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Secaira-Morocho H, Chede A, Gonzalez-de-Salceda L, Garcia-Pichel F, Zhu Q. An evolutionary optimum amid moderate heritability in prokaryotic cell size. Cell Rep 2024; 43:114268. [PMID: 38776226 DOI: 10.1016/j.celrep.2024.114268] [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: 01/04/2024] [Revised: 04/11/2024] [Accepted: 05/08/2024] [Indexed: 05/24/2024] Open
Abstract
We investigate the distribution and evolution of prokaryotic cell size based on a compilation of 5,380 species. Size spans four orders of magnitude, from 100 nm (Mycoplasma) to more than 1 cm (Thiomargarita); however, most species congregate heavily around the mean. The distribution approximates but is distinct from log normality. Comparative phylogenetics suggests that size is heritable, yet the phylogenetic signal is moderate, and the degree of heritability is independent of taxonomic scale (i.e., fractal). Evolutionary modeling indicates the presence of an optimal cell size to which most species gravitate. The size is equivalent to a coccus of 0.70 μm in diameter. Analyses of 1,361 species with sequenced genomes show that genomic traits contribute to size evolution moderately and synergistically. Given our results, scaling theory, and empirical evidence, we discuss potential drivers that may expand or shrink cells around the optimum and propose a stability landscape model for prokaryotic cell size.
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Affiliation(s)
- Henry Secaira-Morocho
- Center for Fundamental and Applied Microbiomics and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Abhinav Chede
- Center for Fundamental and Applied Microbiomics and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Luis Gonzalez-de-Salceda
- Center for Fundamental and Applied Microbiomics and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Ferran Garcia-Pichel
- Center for Fundamental and Applied Microbiomics and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA.
| | - Qiyun Zhu
- Center for Fundamental and Applied Microbiomics and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
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2
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Yamasaki H, Itoh RD, Mizumoto KB, Yoshida YS, Otaki JM, Cohen MF. Spatiotemporal Characteristics Determining the Multifaceted Nature of Reactive Oxygen, Nitrogen, and Sulfur Species in Relation to Proton Homeostasis. Antioxid Redox Signal 2024. [PMID: 38407968 DOI: 10.1089/ars.2023.0544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Significance: Reactive oxygen species (ROS), reactive nitrogen species (RNS), and reactive sulfur species (RSS) act as signaling molecules, regulating gene expression, enzyme activity, and physiological responses. However, excessive amounts of these molecular species can lead to deleterious effects, causing cellular damage and death. This dual nature of ROS, RNS, and RSS presents an intriguing conundrum that calls for a new paradigm. Recent Advances: Recent advancements in the study of photosynthesis have offered significant insights at the molecular level and with high temporal resolution into how the photosystem II oxygen-evolving complex manages to prevent harmful ROS production during the water-splitting process. These findings suggest that a dynamic spatiotemporal arrangement of redox reactions, coupled with strict regulation of proton transfer, is crucial for minimizing unnecessary ROS formation. Critical Issues: To better understand the multifaceted nature of these reactive molecular species in biology, it is worth considering a more holistic view that combines ecological and evolutionary perspectives on ROS, RNS, and RSS. By integrating spatiotemporal perspectives into global, cellular, and biochemical events, we discuss local pH or proton availability as a critical determinant associated with the generation and action of ROS, RNS, and RSS in biological systems. Future Directions: The concept of localized proton availability will not only help explain the multifaceted nature of these ubiquitous simple molecules in diverse systems but also provide a basis for new therapeutic strategies to manage and manipulate these reactive species in neural disorders, pathogenic diseases, and antiaging efforts.
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Affiliation(s)
- Hideo Yamasaki
- Faculty of Science, University of the Ryukyus, Okinawa, Japan
| | - Ryuuichi D Itoh
- Faculty of Science, University of the Ryukyus, Okinawa, Japan
| | | | - Yuki S Yoshida
- Faculty of Science, University of the Ryukyus, Okinawa, Japan
| | - Joji M Otaki
- Faculty of Science, University of the Ryukyus, Okinawa, Japan
| | - Michael F Cohen
- University of California Cooperative Extension, Santa Clara County, San Jose, California, USA
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3
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Thweatt JL, Harman CE, Araújo MN, Marlow JJ, Oliver GC, Sabuda MC, Sevgen S, Wilpiszeki RL. Chapter 6: The Breadth and Limits of Life on Earth. ASTROBIOLOGY 2024; 24:S124-S142. [PMID: 38498824 DOI: 10.1089/ast.2021.0131] [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
Scientific ideas about the potential existence of life elsewhere in the universe are predominantly informed by knowledge about life on Earth. Over the past ∼4 billion years, life on Earth has evolved into millions of unique species. Life now inhabits nearly every environmental niche on Earth that has been explored. Despite the wide variety of species and diverse biochemistry of modern life, many features, such as energy production mechanisms and nutrient requirements, are conserved across the Tree of Life. Such conserved features help define the operational parameters required by life and therefore help direct the exploration and evaluation of habitability in extraterrestrial environments. As new diversity in the Tree of Life continues to expand, so do the known limits of life on Earth and the range of environments considered habitable elsewhere. The metabolic processes used by organisms living on the edge of habitability provide insights into the types of environments that would be most suitable to hosting extraterrestrial life, crucial for planning and developing future astrobiology missions. This chapter will introduce readers to the breadth and limits of life on Earth and show how the study of life at the extremes can inform the broader field of astrobiology.
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Affiliation(s)
- Jennifer L Thweatt
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania, USA. (Former)
| | - C E Harman
- Planetary Systems Branch, NASA Ames Research Center, Moffett Field, California, USA
| | - M N Araújo
- Biochemistry Department, University of São Paulo, São Carlos, Brazil
| | - Jeffrey J Marlow
- Department of Biology, Boston University, Boston, Massachusetts, USA
| | - Gina C Oliver
- Department of Geology, San Bernardino Valley College, San Bernardino, California, 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
| | - Serhat Sevgen
- Institute of Marine Sciences, Middle East Technical University, Erdemli, Mersin, Turkey
- Blue Marble Space Institute of Science, Seattle, Washington, USA
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4
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Benisch R, Andreas MP, Giessen TW. A widespread bacterial protein compartment sequesters and stores elemental sulfur. SCIENCE ADVANCES 2024; 10:eadk9345. [PMID: 38306423 PMCID: PMC10836720 DOI: 10.1126/sciadv.adk9345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 01/03/2024] [Indexed: 02/04/2024]
Abstract
Subcellular compartments often serve to store nutrients or sequester labile or toxic compounds. As bacteria mostly do not possess membrane-bound organelles, they often have to rely on protein-based compartments. Encapsulins are one of the most prevalent protein-based compartmentalization strategies found in prokaryotes. Here, we show that desulfurase encapsulins can sequester and store large amounts of crystalline elemental sulfur. We determine the 1.78-angstrom cryo-EM structure of a 24-nanometer desulfurase-loaded encapsulin. Elemental sulfur crystals can be formed inside the encapsulin shell in a desulfurase-dependent manner with l-cysteine as the sulfur donor. Sulfur accumulation can be influenced by the concentration and type of sulfur source in growth medium. The selectively permeable protein shell allows the storage of redox-labile elemental sulfur by excluding cellular reducing agents, while encapsulation substantially improves desulfurase activity and stability. These findings represent an example of a protein compartment able to accumulate and store elemental sulfur.
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Affiliation(s)
- Robert Benisch
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Michael P. Andreas
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Tobias W. Giessen
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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5
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Hosokawa M, Nishikawa Y. Tools for microbial single-cell genomics for obtaining uncultured microbial genomes. Biophys Rev 2024; 16:69-77. [PMID: 38495448 PMCID: PMC10937852 DOI: 10.1007/s12551-023-01124-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 08/23/2023] [Indexed: 03/19/2024] Open
Abstract
The advent of next-generation sequencing technologies has facilitated the acquisition of large amounts of DNA sequence data at a relatively low cost, leading to numerous breakthroughs in decoding microbial genomes. Among the various genome sequencing activities, metagenomic analysis, which entails the direct analysis of uncultured microbial DNA, has had a profound impact on microbiome research and has emerged as an indispensable technology in this field. Despite its valuable contributions, metagenomic analysis is a "bulk analysis" technique that analyzes samples containing a wide diversity of microbes, such as bacteria, yielding information that is averaged across the entire microbial population. In order to gain a deeper understanding of the heterogeneous nature of the microbial world, there is a growing need for single-cell analysis, similar to its use in human cell biology. With this paradigm shift in mind, comprehensive single-cell genomics technology has become a much-anticipated innovation that is now poised to revolutionize microbiome research. It has the potential to enable the discovery of differences at the strain level and to facilitate a more comprehensive examination of microbial ecosystems. In this review, we summarize the current state-of-the-art in microbial single-cell genomics, highlighting the potential impact of this technology on our understanding of the microbial world. The successful implementation of this technology is expected to have a profound impact in the field, leading to new discoveries and insights into the diversity and evolution of microbes.
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Affiliation(s)
- Masahito Hosokawa
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-Cho, Shinjuku-Ku, Tokyo, 162-8480 Japan
- Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, 3-4-1 Okubo, Shinjuku-Ku, Tokyo, 169-8555 Japan
- Research Organization for Nano and Life Innovation, Waseda University, 513 Wasedatsurumaki-Cho, Shinjuku-Ku, Tokyo, 162-0041 Japan
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, 3-4-1 Okubo, Shinjuku-Ku, Tokyo, 169-8555 Japan
- bitBiome, Inc., 513 Wasedatsurumaki-Cho, Shinjuku-Ku, Tokyo, 162-0041 Japan
| | - Yohei Nishikawa
- Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, 3-4-1 Okubo, Shinjuku-Ku, Tokyo, 169-8555 Japan
- Research Organization for Nano and Life Innovation, Waseda University, 513 Wasedatsurumaki-Cho, Shinjuku-Ku, Tokyo, 162-0041 Japan
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6
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Miao L, Yin Z, Knoll AH, Qu Y, Zhu M. 1.63-billion-year-old multicellular eukaryotes from the Chuanlinggou Formation in North China. SCIENCE ADVANCES 2024; 10:eadk3208. [PMID: 38266082 PMCID: PMC10807817 DOI: 10.1126/sciadv.adk3208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 12/21/2023] [Indexed: 01/26/2024]
Abstract
Multicellularity is key to the functional and ecological success of the Eukarya, underpinning much of their modern diversity in both terrestrial and marine ecosystems. Despite the widespread occurrence of simple multicellular organisms among eukaryotes, when this innovation arose remains an open question. Here, we report cellularly preserved multicellular microfossils (Qingshania magnifica) from the ~1635-million-year-old Chuanlinggou Formation, North China. The fossils consist of large uniseriate, unbranched filaments with cell diameters up to 190 micrometers; spheroidal structures, possibly spores, occur within some cells. In combination with spectroscopic characteristics, the large size and morphological complexity of these fossils support their interpretation as eukaryotes, likely photosynthetic, based on comparisons with extant organisms. The occurrence of multicellular eukaryotes in Paleoproterozoic rocks not much younger than those containing the oldest unambiguous evidence of eukaryotes as a whole supports the hypothesis that simple multicellularity arose early in eukaryotic history, as much as a billion years before complex multicellular organisms diversified in the oceans.
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Affiliation(s)
- Lanyun Miao
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Zongjun Yin
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Andrew H. Knoll
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Yuangao Qu
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
| | - Maoyan Zhu
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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7
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Sannino DR, Arroyo FA, Pepe-Ranney C, Chen W, Volland JM, Elisabeth NH, Angert ER. The exceptional form and function of the giant bacterium Ca. Epulopiscium viviparus revolves around its sodium motive force. Proc Natl Acad Sci U S A 2023; 120:e2306160120. [PMID: 38109545 PMCID: PMC10756260 DOI: 10.1073/pnas.2306160120] [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: 04/16/2023] [Accepted: 11/09/2023] [Indexed: 12/20/2023] Open
Abstract
Epulopiscium spp. are the largest known heterotrophic bacteria; a large cigar-shaped individual is a million times the volume of Escherichia coli. To better understand the metabolic potential and relationship of Epulopiscium sp. type B with its host Naso tonganus, we generated a high-quality draft genome from a population of cells taken from a single fish. We propose the name Candidatus Epulopiscium viviparus to describe populations of this best-characterized Epulopiscium species. Metabolic reconstruction reveals more than 5% of the genome codes for carbohydrate active enzymes, which likely degrade recalcitrant host-diet algal polysaccharides into substrates that may be fermented to acetate, the most abundant short-chain fatty acid in the intestinal tract. Moreover, transcriptome analyses and the concentration of sodium ions in the host intestinal tract suggest that the use of a sodium motive force (SMF) to drive ATP synthesis and flagellar rotation is integral to symbiont metabolism and cellular biology. In natural populations, genes encoding both F-type and V-type ATPases and SMF generation via oxaloacetate decarboxylation are among the most highly expressed, suggesting that ATPases synthesize ATP and balance ion concentrations across the cell membrane. High expression of these and other integral membrane proteins may allow for the growth of its extensive intracellular membrane system. Further, complementary metabolism between microbe and host is implied with the potential provision of nitrogen and B vitamins to reinforce this nutritional symbiosis. The few features shared by all bacterial behemoths include extreme polyploidy, polyphosphate synthesis, and thus far, they have all resisted cultivation in the lab.
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Affiliation(s)
| | | | - Charles Pepe-Ranney
- Soil & Crop Sciences Section, School of Integrative Plant Sciences, Cornell University, Ithaca, NY14853
| | - Wenbo Chen
- Department of Microbiology, Cornell University, Ithaca, NY14853
| | - Jean-Marie Volland
- Laboratory for Research in Complex Systems, Menlo Park, CA94025
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Nathalie H. Elisabeth
- Department of Energy Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA94720
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8
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Baum B, Spang A. On the origin of the nucleus: a hypothesis. Microbiol Mol Biol Rev 2023; 87:e0018621. [PMID: 38018971 PMCID: PMC10732040 DOI: 10.1128/mmbr.00186-21] [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: 11/30/2023] Open
Abstract
SUMMARYIn this hypothesis article, we explore the origin of the eukaryotic nucleus. In doing so, we first look afresh at the nature of this defining feature of the eukaryotic cell and its core functions-emphasizing the utility of seeing the eukaryotic nucleoplasm and cytoplasm as distinct regions of a common compartment. We then discuss recent progress in understanding the evolution of the eukaryotic cell from archaeal and bacterial ancestors, focusing on phylogenetic and experimental data which have revealed that many eukaryotic machines with nuclear activities have archaeal counterparts. In addition, we review the literature describing the cell biology of representatives of the TACK and Asgardarchaeaota - the closest known living archaeal relatives of eukaryotes. Finally, bringing these strands together, we propose a model for the archaeal origin of the nucleus that explains much of the current data, including predictions that can be used to put the model to the test.
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Affiliation(s)
- Buzz Baum
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Anja Spang
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Den Burg, the Netherlands
- Department of Evolutionary & Population Biology, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, the Netherlands
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Den Burg, the Netherlands
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9
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G S J S, Ramakodi MP, T V B P S R. Review of bioaerosols from different sources and their health impacts. ENVIRONMENTAL MONITORING AND ASSESSMENT 2023; 195:1321. [PMID: 37840110 DOI: 10.1007/s10661-023-11935-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 10/04/2023] [Indexed: 10/17/2023]
Abstract
The emission of bioaerosols in the ambient atmosphere from different sources is a cause of concern for human health and the environment. Bioaerosols are a combination of biotic matter like microbes and pollens. The present review emphasizes the understanding of various sources of bioaerosols (industries, municipal solid waste, and medical facilities), their components, and their impact on human health. The study of bioaerosols is of great importance as large numbers of people are estimated to be exposed on the global scale. Bioaerosols exposure in different work environments results in health issues such as infectious diseases, allergies, toxic effects, and respiratory problems. Hence, extensive research is urged to establish an effective assessment of bioaerosols exposure in the workplace, risks involved, distribution, and validation. The present review is intended to explore the relationship between bioaerosols exposure to the atmosphere and its impacts on human health. Some of the preliminary findings, based on our analysis of bioaerosols arising from municipal solid waste at a landfill site and a waste transfer station in Hyderabad, India, are also discussed herein.
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Affiliation(s)
- Shailaja G S J
- CSIR - National Environmental Engineering Research Institute (NEERI), Hyderabad Zonal Centre, IICT Campus, Uppal Road, Hyderabad, 500 007, India.
| | - Meganathan P Ramakodi
- CSIR - National Environmental Engineering Research Institute (NEERI), Hyderabad Zonal Centre, IICT Campus, Uppal Road, Hyderabad, 500 007, India
| | - Ramakrishna T V B P S
- CSIR - National Environmental Engineering Research Institute (NEERI), Hyderabad Zonal Centre, IICT Campus, Uppal Road, Hyderabad, 500 007, India
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10
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López-García P, Gutiérrez-Preciado A, Krupovic M, Ciobanu M, Deschamps P, Jardillier L, López-Pérez M, Rodríguez-Valera F, Moreira D. Metagenome-derived virus-microbe ratios across ecosystems. THE ISME JOURNAL 2023; 17:1552-1563. [PMID: 37169871 PMCID: PMC10504350 DOI: 10.1038/s41396-023-01431-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 04/20/2023] [Accepted: 05/03/2023] [Indexed: 05/13/2023]
Abstract
It is generally assumed that viruses outnumber cells on Earth by at least tenfold. Virus-to-microbe ratios (VMR) are largely based on counts of fluorescently labelled virus-like particles. However, these exclude intracellular viruses and potentially include false positives (DNA-containing vesicles, gene-transfer agents, unspecifically stained inert particles). Here, we develop a metagenome-based VMR estimate (mVRM) that accounts for DNA viruses across all stages of their replication cycles (virion, intracellular lytic and lysogenic) by using normalised RPKM (reads per kilobase of gene sequence per million of mapped metagenome reads) counts of the major capsid protein (MCP) genes and cellular universal single-copy genes (USCGs) as proxies for virus and cell counts, respectively. After benchmarking this strategy using mock metagenomes with increasing VMR, we inferred mVMR across different biomes. To properly estimate mVMR in aquatic ecosystems, we generated metagenomes from co-occurring cellular and viral fractions (>50 kDa-200 µm size-range) in freshwater, seawater and solar saltern ponds (10 metagenomes, 2 control metaviromes). Viruses outnumbered cells in freshwater by ~13 fold and in plankton from marine and saline waters by ~2-4 fold. However, across an additional set of 121 diverse non-aquatic metagenomes including microbial mats, microbialites, soils, freshwater and marine sediments and metazoan-associated microbiomes, viruses, on average, outnumbered cells by barely two-fold. Although viruses likely are the most diverse biological entities on Earth, their global numbers might be closer to those of cells than previously estimated.
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Affiliation(s)
- Purificación López-García
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France.
| | - Ana Gutiérrez-Preciado
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris, France
| | - Maria Ciobanu
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
| | - Philippe Deschamps
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
| | - Ludwig Jardillier
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
| | - Mario López-Pérez
- Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | | | - David Moreira
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
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11
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Geelhoed JS, Thorup CA, Bjerg JJ, Schreiber L, Nielsen LP, Schramm A, Meysman FJR, Marshall IPG. Indications for a genetic basis for big bacteria and description of the giant cable bacterium Candidatus Electrothrix gigas sp. nov. Microbiol Spectr 2023; 11:e0053823. [PMID: 37732806 PMCID: PMC10580974 DOI: 10.1128/spectrum.00538-23] [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: 02/10/2023] [Accepted: 07/21/2023] [Indexed: 09/22/2023] Open
Abstract
Bacterial cells can vary greatly in size, from a few hundred nanometers to hundreds of micrometers in diameter. Filamentous cable bacteria also display substantial size differences, with filament diameters ranging from 0.4 to 8 µm. We analyzed the genomes of cable bacterium filaments from 11 coastal environments of which the resulting 23 new genomes represent 10 novel species-level clades of Candidatus Electrothrix and two clades that putatively represent novel genus-level diversity. Fluorescence in situ hybridization with a species-level probe showed that large-sized cable bacteria belong to a novel species with the proposed name Ca. Electrothrix gigas. Comparative genome analysis suggests genes that play a role in the construction or functioning of large cable bacteria cells: the genomes of Ca. Electrothrix gigas encode a novel actin-like protein as well as a species-specific gene cluster encoding four putative pilin proteins and a putative type II secretion platform protein, which are not present in other cable bacteria. The novel actin-like protein was also found in a number of other giant bacteria, suggesting there could be a genetic basis for large cell size. This actin-like protein (denoted big bacteria protein, Bbp) may have a function analogous to other actin proteins in cell structure or intracellular transport. We contend that Bbp may help overcome the challenges of diffusion limitation and/or morphological complexity presented by the large cells of Ca. Electrothrix gigas and other giant bacteria. IMPORTANCE In this study, we substantially expand the known diversity of marine cable bacteria and describe cable bacteria with a large diameter as a novel species with the proposed name Candidatus Electrothrix gigas. In the genomes of this species, we identified a gene that encodes a novel actin-like protein [denoted big bacteria protein (Bbp)]. The bbp gene was also found in a number of other giant bacteria, predominantly affiliated to Desulfobacterota and Gammaproteobacteria, indicating that there may be a genetic basis for large cell size. Thus far, mostly structural adaptations of giant bacteria, vacuoles, and other inclusions or organelles have been observed, which are employed to overcome nutrient diffusion limitation in their environment. In analogy to other actin proteins, Bbp could fulfill a structural role in the cell or potentially facilitate intracellular transport.
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Affiliation(s)
- Jeanine S. Geelhoed
- Department of Biology, Research Group Geobiology, University of Antwerp, Wilrijk, Belgium
| | - Casper A. Thorup
- Department of Biology, Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
| | - Jesper J. Bjerg
- Department of Biology, Research Group Geobiology, University of Antwerp, Wilrijk, Belgium
- Department of Biology, Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
| | - Lars Schreiber
- Department of Biology, Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
| | - Lars Peter Nielsen
- Department of Biology, Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
| | - Andreas Schramm
- Department of Biology, Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
| | - Filip J. R. Meysman
- Department of Biology, Research Group Geobiology, University of Antwerp, Wilrijk, Belgium
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands
| | - Ian P. G. Marshall
- Department of Biology, Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
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12
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Abstract
The origin of modern eukaryotes is one of the key transitions in life's history, and also one of the least understood. Although the fossil record provides the most direct view of this process, interpreting the fossils of early eukaryotes and eukaryote-grade organisms is not straightforward. We present two end-member models for the evolution of modern (i.e., crown) eukaryotes-one in which modern eukaryotes evolved early, and another in which they evolved late-and interpret key fossils within these frameworks, including where they might fit in eukaryote phylogeny and what they may tell us about the evolution of eukaryotic cell biology and ecology. Each model has different implications for understanding the rise of complex life on Earth, including different roles of Earth surface oxygenation, and makes different predictions that future paleontological studies can test.
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Affiliation(s)
- Susannah M Porter
- Department of Earth Science, University of California at Santa Barbara, Santa Barbara, California, USA;
| | - Leigh Anne Riedman
- Department of Earth Science, University of California at Santa Barbara, Santa Barbara, California, USA;
- Earth Research Institute, University of California at Santa Barbara, Santa Barbara, California, USA;
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13
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Arikawa K, Hosokawa M. Uncultured prokaryotic genomes in the spotlight: An examination of publicly available data from metagenomics and single-cell genomics. Comput Struct Biotechnol J 2023; 21:4508-4518. [PMID: 37771751 PMCID: PMC10523443 DOI: 10.1016/j.csbj.2023.09.010] [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: 06/15/2023] [Revised: 09/10/2023] [Accepted: 09/10/2023] [Indexed: 09/30/2023] Open
Abstract
Owing to the ineffectiveness of traditional culture techniques for the vast majority of microbial species, culture-independent analyses utilizing next-generation sequencing and bioinformatics have become essential for gaining insight into microbial ecology and function. This mini-review focuses on two essential methods for obtaining genetic information from uncultured prokaryotes, metagenomics and single-cell genomics. We analyzed the registration status of uncultured prokaryotic genome data from major public databases and assessed the advantages and limitations of both the methods. Metagenomics generates a significant quantity of sequence data and multiple prokaryotic genomes using straightforward experimental procedures. However, in ecosystems with high microbial diversity, such as soil, most genes are presented as brief, disconnected contigs, and lack association of highly conserved genes and mobile genetic elements with individual species genomes. Although technically more challenging, single-cell genomics offers valuable insights into complex ecosystems by providing strain-resolved genomes, addressing issues in metagenomics. Recent technological advancements, such as long-read sequencing, machine learning algorithms, and in silico protein structure prediction, in combination with vast genomic data, have the potential to overcome the current technical challenges and facilitate a deeper understanding of uncultured microbial ecosystems and microbial dark matter genes and proteins. In light of this, it is imperative that continued innovation in both methods and technologies take place to create high-quality reference genome databases that will support future microbial research and industrial applications.
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Affiliation(s)
- Koji Arikawa
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
- bitBiome, Inc., 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo 162-0041, Japan
| | - Masahito Hosokawa
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
- bitBiome, Inc., 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo 162-0041, Japan
- Research Organization for Nano and Life Innovation, Waseda University, 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo 162-0041, Japan
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
- Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
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14
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Ionescu D, Volland JM, Contarini PE, Gros O. Genomic Mysteries of Giant Bacteria: Insights and Implications. Genome Biol Evol 2023; 15:evad163. [PMID: 37708391 PMCID: PMC10519445 DOI: 10.1093/gbe/evad163] [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: 03/27/2023] [Revised: 08/18/2023] [Accepted: 09/01/2023] [Indexed: 09/16/2023] Open
Abstract
Bacteria and Archaea are traditionally regarded as organisms with a simple morphology constrained to a size of 2-3 µm. Nevertheless, the history of microbial research is rich in the description of giant bacteria exceeding tens and even hundreds of micrometers in length or diameter already from its early days, for example, Beggiatoa spp., to the present, for example, Candidatus Thiomargarita magnifica. While some of these giants are still being studied, some were lost to science, with merely drawings and photomicrographs as evidence for their existence. The physiology and biogeochemical role of giant bacteria have been studied, with a large focus on those involved in the sulfur cycle. With the onset of the genomic era, no special emphasis has been given to this group, in an attempt to gain a novel, evolutionary, and molecular understanding of the phenomenon of bacterial gigantism. The few existing genomic studies reveal a mysterious world of hyperpolyploid bacteria with hundreds to hundreds of thousands of chromosomes that are, in some cases, identical and in others, extremely different. These studies on giant bacteria reveal novel organelles, cellular compartmentalization, and novel mechanisms to combat the accumulation of deleterious mutations in polyploid bacteria. In this perspective paper, we provide a brief overview of what is known about the genomics of giant bacteria and build on that to highlight a few burning questions that await to be addressed.
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Affiliation(s)
- Danny Ionescu
- Department of Plankton and Microbial Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Neuglobsow, Germany
| | - Jean-Marie Volland
- Laboratory for Research in Complex Systems, Menlo Park, California, USA
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Paul-Emile Contarini
- Laboratory for Research in Complex Systems, Menlo Park, California, USA
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Pointe-à-Pitre, France
| | - Olivier Gros
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Pointe-à-Pitre, France
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15
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Gollo G. On the emergence of eukaryotes and other enigmas. Biosystems 2023; 231:104958. [PMID: 37442362 DOI: 10.1016/j.biosystems.2023.104958] [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: 01/30/2023] [Revised: 05/20/2023] [Accepted: 06/15/2023] [Indexed: 07/15/2023]
Abstract
The origin of eukaryotes is one of the most fundamental problems in the entire history of life. How did eukaryotes arise? Previous attempts to solve the problem are very far from an answer, at best they propose a solution to one of the various innovations that ended up culminating in eukaryotes. Based on a hypothetical-deductive methodology, as usual in evolutionary issues, I propose that eukaryotes emerged from the endosymbiotic association between a flagellate parasite and its host, of which the sperm is the main vestige. The hypothesis unifies the solution to the vast array of acquisitions shared by eukaryotes that differentiate them from other beings, remarkably cell nucleus, mitosis, meiosis and sexual reproduction. The solution has a deep impact on understanding the origin and functioning of all complex life forms.
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Affiliation(s)
- Gustavo Gollo
- Universidade de Brasília, Eecologia, Brasilia, DF, Brazil.
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16
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Kurakin G. Lipoxygenase in a Giant Sulfur Bacterium: An Evolutionary Solution for Size and Complexity? BIOCHEMISTRY. BIOKHIMIIA 2023; 88:842-845. [PMID: 37748879 DOI: 10.1134/s0006297923060111] [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: 04/17/2023] [Revised: 04/17/2023] [Accepted: 05/02/2023] [Indexed: 09/27/2023]
Abstract
Discovery of Thiomargarita magnifica - an exceptionally large giant sulfur bacterium - urges us to pay additional attention to the giant sulfur bacteria and to revisit our recent bioinformatic finding of lipoxygenases in the representatives of the genus Beggiatoa. These close relatives of Thiomargarita magnifica meet the similar size requirements by forming multicellular structures. We hypothesize that their lipoxygenases are a part of the oxylipin signaling system that provides high level of cell-to-cell signaling complexity which, in turn, enables them to reach large sizes.
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Affiliation(s)
- Georgy Kurakin
- Pirogov Russian National Research Medical University, Moscow, 117997, Russia.
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17
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Booth JM, Fusi M, Marasco R, Daffonchio D. The microbial landscape in bioturbated mangrove sediment: A resource for promoting nature-based solutions for mangroves. Microb Biotechnol 2023. [PMID: 37209285 PMCID: PMC10364319 DOI: 10.1111/1751-7915.14273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 04/25/2023] [Accepted: 04/30/2023] [Indexed: 05/22/2023] Open
Abstract
Globally, soils and sediments are affected by the bioturbation activities of benthic species. The consequences of these activities are particularly impactful in intertidal sediment, which is generally anoxic and nutrient-poor. Mangrove intertidal sediments are of particular interest because, as the most productive forests and one of the most important stores of blue carbon, they provide global-scale ecosystem services. The mangrove sediment microbiome is fundamental for ecosystem functioning, influencing the efficiency of nutrient cycling and the abundance and distribution of key biological elements. Redox reactions in bioturbated sediment can be extremely complex, with one reaction creating a cascade effect on the succession of respiration pathways. This facilitates the overlap of different respiratory metabolisms important in the element cycles of the mangrove sediment, including carbon, nitrogen, sulphur and iron cycles, among others. Considering that all ecological functions and services provided by mangrove environments involve microorganisms, this work reviews the microbial roles in nutrient cycling in relation to bioturbation by animals and plants, the main mangrove ecosystem engineers. We highlight the diversity of bioturbating organisms and explore the diversity, dynamics and functions of the sediment microbiome, considering both the impacts of bioturbation. Finally, we review the growing evidence that bioturbation, through altering the sediment microbiome and environment, determining a 'halo effect', can ameliorate conditions for plant growth, highlighting the potential of the mangrove microbiome as a nature-based solution to sustain mangrove development and support the role of this ecosystem to deliver essential ecological services.
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Affiliation(s)
- Jenny M Booth
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Centre (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Coastal Research Group, Department of Zoology and Entomology, Rhodes University, Grahamstown, South Africa
| | - Marco Fusi
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Centre (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Centre for Conservation and Restoration Science, School of Applied Sciences, Edinburgh Napier University, Edinburgh, UK
- Joint Nature Conservation Committee, Peterborough, UK
| | - Ramona Marasco
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Centre (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Daniele Daffonchio
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Centre (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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18
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Garcia AC, Pluth MD. Solubilization of elemental sulfur by surfactants promotes reduction to H 2S by thiols. Chem Commun (Camb) 2023; 59:6702-6705. [PMID: 37190948 DOI: 10.1039/d3cc01914d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Elemental sulfur (S8) may contribute to sulfane sulfur (S0) storage in biological systems. We demonstrate that surfactants can solubilize S8 in water and promote S8 reduction to H2S by thiols. Moreover, anionic and cationic surfactants interact differently with intermediate S0 carriers, highlighting how specific hydrophobic microenvironments impact reactive sulfur species.
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Affiliation(s)
- Arman C Garcia
- Department of Chemistry and Biochemistry, Materials Science Institute, Knight Campus for Accelerating Scientific Impact, and Institute of Molecular Biology, University of Oregon, Eugene, Oregon, 97403-12532, USA.
| | - Michael D Pluth
- Department of Chemistry and Biochemistry, Materials Science Institute, Knight Campus for Accelerating Scientific Impact, and Institute of Molecular Biology, University of Oregon, Eugene, Oregon, 97403-12532, USA.
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19
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Li G, Chen L, Pang K, Tang Q, Wu C, Yuan X, Zhou C, Xiao S. Tonian carbonaceous compressions indicate that Horodyskia is one of the oldest multicellular and coenocytic macro-organisms. Commun Biol 2023; 6:399. [PMID: 37046079 PMCID: PMC10097871 DOI: 10.1038/s42003-023-04740-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 03/21/2023] [Indexed: 04/14/2023] Open
Abstract
Macrofossils with unambiguous biogenic origin and predating the one-billion-year-old multicellular fossils Bangiomorpha and Proterocladus interpreted as crown-group eukaryotes are quite rare. Horodyskia is one of these few macrofossils, and it extends from the early Mesoproterozoic Era to the terminal Ediacaran Period. The biological interpretation of this enigmatic fossil, however, has been a matter of controversy since its discovery in 1982, largely because there was no evidence for the preservation of organic walls. Here we report new carbonaceous compressions of Horodyskia from the Tonian successions (~950-720 Ma) in North China. The macrofossils herein with bona fide organic walls reinforce the biogenicity of Horodyskia. Aided by the new material, we reconstruct Horodyskia as a colonial organism composed of a chain of organic-walled vesicles that likely represent multinucleated (coenocytic) cells of early eukaryotes. Two species of Horodyskia are differentiated on the basis of vesicle sizes, and their co-existence in the Tonian assemblage provides a link between the Mesoproterozoic (H. moniliformis) and the Ediacaran (H. minor) species. Our study thus provides evidence that eukaryotes have acquired macroscopic size through the combination of coenocytism and colonial multicellularity at least ~1.48 Ga, and highlights an exceptionally long range and morphological stasis of this Proterozoic macrofossils.
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Affiliation(s)
- Guangjin Li
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Palaeoenvironment, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Lei Chen
- College of Earth Science and Engineering, Shandong University of Science and Technology, Qingdao, 266590, China.
| | - Ke Pang
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Palaeoenvironment, Chinese Academy of Sciences, Nanjing, 210008, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- University of Chinese Academy of Sciences, Nanjing, 211135, China.
| | - Qing Tang
- State Key Laboratory for Mineral Deposits Research, School of Earth Sciences and Engineering, Nanjing University, Nanjing, 210023, China
- Department of Earth Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Chengxi Wu
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Palaeoenvironment, Chinese Academy of Sciences, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xunlai Yuan
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Palaeoenvironment, Chinese Academy of Sciences, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chuanming Zhou
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Palaeoenvironment, Chinese Academy of Sciences, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- University of Chinese Academy of Sciences, Nanjing, 211135, China
| | - Shuhai Xiao
- Department of Geosciences and Global Change Center, Virginia Tech, Blacksburg, VA, 24061, USA
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20
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Qian L, Yu X, Gu H, Liu F, Fan Y, Wang C, He Q, Tian Y, Peng Y, Shu L, Wang S, Huang Z, Yan Q, He J, Liu G, Tu Q, He Z. Vertically stratified methane, nitrogen and sulphur cycling and coupling mechanisms in mangrove sediment microbiomes. MICROBIOME 2023; 11:71. [PMID: 37020239 PMCID: PMC10074775 DOI: 10.1186/s40168-023-01501-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 02/20/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Mangrove ecosystems are considered as hot spots of biogeochemical cycling, yet the diversity, function and coupling mechanism of microbially driven biogeochemical cycling along the sediment depth of mangrove wetlands remain elusive. Here we investigated the vertical profile of methane (CH4), nitrogen (N) and sulphur (S) cycling genes/pathways and their potential coupling mechanisms using metagenome sequencing approaches. RESULTS Our results showed that the metabolic pathways involved in CH4, N and S cycling were mainly shaped by pH and acid volatile sulphide (AVS) along a sediment depth, and AVS was a critical electron donor impacting mangrove sediment S oxidation and denitrification. Gene families involved in S oxidation and denitrification significantly (P < 0.05) decreased along the sediment depth and could be coupled by S-driven denitrifiers, such as Burkholderiaceae and Sulfurifustis in the surface sediment (0-15 cm). Interestingly, all S-driven denitrifier metagenome-assembled genomes (MAGs) appeared to be incomplete denitrifiers with nitrate/nitrite/nitric oxide reductases (Nar/Nir/Nor) but without nitrous oxide reductase (Nos), suggesting such sulphide-utilizing groups might be an important contributor to N2O production in the surface mangrove sediment. Gene families involved in methanogenesis and S reduction significantly (P < 0.05) increased along the sediment depth. Based on both network and MAG analyses, sulphate-reducing bacteria (SRB) might develop syntrophic relationships with anaerobic CH4 oxidizers (ANMEs) by direct electron transfer or zero-valent sulphur, which would pull forward the co-existence of methanogens and SRB in the middle and deep layer sediments. CONCLUSIONS In addition to offering a perspective on the vertical distribution of microbially driven CH4, N and S cycling genes/pathways, this study emphasizes the important role of S-driven denitrifiers on N2O emissions and various possible coupling mechanisms of ANMEs and SRB along the mangrove sediment depth. The exploration of potential coupling mechanisms provides novel insights into future synthetic microbial community construction and analysis. This study also has important implications for predicting ecosystem functions within the context of environmental and global change. Video Abstract.
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Affiliation(s)
- Lu Qian
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Xiaoli Yu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Hang Gu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Fei Liu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Yijun Fan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Cheng Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Qiang He
- Department of Civil and Environmental Engineering, the University of Tennessee, Knoxville, TN 37996 USA
| | - Yun Tian
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, 361005 China
| | - Yisheng Peng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Longfei Shu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Shanquan Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Zhijian Huang
- School of Marine Science, Sun Yat-Sen University, Zhuhai, 519080 China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Jianguo He
- School of Life Science, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Guangli Liu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Qichao Tu
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237 China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
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21
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Cyanobacterial membrane dynamics in the light of eukaryotic principles. Biosci Rep 2023; 43:232406. [PMID: 36602300 PMCID: PMC9950537 DOI: 10.1042/bsr20221269] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/23/2022] [Accepted: 01/03/2023] [Indexed: 01/06/2023] Open
Abstract
Intracellular compartmentalization is a hallmark of eukaryotic cells. Dynamic membrane remodeling, involving membrane fission/fusion events, clearly is crucial for cell viability and function, as well as membrane stabilization and/or repair, e.g., during or after injury. In recent decades, several proteins involved in membrane stabilization and/or dynamic membrane remodeling have been identified and described in eukaryotes. Yet, while typically not having a cellular organization as complex as eukaryotes, also bacteria can contain extra internal membrane systems besides the cytoplasmic membranes (CMs). Thus, also in bacteria mechanisms must have evolved to stabilize membranes and/or trigger dynamic membrane remodeling processes. In fact, in recent years proteins, which were initially defined being eukaryotic inventions, have been recognized also in bacteria, and likely these proteins shape membranes also in these organisms. One example of a complex prokaryotic inner membrane system is the thylakoid membrane (TM) of cyanobacteria, which contains the complexes of the photosynthesis light reaction. Cyanobacteria are evolutionary closely related to chloroplasts, and extensive remodeling of the internal membrane systems has been observed in chloroplasts and cyanobacteria during membrane biogenesis and/or at changing light conditions. We here discuss common principles guiding eukaryotic and prokaryotic membrane dynamics and the proteins involved, with a special focus on the dynamics of the cyanobacterial TMs and CMs.
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22
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Abstract
By chance, we discovered a window of extracellular magnesium (Mg2+) availability that modulates the division frequency of Bacillus subtilis without affecting its growth rate. In this window, cells grown with excess Mg2+ produce shorter cells than do those grown in unsupplemented medium. The Mg2+-responsive adjustment in cell length occurs in both rich and minimal media as well as in domesticated and undomesticated strains. Of other divalent cations tested, manganese (Mn2+) and zinc (Zn2+) also resulted in cell shortening, but this occurred only at concentrations that affected growth. Cell length decreased proportionally with increasing Mg2+ from 0.2 mM to 4.0 mM, with little or no detectable change being observed in labile, intracellular Mg2+, based on a riboswitch reporter. Cells grown in excess Mg2+ had fewer nucleoids and possessed more FtsZ-rings per unit cell length, consistent with the increased division frequency. Remarkably, when shifting cells from unsupplemented to supplemented medium, more than half of the cell length decrease occurred in the first 10 min, consistent with rapid division onset. Relative to unsupplemented cells, cells growing at steady-state with excess Mg2+ showed an enhanced expression of a large number of SigB-regulated genes and the activation of the Fur, MntR, and Zur regulons. Thus, by manipulating the availability of one nutrient, we were able to uncouple the growth rate from the division frequency and identify transcriptional changes that suggest that cell division is accompanied by the general stress response and an enhanced demand to sequester and/or increase the uptake of iron, Mn2+, and Zn2+. IMPORTANCE The signals that cells use to trigger cell division are unknown. Although division is often considered intrinsic to the cell cycle, microorganisms can continue to grow and repeat rounds of DNA replication without dividing, indicating that cycles of division can be skipped. Here, we show that by manipulating a single nutrient, namely, Mg2+, cell division can be uncoupled from the growth rate. This finding can be applied to investigate the nature of the cell division signal(s).
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23
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Spang A. Is an archaeon the ancestor of eukaryotes? Environ Microbiol 2022; 25:775-779. [PMID: 36562617 DOI: 10.1111/1462-2920.16323] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 12/21/2022] [Indexed: 12/24/2022]
Abstract
The origin of complex cellular life is a key puzzle in evolutionary research, which has broad implications for various neighbouring scientific disciplines. Naturally, views on this topic vary widely depending on the world view and context from which this topic is approached. In the following, I will share my perspective about our current scientific knowledge on the origin of eukaryotic cells, that is, eukaryogenesis, from a biological point of view focusing on the question as to whether an archaeon was the ancestor of eukaryotes.
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Affiliation(s)
- Anja Spang
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Utrecht University, AB Den Burg, The Netherlands.,Department of Evolutionary & Population Biology, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
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24
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Berche P. A new giant bacterium reminiscent of eukaryotes. C R Biol 2022; 345:39-42. [PMID: 36847463 DOI: 10.5802/crbiol.87] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 09/05/2022] [Indexed: 11/24/2022]
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25
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Discovering untapped biochemistry in microorganisms from hidden corners. Nat Rev Microbiol 2022; 20:639. [PMID: 36085522 DOI: 10.1038/s41579-022-00795-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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26
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Schavemaker PE, Muñoz-Gómez SA. The role of mitochondrial energetics in the origin and diversification of eukaryotes. Nat Ecol Evol 2022; 6:1307-1317. [PMID: 35915152 PMCID: PMC9575660 DOI: 10.1038/s41559-022-01833-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 06/20/2022] [Indexed: 11/09/2022]
Abstract
The origin of eukaryotic cell size and complexity is often thought to have required an energy excess supplied by mitochondria. Recent observations show energy demands to scale continuously with cell volume, suggesting that eukaryotes do not have higher energetic capacity. However, respiratory membrane area scales superlinearly with the cell surface area. Furthermore, the consequences of the contrasting genomic architectures between prokaryotes and eukaryotes have not been precisely quantified. Here, we investigated (1) the factors that affect the volumes at which prokaryotes become surface area-constrained, (2) the amount of energy divested to DNA due to contrasting genomic architectures and (3) the costs and benefits of respiring symbionts. Our analyses suggest that prokaryotes are not surface area-constrained at volumes of 100‒103 µm3, the genomic architecture of extant eukaryotes is only slightly advantageous at genomes sizes of 106‒107 base pairs and a larger host cell may have derived a greater advantage (lower cost) from harbouring ATP-producing symbionts. This suggests that eukaryotes first evolved without the need for mitochondria since these ranges hypothetically encompass the last eukaryotic common ancestor and its relatives. Our analyses also show that larger and faster-dividing prokaryotes would have a shortage of respiratory membrane area and divest more energy into DNA. Thus, we argue that although mitochondria may not have been required by the first eukaryotes, eukaryote diversification was ultimately dependent on mitochondria.
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Affiliation(s)
- Paul E. Schavemaker
- Center for Mechanisms of Evolution, The Biodesign
Institute, School of Life Sciences, Arizona State University, 727 E. Tyler St.
Tempe, AZ 85281-5001, U.S.A.,Correspondence to:
;
| | - Sergio A. Muñoz-Gómez
- Unité d’Ecologie, Systématique et
Evolution, Université Paris-Saclay, Orsay, France.,Correspondence to:
;
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27
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Afonina IS, Hoffmann E. Infection and immunity: ‘There Are Things Out There You (Don't) Need To Know About’. FEBS J 2022; 289:3920-3925. [DOI: 10.1111/febs.16569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 06/30/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Inna S. Afonina
- Unit of Molecular Signal Transduction in Inflammation VIB‐UGent Center for Inflammation Research Ghent Belgium
- Department of Biomedical Molecular Biology Ghent University Belgium
| | - Eik Hoffmann
- Institute Pasteur Lille Center for Infection and Immunity of Lille (CIIL) France
- European Regimen Accelerator for Tuberculosis (ERA4TB), Innovative Medicines Initiative 2 Joint Undertaking (JU no. 853989)
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28
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Levin PA. A bacterium that is not a microbe. Science 2022; 376:1379-1380. [PMID: 35737764 DOI: 10.1126/science.adc9387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
A new discovery challenges the prevailing view of the boundaries of bacterial cell size.
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Affiliation(s)
- Petra Anne Levin
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
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29
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Sanderson K. Largest bacterium ever found is surprisingly complex. Nature 2022:10.1038/d41586-022-01757-1. [PMID: 35750919 DOI: 10.1038/d41586-022-01757-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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