| | - Johannes Werner
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Rostock, Germany
- High Performance and Cloud Computing Group, Zentrum für Datenverarbeitung (ZDV), Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Thierry Bouvier
- MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | - Nicolas Mouquet
- MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, Montpellier, France
- Centre for the Synthesis and Analysis of Biodiversity, Montpellier, France
| | - Cyrille Violle
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
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13
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Cortez D, Neira G, González C, Vergara E, Holmes DS. A Large-Scale Genome-Based Survey of Acidophilic Bacteria Suggests That Genome Streamlining Is an Adaption for Life at Low pH. Front Microbiol 2022; 13:803241. [PMID: 35387071 PMCID: PMC8978632 DOI: 10.3389/fmicb.2022.803241] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 02/07/2022] [Indexed: 01/04/2023] Open
Abstract
The genome streamlining theory suggests that reduction of microbial genome size optimizes energy utilization in stressful environments. Although this hypothesis has been explored in several cases of low-nutrient (oligotrophic) and high-temperature environments, little work has been carried out on microorganisms from low-pH environments, and what has been reported is inconclusive. In this study, we performed a large-scale comparative genomics investigation of more than 260 bacterial high-quality genome sequences of acidophiles, together with genomes of their closest phylogenetic relatives that live at circum-neutral pH. A statistically supported correlation is reported between reduction of genome size and decreasing pH that we demonstrate is due to gene loss and reduced gene sizes. This trend is independent from other genome size constraints such as temperature and G + C content. Genome streamlining in the evolution of acidophilic bacteria is thus supported by our results. The analyses of predicted Clusters of Orthologous Genes (COG) categories and subcellular location predictions indicate that acidophiles have a lower representation of genes encoding extracellular proteins, signal transduction mechanisms, and proteins with unknown function but are enriched in inner membrane proteins, chaperones, basic metabolism, and core cellular functions. Contrary to other reports for genome streamlining, there was no significant change in paralog frequencies across pH. However, a detailed analysis of COG categories revealed a higher proportion of genes in acidophiles in the following categories: "replication and repair," "amino acid transport," and "intracellular trafficking". This study brings increasing clarity regarding the genomic adaptations of acidophiles to life at low pH while putting elements, such as the reduction of average gene size, under the spotlight of streamlining theory.
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Affiliation(s)
- Diego Cortez
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
| | - Gonzalo Neira
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
| | - Carolina González
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
| | - Eva Vergara
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
| | - David S. Holmes
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastian, Santiago, Chile
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14
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Kim E, Yang SM, Kim D, Kim HY. Complete Genome Sequencing and Comparative Genomics of Three Potential Probiotic Strains, Lacticaseibacillus casei FBL6, Lacticaseibacillus chiayiensis FBL7, and Lacticaseibacillus zeae FBL8. Front Microbiol 2022; 12:794315. [PMID: 35069490 PMCID: PMC8777060 DOI: 10.3389/fmicb.2021.794315] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 12/10/2021] [Indexed: 12/20/2022] Open
Abstract
Lacticaseibacillus casei, Lacticaseibacillus chiayiensis, and Lacticaseibacillus zeae are very closely related Lacticaseibacillus species. L. casei has long been proposed as a probiotic, whereas studies on functional characterization for L. chiayiensis and L. zeae are some compared to L. casei. In this study, L. casei FBL6, L. chiayiensis FBL7, and L. zeae FBL8 were isolated from raw milk, and their probiotic properties were investigated. Genomic analysis demonstrated the role of L. chiayiensis and L. zeae as probiotic candidates. The three strains were tolerant to acid and bile salt, with inhibitory action against pathogenic bacterial strains and capacity of antioxidants. Complete genome sequences of the three strains were analyzed to highlight the probiotic properties at the genetic level, which results in the discovery of genes corresponding to phenotypic characterization. Moreover, genes known to confer probiotic characteristics were identified, including genes related to biosynthesis, defense machinery, adhesion, and stress adaptation. The comparative genomic analysis with other available genomes revealed 256, 214, and 32 unique genes for FBL6, FBL7, and FBL8, respectively. These genomes contained individual genes encoding proteins that are putatively involved in carbohydrate transport and metabolism, prokaryotic immune system for antiviral defense, and physiological control processes. In particular, L. casei FBL6 had a bacteriocin gene cluster that was not present in other genomes of L. casei, resulting in this strain may exhibit a wide range of antimicrobial activity compared to other L. casei strains. Our data can help us understand the probiotic functionalities of the three strains and suggest that L. chiayiensis and L. zeae species, which are closely related to L. casei, can also be considered as novel potential probiotic candidate strains.
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Affiliation(s)
- Eiseul Kim
- Institute of Life Sciences & Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin, South Korea
| | - Seung-Min Yang
- Institute of Life Sciences & Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin, South Korea
| | - Dayoung Kim
- Institute of Life Sciences & Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin, South Korea
| | - Hae-Yeong Kim
- Institute of Life Sciences & Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin, South Korea
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15
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Berrios L. The genus Caulobacter and its role in plant microbiomes. World J Microbiol Biotechnol 2022; 38:43. [PMID: 35064419 DOI: 10.1007/s11274-022-03237-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 01/17/2022] [Indexed: 11/27/2022]
Abstract
Recent omics approaches have revealed the prevalent microbial taxa that constitute the microbiome of various plant species. Across global scales and environmental conditions, strains belonging to the bacterial genus Caulobacter have consistently been found in association with various plant species. Aligned with agroecological relevance and biotechnological advances, many scientific communications have demonstrated that several Caulobacter strains (spanning several Caulobacter species) harbor the potential to enhance plant biomass for various plant species ranging from Arabidopsis to Citrullus and Zea mays. In the past several years, co-occurrence data have driven mechanistically resolved communications about select Caulobacter-plant interactions. Given the long-standing history of Caulobacter as a model organism for cell cycle regulation, genetic studies, and the prevalence of Caulobacter species in various plant microbiomes, the genus Caulobacter offers researchers a unique opportunity to leverage for investigating plant-microbe interactions and realizing targeted biotechnological applications. In this review, recent developments regarding Caulobacter-plant interactions are presented in terms of model utility for future biotechnological investigations.
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Affiliation(s)
- Louis Berrios
- Department of Biology, Stanford University, Stanford, CA, USA.
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16
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Rodríguez-Gijón A, Nuy JK, Mehrshad M, Buck M, Schulz F, Woyke T, Garcia SL. A Genomic Perspective Across Earth's Microbiomes Reveals That Genome Size in Archaea and Bacteria Is Linked to Ecosystem Type and Trophic Strategy. Front Microbiol 2022; 12:761869. [PMID: 35069467 PMCID: PMC8767057 DOI: 10.3389/fmicb.2021.761869] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 12/15/2021] [Indexed: 01/09/2023] Open
Abstract
Our view of genome size in Archaea and Bacteria has remained skewed as the data has been dominated by genomes of microorganisms that have been cultivated under laboratory settings. However, the continuous effort to catalog Earth's microbiomes, specifically propelled by recent extensive work on uncultivated microorganisms, provides an opportunity to revise our perspective on genome size distribution. We present a meta-analysis that includes 26,101 representative genomes from 3 published genomic databases; metagenomic assembled genomes (MAGs) from GEMs and stratfreshDB, and isolates from GTDB. Aquatic and host-associated microbial genomes present on average the smallest estimated genome sizes (3.1 and 3.0 Mbp, respectively). These are followed by terrestrial microbial genomes (average 3.7 Mbp), and genomes from isolated microorganisms (average 4.3 Mbp). On the one hand, aquatic and host-associated ecosystems present smaller genomes sizes in genera of phyla with genome sizes above 3 Mbp. On the other hand, estimated genome size in phyla with genomes under 3 Mbp showed no difference between ecosystems. Moreover, we observed that when using 95% average nucleotide identity (ANI) as an estimator for genetic units, only 3% of MAGs cluster together with genomes from isolated microorganisms. Although there are potential methodological limitations when assembling and binning MAGs, we found that in genome clusters containing both environmental MAGs and isolate genomes, MAGs were estimated only an average 3.7% smaller than isolate genomes. Even when assembly and binning methods introduce biases, estimated genome size of MAGs and isolates are very similar. Finally, to better understand the ecological drivers of genome size, we discuss on the known and the overlooked factors that influence genome size in different ecosystems, phylogenetic groups, and trophic strategies.
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Affiliation(s)
- Alejandro Rodríguez-Gijón
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Julia K. Nuy
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Maliheh Mehrshad
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Moritz Buck
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | | | - Tanja Woyke
- DOE Joint Genome Institute, Berkeley, CA, United States
| | - Sarahi L. Garcia
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
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17
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Zhao J, Wu L, Li W, Wang Y, Zheng H, Sun T, Zhang H, Xi R, Liu W, Sun Z. Genomics landscape of 185 Streptococcus thermophilus and identification of fermentation biomarkers. Food Res Int 2021; 150:110711. [PMID: 34865746 DOI: 10.1016/j.foodres.2021.110711] [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] [Received: 06/08/2021] [Revised: 08/14/2021] [Accepted: 09/07/2021] [Indexed: 01/21/2023]
Abstract
Streptococcus (S.) thermophilus, an indispensable dairy starter, has been used in autochthonous as well as industrial milk fermentation. However, the genetic architecture underlying S. thermophilus traits and phenotypes is largely unknown. Here, we sequenced 185 S. thermophilus strains, isolated from natural fermented dairy products of China and Mongolia and used comparative genomic and genome wide association study to provide novel point for genetic architecture underlying its traits and phenotypes. Genome analysis of S. thermophilus showed association of phylogeny with environmental and phenotypic features and revealed clades with high acid production potential or with substantial genome decay. A few S. thermophilus isolated from areas with high chloramphenicol emissions had a chloramphenicol-resistant gene CatB8. Most importantly, we defined a growth score and identified a missense mutation G1118698T located at the gene AcnA that were both predictive of acidification capability of S. thermophilus. Our findings provide novel insight in S. thermophilus genetic traits, antibiotic resistant and predictive of acidification capability which both may had huge help in culture starter screening.
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Affiliation(s)
- Jie Zhao
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering; Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Linjie Wu
- School of Mathematical Sciences and Center for Statistical Science, Peking University, Beijing 100871, China
| | - Weicheng Li
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering; Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Yu Wang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering; Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Huijuan Zheng
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering; Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Tiansong Sun
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering; Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Heping Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering; Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Ruibin Xi
- School of Mathematical Sciences and Center for Statistical Science, Peking University, Beijing 100871, China
| | - Wenjun Liu
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering; Inner Mongolia Agricultural University, Hohhot 010018, China.
| | - Zhihong Sun
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering; Inner Mongolia Agricultural University, Hohhot 010018, China.
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18
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Nielsen DA, Fierer N, Geoghegan JL, Gillings MR, Gumerov V, Madin JS, Moore L, Paulsen IT, Reddy TBK, Tetu SG, Westoby M. Aerobic bacteria and archaea tend to have larger and more versatile genomes. OIKOS 2021. [DOI: 10.1111/oik.07912] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
| | - Noah Fierer
- Dept of Ecology and Evolutionary Biology, Cooperative Inst. for Research in Environmental Sciences, Univ. of Colorado Boulder CO USA
| | - Jemma L. Geoghegan
- Dept of Biological Sciences, Macquarie Univ. Sydney NSW Australia
- Dept of Microbiology and Immunology, Univ. of Otago New Zealand
| | | | - Vadim Gumerov
- Dept of Microbiology, Ohio State Univ. Columbus Ohio USA
| | - Joshua S. Madin
- Hawaii Inst. of Marine Biology, Univ. of Hawaii Kaneohe HI USA
| | - Lisa Moore
- Dept of Molecular Sciences, Macquarie Univ. Sydney NSW Australia
| | | | - T. B. K. Reddy
- Dept of Molecular Sciences, Macquarie Univ. Sydney NSW Australia
| | - Sasha G. Tetu
- Dept of Molecular Sciences, Macquarie Univ. Sydney NSW Australia
| | - Mark Westoby
- Dept of Biological Sciences, Macquarie Univ. Sydney NSW Australia
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19
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Laurenceau R, Raho N, Forget M, Arellano AA, Chisholm SW. Frequency of mispackaging of Prochlorococcus DNA by cyanophage. THE ISME JOURNAL 2021; 15:129-140. [PMID: 32929209 PMCID: PMC7852597 DOI: 10.1038/s41396-020-00766-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 05/27/2020] [Accepted: 08/27/2020] [Indexed: 01/09/2023]
Abstract
Prochlorococcus cells are the numerically dominant phototrophs in the open ocean. Cyanophages that infect them are a notable fraction of the total viral population in the euphotic zone, and, as vehicles of horizontal gene transfer, appear to drive their evolution. Here we examine the propensity of three cyanophages-a podovirus, a siphovirus, and a myovirus-to mispackage host DNA in their capsids while infecting Prochlorococcus, the first step in phage-mediated horizontal gene transfer. We find the mispackaging frequencies are distinctly different among the three phages. Myoviruses mispackage host DNA at low and seemingly fixed frequencies, while podo- and siphoviruses vary in their mispackaging frequencies by orders of magnitude depending on growth light intensity. We link this difference to the concentration of intracellular reactive oxygen species and protein synthesis rates, both parameters increasing in response to higher light intensity. Based on our findings, we propose a model of mispackaging frequency determined by the imbalance between the production of capsids and the number of phage genome copies during infection: when protein synthesis rate increase to levels that the phage cannot regulate, they lead to an accumulation of empty capsids, in turn triggering more frequent host DNA mispackaging errors.
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Affiliation(s)
- Raphaël Laurenceau
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Nicolas Raho
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mathieu Forget
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institut de Biologie de l'Ecole Normale Supérieure, Département de Biologie, Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France
| | - Aldo A Arellano
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sallie W Chisholm
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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20
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Budaev S, Kristiansen TS, Giske J, Eliassen S. Computational animal welfare: towards cognitive architecture models of animal sentience, emotion and wellbeing. ROYAL SOCIETY OPEN SCIENCE 2020; 7:201886. [PMID: 33489298 PMCID: PMC7813262 DOI: 10.1098/rsos.201886] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 12/04/2020] [Indexed: 05/08/2023]
Abstract
To understand animal wellbeing, we need to consider subjective phenomena and sentience. This is challenging, since these properties are private and cannot be observed directly. Certain motivations, emotions and related internal states can be inferred in animals through experiments that involve choice, learning, generalization and decision-making. Yet, even though there is significant progress in elucidating the neurobiology of human consciousness, animal consciousness is still a mystery. We propose that computational animal welfare science emerges at the intersection of animal behaviour, welfare and computational cognition. By using ideas from cognitive science, we develop a functional and generic definition of subjective phenomena as any process or state of the organism that exists from the first-person perspective and cannot be isolated from the animal subject. We then outline a general cognitive architecture to model simple forms of subjective processes and sentience. This includes evolutionary adaptation which contains top-down attention modulation, predictive processing and subjective simulation by re-entrant (recursive) computations. Thereafter, we show how this approach uses major characteristics of the subjective experience: elementary self-awareness, global workspace and qualia with unity and continuity. This provides a formal framework for process-based modelling of animal needs, subjective states, sentience and wellbeing.
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Affiliation(s)
- Sergey Budaev
- Department of Biological Sciences, University of Bergen, PO Box 7803, 5020 Bergen, Norway
| | - Tore S. Kristiansen
- Research Group Animal Welfare, Institute of Marine Research, PO Box 1870, 5817 Bergen, Norway
| | - Jarl Giske
- Department of Biological Sciences, University of Bergen, PO Box 7803, 5020 Bergen, Norway
| | - Sigrunn Eliassen
- Department of Biological Sciences, University of Bergen, PO Box 7803, 5020 Bergen, Norway
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21
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Li L, Liu Z, Zhang M, Meng D, Liu X, Wang P, Li X, Jiang Z, Zhong S, Jiang C, Yin H. Insights into the Metabolism and Evolution of the Genus Acidiphilium, a Typical Acidophile in Acid Mine Drainage. mSystems 2020; 5:e00867-20. [PMID: 33203689 PMCID: PMC7677001 DOI: 10.1128/msystems.00867-20] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 10/28/2020] [Indexed: 01/05/2023] Open
Abstract
Here, we report three new Acidiphilium genomes, reclassified existing Acidiphilium species, and performed the first comparative genomic analysis on Acidiphilium in an attempt to address the metabolic potential, ecological functions, and evolutionary history of the genus Acidiphilium In the genomes of Acidiphilium, we found an abundant repertoire of horizontally transferred genes (HTGs) contributing to environmental adaption and metabolic expansion, including genes conferring photosynthesis (puf, puh), CO2 assimilation (rbc), capacity for methane metabolism (mmo, mdh, frm), nitrogen source utilization (nar, cyn, hmp), sulfur compound utilization (sox, psr, sqr), and multiple metal and osmotic stress resistance capacities (czc, cop, ect). Additionally, the predicted donors of horizontal gene transfer were present in a cooccurrence network of Acidiphilium Genome-scale positive selection analysis revealed that 15 genes contained adaptive mutations, most of which were multifunctional and played critical roles in the survival of extreme conditions. We proposed that Acidiphilium originated in mild conditions and adapted to extreme environments such as acidic mineral sites after the acquisition of many essential functions.IMPORTANCE Extremophiles, organisms that thrive in extreme environments, are key models for research on biological adaption. They can provide hints for the origin and evolution of life, as well as improve the understanding of biogeochemical cycling of elements. Extremely acidophilic bacteria such as Acidiphilium are widespread in acid mine drainage (AMD) systems, but the metabolic potential, ecological functions, and evolutionary history of this genus are still ambiguous. Here, we sequenced the genomes of three new Acidiphilium strains and performed comparative genomic analysis on this extremely acidophilic bacterial genus. We found in the genomes of Acidiphilium an abundant repertoire of horizontally transferred genes (HTGs) contributing to environmental adaption and metabolic ability expansion, as indicated by phylogenetic reconstruction and gene context comparison. This study has advanced our understanding of microbial evolution and biogeochemical cycling in extreme niches.
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Affiliation(s)
- Liangzhi Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Zhenghua Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Min Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Delong Meng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Pei Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xiutong Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zhen Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Shuiping Zhong
- College of Zijin Mining, Fuzhou University, Fuzhou, China
- National Key Laboratory of Comprehensive Utilization of Low-Grade Refractory Gold Ores, Shanghang, China
| | - Chengying Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
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Abstract
The genomes of bacteria contain fewer genes and substantially less noncoding DNA than those of eukaryotes, and as a result, they have much less raw material to invent new traits. Yet, bacteria are vastly more taxonomically diverse, numerically abundant, and globally successful in colonizing new habitats compared to eukaryotes. Although bacterial genomes are generally considered to be optimized for efficient growth and rapid adaptation, nonadaptive processes have played a major role in shaping the size, contents, and compact organization of bacterial genomes and have allowed the establishment of deleterious traits that serve as the raw materials for genetic innovation.
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Affiliation(s)
- Paul C Kirchberger
- Department of Integrative Biology, University of Texas at Austin, Texas 78712, USA; ; ;
| | - Marian L Schmidt
- Department of Integrative Biology, University of Texas at Austin, Texas 78712, USA; ; ;
| | - Howard Ochman
- Department of Integrative Biology, University of Texas at Austin, Texas 78712, USA; ; ;
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23
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Tian R, Ning D, He Z, Zhang P, Spencer SJ, Gao S, Shi W, Wu L, Zhang Y, Yang Y, Adams BG, Rocha AM, Detienne BL, Lowe KA, Joyner DC, Klingeman DM, Arkin AP, Fields MW, Hazen TC, Stahl DA, Alm EJ, Zhou J. Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicity. MICROBIOME 2020; 8:51. [PMID: 32252814 PMCID: PMC7137472 DOI: 10.1186/s40168-020-00825-w] [Citation(s) in RCA: 140] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 03/13/2020] [Indexed: 05/18/2023]
Abstract
BACKGROUND The newly defined superphylum Patescibacteria such as Parcubacteria (OD1) and Microgenomates (OP11) has been found to be prevalent in groundwater, sediment, lake, and other aquifer environments. Recently increasing attention has been paid to this diverse superphylum including > 20 candidate phyla (a large part of the candidate phylum radiation, CPR) because it refreshed our view of the tree of life. However, adaptive traits contributing to its prevalence are still not well known. RESULTS Here, we investigated the genomic features and metabolic pathways of Patescibacteria in groundwater through genome-resolved metagenomics analysis of > 600 Gbp sequence data. We observed that, while the members of Patescibacteria have reduced genomes (~ 1 Mbp) exclusively, functions essential to growth and reproduction such as genetic information processing were retained. Surprisingly, they have sharply reduced redundant and nonessential functions, including specific metabolic activities and stress response systems. The Patescibacteria have ultra-small cells and simplified membrane structures, including flagellar assembly, transporters, and two-component systems. Despite the lack of CRISPR viral defense, the bacteria may evade predation through deletion of common membrane phage receptors and other alternative strategies, which may explain the low representation of prophage proteins in their genomes and lack of CRISPR. By establishing the linkages between bacterial features and the groundwater environmental conditions, our results provide important insights into the functions and evolution of this CPR group. CONCLUSIONS We found that Patescibacteria has streamlined many functions while acquiring advantages such as avoiding phage invasion, to adapt to the groundwater environment. The unique features of small genome size, ultra-small cell size, and lacking CRISPR of this large lineage are bringing new understandings on life of Bacteria. Our results provide important insights into the mechanisms for adaptation of the superphylum in the groundwater environments, and demonstrate a case where less is more, and small is mighty.
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Affiliation(s)
- Renmao Tian
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Daliang Ning
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Zhili He
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Ping Zhang
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Sarah J Spencer
- Biological Engineering Department, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Shuhong Gao
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Weiling Shi
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Linwei Wu
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Ya Zhang
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Benjamin G Adams
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN, USA
| | - Andrea M Rocha
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA
| | - Brittny L Detienne
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN, USA
| | - Kenneth A Lowe
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA
| | - Dominique C Joyner
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN, USA
| | - Dawn M Klingeman
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA
| | - Adam P Arkin
- Department of Bioengineering, University of California, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Matthew W Fields
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | - Terry C Hazen
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN, USA
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA
| | - David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Eric J Alm
- Biological Engineering Department, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jizhong Zhou
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China.
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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24
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Chiyomaru K, Takemoto K. Revisiting the hypothesis of an energetic barrier to genome complexity between eukaryotes and prokaryotes. ROYAL SOCIETY OPEN SCIENCE 2020; 7:191859. [PMID: 32257343 PMCID: PMC7062059 DOI: 10.1098/rsos.191859] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 01/21/2020] [Indexed: 05/06/2023]
Abstract
The absence of genome complexity in prokaryotes, being the evolutionary precursors to eukaryotic cells comprising all complex life (the prokaryote-eukaryote divide), is a long-standing question in evolutionary biology. A previous study hypothesized that the divide exists because prokaryotic genome size is constrained by bioenergetics (prokaryotic power per gene or genome being significantly lower than eukaryotic ones). However, this hypothesis was evaluated using a relatively small dataset due to lack of data availability at the time, and is therefore controversial. Accordingly, we constructed a larger dataset of genomes, metabolic rates, cell sizes and ploidy levels to investigate whether an energetic barrier to genome complexity exists between eukaryotes and prokaryotes while statistically controlling for the confounding effects of cell size and phylogenetic signals. Notably, we showed that the differences in bioenergetics between prokaryotes and eukaryotes were less significant than those previously reported. More importantly, we found a limited contribution of power per genome and power per gene to the prokaryote-eukaryote dichotomy. Our findings indicate that the prokaryote-eukaryote divide is hard to explain from the energetic perspective. However, our findings may not entirely discount the traditional hypothesis; in contrast, they indicate the need for more careful examination.
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25
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Huan R, Huang J, Liu D, Wang M, Liu C, Zhang Y, Yi C, Xiao D, He H. Genome Sequencing of Mesonia algae K4-1 Reveals Its Adaptation to the Arctic Ocean. Front Microbiol 2019; 10:2812. [PMID: 31866978 PMCID: PMC6905171 DOI: 10.3389/fmicb.2019.02812] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Accepted: 11/20/2019] [Indexed: 12/27/2022] Open
Abstract
The special ecological environment of the Arctic has brought about a large number of salt-tolerant and psychrotolerant microorganisms. We isolated two culturable bacterial strains of the genus Mesonia; one from the Arctic ocean, Mesonia algae K4-1, and one from the tropical sea, Mesonia sp. HuA40. Our genome analysis and phenotypic experiments indicated that Mesonia algae K4-1 is a moderately halophilic and psychrophilic bacterium. Mesonia algae K4-1 can tolerate 3–14% NaCl and grow at a wide range of temperatures from 4 to 50°C. Mesonia sp. HuA40 is a mesophilic bacterium that can only grow with 3–9% NaCl. In addition, the salt adaptation strategy of Mesonia algae K4-1 accumulates organic osmolytes in the cell. RNA helicases, glutathione and organic compatible solutes may play important roles in maintaining the metabolism and physiological function of Mesonia algae K4-1 under cold stress. Moreover, the ability of Mesonia algae K4-1 to adapt to an oligotrophic marine environment is likely due to the synthesis of a large number of extracellular polysaccharides and the secretion of various families of extracellular proteases. This study systematically analyzed the relationship between genomic differentiation and environmental factors of the Mesonia genus and revealed the possible adaptation mechanism of Mesonia algae K4-1 in the extreme Arctic marine environment at the genomic level.
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Affiliation(s)
- Ran Huan
- School of Life Sciences, Central South University, Changsha, China
| | - JiaFeng Huang
- School of Life Sciences, Central South University, Changsha, China
| | - Dan Liu
- School of Life Sciences, Central South University, Changsha, China
| | - Meng Wang
- School of Life Sciences, Central South University, Changsha, China
| | - CongLing Liu
- School of Life Sciences, Central South University, Changsha, China
| | - YunQian Zhang
- School of Life Sciences, Central South University, Changsha, China
| | - CuiPing Yi
- School of Chemistry and Biological Engineering, Changsha University of Science and Technology, Changsha, China
| | - Dong Xiao
- State Key Laboratory of Coal Resources and Safe Mining, China University of Mining and Technology, Xuzhou, China
| | - HaiLun He
- School of Life Sciences, Central South University, Changsha, China
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26
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Pereira-Flores E, Glöckner FO, Fernandez-Guerra A. Fast and accurate average genome size and 16S rRNA gene average copy number computation in metagenomic data. BMC Bioinformatics 2019; 20:453. [PMID: 31488068 PMCID: PMC6727555 DOI: 10.1186/s12859-019-3031-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 08/16/2019] [Indexed: 01/17/2023] Open
Abstract
Background Metagenomics caused a quantum leap in microbial ecology. However, the inherent size and complexity of metagenomic data limit its interpretation. The quantification of metagenomic traits in metagenomic analysis workflows has the potential to improve the exploitation of metagenomic data. Metagenomic traits are organisms’ characteristics linked to their performance. They are measured at the genomic level taking a random sample of individuals in a community. As such, these traits provide valuable information to uncover microorganisms’ ecological patterns. The Average Genome Size (AGS) and the 16S rRNA gene Average Copy Number (ACN) are two highly informative metagenomic traits that reflect microorganisms’ ecological strategies as well as the environmental conditions they inhabit. Results Here, we present the ags.sh and acn.sh tools, which analytically derive the AGS and ACN metagenomic traits. These tools represent an advance on previous approaches to compute the AGS and ACN traits. Benchmarking shows that ags.sh is up to 11 times faster than state-of-the-art tools dedicated to the estimation AGS. Both ags.sh and acn.sh show comparable or higher accuracy than existing tools used to estimate these traits. To exemplify the applicability of both tools, we analyzed the 139 prokaryotic metagenomes of TARA Oceans and revealed the ecological strategies associated with different water layers. Conclusion We took advantage of recent advances in gene annotation to develop the ags.sh and acn.sh tools to combine easy tool usage with fast and accurate performance. Our tools compute the AGS and ACN metagenomic traits on unassembled metagenomes and allow researchers to improve their metagenomic data analysis to gain deeper insights into microorganisms’ ecology. The ags.sh and acn.sh tools are publicly available using Docker container technology at https://github.com/pereiramemo/AGS-and-ACN-tools. Electronic supplementary material The online version of this article (10.1186/s12859-019-3031-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Emiliano Pereira-Flores
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany. .,Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, 28759, Bremen, Germany.
| | - Frank Oliver Glöckner
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany.,Alfred Wegener Institute - Helmholtz Center for Polar- and Marine Research, Am Handelshafen 12, 27570, Bremerhaven, Germany
| | - Antonio Fernandez-Guerra
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany. .,Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, 28759, Bremen, Germany. .,Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, UK.
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27
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Zhang S, Gu S, Ni X, Li X. Genome Size Reversely Correlates With Host Plant Range in Helicoverpa Species. Front Physiol 2019; 10:29. [PMID: 30761014 PMCID: PMC6363812 DOI: 10.3389/fphys.2019.00029] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 01/11/2019] [Indexed: 12/02/2022] Open
Abstract
In organisms with very low percentages of transposable elements (TEs), genome size may positively or negatively correlate with host range, depending on whether host adaptation or host modification is the main route to host generalism. To test if this holds true for insect herbivores with greater percentages of TEs, we conducted flow cytometry to measure the endopolyploidy levels and C-values of the host modification (salivary gland and mandibular gland in head), host adaptation (midgut), and host use-independent tissues (male gonad, hemolymph, and Malpighian tubules) of the generalist Helicoverpa armigera and the head of its older specialist sister H. assulta. Larval salivary gland displayed a consecutive chain of endopolyploidy particles from 8Cx to higher than 32Cx and larval head and midgut had endopolyploidy nuclei clusters of 16Cx and 32Cx, whereas larval male gonad, hemolymph, and Malpighian tubules possessed no endopolyploidy nuclei of higher than 8Cx. The estimated genome size of the Solanaceae plant specialist H. assulta is 430 Mb, significantly larger than that of its older generalist sister Heliothis virescens (408 Mb) and those of its two generalist descendants H. armigera (394 Mb) and H. zea (363 Mb). These data not only reveal a negative correlation between host plant range and genome size in this terminal lineage, but also imply that Helicoverpa species appear to depend more on host modification than on host adaptation to achieve polyphagy.
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Affiliation(s)
- Shen Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shaohua Gu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xinzhi Ni
- USDA-ARS Crop Genetics and Breeding Research Unit, Tifton, GA, United States
| | - Xianchun Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.,Department of Entomology and BIO5 Institute, University of Arizona, Tucson, AZ, United States
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28
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Novel haloarchaeon Natrinema thermophila having the highest growth temperature among haloarchaea with a large genome size. Sci Rep 2018; 8:7777. [PMID: 29773867 PMCID: PMC5958107 DOI: 10.1038/s41598-018-25887-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 04/30/2018] [Indexed: 12/13/2022] Open
Abstract
Environmental temperature is one of the most important factors for the growth and survival of microorganisms. Here we describe a novel extremely halophilic archaeon (haloarchaea) designated as strain CBA1119T isolated from solar salt. Strain CBA1119T had the highest maximum and optimal growth temperatures (66 °C and 55 °C, respectively) and one of the largest genome sizes among haloarchaea (5.1 Mb). It also had the largest number of strain-specific pan-genome orthologous groups and unique pathways among members of the genus Natrinema in the class Halobacteria. A dendrogram based on the presence/absence of genes and a phylogenetic tree constructed based on OrthoANI values highlighted the particularities of strain CBA1119T as compared to other Natrinema species and other haloarchaea members. The large genome of strain CBA1119T may provide information on genes that confer tolerance to extreme environmental conditions, which may lead to the discovery of other thermophilic strains with potential applications in industrial biotechnology.
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29
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Xu Z, Xie J, Yang L, Chen D, Peters BM, Shirtliff ME. Complete Sequence of pCY-CTX, a Plasmid Carrying a Phage-Like Region and an ISEcp1-Mediated Tn2 Element from Enterobacter cloacae. Microb Drug Resist 2017; 24:307-313. [PMID: 28876168 DOI: 10.1089/mdr.2017.0146] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
A plasmid pCY-CTX carrying a phage-like backbone from an extensively drug-resistant Enterobacter cloacae strain Guangzhou-ECL001 (previously known as CY01) was identified in this study. By Illumina MiSeq 2 × 250-bp paired-end sequencing, de novo assembly, and PCR, full sequence of pCY-CTX was obtained. Plasmid pCY-CTX was a circular plasmid with a length of 116,700 bp, harboring 136 putative open reading frames with the average G + C content of 50.8%. The backbone of pCY-CTX showed high identity to previously reported phage-like plasmid pHCM2 and phage SSU5. In addition, pCY-CTX contained a distinctive ISEcp1-mediated Tn2 region with two resistance genes blaTEM-1 and blaCTX-M-3. Transposition unit "ISEcp1- blaCTX-M-3- orf477" was inserted into the Tn2 structure, dividing Tn2 into two parts. This represents the first identification of a plasmid carrying a phage-like backbone and a distinctive ISEcp1-mediated Tn2 region within blaTEM-1 and blaCTX-M-3 in clinical E. cloacae. The finding of phage-like regions located in plasmids provides a new perspective in gene transfer associated with antimicrobial resistance.
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Affiliation(s)
- Zhenbo Xu
- 1 School of Food Science and Technology, South China University of Technology , Guangzhou, China .,2 Department of Microbial Pathogenesis, School of Dentistry, University of Maryland , Baltimore, Maryland
| | - Jinhong Xie
- 1 School of Food Science and Technology, South China University of Technology , Guangzhou, China
| | - Ling Yang
- 3 Department of Laboratory Medicine, First Affiliated Hospital of Guangzhou Medical University , Guangzhou, China
| | - Dingqiang Chen
- 3 Department of Laboratory Medicine, First Affiliated Hospital of Guangzhou Medical University , Guangzhou, China
| | - Brian M Peters
- 4 Department of Clinical Pharmacy, College of Pharmacy, University of Tennessee Health Sciences Center , Memphis, Tennessee
| | - Mark E Shirtliff
- 2 Department of Microbial Pathogenesis, School of Dentistry, University of Maryland , Baltimore, Maryland
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30
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Cobo-Simón M, Tamames J. Relating genomic characteristics to environmental preferences and ubiquity in different microbial taxa. BMC Genomics 2017; 18:499. [PMID: 28662636 PMCID: PMC5492924 DOI: 10.1186/s12864-017-3888-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 06/21/2017] [Indexed: 11/10/2022] Open
Abstract
Background Despite the important role that microorganisms play in environmental processes, the low percentage of cultured microbes (5%) has limited, until now, our knowledge of their ecological strategies. However, the development of high-throughput sequencing has generated a huge amount of genomic and metagenomic data without the need of culturing that can be used to study ecological questions. This study aims to estimate the functional capabilities, genomic sizes and 16S copy number of different taxa in relation to their ubiquity and their environmental preferences. Results To achieve this goal, we compiled data regarding the presence of each prokaryotic genera in diverse environments. Then, genomic characteristics such as genome size, 16S rRNA gene copy number, and functional content of the genomes were related to their ubiquity and different environmental preferences of the corresponding taxa. The results showed clear correlations between genomic characteristics and environmental conditions. Conclusions Ubiquity and adaptation were linked to genome size, while 16S copy number was not directly related to ubiquity. We observed that different combinations of these two characteristics delineate the different environments. Besides, the analysis of functional classes showed some clear signatures linked to particular environments. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3888-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marta Cobo-Simón
- Systems Biology Programme, Centro Nacional de Biotecnología (CNB-CSIC), C/Darwin 3, 28049, Madrid, Spain
| | - Javier Tamames
- Systems Biology Programme, Centro Nacional de Biotecnología (CNB-CSIC), C/Darwin 3, 28049, Madrid, Spain.
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31
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Lear G, Lau K, Perchec AM, Buckley HL, Case BS, Neale M, Fierer N, Leff JW, Handley KM, Lewis G. Following Rapoport's Rule: the geographic range and genome size of bacterial taxa decline at warmer latitudes. Environ Microbiol 2017; 19:3152-3162. [PMID: 28504344 DOI: 10.1111/1462-2920.13797] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 10/11/2016] [Accepted: 05/09/2017] [Indexed: 11/28/2022]
Abstract
We sought to test whether stream bacterial communities conform to Rapoport's Rule, a pattern commonly observed for plants and animals whereby taxa exhibit decreased latitudinal range sizes closer to the equator. Using a DNA sequencing approach, we explored the biogeography of biofilm bacterial communities in 204 streams across a ∼1000 km latitudinal gradient. The range sizes of bacterial taxa were strongly correlated with latitude, decreasing closer to the equator, which coincided with a greater than fivefold increase in bacterial taxonomic richness. The relative richness and range size of bacteria were associated with spatially correlated variation in temperature and rainfall. These patterns were observed despite enormous variability in catchment environmental characteristics. Similar results were obtained when restricting the same analyses to native forest catchments, thereby controlling for spatial biases in land use. We analysed genomic data from ∼500 taxa detected in this study, for which data were available and found that bacterial communities at cooler latitudes also tended to possess greater potential metabolic potential. Collectively, these data provide the first evidence of latitudinal variation in the range size distributions of freshwater bacteria, a trend which may be determined, in part, by a trade-off between bacterial genome size and local variation in climatic conditions.
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Affiliation(s)
- Gavin Lear
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Kelvin Lau
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Anne-Marie Perchec
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Hannah L Buckley
- School of Science, Auckland University of Technology, Private Bag 92006, Auckland, 1142, New Zealand
| | - Bradley S Case
- School of Science, Auckland University of Technology, Private Bag 92006, Auckland, 1142, New Zealand
| | | | - Noah Fierer
- Department of Ecology and Evolutionary Biology and Cooperative Institute for Research in Environmental Biology, University of Colorado at Boulder, Boulder, CO 80309-0216, USA
| | - Jonathan W Leff
- Department of Ecology and Evolutionary Biology and Cooperative Institute for Research in Environmental Biology, University of Colorado at Boulder, Boulder, CO 80309-0216, USA
| | - Kim M Handley
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Gillian Lewis
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
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Gutleben J, Chaib De Mares M, van Elsas JD, Smidt H, Overmann J, Sipkema D. The multi-omics promise in context: from sequence to microbial isolate. Crit Rev Microbiol 2017; 44:212-229. [PMID: 28562180 DOI: 10.1080/1040841x.2017.1332003] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The numbers and diversity of microbes in ecosystems within and around us is unmatched, yet most of these microorganisms remain recalcitrant to in vitro cultivation. Various high-throughput molecular techniques, collectively termed multi-omics, provide insights into the genomic structure and metabolic potential as well as activity of complex microbial communities. Nonetheless, pure or defined cultures are needed to (1) decipher microbial physiology and thus test multi-omics-based ecological hypotheses, (2) curate and improve database annotations and (3) realize novel applications in biotechnology. Cultivation thus provides context. In turn, we here argue that multi-omics information awaits integration into the development of novel cultivation strategies. This can build the foundation for a new era of omics information-guided microbial cultivation technology and reduce the inherent trial-and-error search space. This review discusses how information that can be extracted from multi-omics data can be applied for the cultivation of hitherto uncultured microorganisms. Furthermore, we summarize groundbreaking studies that successfully translated information derived from multi-omics into specific media formulations, screening techniques and selective enrichments in order to obtain novel targeted microbial isolates. By integrating these examples, we conclude with a proposed workflow to facilitate future omics-aided cultivation strategies that are inspired by the microbial complexity of the environment.
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Affiliation(s)
- Johanna Gutleben
- a Laboratory of Microbiology , Wageningen University & Research , Wageningen , The Netherlands
| | - Maryam Chaib De Mares
- b Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences (GELIFES) , Rijksuniversiteit Groningen , Groningen , The Netherlands
| | - Jan Dirk van Elsas
- b Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences (GELIFES) , Rijksuniversiteit Groningen , Groningen , The Netherlands
| | - Hauke Smidt
- a Laboratory of Microbiology , Wageningen University & Research , Wageningen , The Netherlands
| | - Jörg Overmann
- c Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen , Braunschweig , Germany
| | - Detmer Sipkema
- a Laboratory of Microbiology , Wageningen University & Research , Wageningen , The Netherlands
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Takemoto K, Imoto M. Exosomes in mammals with greater habitat variability contain more proteins and RNAs. ROYAL SOCIETY OPEN SCIENCE 2017; 4:170162. [PMID: 28484642 PMCID: PMC5414279 DOI: 10.1098/rsos.170162] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 03/22/2017] [Indexed: 05/08/2023]
Abstract
Factors determining habitat variability are poorly understood despite possible explanations based on genome and physiology. This is because previous studies only focused on primary measures such as genome size and body size. In this study, we hypothesize that specific gene functions determine habitat variability in order to explore new factors beyond primary measures. We comprehensively evaluate the relationship between gene functions and the climate envelope while statistically controlling for potentially confounding effects by using data on the habitat range, genome, body size and metabolism of various mammals. Our analyses show that the number of proteins and RNAs contained in exosomes is predominantly associated with the climate envelope. This finding indicates the importance of exosomes to habitat range expansion of mammals and provides a new hypothesis for the relationship between the genome and habitat variability.
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Bentkowski P, van Oosterhout C, Ashby B, Mock T. The effect of extrinsic mortality on genome size evolution in prokaryotes. THE ISME JOURNAL 2017; 11:1011-1018. [PMID: 27922601 PMCID: PMC5364348 DOI: 10.1038/ismej.2016.165] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 10/06/2016] [Accepted: 10/20/2016] [Indexed: 01/13/2023]
Abstract
Mortality has a significant role in prokaryotic ecology and evolution, yet the impact of variations in extrinsic mortality on prokaryotic genome evolution has received little attention. We used both mathematical and agent-based models to reveal how variations in extrinsic mortality affect prokaryotic genome evolution. Our results suggest that the genome size of bacteria increases with increased mortality. A high extrinsic mortality increases the pool of free resources and shortens life expectancy, which selects for faster reproduction, a phenotype we called 'scramblers'. This phenotype is realised by the expansion of gene families involved in nutrient acquisition and metabolism. In contrast, a low mortality rate increases an individual's life expectancy, which results in natural selection favouring tolerance to starvation when conditions are unfavourable. This leads to the evolution of small, streamlined genomes ('stayers'). Our models predict that large genomes, gene family expansion and horizontal gene transfer should be observed in prokaryotes occupying ecosystems exposed to high abiotic stress, as well as those under strong predator- and/or pathogen-mediated selection. A comparison of genome size of cyanobacteria in relatively stable marine versus more turbulent freshwater environments corroborates our predictions, although other factors between these environments could also be responsible.
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Affiliation(s)
- Piotr Bentkowski
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
- Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Cock van Oosterhout
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Ben Ashby
- Department of Mathematical Sciences, University of Bath, Bath, UK
- Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
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Gweon HS, Bailey MJ, Read DS. Assessment of the bimodality in the distribution of bacterial genome sizes. THE ISME JOURNAL 2017; 11:821-824. [PMID: 27834945 PMCID: PMC5322294 DOI: 10.1038/ismej.2016.142] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 08/12/2016] [Accepted: 09/07/2016] [Indexed: 12/13/2022]
Abstract
Bacterial genome sizes have previously been shown to exhibit a bimodal distribution. This phenomenon has prompted discussion regarding the evolutionary forces driving genome size in bacteria and its ecological significance. We investigated the level of inherent redundancy in the public database and the effect it has on the shape of the apparent bimodal distribution. Our study reveals that there is a significant bias in the genome sequencing efforts towards a certain group of species, and that correcting the bias using species nomenclature and clustering of the 16S rRNA gene, results in a unimodal rather than the previously published bimodal distribution. The true genome size distribution and its wider ecological implications will soon emerge as we are currently witnessing rapid growth in the number of sequenced genomes from diverse environmental niches across a range of habitats at an unprecedented rate.
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Baltrus DA, Dougherty K, Arendt KR, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy TBK, Ngan CY, Daum C, Shapiro N, Markowitz V, Ivanova N, Kyrpides N, Woyke T, Arnold AE. Absence of genome reduction in diverse, facultative endohyphal bacteria. Microb Genom 2017; 3:e000101. [PMID: 28348879 PMCID: PMC5361626 DOI: 10.1099/mgen.0.000101] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 12/04/2016] [Indexed: 01/03/2023] Open
Abstract
Fungi interact closely with bacteria, both on the surfaces of the hyphae and within their living tissues (i.e. endohyphal bacteria, EHB). These EHB can be obligate or facultative symbionts and can mediate diverse phenotypic traits in their hosts. Although EHB have been observed in many lineages of fungi, it remains unclear how widespread and general these associations are, and whether there are unifying ecological and genomic features can be found across EHB strains as a whole. We cultured 11 bacterial strains after they emerged from the hyphae of diverse Ascomycota that were isolated as foliar endophytes of cupressaceous trees, and generated nearly complete genome sequences for all. Unlike the genomes of largely obligate EHB, the genomes of these facultative EHB resembled those of closely related strains isolated from environmental sources. Although all analysed genomes encoded structures that could be used to interact with eukaryotic hosts, pathways previously implicated in maintenance and establishment of EHB symbiosis were not universally present across all strains. Independent isolation of two nearly identical pairs of strains from different classes of fungi, coupled with recent experimental evidence, suggests horizontal transfer of EHB across endophytic hosts. Given the potential for EHB to influence fungal phenotypes, these genomes could shed light on the mechanisms of plant growth promotion or stress mitigation by fungal endophytes during the symbiotic phase, as well as degradation of plant material during the saprotrophic phase. As such, these findings contribute to the illumination of a new dimension of functional biodiversity in fungi.
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Affiliation(s)
- David A Baltrus
- 1School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Kevin Dougherty
- 1School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Kayla R Arendt
- 1School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | | | - Alicia Clum
- 2Joint Genome Institute, Walnut Creek, CA, USA
| | | | | | | | | | | | - T B K Reddy
- 2Joint Genome Institute, Walnut Creek, CA, USA
| | | | - Chris Daum
- 2Joint Genome Institute, Walnut Creek, CA, USA
| | | | | | | | | | - Tanja Woyke
- 2Joint Genome Institute, Walnut Creek, CA, USA
| | - A Elizabeth Arnold
- 1School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA.,3Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
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Hiraoka S, Yang CC, Iwasaki W. Metagenomics and Bioinformatics in Microbial Ecology: Current Status and Beyond. Microbes Environ 2016; 31:204-12. [PMID: 27383682 PMCID: PMC5017796 DOI: 10.1264/jsme2.me16024] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Metagenomic approaches are now commonly used in microbial ecology to study microbial communities in more detail, including many strains that cannot be cultivated in the laboratory. Bioinformatic analyses make it possible to mine huge metagenomic datasets and discover general patterns that govern microbial ecosystems. However, the findings of typical metagenomic and bioinformatic analyses still do not completely describe the ecology and evolution of microbes in their environments. Most analyses still depend on straightforward sequence similarity searches against reference databases. We herein review the current state of metagenomics and bioinformatics in microbial ecology and discuss future directions for the field. New techniques will allow us to go beyond routine analyses and broaden our knowledge of microbial ecosystems. We need to enrich reference databases, promote platforms that enable meta- or comprehensive analyses of diverse metagenomic datasets, devise methods that utilize long-read sequence information, and develop more powerful bioinformatic methods to analyze data from diverse perspectives.
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Affiliation(s)
- Satoshi Hiraoka
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, the University of Tokyo
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Prabha R, Singh DP, Somvanshi P, Rai A. Functional profiling of cyanobacterial genomes and its role in ecological adaptations. GENOMICS DATA 2016; 9:89-94. [PMID: 27408818 PMCID: PMC4932875 DOI: 10.1016/j.gdata.2016.06.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 06/18/2016] [Accepted: 06/18/2016] [Indexed: 11/29/2022]
Abstract
With the availability of complete genome sequences of many cyanobacterial species, it is becoming feasible to study the broad prospective of the environmental adaptation and the overall changes at transcriptional and translational level in these organisms. In the evolutionary phase, niche-specific competitive forces have resulted in specific features of the cyanobacterial genomes. In this study, functional composition of the 84 different cyanobacterial genomes and their adaptations to different environments was examined by identifying the genomic composition for specific cellular processes, which reflect their genomic functional profile and ecological adaptation. It was identified that among cyanobacterial genomes, metabolic genes have major share over other categories and differentiation of genomic functional profile was observed for the species inhabiting different habitats. The cyanobacteria of freshwater and other habitats accumulate large number of poorly characterized genes. Strain specific functions were also reported in many cyanobacterial members, of which an important feature was the occurrence of phage-related sequences. From this study, it can be speculated that habitat is one of the major factors in giving the shape of functional composition of cyanobacterial genomes towards their ecological adaptations.
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Affiliation(s)
- Ratna Prabha
- ICAR-National Bureau of Agriculturally Important Microorganisms, Indian Council of Agricultural Research, Kushmaur, Maunath Bhanjan 275103, India
| | - Dhananjaya P Singh
- ICAR-National Bureau of Agriculturally Important Microorganisms, Indian Council of Agricultural Research, Kushmaur, Maunath Bhanjan 275103, India
| | | | - Anil Rai
- Center for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Indian Council of Agricultural Research, Library Avenue, New Delhi 110012, India
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How Likely Are We? Evolution of Organismal Complexity. Evol Biol 2016. [DOI: 10.1007/978-3-319-41324-2_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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