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Su L, Marshall IPG, Teske AP, Yao H, Li J. Genomic characterization of the bacterial phylum Candidatus Effluviviacota, a cosmopolitan member of the global seep microbiome. mBio 2024:e0099224. [PMID: 38980039 DOI: 10.1128/mbio.00992-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Accepted: 06/17/2024] [Indexed: 07/10/2024] Open
Abstract
The microbial communities of marine seep sediments contain unexplored physiological and phylogenetic diversity. Here, we examined 30 bacterial metagenome-assembled genomes (MAGs) from cold seeps in the South China Sea, the Indian Ocean, the Scotian Basin, and the Gulf of Mexico, as well as from deep-sea hydrothermal sediments in the Guaymas Basin, Gulf of California. Phylogenetic analyses of these MAGs indicate that they form a distinct phylum-level bacterial lineage, which we propose as a new phylum, Candidatus Effluviviacota, in reference to its preferential occurrence at diverse seep areas. Based on tightly clustered high-quality MAGs, we propose two new genus-level candidatus taxa, Candidatus Effluvivivax and Candidatus Effluvibates. Genomic content analyses indicate that Candidatus Effluviviacota are chemoheterotrophs that harbor the Embden-Meyerhof-Parnas glycolysis pathway. They gain energy by fermenting organic substrates. Additionally, they display potential capabilities for the degradation of cellulose, hemicellulose, starch, xylan, and various peptides. Extracellular anaerobic respiration appears to rely on metals as electron acceptors, with electron transfer primarily mediated by multiheme cytochromes and by a flavin-based extracellular electron transfer (EET) mechanism that involves NADH-quinone oxidoreductase-demethylmenaquinone-synthesizing enzymes, uncharacterized membrane proteins, and flavin-binding proteins, also known as the NUO-DMK-EET-FMN complex. The heterogeneity within the Ca. Effluviviacota phylum suggests varying roles in energy metabolism among different genera. While NUO-DMK-EET-FMN electron transfer has been reported predominantly in Gram-positive bacteria, it is now identified in Ca. Effluviviacota as well. We detected the presence of genes associated with bacterial microcompartments in Ca. Effluviviacota, which can promote specific metabolic processes and protect the cytosol from toxic intermediates. IMPORTANCE The newly discovered bacterial phylum Candidatus Effluviviacota is widespread across diverse seepage ecosystems, marine environments, and freshwater environments, with a notable preference for cold seeps. While maintaining an average abundance of approximately 1% in the global gene catalog of cold seep habitats, it has not hitherto been characterized. The metabolic versatility of Ca. Effluviviacota in anaerobic carbon, hydrogen, and metal cycling aligns with its prevalence in anoxic niches, with a preference for cold seep environments. Variations in metabolic potential between Ca. Effluvivivax and Ca. Effluvibates may contribute to shaping their respective habitat distributions.
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Affiliation(s)
- Lei Su
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
- Department of Biology, Center for Electromicrobiology (CEM), Section for Microbiology, Aarhus University, Aarhus, Denmark
| | - Ian P G Marshall
- Department of Biology, Center for Electromicrobiology (CEM), Section for Microbiology, Aarhus University, Aarhus, Denmark
| | - Andreas P Teske
- Department of Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Huiqiang Yao
- MLR Key Laboratory of Marine Mineral Resources, Guangzhou Marine Geological Survey, Guangzhou, China
| | - Jiangtao Li
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
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Li DD, Wang J, Jiang Y, Zhang P, Liu Y, Li YZ, Zhang Z. Quantifying functional redundancy in polysaccharide-degrading prokaryotic communities. MICROBIOME 2024; 12:120. [PMID: 38956705 PMCID: PMC11218364 DOI: 10.1186/s40168-024-01838-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 05/14/2024] [Indexed: 07/04/2024]
Abstract
BACKGROUND Functional redundancy (FR) is widely present, but there is no consensus on its formation process and influencing factors. Taxonomically distinct microorganisms possessing genes for the same function in a community lead to within-community FR, and distinct assemblies of microorganisms in different communities playing the same functional roles are termed between-community FR. We proposed two formulas to respectively quantify the degree of functional redundancy within and between communities and analyzed the FR degrees of carbohydrate degradation functions in global environment samples using the genetic information of glycoside hydrolases (GHs) encoded by prokaryotes. RESULTS Our results revealed that GHs are each encoded by multiple taxonomically distinct prokaryotes within a community, and the enzyme-encoding prokaryotes are further distinct between almost any community pairs. The within- and between-FR degrees are primarily affected by the alpha and beta community diversities, respectively, and are also affected by environmental factors (e.g., pH, temperature, and salinity). The FR degree of the prokaryotic community is determined by deterministic factors. CONCLUSIONS We conclude that the functional redundancy of GHs is a stabilized community characteristic. This study helps to determine the FR formation process and influencing factors and provides new insights into the relationships between prokaryotic community biodiversity and ecosystem functions. Video Abstract.
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Affiliation(s)
- Dan-Dan Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, China
| | - Jianing Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Yiru Jiang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Peng Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Ya Liu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Yue-Zhong Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China.
| | - Zheng Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China.
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Fukuda K, Haro K, Yamasaki K, Ikegami H, Saito M. Surveillance and phylogenetic analysis of a pathogenic bacterium candidate in nasal discharge from children. Microbiol Spectr 2024; 12:e0056624. [PMID: 38785433 PMCID: PMC11218501 DOI: 10.1128/spectrum.00566-24] [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: 03/01/2024] [Accepted: 04/26/2024] [Indexed: 05/25/2024] Open
Abstract
"The infectious organism lurking in human airways (IOLA)" is a candidate pathogenic bacterium detected in bronchoalveolar lavage fluid specimens derived from adult patients with chronic lower respiratory tract infections. Genomic analyses of IOLA have revealed that it possesses the smallest and most AT-rich genome among human-derived bacteria. However, its biological properties remain unclear because no culture method has been established for IOLA. Here, we conducted a large-scale IOLA surveillance study of nasal discharge specimens from children in Japan and investigated the correlation between IOLA detection frequency and patient characteristics. We detected IOLA in 5.4% (103 of 1,920) of pediatric nasal discharge samples. No significant differences were observed in the frequency of detection based on the patient's background. However, with respect to age, the frequency of detection tended to be significantly high at 2-3 and 6 years old. Phylogenetic analysis revealed five phylotypes in the IOLA 16S rRNA gene sequences, and the sequences detected in adult patients with respiratory infections in a previous study belonged to one of the five phylotypes. The involvement of IOLA in the symptoms is not clear, but IOLA is detected at a relatively high frequency in pediatric nasal discharge. Many subjects with detected IOLA were not always IOLA positive, and IOLA was detected transiently. Our findings suggest that IOLA is horizontally transmitted through groups in nursery and elementary schools, and there are differences in biological characteristics among the IOLA phylotypes.IMPORTANCE"The infectious organism lurking in human airways (IOLA)" is a candidate pathogenic bacterium strongly suspected to be infectious to the respiratory tracts of humans and animals. However, a culture method for IOLA has not been established yet, and its properties remain unclear. In this study, IOLA was detected at a relatively high frequency in the nasal discharge of children, and five phylotypes of IOLA were identified. One of these phylotypes was found in the bronchoalveolar lavage fluid from adult patients, suggesting lineage-specific differences in the pathogenicity of IOLA. Moreover, it was suggested that IOLA is horizontally transmitted when children gather in groups such as nursery and elementary schools. These findings strongly indicate that IOLAs have been clinically undetected so far but are spreading among children, with one lineage being involved in respiratory diseases in adults. Examining the presence of IOLA in clinical specimens may help to understand the etiology of respiratory diseases with unknown causes.
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Affiliation(s)
- Kazumasa Fukuda
- Department of Microbiology, University of Occupational and Environmental Health, Japan, Kitakyushu, Fukuoka
| | - Kaoru Haro
- Department of Microbiology, University of Occupational and Environmental Health, Japan, Kitakyushu, Fukuoka
| | - Kei Yamasaki
- Department of Respiratory Medicine, University of Occupational and Environmental Health, Japan, Kitakyushu, Fukuoka
| | - Hiroaki Ikegami
- Department of Respiratory Medicine, University of Occupational and Environmental Health, Japan, Kitakyushu, Fukuoka
| | - Mitsumasa Saito
- Department of Microbiology, University of Occupational and Environmental Health, Japan, Kitakyushu, Fukuoka
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Whitman WB, Venter SN. Commentary on the proposed Section 10 amendments to the International Code of Nomenclature of Prokaryotes regarding Candidatus names. Syst Appl Microbiol 2024; 47:126524. [PMID: 38878497 DOI: 10.1016/j.syapm.2024.126524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 07/06/2024]
Abstract
Amendments were proposed to the International Code of Nomenclature of Prokaryotes (ICNP) in January [Arahal et al. (2024) Int. J Syst. Evol. Microbiol. 74: 006188] that would cause major changes in the treatment of Candidatus names. The amendments introduce Section 10 to name taxa whose names cannot be validly published under the ICNP because of the absence of type strains. This section creates a parallel 'pro-nomenclature' and formalizes alternative material which could serve as nomenclatural types. When conspecific isolates of taxa with Candidatus names are deposited in culture collections as type strains, the names can be validly published, and it is required that the same Candidatus name be used. While the amendments are promoted to provide stable names and rules of nomenclature for uncultivated taxa, the system is deeply flawed. It removes the permanent association between names and types, which will make the meaning of names imprecise and ambiguous. It creates 'pro-nomenclature', which is confusing and unnecessary. Since many taxa which cannot be validly named under the ICNP can already be named under the SeqCode, it duplicates and creates overlap with an established nomenclatural system without providing tangible benefits. As the SeqCode recognizes names formed under the ICNP, the ICNP should recognize names formed under the SeqCode as they have done for the Cyanobacteria named under the International Code of Nomenclature for algae, fungi and plants (ICN). For these reasons, we urge the members of the International Committee of Systematics of Prokaryotes (ICSP) to reject these amendments.
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Affiliation(s)
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
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Teichman S, Lee MD, Willis AD. Analyzing microbial evolution through gene and genome phylogenies. Biostatistics 2024; 25:786-800. [PMID: 37897441 DOI: 10.1093/biostatistics/kxad025] [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: 02/10/2023] [Revised: 08/15/2023] [Accepted: 08/27/2023] [Indexed: 10/30/2023] Open
Abstract
Microbiome scientists critically need modern tools to explore and analyze microbial evolution. Often this involves studying the evolution of microbial genomes as a whole. However, different genes in a single genome can be subject to different evolutionary pressures, which can result in distinct gene-level evolutionary histories. To address this challenge, we propose to treat estimated gene-level phylogenies as data objects, and present an interactive method for the analysis of a collection of gene phylogenies. We use a local linear approximation of phylogenetic tree space to visualize estimated gene trees as points in low-dimensional Euclidean space, and address important practical limitations of existing related approaches, allowing an intuitive visualization of complex data objects. We demonstrate the utility of our proposed approach through microbial data analyses, including by identifying outlying gene histories in strains of Prevotella, and by contrasting Streptococcus phylogenies estimated using different gene sets. Our method is available as an open-source R package, and assists with estimating, visualizing, and interacting with a collection of bacterial gene phylogenies.
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Affiliation(s)
- Sarah Teichman
- University of Washington Department of Statistics, Box 354322, Seattle, WA 98195-4322, USA
| | - Michael D Lee
- KBR NASA Ames Research Center, PO Box 1, Moffett Field, CA 94035-1000
- Blue Marble Space Institute of Science, 600 1st Avenue, 1st Floor, Seattle, WA 98104, USA
| | - Amy D Willis
- University of Washington Department of Biostatistics, Hans Rosling Center for Population Health, Box 351617, Seattle, WA 98195-1617, USA
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Foster AJ, van den Noort M, Poolman B. Bacterial cell volume regulation and the importance of cyclic di-AMP. Microbiol Mol Biol Rev 2024; 88:e0018123. [PMID: 38856222 DOI: 10.1128/mmbr.00181-23] [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] [Indexed: 06/11/2024] Open
Abstract
SUMMARYNucleotide-derived second messengers are present in all domains of life. In prokaryotes, most of their functionality is associated with general lifestyle and metabolic adaptations, often in response to environmental fluctuations of physical parameters. In the last two decades, cyclic di-AMP has emerged as an important signaling nucleotide in many prokaryotic lineages, including Firmicutes, Actinobacteria, and Cyanobacteria. Its importance is highlighted by the fact that both the lack and overproduction of cyclic di-AMP affect viability of prokaryotes that utilize cyclic di-AMP, and that it generates a strong innate immune response in eukaryotes. In bacteria that produce the second messenger, most molecular targets of cyclic di-AMP are associated with cell volume control. Besides, other evidence links the second messenger to cell wall remodeling, DNA damage repair, sporulation, central metabolism, and the regulation of glycogen turnover. In this review, we take a biochemical, quantitative approach to address the main cellular processes that are directly regulated by cyclic di-AMP and show that these processes are very connected and require regulation of a similar set of proteins to which cyclic di-AMP binds. Altogether, we argue that cyclic di-AMP is a master regulator of cell volume and that other cellular processes can be connected with cyclic di-AMP through this core function. We further highlight important directions in which the cyclic di-AMP field has to develop to gain a full understanding of the cyclic di-AMP signaling network and why some processes are regulated, while others are not.
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Affiliation(s)
- Alexander J Foster
- Department of Biochemistry, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Marco van den Noort
- Department of Biochemistry, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Bert Poolman
- Department of Biochemistry, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
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7
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Campos TL, Korhonen PK, Young ND, Wang T, Song J, Marhoefer R, Chang BCH, Selzer PM, Gasser RB. Inference of Essential Genes of the Parasite Haemonchus contortus via Machine Learning. Int J Mol Sci 2024; 25:7015. [PMID: 39000124 PMCID: PMC11240989 DOI: 10.3390/ijms25137015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 06/19/2024] [Accepted: 06/21/2024] [Indexed: 07/16/2024] Open
Abstract
Over the years, comprehensive explorations of the model organisms Caenorhabditis elegans (elegant worm) and Drosophila melanogaster (vinegar fly) have contributed substantially to our understanding of complex biological processes and pathways in multicellular organisms generally. Extensive functional genomic-phenomic, genomic, transcriptomic, and proteomic data sets have enabled the discovery and characterisation of genes that are crucial for life, called 'essential genes'. Recently, we investigated the feasibility of inferring essential genes from such data sets using advanced bioinformatics and showed that a machine learning (ML)-based workflow could be used to extract or engineer features from DNA, RNA, protein, and/or cellular data/information to underpin the reliable prediction of essential genes both within and between C. elegans and D. melanogaster. As these are two distantly related species within the Ecdysozoa, we proposed that this ML approach would be particularly well suited for species that are within the same phylum or evolutionary clade. In the present study, we cross-predicted essential genes within the phylum Nematoda (evolutionary clade V)-between C. elegans and the pathogenic parasitic nematode H. contortus-and then ranked and prioritised H. contortus proteins encoded by these genes as intervention (e.g., drug) target candidates. Using strong, validated predictors, we inferred essential genes of H. contortus that are involved predominantly in crucial biological processes/pathways including ribosome biogenesis, translation, RNA binding/processing, and signalling and which are highly transcribed in the germline, somatic gonad precursors, sex myoblasts, vulva cell precursors, various nerve cells, glia, or hypodermis. The findings indicate that this in silico workflow provides a promising avenue to identify and prioritise panels/groups of drug target candidates in parasitic nematodes for experimental validation in vitro and/or in vivo.
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Affiliation(s)
- Túlio L Campos
- Department of Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia
- Bioinformatics Core Facility, Aggeu Magalhães Institute (Fiocruz), Recife 50740-465, PE, Brazil
| | - Pasi K Korhonen
- Department of Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Neil D Young
- Department of Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Tao Wang
- Department of Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Jiangning Song
- Department of Data Science and AI, Faculty of IT, Monash University, Melbourne, VIC 3800, Australia
- Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
- Monash Data Futures Institute, Monash University, Clayton, VIC 3800, Australia
| | - Richard Marhoefer
- Boehringer Ingelheim Animal Health, Binger Strasse 173, 55216 Ingelheim am Rhein, Germany
| | - Bill C H Chang
- Department of Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Paul M Selzer
- Boehringer Ingelheim Animal Health, Binger Strasse 173, 55216 Ingelheim am Rhein, Germany
| | - Robin B Gasser
- Department of Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia
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Fernando CM, Breaker RR. Bioinformatic prediction of proteins relevant to functions of the bacterial OLE ribonucleoprotein complex. mSphere 2024; 9:e0015924. [PMID: 38771028 DOI: 10.1128/msphere.00159-24] [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: 02/23/2024] [Accepted: 04/19/2024] [Indexed: 05/22/2024] Open
Abstract
OLE (ornate, large, extremophilic) RNAs are members of a noncoding RNA class present in many Gram-positive, extremophilic bacteria. The large size, complex structure, and extensive sequence conservation of OLE RNAs are characteristics consistent with the hypothesis that they likely function as ribozymes. The OLE RNA representative from Halalkalibacterium halodurans is known to localize to the phospholipid membrane and requires at least three essential protein partners: OapA, OapB, and OapC. However, the precise biochemical functions of this unusual ribonucleoprotein (RNP) complex remain unknown. Genetic disruption of OLE RNA or its partners revealed that the complex is beneficial under diverse stress conditions. To search for additional links between OLE RNA and other cellular components, we used phylogenetic profiling to identify proteins that are either correlated or anticorrelated with the presence of OLE RNA in various bacterial species. This analysis revealed strong correlations between the essential protein-binding partners of OLE RNA and organisms that carry the ole gene. Similarly, proteins involved in sporulation are correlated, suggesting a potential role for the OLE RNP complex in spore formation. Intriguingly, the Mg2+ transporter MpfA is strongly anticorrelated with OLE RNA. Evidence indicates that MpfA is structurally related to OapA and therefore MpfA may serve as a functional replacement for some contributions otherwise performed by the OLE RNP complex in species that lack this device. Indeed, OLE RNAs might represent an ancient RNA class that enabled primitive organisms to sense and respond to major cellular stresses.IMPORTANCEOLE (ornate, large, extremophilic) RNAs were first reported nearly 20 years ago, and they represent one of the largest and most intricately folded noncoding RNA classes whose biochemical function remains to be established. Other RNAs with similar size, structural complexity, and extent of sequence conservation have proven to catalyze chemical transformations. Therefore, we speculate that OLE RNAs likewise operate as ribozymes and that they might catalyze a fundamental reaction that has persisted since the RNA World era-a time before the emergence of proteins in evolution. To seek additional clues regarding the function of OLE RNA, we undertook a computational effort to identify potential protein components of the OLE ribonucleoprotein (RNP) complex or other proteins that have functional links to this device. This analysis revealed known protein partners and several additional proteins that might be physically or functionally linked to the OLE RNP complex. Finally, we identified a Mg2+ transporter protein, MpfA, that strongly anticorrelates with the OLE RNP complex. This latter result suggests that MpfA might perform at least some functions that are like those carried out by the OLE RNP complex.
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Affiliation(s)
- Chrishan M Fernando
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Ronald R Breaker
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA
- Howard Hughes Medical Institute, Yale University, New Haven, Connecticut, USA
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Byndloss M, Devkota S, Duca F, Niess JH, Nieuwdorp M, Orho-Melander M, Sanz Y, Tremaroli V, Zhao L. The gut microbiota and diabetes: research, translation, and clinical applications - 2023 Diabetes, Diabetes Care, and Diabetologia Expert Forum. Diabetologia 2024:10.1007/s00125-024-06198-1. [PMID: 38910152 DOI: 10.1007/s00125-024-06198-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 05/23/2024] [Indexed: 06/25/2024]
Abstract
This article summarises the state of the science on the role of the gut microbiota (GM) in diabetes from a recent international expert forum organised by Diabetes, Diabetes Care, and Diabetologia, which was held at the European Association for the Study of Diabetes 2023 Annual Meeting in Hamburg, Germany. Forum participants included clinicians and basic scientists who are leading investigators in the field of the intestinal microbiome and metabolism. Their conclusions were as follows: (1) the GM may be involved in the pathophysiology of type 2 diabetes, as microbially produced metabolites associate both positively and negatively with the disease, and mechanistic links of GM functions (e.g. genes for butyrate production) with glucose metabolism have recently emerged through the use of Mendelian randomisation in humans; (2) the highly individualised nature of the GM poses a major research obstacle, and large cohorts and a deep-sequencing metagenomic approach are required for robust assessments of associations and causation; (3) because single time point sampling misses intraindividual GM dynamics, future studies with repeated measures within individuals are needed; and (4) much future research will be required to determine the applicability of this expanding knowledge to diabetes diagnosis and treatment, and novel technologies and improved computational tools will be important to achieve this goal.
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Affiliation(s)
- Mariana Byndloss
- Vanderbilt University Medical Center, Nashville, TN, USA
- Howard Hughes Medical Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Suzanne Devkota
- Cedars-Sinai Medical Center, Human Microbiome Research Institute, Los Angeles, CA, USA
| | | | - Jan Hendrik Niess
- Department of Biomedicine, University of Basel, Basel, Switzerland
- Department of Gastroenterology and Hepatology, University Digestive Healthcare Center, Clarunis, Basel, Switzerland
| | - Max Nieuwdorp
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Amsterdam, the Netherlands
- Amsterdam Diabeter Center, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Marju Orho-Melander
- Department of Clinical Sciences in Malmö, Lund University Diabetes Centre, Lund University, Malmö, Sweden
| | - Yolanda Sanz
- Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Valencia, Spain.
| | - Valentina Tremaroli
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Liping Zhao
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ, USA
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10
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Ravi J, Anantharaman V, Chen SZ, Brenner EP, Datta P, Aravind L, Gennaro ML. The phage shock protein (PSP) envelope stress response: discovery of novel partners and evolutionary history. mSystems 2024; 9:e0084723. [PMID: 38809013 PMCID: PMC11237479 DOI: 10.1128/msystems.00847-23] [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: 08/28/2023] [Accepted: 03/20/2024] [Indexed: 05/30/2024] Open
Abstract
Bacterial phage shock protein (PSP) systems stabilize the bacterial cell membrane and protect against envelope stress. These systems have been associated with virulence, but despite their critical roles, PSP components are not well characterized outside proteobacteria. Using comparative genomics and protein sequence-structure-function analyses, we systematically identified and analyzed PSP homologs, phyletic patterns, domain architectures, and gene neighborhoods. This approach underscored the evolutionary significance of the system, revealing that its core protein PspA (Snf7 in ESCRT outside bacteria) was present in the last universal common ancestor and that this ancestral functionality has since diversified into multiple novel, distinct PSP systems across life. Several novel partners of the PSP system were identified: (i) the Toastrack domain, likely facilitating assembly of sub-membrane stress-sensing and signaling complexes, (ii) the newly defined HTH-associated α-helical signaling domain-PadR-like transcriptional regulator pair system, and (iii) multiple independent associations with ATPase, CesT/Tir-like chaperone, and Band-7 domains in proteins thought to mediate sub-membrane dynamics. Our work also uncovered links between the PSP components and other domains, such as novel variants of SHOCT-like domains, suggesting roles in assembling membrane-associated complexes of proteins with disparate biochemical functions. Results are available at our interactive web app, https://jravilab.org/psp.IMPORTANCEPhage shock proteins (PSP) are virulence-associated, cell membrane stress-protective systems. They have mostly been characterized in Proteobacteria and Firmicutes. We now show that a minimal PSP system was present in the last universal common ancestor that evolved and diversified into newly identified functional contexts. Recognizing the conservation and evolution of PSP systems across bacterial phyla contributes to our understanding of stress response mechanisms in prokaryotes. Moreover, the newly discovered PSP modularity will likely prompt new studies of lineage-specific cell envelope structures, lifestyles, and adaptation mechanisms. Finally, our results validate the use of domain architecture and genetic context for discovery in comparative genomics.
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Affiliation(s)
- Janani Ravi
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Public Health Research Institute, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - Vivek Anantharaman
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland, USA
| | - Samuel Zorn Chen
- Computer Science Engineering Undergraduate Program, Michigan State University, East Lansing, Michigan, USA
| | - Evan Pierce Brenner
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Pratik Datta
- Public Health Research Institute, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - L. Aravind
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland, USA
| | - Maria Laura Gennaro
- Public Health Research Institute, Rutgers New Jersey Medical School, Newark, New Jersey, USA
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Padalko A, Nair G, Sousa FL. Fusion/fission protein family identification in Archaea. mSystems 2024; 9:e0094823. [PMID: 38700364 PMCID: PMC11237513 DOI: 10.1128/msystems.00948-23] [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: 09/05/2023] [Accepted: 04/02/2024] [Indexed: 05/05/2024] Open
Abstract
The majority of newly discovered archaeal lineages remain without a cultivated representative, but scarce experimental data from the cultivated organisms show that they harbor distinct functional repertoires. To unveil the ecological as well as evolutionary impact of Archaea from metagenomics, new computational methods need to be developed, followed by in-depth analysis. Among them is the genome-wide protein fusion screening performed here. Natural fusions and fissions of genes not only contribute to microbial evolution but also complicate the correct identification and functional annotation of sequences. The products of these processes can be defined as fusion (or composite) proteins, the ones consisting of two or more domains originally encoded by different genes and split proteins, and the ones originating from the separation of a gene in two (fission). Fusion identifications are required for proper phylogenetic reconstructions and metabolic pathway completeness assessments, while mappings between fused and unfused proteins can fill some of the existing gaps in metabolic models. In the archaeal genome-wide screening, more than 1,900 fusion/fission protein clusters were identified, belonging to both newly sequenced and well-studied lineages. These protein families are mainly associated with different types of metabolism, genetic, and cellular processes. Moreover, 162 of the identified fusion/fission protein families are archaeal specific, having no identified fused homolog within the bacterial domain. Our approach was validated by the identification of experimentally characterized fusion/fission cases. However, around 25% of the identified fusion/fission families lack functional annotations for both composite and split states, showing the need for experimental characterization in Archaea.IMPORTANCEGenome-wide fusion screening has never been performed in Archaea on a broad taxonomic scale. The overlay of multiple computational techniques allows the detection of a fine-grained set of predicted fusion/fission families, instead of rough estimations based on conserved domain annotations only. The exhaustive mapping of fused proteins to bacterial organisms allows us to capture fusion/fission families that are specific to archaeal biology, as well as to identify links between bacterial and archaeal lineages based on cooccurrence of taxonomically restricted proteins and their sequence features. Furthermore, the identification of poorly characterized lineage-specific fusion proteins opens up possibilities for future experimental and computational investigations. This approach enhances our understanding of Archaea in general and provides potential candidates for in-depth studies in the future.
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Affiliation(s)
- Anastasiia Padalko
- Genome Evolution and Ecology Group, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Vienna Doctoral School of Ecology and Evolution, University of Vienna, Vienna, Austria
| | - Govind Nair
- Genome Evolution and Ecology Group, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Filipa L. Sousa
- Genome Evolution and Ecology Group, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
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12
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Tsurumaki M, Sato A, Saito M, Kanai A. Comprehensive analysis of insertion sequences within rRNA genes of CPR bacteria and biochemical characterization of a homing endonuclease encoded by these sequences. J Bacteriol 2024:e0007424. [PMID: 38856219 DOI: 10.1128/jb.00074-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 05/11/2024] [Indexed: 06/11/2024] Open
Abstract
The Candidate Phyla Radiation (CPR) represents an extensive bacterial clade comprising primarily uncultured lineages and is distinguished from other bacteria by a significant prevalence of insertion sequences (ISs) within their rRNA genes. However, our understanding of the taxonomic distribution and characteristics of these ISs remains limited. In this study, we used a comprehensive approach to systematically determine the nature of the rRNA ISs in CPR bacteria. The analysis of hundreds of rRNA gene sequences across 65 CPR phyla revealed that ISs are present in 48% of 16S rRNA genes and 82% of 23S rRNA genes, indicating a broad distribution across the CPR clade, with exceptions in the 16S and 23S rRNA genes of Candidatus (Ca.) Saccharibacteria and the 16S rRNA genes of Ca. Peregrinibacteria. Over half the ISs display a group-I-intron-like structure, whereas specific 16S rRNA gene ISs display features reminiscent of group II introns. The ISs frequently encode proteins with homing endonuclease (HE) domains, centered around the LAGLIDADG motif. The LAGLIDADG HE (LHE) proteins encoded by the rRNA ISs of CPR bacteria predominantly have a single-domain structure, deviating from the usual single- or double-domain configuration observed in typical prokaryotic LHEs. Experimental analysis of one LHE protein, I-ShaI from Ca. Shapirobacteria, confirmed that its endonuclease activity targets the DNA sequence of its insertion site, and chemical cross-linking experiments demonstrated its capacity to form homodimers. These results provide robust evidence supporting the hypothesis that the explosive proliferation of rRNA ISs in CPR bacteria was facilitated by mechanisms involving LHEs. IMPORTANCE Insertion sequences (ISs) in rRNA genes are relatively limited and infrequent in most bacterial phyla. With a comprehensive bioinformatic analysis, we show that in CPR bacteria, these ISs occur in 48% of 16S rRNA genes and 82% of 23S rRNA genes. We also report the systematic and biochemical characterization of the LAGLIDADG homing endonucleases (LHEs) encoded by these ISs in the first such analysis of the CPR bacteria. This study significantly extends our understanding of the phylogenetic positions of rRNA ISs within CPR bacteria and the biochemical features of their LHEs.
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Affiliation(s)
- Megumi Tsurumaki
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Asako Sato
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | - Motofumi Saito
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Akio Kanai
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan
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13
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Ameer A, Saleem F, Keating C, Gundogdu O, Ijaz UZ, Javed S. Dataset of 130 metagenome-assembled genomes of healthy and diseased broiler chicken caeca from Pakistan. Data Brief 2024; 54:110487. [PMID: 38764451 PMCID: PMC11098793 DOI: 10.1016/j.dib.2024.110487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 04/23/2024] [Accepted: 04/25/2024] [Indexed: 05/21/2024] Open
Abstract
This article presents metagenomic-assembled genomes (MAGs) of prokaryotic organisms originating from chicken caeca. The samples originate from broiler chickens, one group was infected with Newcastle Disease Virus (NDV) and one uninfected control group. There were four birds per group. Both groups were raised on commercially available antibiotic free feed under a semi-controlled setup. The binning step of the samples identified 130 MAGs with ≥50 % completion, and ≤10 % contamination. The data presented includes sequences in FASTA format, tables of functional annotation of genes, and data from two different approaches for phylogenetic tree construction using these MAGs. Major geochemical cycles at community level including carbon, sulfur, and nitrogen cycles are also presented.
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Affiliation(s)
- Aqsa Ameer
- Department of Biosciences, COMSATS University Islamabad, Pakistan
- Water & Environment Research Group, University of Glasgow, Mazumdar-Shaw Advanced Research Centre, Glasgow, UK
| | - Farrukh Saleem
- Department of Biosciences, COMSATS University Islamabad, Pakistan
| | - Ciara Keating
- Department of Engineering, Durham University, Durham, DH1 3LE, UK
- School of Biodiversity, One Health, and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Ozan Gundogdu
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Umer Zeeshan Ijaz
- Water & Environment Research Group, University of Glasgow, Mazumdar-Shaw Advanced Research Centre, Glasgow, UK
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
- College of Science and Engineering, University of Galway, Ireland
| | - Sundus Javed
- Department of Biosciences, COMSATS University Islamabad, Pakistan
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14
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Tschitschko B, Esti M, Philippi M, Kidane AT, Littmann S, Kitzinger K, Speth DR, Li S, Kraberg A, Tienken D, Marchant HK, Kartal B, Milucka J, Mohr W, Kuypers MMM. Rhizobia-diatom symbiosis fixes missing nitrogen in the ocean. Nature 2024; 630:899-904. [PMID: 38723661 PMCID: PMC11208148 DOI: 10.1038/s41586-024-07495-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 04/30/2024] [Indexed: 06/21/2024]
Abstract
Nitrogen (N2) fixation in oligotrophic surface waters is the main source of new nitrogen to the ocean1 and has a key role in fuelling the biological carbon pump2. Oceanic N2 fixation has been attributed almost exclusively to cyanobacteria, even though genes encoding nitrogenase, the enzyme that fixes N2 into ammonia, are widespread among marine bacteria and archaea3-5. Little is known about these non-cyanobacterial N2 fixers, and direct proof that they can fix nitrogen in the ocean has so far been lacking. Here we report the discovery of a non-cyanobacterial N2-fixing symbiont, 'Candidatus Tectiglobus diatomicola', which provides its diatom host with fixed nitrogen in return for photosynthetic carbon. The N2-fixing symbiont belongs to the order Rhizobiales and its association with a unicellular diatom expands the known hosts for this order beyond the well-known N2-fixing rhizobia-legume symbioses on land6. Our results show that the rhizobia-diatom symbioses can contribute as much fixed nitrogen as can cyanobacterial N2 fixers in the tropical North Atlantic, and that they might be responsible for N2 fixation in the vast regions of the ocean in which cyanobacteria are too rare to account for the measured rates.
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Affiliation(s)
- Bernhard Tschitschko
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria
| | - Mertcan Esti
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Miriam Philippi
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Abiel T Kidane
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Sten Littmann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Katharina Kitzinger
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Daan R Speth
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Shengjie Li
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Alexandra Kraberg
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Daniela Tienken
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Hannah K Marchant
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM - Centre for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Boran Kartal
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- School of Science, Constructor University, Bremen, Germany
| | - Jana Milucka
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Wiebke Mohr
- Max Planck Institute for Marine Microbiology, Bremen, Germany
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15
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Cockell CS, Hallsworth JE, McMahon S, Kane SR, Higgins PM. The Concept of Life on Venus Informs the Concept of Habitability. ASTROBIOLOGY 2024; 24:628-634. [PMID: 38800952 DOI: 10.1089/ast.2023.0106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
An enduring question in astrobiology is how we assess extraterrestrial environments as being suitable for life. We suggest that the most reliable assessments of the habitability of extraterrestrial environments are made with respect to the empirically determined limits to known life. We discuss qualitatively distinct categories of habitability: empirical habitability that is constrained by the observed limits to biological activity; habitability sensu stricto, which is defined with reference to the known or unknown limits to the activity of all known organisms; and habitability sensu lato (habitability in the broadest sense), which is circumscribed by the limit of all possible life in the universe, which is the most difficult (and perhaps impossible) to determine. We use the cloud deck of Venus, which is temperate but incompatible with known life, as an example to elaborate and hypothesize on these limits.
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Affiliation(s)
- Charles S Cockell
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, United Kingdom
| | - John E Hallsworth
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, United Kingdom
| | - Sean McMahon
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, United Kingdom
| | - Stephen R Kane
- Department of Earth and Planetary Sciences, University of California, Riverside, California, USA
| | - Peter M Higgins
- Department of Earth Sciences, University of Toronto, Toronto, Canada
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16
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Saleem F, Ameer A, Star-Shirko B, Keating C, Gundogdu O, Ijaz UZ, Javed S. Dataset of 569 metagenome-assembled genomes from the caeca of multiple chicken breeds from commercial and backyard farming setups of Pakistan. Data Brief 2024; 54:110552. [PMID: 38882194 PMCID: PMC11177053 DOI: 10.1016/j.dib.2024.110552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 05/14/2024] [Accepted: 05/18/2024] [Indexed: 06/18/2024] Open
Abstract
This article focuses the recovery of prokaryotic organisms including bacteria and archaea from 9 different groups of chicken raised in different farm setups in Pakistan. The groups comprise of three different breeds (Broilers, White Layers, and Black Australorp) of chicken raised in different farming setups that include antibiotic-free control, commercial (open and controlled shed), and backyard farms. We have recovered 569 Metagenomics-Assembled Genomes (MAGs) with a completeness of ≥50 % and contamination of ≤10 %. For each MAG, functional annotations were obtained that include KEGG modules, carbohydrate active enzymes (CAZymes), peptidases, geochemical cycles, antibiotic resistance genes, stress genes, and virulence genes. Furthermore, two different sets of Single Copy Genes (SCGs) were used to construct the phylogenetic trees. Based on the reconstructed phylogeny, phylogenetic gain of each MAG is calculated to give an account of novelty.
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Affiliation(s)
- Farrukh Saleem
- Department of Biosciences, COMSATS University Islamabad, Pakistan
| | - Aqsa Ameer
- Department of Biosciences, COMSATS University Islamabad, Pakistan
- Water & Environment Research Group, University of Glasgow, Mazumdar-Shaw Advanced Research Centre, Glasgow, United Kingdom
| | - Banaz Star-Shirko
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Ciara Keating
- Department of Engineering, Durham University, Durham, DH1 3LE, United Kingdom
- School of Biodiversity, One Health, and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Ozan Gundogdu
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Umer Zeeshan Ijaz
- Water & Environment Research Group, University of Glasgow, Mazumdar-Shaw Advanced Research Centre, Glasgow, United Kingdom
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom
- College of Science and Engineering, University of Galway, Ireland
| | - Sundus Javed
- Department of Biosciences, COMSATS University Islamabad, Pakistan
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17
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Zhang S, Sun A, Qian JM, Lin S, Xing W, Yang Y, Zhu HZ, Zhou XY, Guo YS, Liu Y, Meng Y, Jin SL, Song W, Li CP, Li Z, Jin S, Wang JH, Dong MQ, Gao C, Chen C, Bai Y, Liu JJG. Pro-CRISPR PcrIIC1-associated Cas9 system for enhanced bacterial immunity. Nature 2024; 630:484-492. [PMID: 38811729 DOI: 10.1038/s41586-024-07486-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 04/29/2024] [Indexed: 05/31/2024]
Abstract
The CRISPR system is an adaptive immune system found in prokaryotes that defends host cells against the invasion of foreign DNA1. As part of the ongoing struggle between phages and the bacterial immune system, the CRISPR system has evolved into various types, each with distinct functionalities2. Type II Cas9 is the most extensively studied of these systems and has diverse subtypes. It remains uncertain whether members of this family can evolve additional mechanisms to counter viral invasions3,4. Here we identify 2,062 complete Cas9 loci, predict the structures of their associated proteins and reveal three structural growth trajectories for type II-C Cas9. We found that novel associated genes (NAGs) tended to be present within the loci of larger II-C Cas9s. Further investigation revealed that CbCas9 from Chryseobacterium species contains a novel β-REC2 domain, and forms a heterotetrameric complex with an NAG-encoded CRISPR-Cas-system-promoting (pro-CRISPR) protein of II-C Cas9 (PcrIIC1). The CbCas9-PcrIIC1 complex exhibits enhanced DNA binding and cleavage activity, broader compatibility for protospacer adjacent motif sequences, increased tolerance for mismatches and improved anti-phage immunity, compared with stand-alone CbCas9. Overall, our work sheds light on the diversity and 'growth evolutionary' trajectories of II-C Cas9 proteins at the structural level, and identifies many NAGs-such as PcrIIC1, which serves as a pro-CRISPR factor to enhance CRISPR-mediated immunity.
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Affiliation(s)
- Shouyue Zhang
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Ao Sun
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jing-Mei Qian
- State Key Laboratory of Plant Genomics, CAS-JIC Centre of Excellence for Plant and Microbial Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Shuo Lin
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Wenjing Xing
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yun Yang
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Han-Zhou Zhu
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xin-Yi Zhou
- State Key Laboratory of Plant Genomics, CAS-JIC Centre of Excellence for Plant and Microbial Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yan-Shuo Guo
- State Key Laboratory of Plant Genomics, CAS-JIC Centre of Excellence for Plant and Microbial Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yun Liu
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yu Meng
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Shu-Lin Jin
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Wenhao Song
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Cheng-Ping Li
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Zhaofu Li
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Shuai Jin
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Jian-Hua Wang
- National Institute of Biological Sciences, Beijing, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
| | - Caixia Gao
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Chunlai Chen
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.
| | - Yang Bai
- State Key Laboratory of Plant Genomics, CAS-JIC Centre of Excellence for Plant and Microbial Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing, China.
| | - Jun-Jie Gogo Liu
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.
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18
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Rodríguez-Cruz UE, Castelán-Sánchez HG, Madrigal-Trejo D, Eguiarte LE, Souza V. Uncovering novel bacterial and archaeal diversity: genomic insights from metagenome-assembled genomes in Cuatro Cienegas, Coahuila. Front Microbiol 2024; 15:1369263. [PMID: 38873164 PMCID: PMC11169877 DOI: 10.3389/fmicb.2024.1369263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 05/03/2024] [Indexed: 06/15/2024] Open
Abstract
A comprehensive study was conducted in the Cuatro Ciénegas Basin (CCB) in Coahuila, Mexico, which is known for its diversity of microorganisms and unique physicochemical properties. The study focused on the "Archaean Domes" (AD) site in the CCB, which is characterized by an abundance of hypersaline, non-lithifying microbial mats. In AD, we analyzed the small domes and circular structures using metagenome assembly genomes (MAGs) with the aim of expanding our understanding of the prokaryotic tree of life by uncovering previously unreported lineages, as well as analyzing the diversity of bacteria and archaea in the CCB. A total of 325 MAGs were identified, including 48 Archaea and 277 Bacteria. Remarkably, 22 archaea and 104 bacteria could not be classified even at the genus level, highlighting the remarkable novel diversity of the CCB. Besides, AD site exhibited significant diversity at the phylum level, with Proteobacteria being the most abundant, followed by Desulfobacteria, Spirochaetes, Bacteroidetes, Nanoarchaeota, Halobacteriota, Cyanobacteria, Planctomycetota, Verrucomicrobiota, Actinomycetes and Chloroflexi. In Archaea, the monophyletic groups of MAGs belonged to the Archaeoglobi, Aenigmarchaeota, Candidate Nanoarchaeota, and Halobacteriota. Among Bacteria, monophyletic groups were also identified, including Spirochaetes, Proteobacteria, Planctomycetes, Actinobacteria, Verrucomicrobia, Bacteroidetes, Candidate Bipolaricaulota, Desulfobacteria, and Cyanobacteria. These monophyletic groups were possibly influenced by geographic isolation, as well as the extreme and fluctuating environmental conditions in the pond AD, such as stoichiometric imbalance of C:N:P of 122:42:1, fluctuating pH (5-9.8) and high salinity (5.28% to saturation).
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Affiliation(s)
- Ulises E. Rodríguez-Cruz
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | | | - David Madrigal-Trejo
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Luis E. Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Valeria Souza
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- Centro de Estudios del Cuaternario de Fuego, Patagonia y Antártica (CEQUA), Punta Arenas, Chile
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19
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Masuda Y, Mise K, Xu Z, Zhang Z, Shiratori Y, Senoo K, Itoh H. Global soil metagenomics reveals distribution and predominance of Deltaproteobacteria in nitrogen-fixing microbiome. MICROBIOME 2024; 12:95. [PMID: 38790049 PMCID: PMC11127431 DOI: 10.1186/s40168-024-01812-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 04/09/2024] [Indexed: 05/26/2024]
Abstract
BACKGROUND Biological nitrogen fixation is a fundamental process sustaining all life on earth. While distribution and diversity of N2-fixing soil microbes have been investigated by numerous PCR amplicon sequencing of nitrogenase genes, their comprehensive understanding has been hindered by lack of de facto standard protocols for amplicon surveys and possible PCR biases. Here, by fully leveraging the planetary collections of soil shotgun metagenomes along with recently expanded culture collections, we evaluated the global distribution and diversity of terrestrial diazotrophic microbiome. RESULTS After the extensive analysis of 1,451 soil metagenomic samples, we revealed that the Anaeromyxobacteraceae and Geobacteraceae within Deltaproteobacteria are ubiquitous groups of diazotrophic microbiome in the soils with different geographic origins and land usage types, with particular predominance in anaerobic soils (paddy soils and sediments). CONCLUSION Our results indicate that Deltaproteobacteria is a core bacterial taxon in the potential soil nitrogen fixation population, especially in anaerobic environments, which encourages a careful consideration on deltaproteobacterial diazotrophs in understanding terrestrial nitrogen cycling. Video Abstract.
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Affiliation(s)
- Yoko Masuda
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
| | - Kazumori Mise
- National Institute of Advanced Industrial Science and Technology (AIST) Hokkaido, 2-17-2-1 Tsukisamu-higashi, Toyohira, Sapporo, Hokkaido, 062-8517, Japan.
| | - Zhenxing Xu
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Zhengcheng Zhang
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yutaka Shiratori
- Niigata Agricultural Research Institute, 857 Nagakura-machi, Nagaoka, Niigata, 940-0826, Japan
| | - Keishi Senoo
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Hideomi Itoh
- National Institute of Advanced Industrial Science and Technology (AIST) Hokkaido, 2-17-2-1 Tsukisamu-higashi, Toyohira, Sapporo, Hokkaido, 062-8517, Japan.
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20
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Dewar AE, Hao C, Belcher LJ, Ghoul M, West SA. Bacterial lifestyle shapes pangenomes. Proc Natl Acad Sci U S A 2024; 121:e2320170121. [PMID: 38743630 PMCID: PMC11126918 DOI: 10.1073/pnas.2320170121] [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: 11/16/2023] [Accepted: 04/06/2024] [Indexed: 05/16/2024] Open
Abstract
Pangenomes vary across bacteria. Some species have fluid pangenomes, with a high proportion of genes varying between individual genomes. Other species have less fluid pangenomes, with different genomes tending to contain the same genes. Two main hypotheses have been suggested to explain this variation: differences in species' bacterial lifestyle and effective population size. However, previous studies have not been able to test between these hypotheses because the different features of lifestyle and effective population size are highly correlated with each other, and phylogenetically conserved, making it hard to disentangle their relative importance. We used phylogeny-based analyses, across 126 bacterial species, to tease apart the causal role of different factors. We found that pangenome fluidity was lower in i) host-associated compared with free-living species and ii) host-associated species that are obligately dependent on a host, live inside cells, and are more pathogenic and less motile. In contrast, we found no support for the competing hypothesis that larger effective population sizes lead to more fluid pangenomes. Effective population size appears to correlate with pangenome variation because it is also driven by bacterial lifestyle, rather than because of a causal relationship.
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Affiliation(s)
- Anna E. Dewar
- Department of Biology, University of Oxford, OxfordOX1 3SZ, United Kingdom
| | - Chunhui Hao
- Department of Biology, University of Oxford, OxfordOX1 3SZ, United Kingdom
| | | | - Melanie Ghoul
- Department of Biology, University of Oxford, OxfordOX1 3SZ, United Kingdom
| | - Stuart A. West
- Department of Biology, University of Oxford, OxfordOX1 3SZ, United Kingdom
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21
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Zou Y, Zhang Z, Zeng Y, Hu H, Hao Y, Huang S, Li B. Common Methods for Phylogenetic Tree Construction and Their Implementation in R. Bioengineering (Basel) 2024; 11:480. [PMID: 38790347 PMCID: PMC11117635 DOI: 10.3390/bioengineering11050480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 05/04/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
A phylogenetic tree can reflect the evolutionary relationships between species or gene families, and they play a critical role in modern biological research. In this review, we summarize common methods for constructing phylogenetic trees, including distance methods, maximum parsimony, maximum likelihood, Bayesian inference, and tree-integration methods (supermatrix and supertree). Here we discuss the advantages, shortcomings, and applications of each method and offer relevant codes to construct phylogenetic trees from molecular data using packages and algorithms in R. This review aims to provide comprehensive guidance and reference for researchers seeking to construct phylogenetic trees while also promoting further development and innovation in this field. By offering a clear and concise overview of the different methods available, we hope to enable researchers to select the most appropriate approach for their specific research questions and datasets.
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Affiliation(s)
- Yue Zou
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China; (Y.Z.); (Z.Z.); (Y.Z.); (H.H.); (Y.H.)
| | - Zixuan Zhang
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China; (Y.Z.); (Z.Z.); (Y.Z.); (H.H.); (Y.H.)
| | - Yujie Zeng
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China; (Y.Z.); (Z.Z.); (Y.Z.); (H.H.); (Y.H.)
| | - Hanyue Hu
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China; (Y.Z.); (Z.Z.); (Y.Z.); (H.H.); (Y.H.)
| | - Youjin Hao
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China; (Y.Z.); (Z.Z.); (Y.Z.); (H.H.); (Y.H.)
| | - Sheng Huang
- Animal Nutrition Institute, Chongqing Academy of Animal Science, Chongqing 402460, China
| | - Bo Li
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China; (Y.Z.); (Z.Z.); (Y.Z.); (H.H.); (Y.H.)
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22
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Cui Z, Li Y, Jing X, Luan X, Liu N, Liu J, Meng Y, Xu J, Valentine DL. Cycloalkane degradation by an uncultivated novel genus of Gammaproteobacteria derived from China's marginal seas. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:133904. [PMID: 38422739 DOI: 10.1016/j.jhazmat.2024.133904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 01/30/2024] [Accepted: 02/25/2024] [Indexed: 03/02/2024]
Abstract
The consumption of cycloalkanes is prevalent in low-temperature marine environments, likely influenced by psychrophilic microorganisms. Despite their significance, the primary active species responsible for marine cycloalkane degradation remain largely unidentified due to cultivation challenges. In this study, we provide compelling evidence indicating that the uncultured genus C1-B045 of Gammaproteobacteria is a pivotal participant in cycloalkane decomposition within China's marginal seas. Notably, the relative abundance of C1-B045 surged from 15.9% in the methylcyclohexane (MCH)-consuming starter culture to as high as 97.5% in MCH-utilizing extinction cultures following successive dilution-to-extinction and incubation cycles. We used stable isotope probing, Raman-activated gravity-driven encapsulation, and 16 S rRNA gene sequencing to link cycloalkane-metabolizing phenotype to genotype at the single-cell level. By annotating key enzymes (e.g., alkane monooxygenase, cyclohexanone monooxygenase, and 6-hexanolactone hydrolase) involved in MCH metabolism within C1-B045's representative metagenome-assembled genome, we developed a putative MCH degradation pathway.
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Affiliation(s)
- Zhisong Cui
- Marine Bioresource and Environment Research Center, Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources of China, Qingdao 266061, People's Republic of China.
| | - Yingchao Li
- Marine Bioresource and Environment Research Center, Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources of China, Qingdao 266061, People's Republic of China
| | - Xiaoyan Jing
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, People's Republic of China
| | - Xiao Luan
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing 100048, People's Republic of China
| | - Na Liu
- Department of Earth Science and Marine Science Institute, University of California, Santa Barbara, CA 93106, USA
| | - Jinyan Liu
- Marine Bioresource and Environment Research Center, Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources of China, Qingdao 266061, People's Republic of China
| | - Yu Meng
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, People's Republic of China
| | - Jian Xu
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, People's Republic of China
| | - David L Valentine
- Department of Earth Science and Marine Science Institute, University of California, Santa Barbara, CA 93106, USA.
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23
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de la Fuente I, Manzano-Morales S, Sanz D, Prieto A, Barriuso J. Quorum sensing in bacteria: in silico protein analysis, ecophysiology, and reconstruction of their evolutionary history. BMC Genomics 2024; 25:441. [PMID: 38702600 PMCID: PMC11069264 DOI: 10.1186/s12864-024-10355-6] [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: 01/31/2024] [Accepted: 04/25/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND Quorum sensing (QS) is a sophisticated cell-to-cell signalling mechanism that allows the coordination of important processes in microbial populations. The AI-1 and AI-2 autoinducer systems are among the best characterized bacterial QS systems at the genetic level. RESULTS In this study, we present data derived from in silico screening of QS proteins from bacterial genomes available in public databases. Sequence analyses allowed identifying candidate sequences of known QS systems that were used to build phylogenetic trees. Eight categories were established according to the number of genes from the two major QS systems present in each genome, revealing a correlation with specific taxa, lifestyles or metabolic traits. Many species had incomplete QS systems, encoding the receptor protein but not the biosynthesis of the quorum sensing molecule (QSMs). Reconstruction of the evolutionary history of the LuxR family and prediction of the 3D structure of the ancestral protein suggested their monomeric configuration in the absence of the signal molecule and the presence of a cavity for its binding. CONCLUSIONS Here we correlate the taxonomic affiliation and lifestyle of bacteria from different genera with the QS systems encoded in their genomes. Moreover, we present the first ancestral reconstruction of the LuxR QS receptors, providing further insight in their evolutionary history.
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Affiliation(s)
- Iñigo de la Fuente
- Centro de Investigaciones Biológicas (CIB Margarita Salas), Department of Microbial and Plant Biotechnology, Consejo Superior de Investigaciones Científicas (CSIC), Ramiro de Maeztu 9, Madrid, 28040, Spain
| | - Saioa Manzano-Morales
- Centro de Investigaciones Biológicas (CIB Margarita Salas), Department of Microbial and Plant Biotechnology, Consejo Superior de Investigaciones Científicas (CSIC), Ramiro de Maeztu 9, Madrid, 28040, Spain
| | - David Sanz
- Centro de Investigaciones Biológicas (CIB Margarita Salas), Department of Microbial and Plant Biotechnology, Consejo Superior de Investigaciones Científicas (CSIC), Ramiro de Maeztu 9, Madrid, 28040, Spain
| | - Alicia Prieto
- Centro de Investigaciones Biológicas (CIB Margarita Salas), Department of Microbial and Plant Biotechnology, Consejo Superior de Investigaciones Científicas (CSIC), Ramiro de Maeztu 9, Madrid, 28040, Spain
| | - Jorge Barriuso
- Centro de Investigaciones Biológicas (CIB Margarita Salas), Department of Microbial and Plant Biotechnology, Consejo Superior de Investigaciones Científicas (CSIC), Ramiro de Maeztu 9, Madrid, 28040, Spain.
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24
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Liao T, Wang S, Zhang H, Stüeken EE, Luo H. Dating Ammonia-Oxidizing Bacteria with Abundant Eukaryotic Fossils. Mol Biol Evol 2024; 41:msae096. [PMID: 38776415 PMCID: PMC11135946 DOI: 10.1093/molbev/msae096] [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: 01/09/2024] [Revised: 04/21/2024] [Accepted: 05/14/2024] [Indexed: 05/25/2024] Open
Abstract
Evolution of a complete nitrogen (N) cycle relies on the onset of ammonia oxidation, which aerobically converts ammonia to nitrogen oxides. However, accurate estimation of the antiquity of ammonia-oxidizing bacteria (AOB) remains challenging because AOB-specific fossils are absent and bacterial fossils amenable to calibrate molecular clocks are rare. Leveraging the ancient endosymbiosis of mitochondria and plastid, as well as using state-of-the-art Bayesian sequential dating approach, we obtained a timeline of AOB evolution calibrated largely by eukaryotic fossils. We show that the first AOB evolved in marine Gammaproteobacteria (Gamma-AOB) and emerged between 2.1 and 1.9 billion years ago (Ga), thus postdating the Great Oxidation Event (GOE; 2.4 to 2.32 Ga). To reconcile the sedimentary N isotopic signatures of ammonia oxidation occurring near the GOE, we propose that ammonia oxidation likely occurred at the common ancestor of Gamma-AOB and Gammaproteobacterial methanotrophs, or the actinobacterial/verrucomicrobial methanotrophs which are known to have ammonia oxidation activities. It is also likely that nitrite was transported from the terrestrial habitats where ammonia oxidation by archaea took place. Further, we show that the Gamma-AOB predated the anaerobic ammonia-oxidizing (anammox) bacteria, implying that the emergence of anammox was constrained by the availability of dedicated ammonia oxidizers which produce nitrite to fuel anammox. Our work supports a new hypothesis that N redox cycle involving nitrogen oxides evolved rather late in the ocean.
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Affiliation(s)
- Tianhua Liao
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - Sishuo Wang
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - Hao Zhang
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - Eva E Stüeken
- School of Earth and Environmental Sciences and Centre for Exoplanet Science, University of St Andrews, Queen's Terrace, KY16 9TS, UK
| | - Haiwei Luo
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
- Earth and Environmental Sciences Programme, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
- Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
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25
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Boden JS, Zhong J, Anderson RE, Stüeken EE. Timing the evolution of phosphorus-cycling enzymes through geological time using phylogenomics. Nat Commun 2024; 15:3703. [PMID: 38697988 PMCID: PMC11066067 DOI: 10.1038/s41467-024-47914-0] [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: 08/20/2023] [Accepted: 04/11/2024] [Indexed: 05/05/2024] Open
Abstract
Phosphorus plays a crucial role in controlling biological productivity, but geological estimates of phosphate concentrations in the Precambrian ocean, during life's origin and early evolution, vary over several orders of magnitude. While reduced phosphorus species may have served as alternative substrates to phosphate, their bioavailability on the early Earth remains unknown. Here, we reconstruct the phylogenomic record of life on Earth and find that phosphate transporting genes (pnas) evolved in the Paleoarchean (ca. 3.6-3.2 Ga) and are consistent with phosphate concentrations above modern levels ( > 3 µM). The first gene optimized for low phosphate levels (pstS; <1 µM) appeared around the same time or in the Mesoarchean depending on the reconstruction method. Most enzymatic pathways for metabolising reduced phosphorus emerged and expanded across the tree of life later. This includes phosphonate-catabolising CP-lyases, phosphite-oxidising pathways and hypophosphite-oxidising pathways. CP-lyases are particularly abundant in dissolved phosphate concentrations below 0.1 µM. Our results thus indicate at least local regions of declining phosphate levels through the Archean, possibly linked to phosphate-scavenging Fe(III), which may have limited productivity. However, reduced phosphorus species did not become widely used until after the Paleoproterozoic Great Oxidation Event (2.3 Ga), possibly linked to expansion of the biosphere at that time.
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Affiliation(s)
- Joanne S Boden
- School of Earth and Environmental Sciences, University of St. Andrews, Bute Building, Queen's terrace, St. Andrews, Fife, United Kingdom.
| | - Juntao Zhong
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Rika E Anderson
- Department of Biology, Carleton College, Northfield, MN, USA
| | - Eva E Stüeken
- School of Earth and Environmental Sciences, University of St. Andrews, Bute Building, Queen's terrace, St. Andrews, Fife, United Kingdom
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26
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Owens SL, Ahmed SR, Lang Harman RM, Stewart LE, Mori S. Natural Products That Contain Higher Homologated Amino Acids. Chembiochem 2024; 25:e202300822. [PMID: 38487927 DOI: 10.1002/cbic.202300822] [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: 12/04/2023] [Revised: 03/13/2024] [Indexed: 04/11/2024]
Abstract
This review focuses on discussing natural products (NPs) that contain higher homologated amino acids (homoAAs) in the structure as well as the proposed and characterized biosynthesis of these non-proteinogenic amino acids. Homologation of amino acids includes the insertion of a methylene group into its side chain. It is not a very common modification found in NP biosynthesis as approximately 450 homoAA-containing NPs have been isolated from four bacterial phyla (Cyanobacteria, Actinomycetota, Myxococcota, and Pseudomonadota), two fungal phyla (Ascomycota and Basidiomycota), and one animal phylum (Porifera), except for a few examples. Amino acids that are found to be homologated and incorporated in the NP structures include the following ten amino acids: alanine, arginine, cysteine, isoleucine, glutamic acid, leucine, phenylalanine, proline, serine, and tyrosine, where isoleucine, leucine, phenylalanine, and tyrosine share the comparable enzymatic pathway. Other amino acids have their individual homologation pathway (arginine, proline, and glutamic acid for bacteria), likely utilize the primary metabolic pathway (alanine and glutamic acid for fungi), or have not been reported (cysteine and serine). Despite its possible high potential in the drug discovery field, the biosynthesis of homologated amino acids has a large room to explore for future combinatorial biosynthesis and metabolic engineering purpose.
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Affiliation(s)
- Skyler L Owens
- Department of Chemistry and Biochemistry, Augusta University, 1120 15th Street, Augusta, GA 30912
| | - Shopno R Ahmed
- Department of Chemistry and Biochemistry, Augusta University, 1120 15th Street, Augusta, GA 30912
| | - Rebecca M Lang Harman
- Department of Chemistry and Biochemistry, Augusta University, 1120 15th Street, Augusta, GA 30912
| | - Laura E Stewart
- Department of Chemistry and Biochemistry, Augusta University, 1120 15th Street, Augusta, GA 30912
| | - Shogo Mori
- Department of Chemistry and Biochemistry, Augusta University, 1120 15th Street, Augusta, GA 30912
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27
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Gómez-Márquez J. The Lithbea Domain. Adv Biol (Weinh) 2024; 8:e2300679. [PMID: 38386280 DOI: 10.1002/adbi.202300679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 02/09/2024] [Indexed: 02/23/2024]
Abstract
The tree of life is the evolutionary metaphor for the past and present connections of all cellular organisms. Today, to speak of biodiversity is not only to speak of archaea, bacteria, and eukaryotes, but they should also consider the "new biodiversity" that includes viruses and synthetic organisms, which represent the new forms of life created in laboratories. There is even a third group of artificial entities that, although not living systems, pretend to imitate the living. To embrace and organize all this new biodiversity, I propose the creation of a new domain, with the name Lithbea (from life-on-the-border entites) The criteria for inclusion as members of Lithbea are: i) the acellular nature of the living system, ii) its origin in laboratory manipulation, iii) showing new biological traits, iv) the presence of exogenous genetic elements, v) artificial or inorganic nature. Within Lithbea there are two subdomains: Virworld (from virus world) which includes all viruses, regarded as lifeless living systems, and classified according to the International Committee on Taxonomy of Viruses (ICTV), and ii) Humade (from human-made) which includes all synthetic organisms and artificial entities. The relationships of Lithbea members to the three classical woesian domains and their implications are briefly discussed.
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Affiliation(s)
- Jaime Gómez-Márquez
- Department of Biochemistry and Molecular Biology, University of Santiago de Compostela, Santiago de Compostela, Galicia, 15782, Spain
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28
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McCoy JA, Burris HH, Gerson KD, McCarthy C, Ravel J, Elovitz MA. Cervicovaginal Microbial-Immune State and Group B Streptococcus Colonization in Pregnancy. Am J Perinatol 2024; 41:e2539-e2546. [PMID: 37557898 PMCID: PMC10853487 DOI: 10.1055/s-0043-1772226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
OBJECTIVE Maternal colonization with Group B Streptococcus (GBS) is a significant risk factor for serious neonatal morbidity. There are limited data on how the cervicovaginal (CV) microbiota and host immune factor β-defensin-2 might influence GBS colonization in pregnant individuals. This study sought to determine if the CV microbiota is associated with GBS colonization in pregnant individuals, and if β-defensin-2 modifies this relationship. STUDY DESIGN This was a secondary analysis of a prospective cohort study of pregnant individuals with singleton pregnancies who had CV microbiota specimens analyzed at 16 to 20, 20 to 24, and 24 to 28 weeks' gestation, along with a third trimester GBS rectovaginal (RV) culture (n = 492). Microbiota data were analyzed with 16S rRNA gene sequencing and classified into community state types (CSTs). Log-binomial multivariable regression was used to model associations between CST and GBS RV status and to calculate risk ratios. β-defensin-2, an immune factor known to modulate the relationship between CST and pregnancy outcomes, was examined as an effect modifier. RESULTS Of 492 individuals, 34.3% were GBS RV + . Compared with individuals with CST I at 16 to 20 weeks, individuals with CST IV-A and CST II had a significantly elevated relative risk of subsequent GBS RV+ status. When stratified by high and low β-defensin-2 levels, β-defensin-2 was found to be an effect modifier of the association between CST IV-A and GBS RV+ status. In individuals with low β-defensin-2 levels, CST VI-A was associated with GBS RV+ status, but among individuals with high β-defensin-2 levels, there was no such association (interaction p-value = 0.03). CONCLUSION Pregnant individuals with CV microbiota characterized by CST IV-A and CST II had significantly elevated risk of GBS RV colonization in the third trimester compared with those with CST I, and β-defensin-2 was an effect modifier of the association between CST IV-A and GBS RV+ status. Future research should investigate if manipulation of the CV microbiota can prevent GBS colonization, thereby reducing intrapartum antibiotic prophylaxis and the risks of neonatal GBS infection. KEY POINTS · The relationship between the CV microbiota and GBS RV colonization is unknown.. · A Lactobacillus-deficient, anaerobic rich vaginal community, CST IV-A, is associated with increased risk of GBS RV colonization.. · β-defensin-2 is an effect modifier of the association between CST IV-A and GBS RV+ status..
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Affiliation(s)
- Jennifer A. McCoy
- Department of OB/GYN, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Heather H. Burris
- Department of OB/GYN, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Kristin D. Gerson
- Department of OB/GYN, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Clare McCarthy
- Department of OB/GYN, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jacques Ravel
- Department of Microbiology and Immunology, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland
| | - Michal A. Elovitz
- Department of Obstetrics, Gynecology and Reproductive Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
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29
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Mulay SA, Hahn CR, Klingeman DM, Elshahed MS, Youssef NH, Podar M. Metagenomic sequencing of a Patescibacteria-containing enrichment from Zodletone spring in Oklahoma, USA. Microbiol Resour Announc 2024; 13:e0011424. [PMID: 38497626 PMCID: PMC11008151 DOI: 10.1128/mra.00114-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 03/06/2024] [Indexed: 03/19/2024] Open
Abstract
An enrichment of sulfidic sediments from Zodletone spring was sequenced as a metagenome. Draft genomes representing Cloacimonadota, Deltabacterota, Firmicutes, and Patescibacteria were binned and annotated and will aid functional genomics and cultivation efforts.
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Affiliation(s)
- Sayali A. Mulay
- Department of Microbiology, University of Tennessee Knoxville, Knoxville, Tennessee, USA
| | - C. Ryan Hahn
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Dawn M. Klingeman
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Mostafa S. Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Noha H. Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Mircea Podar
- Department of Microbiology, University of Tennessee Knoxville, Knoxville, Tennessee, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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30
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Frey B, Aiesi M, Rast BM, Rüthi J, Julmi J, Stierli B, Qi W, Brunner I. Searching for new plastic-degrading enzymes from the plastisphere of alpine soils using a metagenomic mining approach. PLoS One 2024; 19:e0300503. [PMID: 38578779 PMCID: PMC10997104 DOI: 10.1371/journal.pone.0300503] [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: 01/03/2024] [Accepted: 02/28/2024] [Indexed: 04/07/2024] Open
Abstract
Plastic materials, including microplastics, accumulate in all types of ecosystems, even in remote and cold environments such as the European Alps. This pollution poses a risk for the environment and humans and needs to be addressed. Using shotgun DNA metagenomics of soils collected in the eastern Swiss Alps at about 3,000 m a.s.l., we identified genes and their proteins that potentially can degrade plastics. We screened the metagenomes of the plastisphere and the bulk soil with a differential abundance analysis, conducted similarity-based screening with specific databases dedicated to putative plastic-degrading genes, and selected those genes with a high probability of signal peptides for extracellular export and a high confidence for functional domains. This procedure resulted in a final list of nine candidate genes. The lengths of the predicted proteins were between 425 and 845 amino acids, and the predicted genera producing these proteins belonged mainly to Caballeronia and Bradyrhizobium. We applied functional validation, using heterologous expression followed by enzymatic assays of the supernatant. Five of the nine proteins tested showed significantly increased activities when we used an esterase assay, and one of these five proteins from candidate genes, a hydrolase-type esterase, clearly had the highest activity, by more than double. We performed the fluorescence assays for plastic degradation of the plastic types BI-OPL and ecovio® only with proteins from the five candidate genes that were positively active in the esterase assay, but like the negative controls, these did not show any significantly increased activity. In contrast, the activity of the positive control, which contained a PLA-degrading gene insert known from the literature, was more than 20 times higher than that of the negative controls. These findings suggest that in silico screening followed by functional validation is suitable for finding new plastic-degrading enzymes. Although we only found one new esterase enzyme, our approach has the potential to be applied to any type of soil and to plastics in various ecosystems to search rapidly and efficiently for new plastic-degrading enzymes.
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Affiliation(s)
- Beat Frey
- Swiss Federal Institute for Forest, Forest Soils and Biogeochemistry, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Margherita Aiesi
- Swiss Federal Institute for Forest, Forest Soils and Biogeochemistry, Snow and Landscape Research WSL, Birmensdorf, Switzerland
- Facoltà de Science Agrarie e Alimentari, University Degli Studi di Milano, Milano, Italy
| | - Basil M. Rast
- Swiss Federal Institute for Forest, Forest Soils and Biogeochemistry, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Joel Rüthi
- Swiss Federal Institute for Forest, Forest Soils and Biogeochemistry, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Jérôme Julmi
- Swiss Federal Institute for Forest, Forest Soils and Biogeochemistry, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Beat Stierli
- Swiss Federal Institute for Forest, Forest Soils and Biogeochemistry, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Weihong Qi
- Functional Genomics Center Zürich, ETH Zürich and University of Zürich, Zürich, Switzerland
- Swiss Institute of Bioinformatics SIB, Geneva, Switzerland
| | - Ivano Brunner
- Swiss Federal Institute for Forest, Forest Soils and Biogeochemistry, Snow and Landscape Research WSL, Birmensdorf, Switzerland
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Yin X, Zhou G, Cai M, Richter-Heitmann T, Zhu QZ, Maeke M, Kulkarni AC, Nimzyk R, Elvert M, Friedrich MW. Physiological versatility of ANME-1 and Bathyarchaeotoa-8 archaea evidenced by inverse stable isotope labeling. MICROBIOME 2024; 12:68. [PMID: 38570877 PMCID: PMC10988981 DOI: 10.1186/s40168-024-01779-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 02/15/2024] [Indexed: 04/05/2024]
Abstract
BACKGROUND The trophic strategy is one key principle to categorize microbial lifestyles, by broadly classifying microorganisms based on the combination of their preferred carbon sources, electron sources, and electron sinks. Recently, a novel trophic strategy, i.e., chemoorganoautotrophy-the utilization of organic carbon as energy source but inorganic carbon as sole carbon source-has been specifically proposed for anaerobic methane oxidizing archaea (ANME-1) and Bathyarchaeota subgroup 8 (Bathy-8). RESULTS To further explore chemoorganoautotrophy, we employed stable isotope probing (SIP) of nucleic acids (rRNA or DNA) using unlabeled organic carbon and 13C-labeled dissolved inorganic carbon (DIC), i.e., inverse stable isotope labeling, in combination with metagenomics. We found that ANME-1 archaea actively incorporated 13C-DIC into RNA in the presence of methane and lepidocrocite when sulfate was absent, but assimilated organic carbon when cellulose was added to incubations without methane additions. Bathy-8 archaea assimilated 13C-DIC when lignin was amended; however, their DNA was derived from both inorganic and organic carbon sources rather than from inorganic carbon alone. Based on SIP results and supported by metagenomics, carbon transfer between catabolic and anabolic branches of metabolism is possible in these archaeal groups, indicating their anabolic versatility. CONCLUSION We provide evidence for the incorporation of the mixed organic and inorganic carbon by ANME-1 and Bathy-8 archaea in the environment. Video Abstract.
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Affiliation(s)
- Xiuran Yin
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Renmin Ave. No.58, Haikou, 570228, China.
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, James-Watt-Strasse 1, Bremen, D-28359, Germany.
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
- MARUM-Center for Marine Environmental Sciences, University of Bremen, Leobener Straße 8, Bremen, D-28359, Germany.
| | - Guowei Zhou
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Renmin Ave. No.58, Haikou, 570228, China
- School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui, China
| | - Mingwei Cai
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen, China
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Tim Richter-Heitmann
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, James-Watt-Strasse 1, Bremen, D-28359, Germany
| | - Qing-Zeng Zhu
- MARUM-Center for Marine Environmental Sciences, University of Bremen, Leobener Straße 8, Bremen, D-28359, Germany
| | - Mara Maeke
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, James-Watt-Strasse 1, Bremen, D-28359, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM-Center for Marine Environmental Sciences, University of Bremen, Leobener Straße 8, Bremen, D-28359, Germany
| | - Ajinkya C Kulkarni
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, James-Watt-Strasse 1, Bremen, D-28359, Germany
| | - Rolf Nimzyk
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, James-Watt-Strasse 1, Bremen, D-28359, Germany
| | - Marcus Elvert
- MARUM-Center for Marine Environmental Sciences, University of Bremen, Leobener Straße 8, Bremen, D-28359, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Michael W Friedrich
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, James-Watt-Strasse 1, Bremen, D-28359, Germany
- MARUM-Center for Marine Environmental Sciences, University of Bremen, Leobener Straße 8, Bremen, D-28359, Germany
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Giacomini JJ, Torres-Morales J, Tang J, Dewhirst FE, Borisy GG, Mark Welch JL. Spatial ecology of Haemophilus and Aggregatibacter in the human oral cavity. Microbiol Spectr 2024; 12:e0401723. [PMID: 38488280 PMCID: PMC10986600 DOI: 10.1128/spectrum.04017-23] [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: 11/23/2023] [Accepted: 01/26/2024] [Indexed: 04/06/2024] Open
Abstract
Haemophilus and Aggregatibacter are two of the most common bacterial genera in the human oral cavity, encompassing both commensals and pathogens of substantial ecological and medical significance. In this study, we conducted a metapangenomic analysis of oral Haemophilus and Aggregatibacter species to uncover genomic diversity, phylogenetic relationships, and habitat specialization within the human oral cavity. Using three metrics-pangenomic gene content, phylogenomics, and average nucleotide identity (ANI)-we first identified distinct species and sub-species groups among these genera. Mapping of metagenomic reads then revealed clear patterns of habitat specialization, such as Aggregatibacter species predominantly in dental plaque, a distinctive Haemophilus parainfluenzae sub-species group on the tongue dorsum, and H. sp. HMT-036 predominantly in keratinized gingiva and buccal mucosa. In addition, we found that supragingival plaque samples contained predominantly only one out of the three taxa, H. parainfluenzae, Aggregatibacter aphrophilus, and A. sp. HMT-458, suggesting independent niches or a competitive relationship. Functional analyses revealed the presence of key metabolic genes, such as oxaloacetate decarboxylase, correlated with habitat specialization, suggesting metabolic versatility as a driving force. Additionally, heme synthesis distinguishes H. sp. HMT-036 from closely related Haemophilus haemolyticus, suggesting that the availability of micronutrients, particularly iron, was important in the evolutionary ecology of these species. Overall, our study exemplifies the power of metapangenomics to identify factors that may affect ecological interactions within microbial communities, including genomic diversity, habitat specialization, and metabolic versatility. IMPORTANCE Understanding the microbial ecology of the mouth is essential for comprehending human physiology. This study employs metapangenomics to reveal that various Haemophilus and Aggregatibacter species exhibit distinct ecological preferences within the oral cavity of healthy individuals, thereby supporting the site-specialist hypothesis. Additionally, it was observed that the gene pool of different Haemophilus species correlates with their ecological niches. These findings shed light on the significance of key metabolic functions in shaping microbial distribution patterns and interspecies interactions in the oral ecosystem.
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Affiliation(s)
| | | | - Jonathan Tang
- The Forsyth Institute, Cambridge, Massachusetts, USA
| | - Floyd E. Dewhirst
- The Forsyth Institute, Cambridge, Massachusetts, USA
- Harvard School of Dental Medicine, Boston, Massachusetts, USA
| | | | - Jessica L. Mark Welch
- The Forsyth Institute, Cambridge, Massachusetts, USA
- Marine Biological Laboratory, Woods Hole, Massachusetts, USA
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Eme L, Tamarit D. Microbial Diversity and Open Questions about the Deep Tree of Life. Genome Biol Evol 2024; 16:evae053. [PMID: 38620144 PMCID: PMC11018274 DOI: 10.1093/gbe/evae053] [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] [Accepted: 03/11/2024] [Indexed: 04/17/2024] Open
Abstract
In this perspective, we explore the transformative impact and inherent limitations of metagenomics and single-cell genomics on our understanding of microbial diversity and their integration into the Tree of Life. We delve into the key challenges associated with incorporating new microbial lineages into the Tree of Life through advanced phylogenomic approaches. Additionally, we shed light on enduring debates surrounding various aspects of the microbial Tree of Life, focusing on recent advances in some of its deepest nodes, such as the roots of bacteria, archaea, and eukaryotes. We also bring forth current limitations in genome recovery and phylogenomic methodology, as well as new avenues of research to uncover additional key microbial lineages and resolve the shape of the Tree of Life.
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Affiliation(s)
- Laura Eme
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif sur-Yvette, France
| | - Daniel Tamarit
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht 3584CH, The Netherlands
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Ray M, Manu S, Rastogi G, Umapathy G. Cyanobacterial Genomes from a Brackish Coastal Lagoon Reveal Potential for Novel Biogeochemical Functions and Their Evolution. J Mol Evol 2024; 92:121-137. [PMID: 38489069 DOI: 10.1007/s00239-024-10159-y] [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: 10/14/2023] [Accepted: 01/24/2024] [Indexed: 03/17/2024]
Abstract
Cyanobacteria are recognised for their pivotal roles in aquatic ecosystems, serving as primary producers and major agents in diazotrophic processes. Currently, the primary focus of cyanobacterial research lies in gaining a more detailed understanding of these well-established ecosystem functions. However, their involvement and impact on other crucial biogeochemical cycles remain understudied. This knowledge gap is partially attributed to the challenges associated with culturing cyanobacteria in controlled laboratory conditions and the limited understanding of their specific growth requirements. This can be circumvented partially by the culture-independent methods which can shed light on the genomic potential of cyanobacterial species and answer more profound questions about the evolution of other key biogeochemical functions. In this study, we assembled 83 cyanobacterial genomes from metagenomic data generated from environmental DNA extracted from a brackish water lagoon (Chilika Lake, India). We taxonomically classified these metagenome-assembled genomes (MAGs) and found that about 92.77% of them are novel genomes at the species level. We then annotated these cyanobacterial MAGs for all the encoded functions using KEGG Orthology. Interestingly, we found two previously unreported functions in Cyanobacteria, namely, DNRA (Dissimilatory Nitrate Reduction to Ammonium) and DMSP (Dimethylsulfoniopropionate) synthesis in multiple MAGs using nirBD and dsyB genes as markers. We validated their presence in several publicly available cyanobacterial isolate genomes. Further, we identified incongruities between the evolutionary patterns of species and the marker genes and elucidated the underlying reasons for these discrepancies. This study expands our overall comprehension of the contribution of cyanobacteria to the biogeochemical cycling in coastal brackish ecosystems.
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Affiliation(s)
- Manisha Ray
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, 500007, India
| | - Shivakumara Manu
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, 500007, India
| | - Gurdeep Rastogi
- Wetland Research and Training Centre, Chilika Development Authority, Balugaon, Odisha, 752030, India
| | - Govindhaswamy Umapathy
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, 500007, India.
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Machulin AV, Deryusheva EI, Galzitskaya OV. Variation in base composition, structure-function relationships, and origins of structural repetition in bacterial rpsA gene. Biosystems 2024; 238:105196. [PMID: 38537772 DOI: 10.1016/j.biosystems.2024.105196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 03/22/2024] [Accepted: 03/22/2024] [Indexed: 04/12/2024]
Abstract
Protein domain repeats are known to arise due to tandem duplications of internal genes. However, the understanding of the underlying mechanisms of this process is incomplete. The goal of this work was to investigate the mechanism of occurrence of repeat expansion based on studying the sequences of 1324 rpsA genes of bacterial S1 ribosomal proteins containing different numbers of S1 structural domains. The rpsA gene encodes ribosomal S1 protein, which is essential for cell viability as it interacts with both mRNA and proteins. Gene ontology (GO) analysis of S1 domains in ribosomal S1 proteins revealed that bacterial protein sequences in S1 mainly have 3 types of molecular functions: RNA binding activity, nucleic acid activity, and ribosome structural component. Our results show that the maximum value of rpsA gene identity for full-length proteins was found for S1 proteins containing six structural domains (58%). Analysis of consensus sequences showed that parts of the rpsA gene encoding separate S1 domains have no a strictly repetitive structure between groups containing different numbers of S1 domains. At the same time, gene regions encoding some conserved residues that form the RNA-binding site remain conserved. The detected phylogenetic similarity suggests that the proposed fold of the rpsA translation initiation region of Escherichia coli has functional value and is important for translational control of rpsA gene expression in other bacterial phyla, but not only in gamma Proteobacteria.
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Affiliation(s)
- Andrey V Machulin
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", 142290, Pushchino, Moscow Region, Russia
| | - Evgeniya I Deryusheva
- Institute for Biological Instrumentation, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", 142290, Pushchino, Moscow Region, Russia
| | - Oxana V Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, 142290, Pushchino, Moscow Region, Russia; Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290, Pushchino, Moscow Region, Russia.
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McGrath AH, Lema K, Egan S, Wood G, Gonzalez SV, Kjelleberg S, Steinberg PD, Marzinelli EM. Disentangling direct vs indirect effects of microbiome manipulations in a habitat-forming marine holobiont. NPJ Biofilms Microbiomes 2024; 10:33. [PMID: 38553475 PMCID: PMC10980776 DOI: 10.1038/s41522-024-00503-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 03/14/2024] [Indexed: 04/02/2024] Open
Abstract
Host-associated microbiota are critical for eukaryotic host functioning, to the extent that hosts and their associated microbial communities are often considered "holobionts". Most studies of holobionts have focused on descriptive approaches or have used model systems, usually in the laboratory, to understand host-microbiome interactions. To advance our understanding of host-microbiota interactions and their wider ecological impacts, we need experimental frameworks that can explore causation in non-model hosts, which often have highly diverse microbiota, and in their natural ecological setting (i.e. in the field). We used a dominant habitat-forming seaweed, Hormosira banksii, to explore these issues and to experimentally test host-microbiota interactions in a non-model holobiont. The experimental protocols were aimed at trying to disentangle microbially mediated effects on hosts from direct effects on hosts associated with the methods employed to manipulate host-microbiota. This was done by disrupting the microbiome, either through removal/disruption using a combination of antimicrobial treatments, or additions of specific taxa via inoculations, or a combination of thew two. The experiments were done in mesocosms and in the field. Three different antibiotic treatments were used to disrupt seaweed-associated microbiota to test whether disturbances of microbiota, particularly bacteria, would negatively affect host performance. Responses of bacteria to these disturbances were complex and differed substantially among treatments, with some antibacterial treatments having little discernible effect. However, the temporal sequence of responses antibiotic treatments, changes in bacterial diversity and subsequent decreases in host performance, strongly suggested an effect of the microbiota on host performance in some treatments, as opposed to direct effects of the antibiotics. To further test these effects, we used 16S-rRNA-gene sequencing to identify bacterial taxa that were either correlated, or uncorrelated, with poor host performance following antibiotic treatment. These were then isolated and used in inoculation experiments, independently or in combination with the previously used antibiotic treatments. Negative effects on host performance were strongest where specific microbial antimicrobials treatments were combined with inoculations of strains that were correlated with poor host performance. For these treatments, negative host effects persisted the entire experimental period (12 days), even though treatments were only applied at the beginning of the experiment. Host performance recovered in all other treatments. These experiments provide a framework for exploring causation and disentangling microbially mediated vs. direct effects on hosts for ecologically important, non-model holobionts in the field. This should allow for better predictions of how these systems will respond to, and potentially mitigate, environmental disturbances in their natural context.
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Affiliation(s)
- Alexander Harry McGrath
- The University of Sydney, School of Life and Environmental Sciences, Sydney, NSW, Australia.
- Sydney Institute of Marine Science, Mosman, NSW, Australia.
| | - Kimberley Lema
- Sydney Institute of Marine Science, Mosman, NSW, Australia
- Centre for Marine Science and Innovation, School of Biological, Earth, and Environmental Science, University of New South Wales, Sydney, NSW, Australia
| | - Suhelen Egan
- Sydney Institute of Marine Science, Mosman, NSW, Australia
- Centre for Marine Science and Innovation, School of Biological, Earth, and Environmental Science, University of New South Wales, Sydney, NSW, Australia
| | - Georgina Wood
- The University of Sydney, School of Life and Environmental Sciences, Sydney, NSW, Australia
- Sydney Institute of Marine Science, Mosman, NSW, Australia
- UWA Oceans Institute & School of Biological Sciences, Indian Ocean Marine Research Centre, The University of Western Australia, Sydney, Australia
| | - Sebastian Vadillo Gonzalez
- The University of Sydney, School of Life and Environmental Sciences, Sydney, NSW, Australia
- Sydney Institute of Marine Science, Mosman, NSW, Australia
| | - Staffan Kjelleberg
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, SBS-01N-27, Singapore, 637551, Singapore
| | - Peter D Steinberg
- Sydney Institute of Marine Science, Mosman, NSW, Australia
- Centre for Marine Science and Innovation, School of Biological, Earth, and Environmental Science, University of New South Wales, Sydney, NSW, Australia
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, SBS-01N-27, Singapore, 637551, Singapore
| | - Ezequiel M Marzinelli
- The University of Sydney, School of Life and Environmental Sciences, Sydney, NSW, Australia
- Sydney Institute of Marine Science, Mosman, NSW, Australia
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, SBS-01N-27, Singapore, 637551, Singapore
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Edwin NR, Fitzpatrick AH, Brennan F, Abram F, O'Sullivan O. An in-depth evaluation of metagenomic classifiers for soil microbiomes. ENVIRONMENTAL MICROBIOME 2024; 19:19. [PMID: 38549112 PMCID: PMC10979606 DOI: 10.1186/s40793-024-00561-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 03/11/2024] [Indexed: 04/01/2024]
Abstract
BACKGROUND Recent endeavours in metagenomics, exemplified by projects such as the human microbiome project and TARA Oceans, have illuminated the complexities of microbial biomes. A robust bioinformatic pipeline and meticulous evaluation of their methodology have contributed to the success of these projects. The soil environment, however, with its unique challenges, requires a specialized methodological exploration to maximize microbial insights. A notable limitation in soil microbiome studies is the dearth of soil-specific reference databases available to classifiers that emulate the complexity of soil communities. There is also a lack of in-vitro mock communities derived from soil strains that can be assessed for taxonomic classification accuracy. RESULTS In this study, we generated a custom in-silico mock community containing microbial genomes commonly observed in the soil microbiome. Using this mock community, we simulated shotgun sequencing data to evaluate the performance of three leading metagenomic classifiers: Kraken2 (supplemented with Bracken, using a custom database derived from GTDB-TK genomes along with its own default database), Kaiju, and MetaPhlAn, utilizing their respective default databases for a robust analysis. Our results highlight the importance of optimizing taxonomic classification parameters, database selection, as well as analysing trimmed reads and contigs. Our study showed that classifiers tailored to the specific taxa present in our samples led to fewer errors compared to broader databases including microbial eukaryotes, protozoa, or human genomes, highlighting the effectiveness of targeted taxonomic classification. Notably, an optimal classifier performance was achieved when applying a relative abundance threshold of 0.001% or 0.005%. The Kraken2 supplemented with bracken, with a custom database demonstrated superior precision, sensitivity, F1 score, and overall sequence classification. Using a custom database, this classifier classified 99% of in-silico reads and 58% of real-world soil shotgun reads, with the latter identifying previously overlooked phyla using a custom database. CONCLUSION This study underscores the potential advantages of in-silico methodological optimization in metagenomic analyses, especially when deciphering the complexities of soil microbiomes. We demonstrate that the choice of classifier and database significantly impacts microbial taxonomic profiling. Our findings suggest that employing Kraken2 with Bracken, coupled with a custom database of GTDB-TK genomes and fungal genomes at a relative abundance threshold of 0.001% provides optimal accuracy in soil shotgun metagenome analysis.
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Affiliation(s)
- Niranjana Rose Edwin
- Teagasc, Moorepark Food Research Centre, Moorepark, Fermoy, Cork, Ireland
- Functional Environmental Microbiology, School of Biological and Chemical Sciences, Ryan Institute, University of Galway, Galway, Ireland
- VistaMilk SFI Research Centre, Cork, Ireland
| | | | - Fiona Brennan
- Teagasc, Soils, Environment and Landuse Department, Johnstown Castle, Wexford, Ireland
- VistaMilk SFI Research Centre, Cork, Ireland
| | - Florence Abram
- Functional Environmental Microbiology, School of Biological and Chemical Sciences, Ryan Institute, University of Galway, Galway, Ireland
| | - Orla O'Sullivan
- Teagasc, Moorepark Food Research Centre, Moorepark, Fermoy, Cork, Ireland.
- VistaMilk SFI Research Centre, Cork, Ireland.
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Giordano N, Gaudin M, Trottier C, Delage E, Nef C, Bowler C, Chaffron S. Genome-scale community modelling reveals conserved metabolic cross-feedings in epipelagic bacterioplankton communities. Nat Commun 2024; 15:2721. [PMID: 38548725 PMCID: PMC10978986 DOI: 10.1038/s41467-024-46374-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 02/26/2024] [Indexed: 04/01/2024] Open
Abstract
Marine microorganisms form complex communities of interacting organisms that influence central ecosystem functions in the ocean such as primary production and nutrient cycling. Identifying the mechanisms controlling their assembly and activities is a major challenge in microbial ecology. Here, we integrated Tara Oceans meta-omics data to predict genome-scale community interactions within prokaryotic assemblages in the euphotic ocean. A global genome-resolved co-activity network revealed a significant number of inter-lineage associations across diverse phylogenetic distances. Identified co-active communities include species displaying smaller genomes but encoding a higher potential for quorum sensing, biofilm formation, and secondary metabolism. Community metabolic modelling reveals a higher potential for interaction within co-active communities and points towards conserved metabolic cross-feedings, in particular of specific amino acids and group B vitamins. Our integrated ecological and metabolic modelling approach suggests that genome streamlining and metabolic auxotrophies may act as joint mechanisms shaping bacterioplankton community assembly in the global ocean surface.
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Affiliation(s)
- Nils Giordano
- Nantes Université, École Centrale Nantes, CNRS, LS2N, UMR 6004, F-44000, Nantes, France
| | - Marinna Gaudin
- Nantes Université, École Centrale Nantes, CNRS, LS2N, UMR 6004, F-44000, Nantes, France
| | - Camille Trottier
- Nantes Université, École Centrale Nantes, CNRS, LS2N, UMR 6004, F-44000, Nantes, France
| | - Erwan Delage
- Nantes Université, École Centrale Nantes, CNRS, LS2N, UMR 6004, F-44000, Nantes, France
| | - Charlotte Nef
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, F-75016, Paris, France
| | - Chris Bowler
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, F-75016, Paris, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, F-75016, Paris, France
| | - Samuel Chaffron
- Nantes Université, École Centrale Nantes, CNRS, LS2N, UMR 6004, F-44000, Nantes, France.
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, F-75016, Paris, France.
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Fry M. The discovery of archaea: from observed anomaly to consequential restructuring of the phylogenetic tree. HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES 2024; 46:16. [PMID: 38530473 PMCID: PMC10965645 DOI: 10.1007/s40656-024-00616-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 02/14/2024] [Indexed: 03/28/2024]
Abstract
Observational and experimental discoveries of new factual entities such as objects, systems, or processes, are major contributors to some advances in the life sciences. Yet, whereas discovery of theories was extensively deliberated by philosophers of science, very little philosophical attention was paid to the discovery of factual entities. This paper examines historical and philosophical aspects of the experimental discovery by Carl Woese of archaea, prokaryotes that comprise one of the three principal domains of the phylogenetic tree. Borrowing Kuhn's terminology, this discovery of a major biological entity was made during a 'normal science' project of building molecular taxonomy for prokaryotes. Unexpectedly, however, an observed anomaly instigated the discovery of archaea. Substantiation of the existence of the new archaeal entity and consequent reconstruction of the phylogenetic tree prompted replacement of a long-held model of a prokarya and eukarya bipartite tree of life by a new model of a tripartite tree comprising of bacteria, archaea, and eukarya. This paper explores the history and philosophical implications of the progression of Woese's project from normal science to anomaly-instigated model-changing discovery. It is also shown that the consequential discoveries of RNA splicing and of ribozymes were similarly prompted by unexpected irregularities during normal science activities. It is thus submitted that some discoveries of factual biological entities are triggered by unforeseen observational or experimental anomalies.
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Affiliation(s)
- Michael Fry
- Department of Biochemistry, Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Efron St., Bat Galim, POB 9649, Haifa, 31096, Israel.
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Stewart RD, Myers KS, Amstadt C, Seib M, McMahon KD, Noguera DR. Refinement of the " Candidatus Accumulibacter" genus based on metagenomic analysis of biological nutrient removal (BNR) pilot-scale plants operated with reduced aeration. mSystems 2024; 9:e0118823. [PMID: 38415636 PMCID: PMC10949500 DOI: 10.1128/msystems.01188-23] [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: 11/18/2023] [Accepted: 01/31/2024] [Indexed: 02/29/2024] Open
Abstract
Members of the "Candidatus Accumulibacter" genus are widely studied as key polyphosphate-accumulating organisms (PAOs) in biological nutrient removal (BNR) facilities performing enhanced biological phosphorus removal (EBPR). This diverse lineage includes 18 "Ca. Accumulibacter" species, which have been proposed based on the phylogenetic divergence of the polyphosphate kinase 1 (ppk1) gene and genome-scale comparisons of metagenome-assembled genomes (MAGs). Phylogenetic classification based on the 16S rRNA genetic marker has been difficult to attain because most "Ca. Accumulibacter" MAGs are incomplete and often do not include the rRNA operon. Here, we investigate the "Ca. Accumulibacter" diversity in pilot-scale treatment trains performing BNR under low dissolved oxygen (DO) conditions using genome-resolved metagenomics. Using long-read sequencing, we recovered medium- and high-quality MAGs for 5 of the 18 "Ca. Accumulibacter" species, all with rRNA operons assembled, which allowed a reassessment of the 16S rRNA-based phylogeny of this genus and an analysis of phylogeny based on the 23S rRNA gene. In addition, we recovered a cluster of MAGs that based on 16S rRNA, 23S rRNA, ppk1, and genome-scale phylogenetic analyses do not belong to any of the currently recognized "Ca. Accumulibacter" species for which we propose the new species designation "Ca. Accumulibacter jenkinsii" sp. nov. Relative abundance evaluations of the genus across all pilot plant operations revealed that regardless of the operational mode, "Ca. A. necessarius" and "Ca. A. propinquus" accounted for more than 40% of the "Ca. Accumulibacter" community, whereas the newly proposed "Ca. A. jenkinsii" accounted for about 5% of the "Ca. Accumulibacter" community.IMPORTANCEOne of the main drivers of energy use and operational costs in activated sludge processes is the amount of oxygen provided to enable biological phosphorus and nitrogen removal. Wastewater treatment facilities are increasingly considering reduced aeration to decrease energy consumption, and whereas successful BNR has been demonstrated in systems with minimal aeration, an adequate understanding of the microbial communities that facilitate nutrient removal under these conditions is still lacking. In this study, we used genome-resolved metagenomics to evaluate the diversity of the "Candidatus Accumulibacter" genus in pilot-scale plants operating with minimal aeration. We identified the "Ca. Accumulibacter" species enriched under these conditions, including one novel species for which we propose "Ca. Accumulibacter jenkinsii" sp. nov. as its designation. Furthermore, the MAGs obtained for five additional "Ca. Accumulibacter" species further refine the phylogeny of the "Ca. Accumulibacter" genus and provide new insight into its diversity within unconventional biological nutrient removal systems.
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Affiliation(s)
- Rachel D. Stewart
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Kevin S. Myers
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Carly Amstadt
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Matt Seib
- Madison Metropolitan Sewerage District, Madison, Wisconsin, USA
| | - Katherine D. McMahon
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Daniel R. Noguera
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
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Li X, Xu L, Demaree B, Noecker C, Bisanz JE, Weisgerber DW, Modavi C, Turnbaugh PJ, Abate AR. Microbiome single cell atlases generated with a commercial instrument. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.08.551713. [PMID: 37609281 PMCID: PMC10441329 DOI: 10.1101/2023.08.08.551713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Single cell sequencing is useful for resolving complex systems into their composite cell types and computationally mining them for unique features that are masked in pooled sequencing. However, while commercial instruments have made single cell analysis widespread for mammalian cells, analogous tools for microbes are limited. Here, we present EASi-seq (Easily Accessible Single microbe sequencing). By adapting the single cell workflow of the commercial Mission Bio Tapestri instrument, this method allows for efficient sequencing of individual microbes' genomes. EASi-seq allows thousands of microbes to be sequenced per run and, as we show, can generate detailed atlases of human and environmental microbiomes. The ability to capture large shotgun genome datasets from thousands of single microbes provides new opportunities in discovering and analyzing species subpopulations. To facilitate this, we develop a companion bioinformatic pipeline that clusters microbes by similarity, improving whole genome assembly, strain identification, taxonomic classification, and gene annotation. In addition, we demonstrate integration of metagenomic contigs with the EASi-seq datasets to reduce capture bias and increase coverage. Overall, EASi-seq enables high quality single cell genomic data for microbiome samples using an accessible workflow that can be run on a commercially available platform.
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Hu H, Kristensen JM, Herbold CW, Pjevac P, Kitzinger K, Hausmann B, Dueholm MKD, Nielsen PH, Wagner M. Global abundance patterns, diversity, and ecology of Patescibacteria in wastewater treatment plants. MICROBIOME 2024; 12:55. [PMID: 38493180 PMCID: PMC10943839 DOI: 10.1186/s40168-024-01769-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 01/23/2024] [Indexed: 03/18/2024]
Abstract
BACKGROUND Microorganisms are responsible for nutrient removal and resource recovery in wastewater treatment plants (WWTPs), and their diversity is often studied by 16S rRNA gene amplicon sequencing. However, this approach underestimates the abundance and diversity of Patescibacteria due to the low coverage of commonly used PCR primers for this highly divergent bacterial phylum. Therefore, our current understanding of the global diversity, distribution, and ecological role of Patescibacteria in WWTPs is very incomplete. This is particularly relevant as Patescibacteria are considered to be associated with microbial host cells and can therefore influence the abundance and temporal variability of other microbial groups that are important for WWTP functioning. RESULTS Here, we evaluated the in silico coverage of widely used 16S rRNA gene-targeted primer pairs and redesigned a primer pair targeting the V4 region of bacterial and archaeal 16S rRNA genes to expand its coverage for Patescibacteria. We then experimentally evaluated and compared the performance of the original and modified V4-targeted primers on 565 WWTP samples from the MiDAS global sample collection. Using the modified primer pair, the percentage of ASVs classified as Patescibacteria increased from 5.9 to 23.8%, and the number of detected patescibacterial genera increased from 560 to 1576, while the detected diversity of the remaining microbial community remained similar. Due to this significantly improved coverage of Patescibacteria, we identified 23 core genera of Patescibacteria in WWTPs and described the global distribution pattern of these unusual microbes in these systems. Finally, correlation network analysis revealed potential host organisms that might be associated with Patescibacteria in WWTPs. Interestingly, strong indications were found for an association between Patescibacteria of the Saccharimonadia and globally abundant polyphosphate-accumulating organisms of the genus Ca. Phosphoribacter. CONCLUSIONS Our study (i) provides an improved 16S rRNA gene V4 region-targeted amplicon primer pair inclusive of Patescibacteria with little impact on the detection of other taxa, (ii) reveals the diversity and distribution patterns of Patescibacteria in WWTPs on a global scale, and (iii) provides new insights into the ecological role and potential hosts of Patescibacteria in WWTPs. Video Abstract.
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Affiliation(s)
- Huifeng Hu
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Universitätsring 1, 1010, Vienna, Austria
| | - Jannie Munk Kristensen
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Craig William Herbold
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
- Te Kura Putaiao Koiora, School of Biological Sciences, Te Whare Wananga o Waitaha, University of Canterbury, Otautahi, Christchurch, Aotearoa, New Zealand
| | - Petra Pjevac
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
- Joint Microbiome Facility of the Medical University of Vienna , University of Vienna, Vienna, Austria
| | - Katharina Kitzinger
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna , University of Vienna, Vienna, Austria
- Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Morten Kam Dahl Dueholm
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Per Halkjaer Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Michael Wagner
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria.
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.
- Joint Microbiome Facility of the Medical University of Vienna , University of Vienna, Vienna, Austria.
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Campbell BC, Greenfield P, Barnhart EP, Gong S, Midgley DJ, Paulsen IT, George SC. Krumholzibacteriota and Deltaproteobacteria contain rare genetic potential to liberate carbon from monoaromatic compounds in subsurface coal seams. mBio 2024; 15:e0173523. [PMID: 38345372 PMCID: PMC10936416 DOI: 10.1128/mbio.01735-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 01/09/2024] [Indexed: 03/14/2024] Open
Abstract
Biogenic methane in subsurface coal seam environments is produced by diverse consortia of microbes. Although this methane is useful for global energy security, it remains unclear which microbes can liberate carbon from the coal. Most of this carbon is relatively resistant to biodegradation, as it is contained within aromatic rings. Thus, to explore for coal-degrading taxa in the subsurface, this study reconstructed relevant metagenome-assembled genomes (MAGs) from coal seams by using a key genomic marker for the anaerobic degradation of monoaromatic compounds as a guide: the benzoyl-CoA reductase gene (bcrABCD). Three MAGs were identified with this genetic potential. The first represented a novel taxon from the Krumholzibacteriota phylum, which this study is the first to describe. This Krumholzibacteriota MAG contained a full set of genes for benzoyl-CoA dearomatization, in addition to other genes for anaerobic catabolism of monoaromatics. Analysis of Krumholzibacteriota MAGs from other environments revealed that this genetic potential may be common, and thus, Krumholzibacteriota may be important organisms for the liberation of recalcitrant carbon in a broad range of environments. Moreover, the assembly and characterization of two Syntrophorhabdus aromaticivorans MAGs from different continents and a Syntrophaceae sp. MAG implicate the Deltaproteobacteria class in coal seam monoaromatic degradation. Each of these taxa are potential rate-limiting organisms for subsurface coal-to-methane biodegradation. Their description here provides some understanding of their function within the coal seam microbiome and will help inform future efforts in coal bed methane stimulation, anoxic bioremediation of organic pollutants, and assessments of anoxic, subsurface carbon cycling and emissions.IMPORTANCESubsurface coal seams are highly anoxic, oligotrophic environments, where the main source of carbon is "locked away" within aromatic rings. Despite these challenges, many coal seams accumulate biogenic methane, implying that the coal seam microbiome is "unlocking" this carbon source in situ. For over two decades, researchers have endeavored to understand which organisms perform these processes. This study provides the first descriptions of organisms with this genetic potential from the coal seam environment. Here, we report metagenomic insights into carbon liberation from aromatic molecules and the degradation pathways involved and describe a Krumholzibacteriota, two Syntrophorhabdus aromaticivorans, and a Syntrophaceae MAG that contain this genetic potential. This is also the first time that the Krumholzibacteriota phylum has been implicated in anaerobic dearomatization of aromatic hydrocarbons. This potential is identified here in numerous MAGs from other terrestrial and marine subsurface habitats, implicating the Krumholzibacteriota in carbon-cycling processes across a broad range of environments.
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Affiliation(s)
- Bronwyn C. Campbell
- Environment Business Unit, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Floreat, Western Australia, Australia
- School of Natural Sciences, Macquarie University, North Ryde, New South Wales, Australia
| | - Paul Greenfield
- School of Natural Sciences, Macquarie University, North Ryde, New South Wales, Australia
- Energy Business Unit, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Lindfield, New South Wales, Australia
| | - Elliott P. Barnhart
- U.S. Geological Survey, Wyoming-Montana Water Science Center, Helena, Montana, USA
| | - Se Gong
- Energy Business Unit, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Lindfield, New South Wales, Australia
| | - David J. Midgley
- Energy Business Unit, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Lindfield, New South Wales, Australia
| | - Ian T. Paulsen
- School of Natural Sciences, Macquarie University, North Ryde, New South Wales, Australia
| | - Simon C. George
- School of Natural Sciences, Macquarie University, North Ryde, New South Wales, Australia
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Zhang IH, Borer B, Zhao R, Wilbert S, Newman DK, Babbin AR. Uncultivated DPANN archaea are ubiquitous inhabitants of global oxygen-deficient zones with diverse metabolic potential. mBio 2024; 15:e0291823. [PMID: 38380943 PMCID: PMC10936187 DOI: 10.1128/mbio.02918-23] [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: 10/26/2023] [Accepted: 01/22/2024] [Indexed: 02/22/2024] Open
Abstract
Archaea belonging to the DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota) superphylum have been found in an expanding number of environments and perform a variety of biogeochemical roles, including contributing to carbon, sulfur, and nitrogen cycling. Generally characterized by ultrasmall cell sizes and reduced genomes, DPANN archaea may form mutualistic, commensal, or parasitic interactions with various archaeal and bacterial hosts, influencing the ecology and functioning of microbial communities. While DPANN archaea reportedly comprise a sizeable fraction of the archaeal community within marine oxygen-deficient zone (ODZ) water columns, little is known about their metabolic capabilities in these ecosystems. We report 33 novel metagenome-assembled genomes (MAGs) belonging to the DPANN phyla Nanoarchaeota, Pacearchaeota, Woesearchaeota, Undinarchaeota, Iainarchaeota, and SpSt-1190 from pelagic ODZs in the Eastern Tropical North Pacific and the Arabian Sea. We find these archaea to be permanent, stable residents of all three major ODZs only within anoxic depths, comprising up to 1% of the total microbial community and up to 25%-50% of archaea as estimated from read mapping to MAGs. ODZ DPANN appear to be capable of diverse metabolic functions, including fermentation, organic carbon scavenging, and the cycling of sulfur, hydrogen, and methane. Within a majority of ODZ DPANN, we identify a gene homologous to nitrous oxide reductase. Modeling analyses indicate the feasibility of a nitrous oxide reduction metabolism for host-attached symbionts, and the small genome sizes and reduced metabolic capabilities of most DPANN MAGs suggest host-associated lifestyles within ODZs. IMPORTANCE Archaea from the DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota) superphylum have diverse metabolic capabilities and participate in multiple biogeochemical cycles. While metagenomics and enrichments have revealed that many DPANN are characterized by ultrasmall genomes, few biosynthetic genes, and episymbiotic lifestyles, much remains unknown about their biology. We report 33 new DPANN metagenome-assembled genomes originating from the three global marine oxygen-deficient zones (ODZs), the first from these regions. We survey DPANN abundance and distribution within the ODZ water column, investigate their biosynthetic capabilities, and report potential roles in the cycling of organic carbon, methane, and nitrogen. We test the hypothesis that nitrous oxide reductases found within several ODZ DPANN genomes may enable ultrasmall episymbionts to serve as nitrous oxide consumers when attached to a host nitrous oxide producer. Our results indicate DPANN archaea as ubiquitous residents within the anoxic core of ODZs with the potential to produce or consume key compounds.
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Affiliation(s)
- Irene H. Zhang
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Benedict Borer
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Rui Zhao
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Steven Wilbert
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Dianne K. Newman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, USA
| | - Andrew R. Babbin
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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Geesink P, ter Horst J, Ettema TJG. More than the sum of its parts: uncovering emerging effects of microbial interactions in complex communities. FEMS Microbiol Ecol 2024; 100:fiae029. [PMID: 38444203 PMCID: PMC10950044 DOI: 10.1093/femsec/fiae029] [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: 11/15/2023] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 03/07/2024] Open
Abstract
Microbial communities are not only shaped by the diversity of microorganisms and their individual metabolic potential, but also by the vast amount of intra- and interspecies interactions that can occur pairwise interactions among microorganisms, we suggest that more attention should be drawn towards the effects on the entire microbiome that emerge from individual interactions between community members. The production of certain metabolites that can be tied to a specific microbe-microbe interaction might subsequently influence the physicochemical parameters of the habitat, stimulate a change in the trophic network of the community or create new micro-habitats through the formation of biofilms, similar to the production of antimicrobial substances which might negatively affect only one microorganism but cause a ripple effect on the abundance of other community members. Here, we argue that combining established as well as innovative laboratory and computational methods is needed to predict novel interactions and assess their secondary effects. Such efforts will enable future microbiome studies to expand our knowledge on the dynamics of complex microbial communities.
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Affiliation(s)
- Patricia Geesink
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Jolanda ter Horst
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Thijs J G Ettema
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
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Bozdag GO, Szeinbaum N, Conlin PL, Chen K, Fos SM, Garcia A, Penev PI, Schaible GA, Trubl G. Chapter 5: Major Biological Innovations in the History of Life on Earth. ASTROBIOLOGY 2024; 24:S107-S123. [PMID: 38498818 PMCID: PMC11071111 DOI: 10.1089/ast.2021.0119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 11/14/2023] [Indexed: 03/20/2024]
Abstract
All organisms living on Earth descended from a single, common ancestral population of cells, known as LUCA-the last universal common ancestor. Since its emergence, the diversity and complexity of life have increased dramatically. This chapter focuses on four key biological innovations throughout Earth's history that had a significant impact on the expansion of phylogenetic diversity, organismal complexity, and ecospace habitation. First is the emergence of the last universal common ancestor, LUCA, which laid the foundation for all life-forms on Earth. Second is the evolution of oxygenic photosynthesis, which resulted in global geochemical and biological transformations. Third is the appearance of a new type of cell-the eukaryotic cell-which led to the origin of a new domain of life and the basis for complex multicellularity. Fourth is the multiple independent origins of multicellularity, resulting in the emergence of a new level of complex individuality. A discussion of these four key events will improve our understanding of the intertwined history of our planet and its inhabitants and better inform the extent to which we can expect life at different degrees of diversity and complexity elsewhere.
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Affiliation(s)
- G. Ozan Bozdag
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Nadia Szeinbaum
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Peter L. Conlin
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Kimberly Chen
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Santiago Mestre Fos
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Amanda Garcia
- Department of Bacteriology, University of Wisconsin–Madison, Wisconsin, USA
| | - Petar I. Penev
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - George A. Schaible
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Gareth Trubl
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
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Bernabeu M, Manzano-Morales S, Gabaldón T. On the impact of incomplete taxon sampling on the relative timing of gene transfer events. PLoS Biol 2024; 22:e3002460. [PMID: 38498548 PMCID: PMC10947667 DOI: 10.1371/journal.pbio.3002460] [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: 07/24/2023] [Accepted: 12/04/2023] [Indexed: 03/20/2024] Open
Abstract
A recent study questioned the use of branch length methods to assess the relative timing of horizontal gene transfers because of the effects of so-called "ghost" lineages. This Formal Comment discusses key considerations regarding the potential effect of missing lineages when assessing relative timing of evolutionary events.
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Affiliation(s)
- Moisès Bernabeu
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Saioa Manzano-Morales
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Toni Gabaldón
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
- Centro de Investigación Biomédica En Red de Enfermedades Infecciosas (CIBERINFEC), Barcelona, Spain
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Orgeur M, Sous C, Madacki J, Brosch R. Evolution and emergence of Mycobacterium tuberculosis. FEMS Microbiol Rev 2024; 48:fuae006. [PMID: 38365982 PMCID: PMC10906988 DOI: 10.1093/femsre/fuae006] [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: 11/09/2023] [Revised: 01/12/2024] [Accepted: 02/13/2024] [Indexed: 02/18/2024] Open
Abstract
Tuberculosis (TB) remains one of the deadliest infectious diseases in human history, prevailing even in the 21st century. The causative agents of TB are represented by a group of closely related bacteria belonging to the Mycobacterium tuberculosis complex (MTBC), which can be subdivided into several lineages of human- and animal-adapted strains, thought to have shared a last common ancestor emerged by clonal expansion from a pool of recombinogenic Mycobacterium canettii-like tubercle bacilli. A better understanding of how MTBC populations evolved from less virulent mycobacteria may allow for discovering improved TB control strategies and future epidemiologic trends. In this review, we highlight new insights into the evolution of mycobacteria at the genus level, describing different milestones in the evolution of mycobacteria, with a focus on the genomic events that have likely enabled the emergence and the dominance of the MTBC. We also review the recent literature describing the various MTBC lineages and highlight their particularities and differences with a focus on host preferences and geographic distribution. Finally, we discuss on putative mechanisms driving the evolution of tubercle bacilli and mycobacteria in general, by taking the mycobacteria-specific distributive conjugal transfer as an example.
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Affiliation(s)
- Mickael Orgeur
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Unit for Integrated Mycobacterial Pathogenomics, 75015 Paris, France
| | - Camille Sous
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Unit for Integrated Mycobacterial Pathogenomics, 75015 Paris, France
| | - Jan Madacki
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Unit for Integrated Mycobacterial Pathogenomics, 75015 Paris, France
- Institut Pasteur, Université Paris Cité, CNRS UMR 2000, Unit for Human Evolutionary Genetics, 75015 Paris, France
| | - Roland Brosch
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Unit for Integrated Mycobacterial Pathogenomics, 75015 Paris, France
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Schaible MJ, Szeinbaum N, Bozdag GO, Chou L, Grefenstette N, Colón-Santos S, Rodriguez LE, Styczinski MJ, Thweatt JL, Todd ZR, Vázquez-Salazar A, Adams A, Araújo MN, Altair T, Borges S, Burton D, Campillo-Balderas JA, Cangi EM, Caro T, Catalano E, Chen K, Conlin PL, Cooper ZS, Fisher TM, Fos SM, Garcia A, Glaser DM, Harman CE, Hermis NY, Hooks M, Johnson-Finn K, Lehmer O, Hernández-Morales R, Hughson KHG, Jácome R, Jia TZ, Marlow JJ, McKaig J, Mierzejewski V, Muñoz-Velasco I, Nural C, Oliver GC, Penev PI, Raj CG, Roche TP, Sabuda MC, Schaible GA, Sevgen S, Sinhadc P, Steller LH, Stelmach K, Tarnas J, Tavares F, Trubl G, Vidaurri M, Vincent L, Weber JM, Weng MM, Wilpiszeki RL, Young A. Chapter 1: The Astrobiology Primer 3.0. ASTROBIOLOGY 2024; 24:S4-S39. [PMID: 38498816 DOI: 10.1089/ast.2021.0129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
The Astrobiology Primer 3.0 (ABP3.0) is a concise introduction to the field of astrobiology for students and others who are new to the field of astrobiology. It provides an entry into the broader materials in this supplementary issue of Astrobiology and an overview of the investigations and driving hypotheses that make up this interdisciplinary field. The content of this chapter was adapted from the other 10 articles in this supplementary issue and thus represents the contribution of all the authors who worked on these introductory articles. The content of this chapter is not exhaustive and represents the topics that the authors found to be the most important and compelling in a dynamic and changing field.
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Affiliation(s)
- Micah J Schaible
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Nadia Szeinbaum
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - G Ozan Bozdag
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Luoth Chou
- NASA Goddard Space Flight Center, Greenbelt, Maryland, USA
- Center for Space Sciences and Technology, University of Maryland, Baltimore, Maryland, USA
- Georgetown University, Washington DC, USA
| | - Natalie Grefenstette
- Santa Fe Institute, Santa Fe, New Mexico, USA
- Blue Marble Space Institute of Science, Seattle, Washington, USA
| | - Stephanie Colón-Santos
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Wisconsin, USA
- Department of Botany, University of Wisconsin-Madison, Wisconsin, USA
| | - Laura E Rodriguez
- Lunar and Planetary Institute, Universities Space Research Association, Houston, Texas, USA
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - M J Styczinski
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
- University of Washington, Seattle, Washington, USA
| | - Jennifer L Thweatt
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania, USA
| | - Zoe R Todd
- Department of Earth and Space Sciences, University of Washington, Seattle, Washington, USA
| | - Alberto Vázquez-Salazar
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles, California, USA
| | - Alyssa Adams
- Center for Space Sciences and Technology, University of Maryland, Baltimore, Maryland, USA
| | - M N Araújo
- Biochemistry Department, University of São Paulo, São Carlos, Brazil
| | - Thiago Altair
- Institute of Chemistry of São Carlos, Universidade de São Paulo, São Carlos, Brazil
- Department of Chemistry, College of the Atlantic, Bar Harbor, Maine, USA
| | | | - Dana Burton
- Department of Anthropology, George Washington University, Washington DC, USA
| | | | - Eryn M Cangi
- Laboratory for Atmospheric and Space Physics, University of Colorado Boulder, Boulder, Colorado, USA
| | - Tristan Caro
- Department of Geological Sciences, University of Colorado Boulder, Boulder, Colorado, USA
| | - Enrico Catalano
- Sant'Anna School of Advanced Studies, The BioRobotics Institute, Pisa, Italy
| | - Kimberly Chen
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Peter L Conlin
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Z S Cooper
- Department of Earth and Space Sciences, University of Washington, Seattle, Washington, USA
| | - Theresa M Fisher
- School of Earth and Space Exploration, Arizona State University, Tempe, Arizona, USA
| | - Santiago Mestre Fos
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Amanda Garcia
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin, USA
| | - D M Glaser
- Arizona State University, Tempe, Arizona, USA
| | - Chester E Harman
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Ninos Y Hermis
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
- Department of Physics and Space Sciences, University of Granada, Granada, Spain
| | - M Hooks
- NASA Johnson Space Center, Houston, Texas, USA
| | - K Johnson-Finn
- Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo, Japan
- Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Owen Lehmer
- Department of Earth and Space Sciences, University of Washington, Seattle, Washington, USA
| | - Ricardo Hernández-Morales
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Kynan H G Hughson
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Rodrigo Jácome
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Tony Z Jia
- Blue Marble Space Institute of Science, Seattle, Washington, USA
- Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo, Japan
| | - Jeffrey J Marlow
- Department of Biology, Boston University, Boston, Massachusetts, USA
| | - Jordan McKaig
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Veronica Mierzejewski
- School of Earth and Space Exploration, Arizona State University, Tempe, Arizona, USA
| | - Israel Muñoz-Velasco
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Ceren Nural
- Istanbul Technical University, Istanbul, Turkey
| | - Gina C Oliver
- Department of Geology, San Bernardino Valley College, San Bernardino, California, USA
| | - Petar I Penev
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Chinmayee Govinda Raj
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Tyler P Roche
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Mary C Sabuda
- Department of Earth and Environmental Sciences, University of Minnesota-Twin Cities, Minneapolis, Minnesota, USA
- Biotechnology Institute, University of Minnesota-Twin Cities, St. Paul, Minnesota, USA
| | - George A Schaible
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Serhat Sevgen
- Blue Marble Space Institute of Science, Seattle, Washington, USA
- Institute of Marine Sciences, Middle East Technical University, Erdemli, Mersin, Turkey
| | - Pritvik Sinhadc
- BEYOND: Center For Fundamental Concepts in Science, Arizona State University, Arizona, USA
- Dubai College, Dubai, United Arab Emirates
| | - Luke H Steller
- Australian Centre for Astrobiology, and School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington, Australia
| | - Kamil Stelmach
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, USA
| | - J Tarnas
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Frank Tavares
- Space Enabled Research Group, MIT Media Lab, Cambridge, Massachusetts, USA
| | - Gareth Trubl
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Monica Vidaurri
- Center for Space Sciences and Technology, University of Maryland, Baltimore, Maryland, USA
- Department of Physics and Astronomy, Howard University, Washington DC, USA
| | - Lena Vincent
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Wisconsin, USA
| | - Jessica M Weber
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | | | | | - Amber Young
- NASA Goddard Space Flight Center, Greenbelt, Maryland, USA
- Northern Arizona University, Flagstaff, Arizona, USA
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Colón-Santos S, Vázquez-Salazar A, Adams A, Campillo-Balderas JA, Hernández-Morales R, Jácome R, Muñoz-Velasco I, Rodriguez LE, Schaible MJ, Schaible GA, Szeinbaum N, Thweatt JL, Trubl G. Chapter 2: What Is Life? ASTROBIOLOGY 2024; 24:S40-S56. [PMID: 38498820 DOI: 10.1089/ast.2021.0116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
The question "What is life?" has existed since the beginning of recorded history. However, the scientific and philosophical contexts of this question have changed and been refined as advancements in technology have revealed both fine details and broad connections in the network of life on Earth. Understanding the framework of the question "What is life?" is central to formulating other questions such as "Where else could life be?" and "How do we search for life elsewhere?" While many of these questions are addressed throughout the Astrobiology Primer 3.0, this chapter gives historical context for defining life, highlights conceptual characteristics shared by all life on Earth as well as key features used to describe it, discusses why it matters for astrobiology, and explores both challenges and opportunities for finding an informative operational definition.
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Affiliation(s)
- Stephanie Colón-Santos
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Wisconsin, USA
- Department of Botany, University of Wisconsin-Madison, Wisconsin, USA
| | - Alberto Vázquez-Salazar
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles, California, USA
| | - Alyssa Adams
- Department of Botany, University of Wisconsin-Madison, Wisconsin, USA
| | | | - Ricardo Hernández-Morales
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Rodrigo Jácome
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Israel Muñoz-Velasco
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Laura E Rodriguez
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
- Lunar and Planetary Institute, Universities Space Research Association, Houston, Texas, USA
| | - Micah J Schaible
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - George A Schaible
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Nadia Szeinbaum
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Jennifer L Thweatt
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania, USA. (Former)
| | - Gareth Trubl
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
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