1
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Barzkar N, Sukhikh S, Babich O. A comprehensive review of marine sponge metabolites, with emphasis on Neopetrosia sp. Int J Biol Macromol 2024; 280:135823. [PMID: 39313052 DOI: 10.1016/j.ijbiomac.2024.135823] [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: 07/13/2024] [Revised: 09/18/2024] [Accepted: 09/18/2024] [Indexed: 09/25/2024]
Abstract
The secondary metabolites that marine sponges create are essential to the advancement of contemporary medicine and are often employed in clinical settings. Over the past five years, microbes associated with sponges have yielded the identification of 140 novel chemicals. Statistics show that most are derived from actinomycetes (bacteria) and ascomycotes (fungi). The aim of this study was to investigate the biological activity of metabolites from marine sponges. Chlocarbazomycins A-D, which are a group of novel chlorinated carbazole alkaloids isolated from the sponge Neopetrosia fennelliae KUFA 0811, exhibit antimicrobial, cytotoxic, and enzyme inhibitory activities. Recently, marine sponges of the genus Neopetrosia have attracted attention due to the unique chemical composition of the compounds they produce, including alkaloids of potential importance in drug discovery. Fridamycin H and fridamycin I are two novel type II polyketides synthesized by sponge-associated bacteria exhibit antitrypanosomal activity. Fintiamin, composed of amino acids and terpenoid moieties, shows affinity for the cannabinoid receptor CB 1. It was found that out of 27 species of Neopetrosia sponges, the chemical composition of only 9 species has been studied. These species mainly produce bioactive substances such as alkaloids, quinones, sterols, and terpenoids. The presence of motuporamines is a marker of the species Neopetrosia exigua. Terpenoids are specific markers of Neopetrosia vanilla species. Although recently discovered, secondary metabolites from marine sponges have been shown to have diverse biological activities, antimicrobial, antiviral, antibacterial, antimicrobial, antioxidant, antimalarial, and anticancer properties, providing many lead compounds for drug development. The data presented in this review on known and future natural products derived from sponges will further clarify the role and importance of microbes in marine sponges and trace the prospects of their applications, especially in medicine, cosmeceuticals, environmental protection, and manufacturing industries.
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Affiliation(s)
- Noora Barzkar
- Higher Institution Center of Excellence, Borneo Marine Research Institute, Universiti Malaysia Sabah, Kota Kinabalu 88400, Sabah, Malaysia.
| | - Stanislav Sukhikh
- SEC "Applied Biotechnologies", Immanuel Kant Baltic Federal University, A. Nevskogo Street 14, Kaliningrad, 236016, Russia
| | - Olga Babich
- SEC "Applied Biotechnologies", Immanuel Kant Baltic Federal University, A. Nevskogo Street 14, Kaliningrad, 236016, Russia
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2
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Liu H, Steenwyk JL, Zhou X, Schultz DT, Kocot KM, Shen XX, Rokas A, Li Y. A taxon-rich and genome-scale phylogeny of Opisthokonta. PLoS Biol 2024; 22:e3002794. [PMID: 39283949 PMCID: PMC11426530 DOI: 10.1371/journal.pbio.3002794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 09/26/2024] [Accepted: 08/07/2024] [Indexed: 09/27/2024] Open
Abstract
Ancient divergences within Opisthokonta-a major lineage that includes organisms in the kingdoms Animalia, Fungi, and their unicellular relatives-remain contentious. To assess progress toward a genome-scale Opisthokonta phylogeny, we conducted the most taxon rich phylogenomic analysis using sets of genes inferred with different orthology inference methods and established the geological timeline of Opisthokonta diversification. We also conducted sensitivity analysis by subsampling genes or taxa from the full data matrix based on filtering criteria previously shown to improve phylogenomic inference. We found that approximately 85% of internal branches were congruent across data matrices and the approaches used. Notably, the use of different orthology inference methods was a substantial contributor to the observed incongruence: analyses using the same set of orthologs showed high congruence of 97% to 98%, whereas different sets of orthologs resulted in somewhat lower congruence (87% to 91%). Examination of unicellular Holozoa relationships suggests that the instability observed across varying gene sets may stem from weak phylogenetic signals. Our results provide a comprehensive Opisthokonta phylogenomic framework that will be useful for illuminating ancient evolutionary episodes concerning the origin and diversification of the 2 major eukaryotic kingdoms and emphasize the importance of investigating effects of orthology inference on phylogenetic analyses to resolve ancient divergences.
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Affiliation(s)
- Hongyue Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Jacob L Steenwyk
- Howards Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Xiaofan Zhou
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Darrin T Schultz
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, California, United States of America
- Monterey Bay Aquarium Research Institute, Moss Landing, California, United States of America
| | - Kevin M Kocot
- University of Alabama, Department of Biological Sciences & Alabama Museum of Natural History, Tuscaloosa, Alabama, United States of America
| | - Xing-Xing Shen
- Institute of Insect Sciences and Centre for Evolutionary and Organismal Biology, Zhejiang University, Hangzhou, China
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Yuanning Li
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China
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3
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Gastaldi M, Pankey MS, Svendsen G, Medina A, Firstater F, Narvarte M, Lozada M, Lesser M. Holobiont dysbiosis or acclimatation? Shift in the microbial taxonomic diversity and functional composition of a cosmopolitan sponge subjected to chronic pollution in a Patagonian bay. PeerJ 2024; 12:e17707. [PMID: 39184395 PMCID: PMC11344537 DOI: 10.7717/peerj.17707] [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: 02/05/2024] [Accepted: 06/18/2024] [Indexed: 08/27/2024] Open
Abstract
Dysbiosis and acclimatization are two starkly opposing outcomes of altered holobiont associations in response to environmental pollution. This study assesses whether shifts in microbial taxonomic composition and functional profiles of the cosmopolitan sponge Hymeniacidon perlevis indicate dysbiotic or acclimatized responses to water pollution. To do so, sponge and water samples were collected in a semi-enclosed environment (San Antonio Bay, Patagonia, Argentina) from variably polluted sites (i.e., eutrophication, heavy metal contamination). We found significant differences in the microbiome of H. perlevis with respect to the pollution history of the sites. Several indicators suggested that acclimatization, rather than dysbiosis, explained the microbiome response to higher pollution: 1) the distinction of the sponge microbiome from the water microbiome; 2) low similarity between the sponge and water microbiomes at the most polluted site; 3) the change in microbiome composition between sponges from the different sites; 4) a high similarity in the microbiome among sponge individuals within sites; 5) a similar ratio of common sponge microbes to opportunistic microbes between sponges at the most and least polluted sites; and 6) a distinctive functional profile of the sponge microbiome at the most polluted site. This profile indicated a more expansive metabolic repertoire, including the degradation of pollutants and the biosynthesis of secondary metabolites, suggesting a relevant role of these microbial communities in the adaptation of the holobiont to organic pollution. Our results shed light on the rearrangement of the H. perlevis microbiome that could allow it to successfully colonize sites with high anthropogenic impact while resisting dysbiosis.
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Affiliation(s)
- Marianela Gastaldi
- Escuela Superior de Ciencias Marinas, Universidad Nacional del Comahue, San Antonio Oeste, Río Negro, Argentina
- Laboratorio de Biodiversidad y Servicios Ecosistémicos, CIMAS-CONICET, San Antonio Oeste, Río Negro, Argentina
| | - M. Sabrina Pankey
- Department of Molecular, Cellular and Biomedical Sciences and School of Marine Science and Ocean Engineering, University of New Hampshire, Durham, New England, United States
| | - Guillermo Svendsen
- Escuela Superior de Ciencias Marinas, Universidad Nacional del Comahue, San Antonio Oeste, Río Negro, Argentina
- Laboratorio de Modelado Ecológico y Pesquero, CIMAS-CONICET, San Antonio Oeste, Río Negro, Argentina
| | - Alonso Medina
- Escuela Superior de Ciencias Marinas, Universidad Nacional del Comahue, San Antonio Oeste, Río Negro, Argentina
| | - Fausto Firstater
- Escuela Superior de Ciencias Marinas, Universidad Nacional del Comahue, San Antonio Oeste, Río Negro, Argentina
- Laboratorio de Biodiversidad y Servicios Ecosistémicos, CIMAS-CONICET, San Antonio Oeste, Río Negro, Argentina
| | - Maite Narvarte
- Escuela Superior de Ciencias Marinas, Universidad Nacional del Comahue, San Antonio Oeste, Río Negro, Argentina
- Laboratorio de Biodiversidad y Servicios Ecosistémicos, CIMAS-CONICET, San Antonio Oeste, Río Negro, Argentina
| | - Mariana Lozada
- Laboratorio de Microbiología Ambiental, IBIOMAR-CONICET, Puerto Madryn, Chubut, Argentina
| | - Michael Lesser
- Department of Molecular, Cellular and Biomedical Sciences and School of Marine Science and Ocean Engineering, University of New Hampshire, Durham, New England, United States
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Morais L, Freitas BT, Fairchild TR, Clavijo Arcos RE, Guillong M, Vance D, de Campos MDR, Babinski M, Pereira LG, Leme JM, Boggiani PC, Osés GL, Rudnitzki ID, Galante D, Rodrigues F, Trindade RIF. Dawn of diverse shelled and carbonaceous animal microfossils at ~ 571 Ma. Sci Rep 2024; 14:14916. [PMID: 38942912 PMCID: PMC11213954 DOI: 10.1038/s41598-024-65671-4] [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: 10/30/2023] [Accepted: 06/23/2024] [Indexed: 06/30/2024] Open
Abstract
The Ediacaran-Cambrian transition documents a critical stage in the diversification of animals. The global fossil record documents the appearance of cloudinomorphs and other shelled tubular organisms followed by non-biomineralized small carbonaceous fossils and by the highly diversified small shelly fossils between ~ 550 and 530 Ma. Here, we report diverse microfossils in thin sections and hand samples from the Ediacaran Bocaina Formation, Brazil, separated into five descriptive categories: elongate solid structures (ES); elongate filled structures (EF); two types of equidimensional structures (EQ 1 and 2) and elongate hollow structures with coiled ends (CE). These specimens, interpreted as diversified candidate metazoans, predate the latest Ediacaran biomineralized index macrofossils of the Cloudina-Corumbella-Namacalathus biozone in the overlying Tamengo Formation. Our new carbonate U-Pb ages for the Bocaina Formation, position this novel fossil record at 571 ± 9 Ma (weighted mean age). Thus, our data point to diversification of metazoans, including biomineralized specimens reminiscent of sections of cloudinids, protoconodonts, anabaritids, and hyolithids, in addition to organo-phosphatic surficial coverings of animals, demonstrably earlier than the record of the earliest known skeletonized metazoan fossils.
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Affiliation(s)
- Luana Morais
- Department of Geophysics, Institute of Astronomy, Geophysics and Atmospheric Sciences, University of São Paulo (USP), São Paulo, SP, Brazil.
- Department of Geology, São Paulo State University (UNESP), Rio Claro, 13506-900, Brazil.
| | | | | | - Rolando Esteban Clavijo Arcos
- Institute of Geochemistry and Petrology, Department of Earth Sciences, ETH Zurich, Clausiusstrasse 25, 8092, Zurich, Switzerland
| | - Marcel Guillong
- Institute of Geochemistry and Petrology, Department of Earth Sciences, ETH Zurich, Clausiusstrasse 25, 8092, Zurich, Switzerland
| | - Derek Vance
- Institute of Geochemistry and Petrology, Department of Earth Sciences, ETH Zurich, Clausiusstrasse 25, 8092, Zurich, Switzerland
| | | | - Marly Babinski
- Institute of Geosciences, University of São Paulo (USP), São Paulo, SP, Brazil
| | | | - Juliana M Leme
- Institute of Geosciences, University of São Paulo (USP), São Paulo, SP, Brazil
| | - Paulo C Boggiani
- Institute of Geosciences, University of São Paulo (USP), São Paulo, SP, Brazil
| | - Gabriel L Osés
- Programa de Pós-Doutorado, Instituto de Física, Universidade de São Paulo (USP), Rua do Matão, 1371, São Paulo, 05508090, Brazil
- Laboratório de Arqueometria e Ciências Aplicadas ao Patrimônio Cultural, Instituto de Física, Universidade de São Paulo (USP), Rua do Matão, 1371, São Paulo, 05508090, Brazil
| | - Isaac D Rudnitzki
- Departament of Geology, Federal University of Ouro Preto (UFOP), Ouro Preto, MG, Brazil
| | - Douglas Galante
- Institute of Geosciences, University of São Paulo (USP), São Paulo, SP, Brazil
- Laboratório Nacional de Luz Síncrotron, Campinas, SP, Brazil
| | - Fabio Rodrigues
- Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo (USP), São Paulo, SP, Brazil
| | - Ricardo I F Trindade
- Department of Geophysics, Institute of Astronomy, Geophysics and Atmospheric Sciences, University of São Paulo (USP), São Paulo, SP, Brazil
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5
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Wang X, Liu AG, Chen Z, Wu C, Liu Y, Wan B, Pang K, Zhou C, Yuan X, Xiao S. A late-Ediacaran crown-group sponge animal. Nature 2024; 630:905-911. [PMID: 38839967 DOI: 10.1038/s41586-024-07520-y] [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: 07/29/2023] [Accepted: 05/03/2024] [Indexed: 06/07/2024]
Abstract
Sponges are the most basal metazoan phylum1 and may have played important roles in modulating the redox architecture of Neoproterozoic oceans2. Although molecular clocks predict that sponges diverged in the Neoproterozoic era3,4, their fossils have not been unequivocally demonstrated before the Cambrian period5-8, possibly because Precambrian sponges were aspiculate and non-biomineralized9. Here we describe a late-Ediacaran fossil, Helicolocellus cantori gen. et sp. nov., from the Dengying Formation (around 551-539 million years ago) of South China. This fossil is reconstructed as a large, stemmed benthic organism with a goblet-shaped body more than 0.4 m in height, with a body wall consisting of at least three orders of nested grids defined by quadrate fields, resembling a Cantor dust fractal pattern. The resulting lattice is interpreted as an organic skeleton comprising orthogonally arranged cruciform elements, architecturally similar to some hexactinellid sponges, although the latter are built with biomineralized spicules. A Bayesian phylogenetic analysis resolves H. cantori as a crown-group sponge related to the Hexactinellida. H. cantori confirms that sponges diverged and existed in the Precambrian as non-biomineralizing animals with an organic skeleton. Considering that siliceous biomineralization may have evolved independently among sponge classes10-13, we question the validity of biomineralized spicules as a necessary criterion for the identification of Precambrian sponge fossils.
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Affiliation(s)
- Xiaopeng Wang
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
- Department of Earth Sciences, University of Cambridge, Cambridge, UK
| | - Alexander G Liu
- Department of Earth Sciences, University of Cambridge, Cambridge, UK
| | - Zhe Chen
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chengxi Wu
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yarong Liu
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bin Wan
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Ke Pang
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chuanming Zhou
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Nanjing, Nanjing, China
| | - Xunlai Yuan
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Shuhai Xiao
- Department of Geosciences and Global Change Centre, Virginia Tech, Blacksburg, VA, USA.
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6
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Crockett WW, Shaw JO, Simpson C, Kempes CP. Physical constraints during Snowball Earth drive the evolution of multicellularity. Proc Biol Sci 2024; 291:20232767. [PMID: 38924758 PMCID: PMC11271684 DOI: 10.1098/rspb.2023.2767] [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: 12/07/2023] [Accepted: 05/09/2024] [Indexed: 06/28/2024] Open
Abstract
Molecular and fossil evidence suggests that complex eukaryotic multicellularity evolved during the late Neoproterozoic era, coincident with Snowball Earth glaciations, where ice sheets covered most of the globe. During this period, environmental conditions-such as seawater temperature and the availability of photosynthetically active light in the oceans-likely changed dramatically. Such changes would have had significant effects on both resource availability and optimal phenotypes. Here, we construct and apply mechanistic models to explore (i) how environmental changes during Snowball Earth and biophysical constraints generated selective pressures, and (ii) how these pressures may have had differential effects on organisms with different forms of biological organization. By testing a series of alternative-and commonly debated-hypotheses, we demonstrate how multicellularity was likely acquired differently in eukaryotes and prokaryotes owing to selective differences on their size due to the biophysical and metabolic regimes they inhabit: decreasing temperatures and resource availability instigated by the onset of glaciations generated selective pressures towards smaller sizes in organisms in the diffusive regime and towards larger sizes in motile heterotrophs. These results suggest that changing environmental conditions during Snowball Earth glaciations gave multicellular eukaryotes an evolutionary advantage, paving the way for the complex multicellular lineages that followed.
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Affiliation(s)
- William W. Crockett
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Santa Fe Institute, Santa Fe, NM 87501, USA
| | | | - Carl Simpson
- Department of Geological Sciences and University of Colorado Museum of Natural History, University of Colorado, Boulder, CO 80309, USA
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7
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Sun W, Yin Z, Liu P, Zhu M, Donoghue P. Developmental biology of Spiralicellula and the Ediacaran origin of crown metazoans. Proc Biol Sci 2024; 291:20240101. [PMID: 38808442 DOI: 10.1098/rspb.2024.0101] [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: 01/13/2024] [Accepted: 04/23/2024] [Indexed: 05/30/2024] Open
Abstract
The early Ediacaran Weng'an biota (Doushantuo Formation, South China) provides a rare window onto the period of Earth history in which molecular timescales have inferred the initial phase of crown-metazoan diversification. Interpretation of the embryo-like fossils that dominate the biota remains contentious because they are morphologically simple and so difficult to constrain phylogenetically. Spiralicellula from the Weng'an biota is distinguished by spiral internal bodies, allied through development to Megasphaera or Helicoforamina and interpreted variously as metazoan embryos, encysting protists, or chlorophycean green algae. Here we show, using X-ray microtomography, that Spiralicellula has a single-layered outer envelope and no more than 32 internal cells, often preserving a nucleus and yolk granules. There is no correlation between the extent of spiral development and the number of component cells; rather, the spiral developed with each palintomic stage, associated with cell disaggregation and reorientation. Evidence for envelope thinning and cell loss was observed in all developmental stages, reflecting non-deterministic shedding of gametes or amoebae. The developmental biology of Spiralicellula is similar to Megasphaera and Helicoforamina, which otherwise exhibit more rounds of palintomy. We reject a crown-metazoan affinity for Spiralicellula and all other components of the Weng'an biota, diminishing the probability of crown-metazoan diversification before the early Ediacaran.
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Affiliation(s)
- Weichen Sun
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, People's Republic of China
| | - Zongjun Yin
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, People's Republic of China
- Nanjing College, University of Chinese Academy of Sciences, Nanjing 211135, People's Republic of China
| | - Pengju Liu
- Institute of Geology, Chinese Academy of Geological Sciences, Beijing 100037, People's Republic of China
| | - Maoyan Zhu
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, People's Republic of China
- Nanjing College, University of Chinese Academy of Sciences, Nanjing 211135, People's Republic of China
| | - Philip Donoghue
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
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8
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Ramme L, Ilyina T, Marotzke J. Moderate greenhouse climate and rapid carbonate formation after Marinoan snowball Earth. Nat Commun 2024; 15:3571. [PMID: 38670992 PMCID: PMC11053170 DOI: 10.1038/s41467-024-47873-6] [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: 08/31/2023] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
When the Marinoan snowball Earth deglaciated in response to high atmospheric carbon dioxide (CO2) concentrations, the planet warmed rapidly. It is commonly hypothesized that the ensuing supergreenhouse climate then declined slowly over hundreds of thousands of years through continental weathering. However, how the ocean affected atmospheric CO2 in the snowball Earth aftermath has never been quantified. Here we show that the ocean's carbon cycle drives the supergreenhouse climate evolution via a set of different mechanisms, triggering scenarios ranging from a rapid decline to an intensification of the supergreenhouse climate. We further identify the rapid formation of carbonate sediments from pre-existing ocean alkalinity as a possible explanation for the enigmatic origin of Marinoan cap dolostones. This work demonstrates that a moderate and relatively short-lived supergreenhouse climate following the Marinoan snowball Earth is a plausible scenario that is in accordance with geological data, challenging the previous hypothesis.
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Affiliation(s)
- Lennart Ramme
- Max Planck Institute for Meteorology, Hamburg, Germany.
- International Max Planck Research School on Earth System Modelling, Hamburg, Germany.
| | - Tatiana Ilyina
- Max Planck Institute for Meteorology, Hamburg, Germany
- Center for Earth System Research and Sustainability (CEN), Universität Hamburg, Hamburg, Germany
- Helmholtz-Zentrum Hereon, Geesthacht, Germany
| | - Jochem Marotzke
- Max Planck Institute for Meteorology, Hamburg, Germany
- Center for Earth System Research and Sustainability (CEN), Universität Hamburg, Hamburg, Germany
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9
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Shimizu K, Nishi M, Sakate Y, Kawanami H, Bito T, Arima J, Leria L, Maldonado M. Silica-associated proteins from hexactinellid sponges support an alternative evolutionary scenario for biomineralization in Porifera. Nat Commun 2024; 15:181. [PMID: 38185711 PMCID: PMC10772126 DOI: 10.1038/s41467-023-44226-7] [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: 03/30/2023] [Accepted: 12/04/2023] [Indexed: 01/09/2024] Open
Abstract
Metazoans use silicon traces but rarely develop extensive silica skeletons, except for the early-diverging lineage of sponges. The mechanisms underlying metazoan silicification remain incompletely understood, despite significant biotechnological and evolutionary implications. Here, the characterization of two proteins identified from hexactinellid sponge silica, hexaxilin and perisilin, supports that the three classes of siliceous sponges (Hexactinellida, Demospongiae, and Homoscleromorpha) use independent protein machineries to build their skeletons, which become non-homologous structures. Hexaxilin forms the axial filament to intracellularly pattern the main symmetry of the skeletal parts, while perisilin appears to operate in their thickening, guiding extracellular deposition of peripheral silica, as does glassin, a previously characterized hexactinellid silicifying protein. Distant hexaxilin homologs occur in some bilaterians with siliceous parts, suggesting putative conserved silicifying activity along metazoan evolution. The findings also support that ancestral Porifera were non-skeletonized, acquiring silica skeletons only after diverging into major classes, what reconciles molecular-clock dating and the fossil record.
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Affiliation(s)
- Katsuhiko Shimizu
- Platform for Community-based Research and Education, Tottori University, 4-101, Koyama-cho, Minami, Tottori, 680-8550, Japan.
| | - Michika Nishi
- Division of Agricultural Science, Graduate studies of Sustainability Science, Tottori University Graduate School, 4-101, Koyama-cho, Minami, Tottori, 680-8553, Japan
| | - Yuto Sakate
- Division of Agricultural Science, Graduate studies of Sustainability Science, Tottori University Graduate School, 4-101, Koyama-cho, Minami, Tottori, 680-8553, Japan
| | - Haruka Kawanami
- Department of Life Environmental Agriculture, Faculty of Agriculture, Tottori University, 4-101, Koyama-cho, Minami, Tottori, 680-8553, Japan
| | - Tomohiro Bito
- Department of Life Environmental Agriculture, Faculty of Agriculture, Tottori University, 4-101, Koyama-cho, Minami, Tottori, 680-8553, Japan
| | - Jiro Arima
- Department of Life Environmental Agriculture, Faculty of Agriculture, Tottori University, 4-101, Koyama-cho, Minami, Tottori, 680-8553, Japan
| | - Laia Leria
- Sponge Ecobiology and Biotechnology Group, Center for Advanced Studies of Blanes (CEAB, CSIC), Blanes, 17300, Spain
| | - Manuel Maldonado
- Sponge Ecobiology and Biotechnology Group, Center for Advanced Studies of Blanes (CEAB, CSIC), Blanes, 17300, Spain.
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10
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Belato FA, Mello B, Coates CJ, Halanych KM, Brown FD, Morandini AC, de Moraes Leme J, Trindade RIF, Costa-Paiva EM. Divergence time estimates for the hypoxia-inducible factor-1 alpha (HIF1α) reveal an ancient emergence of animals in low-oxygen environments. GEOBIOLOGY 2024; 22:e12577. [PMID: 37750460 DOI: 10.1111/gbi.12577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 07/13/2023] [Accepted: 09/07/2023] [Indexed: 09/27/2023]
Abstract
Unveiling the tempo and mode of animal evolution is necessary to understand the links between environmental changes and biological innovation. Although the earliest unambiguous metazoan fossils date to the late Ediacaran period, molecular clock estimates agree that the last common ancestor (LCA) of all extant animals emerged ~850 Ma, in the Tonian period, before the oldest evidence for widespread ocean oxygenation at ~635-560 Ma in the Ediacaran period. Metazoans are aerobic organisms, that is, they are dependent on oxygen to survive. In low-oxygen conditions, most animals have an evolutionarily conserved pathway for maintaining oxygen homeostasis that triggers physiological changes in gene expression via the hypoxia-inducible factor (HIFa). However, here we confirm the absence of the characteristic HIFa protein domain responsible for the oxygen sensing of HIFa in sponges and ctenophores, indicating the LCA of metazoans lacked the functional protein domain as well, and so could have maintained their transcription levels unaltered under the very low-oxygen concentrations of their environments. Using Bayesian relaxed molecular clock dating, we inferred that the ancestral gene lineage responsible for HIFa arose in the Mesoproterozoic Era, ~1273 Ma (Credibility Interval 957-1621 Ma), consistent with the idea that important genetic machinery associated with animals evolved much earlier than the LCA of animals. Our data suggest at least two duplication events in the evolutionary history of HIFa, which generated three vertebrate paralogs, products of the two successive whole-genome duplications that occurred in the vertebrate LCA. Overall, our results support the hypothesis of a pre-Tonian emergence of metazoans under low-oxygen conditions, and an increase in oxygen response elements during animal evolution.
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Affiliation(s)
- Flavia A Belato
- Institute of Biosciences, Department of Zoology, University of Sao Paulo, São Paulo - SP, Brazil
| | - Beatriz Mello
- Biology Institute, Genetics Department, Federal University of Rio de Janeiro, Rio de Janeiro - RJ, Brazil
| | - Christopher J Coates
- Zoology, Ryan Institute, School of Natural Sciences, University of Galway, Galway, Ireland
| | - Kenneth M Halanych
- Center for Marine Science, University of North Carolina Wilmington, Wilmington, North Carolina, USA
| | - Federico D Brown
- Institute of Biosciences, Department of Zoology, University of Sao Paulo, São Paulo - SP, Brazil
| | - André C Morandini
- Institute of Biosciences, Department of Zoology, University of Sao Paulo, São Paulo - SP, Brazil
| | | | - Ricardo I F Trindade
- Institute of Astronomy, Geophysics and Atmospheric Sciences, University of Sao Paulo, São Paulo - SP, Brazil
| | - Elisa Maria Costa-Paiva
- Institute of Biosciences, Department of Zoology, University of Sao Paulo, São Paulo - SP, Brazil
- Institute of Astronomy, Geophysics and Atmospheric Sciences, University of Sao Paulo, São Paulo - SP, Brazil
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11
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Lavrov DV, Diaz MC, Maldonado M, Morrow CC, Perez T, Pomponi SA, Thacker RW. Phylomitogenomics bolsters the high-level classification of Demospongiae (phylum Porifera). PLoS One 2023; 18:e0287281. [PMID: 38048310 PMCID: PMC10695373 DOI: 10.1371/journal.pone.0287281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 11/15/2023] [Indexed: 12/06/2023] Open
Abstract
Class Demospongiae is the largest in the phylum Porifera (Sponges) and encompasses nearly 8,000 accepted species in three subclasses: Keratosa, Verongimorpha, and Heteroscleromorpha. Subclass Heteroscleromorpha contains ∼90% of demosponge species and is subdivided into 17 orders. The higher level classification of demosponges underwent major revision as the result of nearly three decades of molecular studies. However, because most of the previous molecular work only utilized partial data from a small number of nuclear and mitochondrial (mt) genes, this classification scheme needs to be tested by larger datasets. Here we compiled a mt dataset for 136 demosponge species-including 64 complete or nearly complete and six partial mt-genome sequences determined or assembled for this study-and used it to test phylogenetic relationships among Demospongiae in general and Heteroscleromorpha in particular. We also investigated the phylogenetic position of Myceliospongia araneosa, a highly unusual demosponge without spicules and spongin fibers, currently classified as Demospongiae incertae sedis, for which molecular data were not available. Our results support the previously inferred sister-group relationship between Heteroscleromorpha and Keratosa + Verongimorpha and suggest five main clades within Heteroscleromorpha: Clade C0 composed of order Haplosclerida; Clade C1 composed of Scopalinida, Sphaerocladina, and Spongillida; Clade C2 composed of Axinellida, Biemnida, Bubarida; Clade C3 composed of Tetractinellida; and Clade C4 composed of Agelasida, Clionaida, Desmacellida, Merliida, Suberitida, Poecilosclerida, Polymastiida, and Tethyida. The inferred relationships among these clades were (C0(C1(C2(C3+C4)))). Analysis of molecular data from M. araneosa placed it in the C3 clade as a sister taxon to the highly skeletonized tetractinellids Microscleroderma sp. and Leiodermatium sp. Molecular clock analysis dated divergences among the major clades in Heteroscleromorpha from the Cambrian to the Early Silurian, the origins of most heteroscleromorph orders in the middle Paleozoic, and the most basal splits within these orders around the Paleozoic to Mesozoic transition. Overall, the results of this study are mostly congruent with the accepted classification of Heteroscleromorpha, but add temporal perspective and new resolution to phylogenetic relationships within this subclass.
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Affiliation(s)
- Dennis V. Lavrov
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa, United States of America
| | - Maria C. Diaz
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, Florida, United States of America
- Museo Marino de Margarita, Boca de Río, Nueva Esparta, Venezuela
| | - Manuel Maldonado
- Department of Marine Ecology, Centro de Estudios Avanzados de Blanes (CEAB-CSIC), Girona, Spain
| | - Christine C. Morrow
- Zoology Department, School of Natural Sciences & Ryan Institute, NUI Galway, University Road, Galway, Ireland
- Ireland and Queen’s University Marine Laboratory, Portaferry, Northern Ireland
| | - Thierry Perez
- Institut Méditerranéen de la Biodiversité et d’Ecologie marine et continentale (IMBE), CNRS, Aix-Marseille Université, IRD, Avignon Université City, Provence, France
| | - Shirley A. Pomponi
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, Florida, United States of America
| | - Robert W. Thacker
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, United States of America
- Smithsonian Tropical Research Institute, Balboa, Panama City, Republic of Panama
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12
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Brunoir T, Mulligan C, Sistiaga A, Vuu KM, Shih PM, O'Reilly SS, Summons RE, Gold DA. Common origin of sterol biosynthesis points to a feeding strategy shift in Neoproterozoic animals. Nat Commun 2023; 14:7941. [PMID: 38040676 PMCID: PMC10692144 DOI: 10.1038/s41467-023-43545-z] [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: 03/06/2023] [Accepted: 11/13/2023] [Indexed: 12/03/2023] Open
Abstract
Steranes preserved in sedimentary rocks serve as molecular fossils, which are thought to record the expansion of eukaryote life through the Neoproterozoic Era ( ~ 1000-541 Ma). Scientists hypothesize that ancient C27 steranes originated from cholesterol, the major sterol produced by living red algae and animals. Similarly, C28 and C29 steranes are thought to be derived from the sterols of prehistoric fungi, green algae, and other microbial eukaryotes. However, recent work on annelid worms-an advanced group of eumetazoan animals-shows that they are also capable of producing C28 and C29 sterols. In this paper, we explore the evolutionary history of the 24-C sterol methyltransferase (smt) gene in animals, which is required to make C28+ sterols. We find evidence that the smt gene was vertically inherited through animals, suggesting early eumetazoans were capable of C28+ sterol synthesis. Our molecular clock of the animal smt gene demonstrates that its diversification coincides with the rise of C28 and C29 steranes in the Neoproterozoic. This study supports the hypothesis that early eumetazoans were capable of making C28+ sterols and that many animal lineages independently abandoned its biosynthesis around the end-Neoproterozoic, coinciding with the rise of abundant eukaryotic prey.
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Affiliation(s)
- T Brunoir
- Department of Earth and Planetary Sciences, University of California, Davis, Davis, CA, USA
| | - C Mulligan
- Department of Earth and Planetary Sciences, University of California, Davis, Davis, CA, USA
| | - A Sistiaga
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - K M Vuu
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - P M Shih
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - S S O'Reilly
- Department of Life Sciences, Atlantic Technological University, ATU Sligo, Ash Lane, Sligo, Ireland
| | - R E Summons
- Department of Earth, Atmospheric, and Planetary Sciences. Massachusetts Institute of Technology, Cambridge, MA, USA
| | - D A Gold
- Department of Earth and Planetary Sciences, University of California, Davis, Davis, CA, USA.
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13
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Li M, Xu Y, Sun L, Chen J, Zhang K, Li D, Farquhar J, Zhang X, Sun R, Macdonald FA, Grasby SE, Fu Y, Shen Y. Deglacial volcanism and reoxygenation in the aftermath of the Sturtian Snowball Earth. SCIENCE ADVANCES 2023; 9:eadh9502. [PMID: 37672591 PMCID: PMC10482342 DOI: 10.1126/sciadv.adh9502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 08/02/2023] [Indexed: 09/08/2023]
Abstract
The Cryogenian Sturtian and Marinoan Snowball Earth glaciations bracket a nonglacial interval during which Demosponge and green-algal biomarkers first appear. To understand the relationships between environmental perturbations and early animal evolution, we measured sulfur and mercury isotopes from the Datangpo Formation from South China. Hg enrichment with positive Δ199Hg excursion suggests enhanced volcanism, potentially due to depressurization of terrestrial magma chambers during deglaciation. A thick stratigraphic interval of negative Δ33Spy indicates that the nonglacial interlude was characterized by low but rising sulfate levels. Model results reveal a mechanism to produce the Δ33S anomalies down to -0.284‰ through Rayleigh distillation. We propose that extreme temperatures and anoxia contributed to the apparent delay in green algal production in the aftermath of the Sturtian glaciation and the subsequent reoxygenation of the iron-rich and sulfate-depleted ocean paved the way for evolution of animals.
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Affiliation(s)
- Menghan Li
- School of Earth and Space Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Yilun Xu
- School of Earth and Space Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Lilin Sun
- School of Earth and Space Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Jiubin Chen
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300350, China
| | - Ke Zhang
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300350, China
| | - Dandan Li
- School of Earth and Space Sciences, University of Science and Technology of China, Hefei 230026, China
| | - James Farquhar
- Department of Geology and ESSIC, University of Maryland, College Park, MD 20742, USA
| | - Xiaolin Zhang
- School of Earth and Space Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Ruoyu Sun
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300350, China
| | - Francis A. Macdonald
- Department of Earth Science, University of California–Santa Barbara, Santa Barbara, CA 93106, USA
| | - Stephen E. Grasby
- Geological Survey of Canada, Natural Resources Canada, Calgary, Alberta T2L 2A7, Canada
| | - Yong Fu
- College of Resource and Environmental Engineering, Guizhou University, Guiyang 550012, China
| | - Yanan Shen
- School of Earth and Space Sciences, University of Science and Technology of China, Hefei 230026, China
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14
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Ostrander CM, Bjerrum CJ, Ahm ASC, Stenger SR, Bergmann KD, El-Ghali MAK, Harthi AR, Aisri Z, Nielsen SG. Widespread seafloor anoxia during generation of the Ediacaran Shuram carbon isotope excursion. GEOBIOLOGY 2023; 21:556-570. [PMID: 37157927 DOI: 10.1111/gbi.12557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 04/13/2023] [Accepted: 04/25/2023] [Indexed: 05/10/2023]
Abstract
Reconstructing the oxygenation history of Earth's oceans during the Ediacaran period (635 to 539 million years ago) has been challenging, and this has led to a polarizing debate about the environmental conditions that played host to the rise of animals. One focal point of this debate is the largest negative inorganic C-isotope excursion recognized in the geologic record, the Shuram excursion, and whether this relic tracks the global-scale oxygenation of Earth's deep oceans. To help inform this debate, we conducted a detailed geochemical investigation of two siliciclastic-dominated successions from Oman deposited through the Shuram Formation. Iron speciation data from both successions indicate formation beneath an intermittently anoxic local water column. Authigenic thallium (Tl) isotopic compositions leached from both successions are indistinguishable from bulk upper continental crust (ε205 TlA ≈ -2) and, by analogy with modern equivalents, likely representative of the ancient seawater ε205 Tl value. A crustal seawater ε205 Tl value requires limited manganese (Mn) oxide burial on the ancient seafloor, and by extension widely distributed anoxic sediment porewaters. This inference is supported by muted redox-sensitive element enrichments (V, Mo, and U) and consistent with some combination of widespread (a) bottom water anoxia and (b) high sedimentary organic matter loading. Contrary to a classical hypothesis, our interpretations place the Shuram excursion, and any coeval animal evolutionary events, in a predominantly anoxic global ocean.
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Affiliation(s)
- Chadlin M Ostrander
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
- NIRVANA Laboratories, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
- Department of Geology and Geophysics, University of Utah, Salt Lake City, Utah, USA
| | - Christian J Bjerrum
- Department of Geoscience and Natural Resource Management, Nordic Center for Earth Evolution, University of Copenhagen, Copenhagen K, Denmark
| | - Anne-Sofie C Ahm
- Department of Geoscience and Natural Resource Management, Nordic Center for Earth Evolution, University of Copenhagen, Copenhagen K, Denmark
- School of Earth and Ocean Sciences, University of Victoria, Victoria, British Columbia, Canada
| | - Simon R Stenger
- Department of Geoscience and Natural Resource Management, Nordic Center for Earth Evolution, University of Copenhagen, Copenhagen K, Denmark
- Norwegian Geotechnical Institute, Trondheim, Norway
| | - Kristin D Bergmann
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Mohamed A K El-Ghali
- Department of Earth Sciences and Earth Sciences Research Centre, Sultan Qaboos University, Muscat, Oman
| | | | | | - Sune G Nielsen
- NIRVANA Laboratories, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
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15
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Bowyer FT, Krause AJ, Song Y, Huang KJ, Fu Y, Shen B, Li J, Zhu XK, Kipp MA, van Maldegem LM, Brocks JJ, Shields GA, Le Hir G, Mills BJW, Poulton SW. Biological diversification linked to environmental stabilization following the Sturtian Snowball glaciation. SCIENCE ADVANCES 2023; 9:eadf9999. [PMID: 37624887 PMCID: PMC10456883 DOI: 10.1126/sciadv.adf9999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 05/17/2023] [Accepted: 07/25/2023] [Indexed: 08/27/2023]
Abstract
The body fossil and biomarker records hint at an increase in biotic complexity between the two Cryogenian Snowball Earth episodes (ca. 661 million to ≤650 million years ago). Oxygen and nutrient availability can promote biotic complexity, but nutrient (particularly phosphorus) and redox dynamics across this interval remain poorly understood. Here, we present high-resolution paleoredox and phosphorus phase association data from multiple globally distributed drill core records through the non-glacial interval. These data are first correlated regionally by litho- and chemostratigraphy, and then calibrated within a series of global chronostratigraphic frameworks. The combined data show that regional differences in postglacial redox stabilization were partly controlled by the intensity of phosphorus recycling from marine sediments. The apparent increase in biotic complexity followed a global transition to more stable and less reducing conditions in shallow to mid-depth marine environments and occurred within a tolerable climatic window during progressive cooling after post-Snowball super-greenhouse conditions.
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Affiliation(s)
- Fred T. Bowyer
- School of GeoSciences, University of Edinburgh, James Hutton Road, Edinburgh EH9 3FE, UK
- School of Earth and Environment, University of Leeds, Leeds LS2 9JT, UK
| | - Alexander J. Krause
- School of Earth and Environment, University of Leeds, Leeds LS2 9JT, UK
- Department of Earth Sciences, University College London, London WC1E 6BT, UK
| | - Yafang Song
- School of Earth and Environment, University of Leeds, Leeds LS2 9JT, UK
| | - Kang-Jun Huang
- Department of Geology, Northwest University, 229 North Taibai Road, Xi’an 710069, Shaanxi Province, China
| | - Yong Fu
- College of Resource and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang 550025, China
| | - Bing Shen
- Ministry of Education Key Laboratory of Orogenic Belts and Crustal Evolution, School of Earth and Space Sciences, Peking University, Beijing 100871, China
| | - Jin Li
- MNR Key Laboratory of Isotope Geology, MNR Key Laboratory of Deep-Earth Dynamics, Institute of Geology, Chinese Academy of Geological Sciences, Beijing 100037, China
| | - Xiang-Kun Zhu
- MNR Key Laboratory of Isotope Geology, MNR Key Laboratory of Deep-Earth Dynamics, Institute of Geology, Chinese Academy of Geological Sciences, Beijing 100037, China
| | - Michael A. Kipp
- Division of Geological and Planetary Sciences, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Lennart M. van Maldegem
- Research School of Earth Sciences, The Australian National University, Canberra, ACT 2601, Australia
| | - Jochen J. Brocks
- Research School of Earth Sciences, The Australian National University, Canberra, ACT 2601, Australia
| | - Graham A. Shields
- Department of Earth Sciences, University College London, London WC1E 6BT, UK
| | - Guillaume Le Hir
- Université Paris, Institut de Physique du Globe de Paris, CNRS, 1 rue Jussieu, 75005 Paris, France
| | | | - Simon W. Poulton
- School of Earth and Environment, University of Leeds, Leeds LS2 9JT, UK
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16
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Mateos K, Chappell G, Klos A, Le B, Boden J, Stüeken E, Anderson R. The evolution and spread of sulfur cycling enzymes reflect the redox state of the early Earth. SCIENCE ADVANCES 2023; 9:eade4847. [PMID: 37418533 PMCID: PMC10328410 DOI: 10.1126/sciadv.ade4847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 02/06/2023] [Accepted: 06/05/2023] [Indexed: 07/09/2023]
Abstract
The biogeochemical sulfur cycle plays a central role in fueling microbial metabolisms, regulating the Earth's redox state, and affecting climate. However, geochemical reconstructions of the ancient sulfur cycle are confounded by ambiguous isotopic signals. We use phylogenetic reconciliation to ascertain the timing of ancient sulfur cycling gene events across the tree of life. Our results suggest that metabolisms using sulfide oxidation emerged in the Archean, but those involving thiosulfate emerged only after the Great Oxidation Event. Our data reveal that observed geochemical signatures resulted not from the expansion of a single type of organism but were instead associated with genomic innovation across the biosphere. Moreover, our results provide the first indication of organic sulfur cycling from the Mid-Proterozoic onwards, with implications for climate regulation and atmospheric biosignatures. Overall, our results provide insights into how the biological sulfur cycle evolved in tandem with the redox state of the early Earth.
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Affiliation(s)
- Katherine Mateos
- Carleton College, Northfield, MN, USA
- Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Garrett Chappell
- Carleton College, Northfield, MN, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Aya Klos
- Carleton College, Northfield, MN, USA
| | - Bryan Le
- Carleton College, Northfield, MN, USA
| | - Joanne Boden
- University of St. Andrews, School of Earth and Environmental Sciences, Bute Building, Queen’s Terrace, St Andrews, Fife KY16 9TS, UK
| | - Eva Stüeken
- University of St. Andrews, School of Earth and Environmental Sciences, Bute Building, Queen’s Terrace, St Andrews, Fife KY16 9TS, UK
| | - Rika Anderson
- Carleton College, Northfield, MN, USA
- NASA NExSS Virtual Planetary Laboratory, University of Washington, Seattle, WA, USA
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17
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Beinsteiner B, Billas IML, Moras D. Structural insights into the HNF4 biology. Front Endocrinol (Lausanne) 2023; 14:1197063. [PMID: 37404310 PMCID: PMC10315846 DOI: 10.3389/fendo.2023.1197063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 06/01/2023] [Indexed: 07/06/2023] Open
Abstract
Hepatocyte Nuclear Factor 4 (HNF4) is a transcription factor (TF) belonging to the nuclear receptor (NR) family that is expressed in liver, kidney, intestine and pancreas. It is a master regulator of liver-specific gene expression, in particular those genes involved in lipid transport and glucose metabolism and is crucial for the cellular differentiation during development. Dysregulation of HNF4 is linked to human diseases, such as type I diabetes (MODY1) and hemophilia. Here, we review the structures of the isolated HNF4 DNA binding domain (DBD) and ligand binding domain (LBD) and that of the multidomain receptor and compare them with the structures of other NRs. We will further discuss the biology of the HNF4α receptors from a structural perspective, in particular the effect of pathological mutations and of functionally critical post-translational modifications on the structure-function of the receptor.
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Affiliation(s)
- Brice Beinsteiner
- Laboratory IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Centre for Integrative Biology (CBI), Illkirch, France
- Université de Strasbourg (Unistra), Strasbourg, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) U1258, Illkirch, France
- Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France
| | - Isabelle M. L. Billas
- Laboratory IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Centre for Integrative Biology (CBI), Illkirch, France
- Université de Strasbourg (Unistra), Strasbourg, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) U1258, Illkirch, France
- Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France
| | - Dino Moras
- Laboratory IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Centre for Integrative Biology (CBI), Illkirch, France
- Université de Strasbourg (Unistra), Strasbourg, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) U1258, Illkirch, France
- Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France
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18
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Abstract
Immunity to infection has been extensively studied in humans and mice bearing naturally occurring or experimentally introduced germline mutations. Mouse studies are sometimes neglected by human immunologists, on the basis that mice are not humans and the infections studied are experimental and not natural. Conversely, human studies are sometimes neglected by mouse immunologists, on the basis of the uncontrolled conditions of study and small numbers of patients. However, both sides would agree that the infectious phenotypes of patients with inborn errors of immunity often differ from those of the corresponding mutant mice. Why is that? We argue that this important question is best addressed by revisiting and reinterpreting the findings of both mouse and human studies from a genetic perspective. Greater caution is required for reverse-genetics studies than for forward-genetics studies, but genetic analysis is sufficiently strong to define the studies likely to stand the test of time. Genetically robust mouse and human studies can provide invaluable complementary insights into the mechanisms of immunity to infection common and specific to these two species.
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Affiliation(s)
- Philippe Gros
- McGill University Research Center on Complex Traits, Department of Biochemistry, and Department of Human Genetics, McGill University, Montréal, Québec, Canada;
| | - Jean-Laurent Casanova
- Howard Hughes Medical Institute and St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA;
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM, and University of Paris Cité, Imagine Institute and Necker Hospital for Sick Children, Paris, France
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19
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Shi H, Ruan L, Chen Z, Liao Y, Wu W, Liu L, Xu X. Sulfur, sterol and trehalose metabolism in the deep-sea hydrocarbon seep tubeworm Lamellibrachia luymesi. BMC Genomics 2023; 24:175. [PMID: 37020304 PMCID: PMC10077716 DOI: 10.1186/s12864-023-09267-8] [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: 02/12/2022] [Accepted: 03/20/2023] [Indexed: 04/07/2023] Open
Abstract
BACKGROUND Lamellibrachia luymesi dominates cold sulfide-hydrocarbon seeps and is known for its ability to consume bacteria for energy. The symbiotic relationship between tubeworms and bacteria with particular adaptations to chemosynthetic environments has received attention. However, metabolic studies have primarily focused on the mechanisms and pathways of the bacterial symbionts, while studies on the animal hosts are limited. RESULTS Here, we sequenced the transcriptome of L. luymesi and generated a transcriptomic database containing 79,464 transcript sequences. Based on GO and KEGG annotations, we identified transcripts related to sulfur metabolism, sterol biosynthesis, trehalose synthesis, and hydrolysis. Our in-depth analysis identified sulfation pathways in L. luymesi, and sulfate activation might be an important detoxification pathway for promoting sulfur cycling, reducing byproducts of sulfide metabolism, and converting sulfur compounds to sulfur-containing organics, which are essential for symbiotic survival. Moreover, sulfide can serve directly as a sulfur source for cysteine synthesis in L. luymesi. The existence of two pathways for cysteine synthesis might ensure its participation in the formation of proteins, heavy metal detoxification, and the sulfide-binding function of haemoglobin. Furthermore, our data suggested that cold-seep tubeworm is capable of de novo sterol biosynthesis, as well as incorporation and transformation of cycloartenol and lanosterol into unconventional sterols, and the critical enzyme involved in this process might have properties similar to those in the enzymes from plants or fungi. Finally, trehalose synthesis in L. luymesi occurs via the trehalose-6-phosphate synthase (TPS) and trehalose-6-phosphate phosphatase (TPP) pathways. The TPP gene has not been identified, whereas the TPS gene encodes a protein harbouring conserved TPS/OtsA and TPP/OtsB domains. The presence of multiple trehalases that catalyse trehalose hydrolysis could indicate the different roles of trehalase in cold-seep tubeworms. CONCLUSIONS We elucidated several molecular pathways of sulfate activation, cysteine and cholesterol synthesis, and trehalose metabolism. Contrary to the previous analysis, two pathways for cysteine synthesis and the cycloartenol-C-24-methyltransferase gene were identified in animals for the first time. The present study provides new insights into particular adaptations to chemosynthetic environments in L. luymesi and can serve as the basis for future molecular studies on host-symbiont interactions and biological evolution.
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Affiliation(s)
- Hong Shi
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Ministry of Natural Resources, Third Institute of Oceanography, Ministry of Natural Resources, Fujian Key Laboratory of Marine Genetic Resources, No. 178 Daxue Road, Xiamen, Fujian, 361005, People's Republic of China.
| | - Lingwei Ruan
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Ministry of Natural Resources, Third Institute of Oceanography, Ministry of Natural Resources, Fujian Key Laboratory of Marine Genetic Resources, No. 178 Daxue Road, Xiamen, Fujian, 361005, People's Republic of China.
- College of Marine Biology, Xiamen ocean vocational college, 361100, Xiamen, People's Republic of China.
- Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang, 222005, People's Republic of China.
| | - Zimeng Chen
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Ministry of Natural Resources, Third Institute of Oceanography, Ministry of Natural Resources, Fujian Key Laboratory of Marine Genetic Resources, No. 178 Daxue Road, Xiamen, Fujian, 361005, People's Republic of China
| | - Yifei Liao
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Ministry of Natural Resources, Third Institute of Oceanography, Ministry of Natural Resources, Fujian Key Laboratory of Marine Genetic Resources, No. 178 Daxue Road, Xiamen, Fujian, 361005, People's Republic of China
- School of Advanced Manufacturing, Fuzhou University, Fuzhou, 362200, People's Republic of China
| | - Wenhao Wu
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Ministry of Natural Resources, Third Institute of Oceanography, Ministry of Natural Resources, Fujian Key Laboratory of Marine Genetic Resources, No. 178 Daxue Road, Xiamen, Fujian, 361005, People's Republic of China
- Department of Biology and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, People's Republic of China
| | - Linmin Liu
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Ministry of Natural Resources, Third Institute of Oceanography, Ministry of Natural Resources, Fujian Key Laboratory of Marine Genetic Resources, No. 178 Daxue Road, Xiamen, Fujian, 361005, People's Republic of China
| | - Xun Xu
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Ministry of Natural Resources, Third Institute of Oceanography, Ministry of Natural Resources, Fujian Key Laboratory of Marine Genetic Resources, No. 178 Daxue Road, Xiamen, Fujian, 361005, People's Republic of China
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20
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Song H, An Z, Ye Q, Stüeken EE, Li J, Hu J, Algeo TJ, Tian L, Chu D, Song H, Xiao S, Tong J. Mid-latitudinal habitable environment for marine eukaryotes during the waning stage of the Marinoan snowball glaciation. Nat Commun 2023; 14:1564. [PMID: 37015913 PMCID: PMC10073137 DOI: 10.1038/s41467-023-37172-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 03/06/2023] [Indexed: 04/06/2023] Open
Abstract
During the Marinoan Ice Age (ca. 654-635 Ma), one of the 'Snowball Earth' events in the Cryogenian Period, continental icesheets reached the tropical oceans. Oceanic refugia must have existed for aerobic marine eukaryotes to survive this event, as evidenced by benthic phototrophic macroalgae of the Songluo Biota preserved in black shales interbedded with glacial diamictites of the late Cryogenian Nantuo Formation in South China. However, the environmental conditions that allowed these organisms to thrive are poorly known. Here, we report carbon-nitrogen-iron geochemical data from the fossiliferous black shales and adjacent diamictites of the Nantuo Formation. Iron-speciation data document dysoxic-anoxic conditions in bottom waters, whereas nitrogen isotopes record aerobic nitrogen cycling perhaps in surface waters. These findings indicate that habitable open-ocean conditions were more extensive than previously thought, extending into mid-latitude coastal oceans and providing refugia for eukaryotic organisms during the waning stage of the Marinoan Ice Age.
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Affiliation(s)
- Huyue Song
- State Key Laboratory of Biogeology and Environmental Geology, School of Earth Science, China University of Geosciences, Wuhan, 430074, China.
| | - Zhihui An
- Wuhan Center of China Geological Survey, Wuhan, 430205, China
| | - Qin Ye
- State Key Laboratory of Biogeology and Environmental Geology, School of Earth Science, China University of Geosciences, Wuhan, 430074, China
| | - Eva E Stüeken
- School of Earth & Environmental Sciences, University of St. Andrews, St. Andrews, KY16 9AL, UK
| | - Jing Li
- State Key Laboratory of Biogeology and Environmental Geology, School of Earth Science, China University of Geosciences, Wuhan, 430074, China
| | - Jun Hu
- State Key Laboratory of Biogeology and Environmental Geology, School of Earth Science, China University of Geosciences, Wuhan, 430074, China
| | - Thomas J Algeo
- State Key Laboratory of Biogeology and Environmental Geology, School of Earth Science, China University of Geosciences, Wuhan, 430074, China
- State Key Laboratory of Geological Processes and Mineral Resources, China University of Geosciences, Wuhan, 430074, China
- Department of Geosciences, University of Cincinnati, Cincinnati, OH, 45221-0013, USA
| | - Li Tian
- State Key Laboratory of Biogeology and Environmental Geology, School of Earth Science, China University of Geosciences, Wuhan, 430074, China
| | - Daoliang Chu
- State Key Laboratory of Biogeology and Environmental Geology, School of Earth Science, China University of Geosciences, Wuhan, 430074, China
| | - Haijun Song
- State Key Laboratory of Biogeology and Environmental Geology, School of Earth Science, China University of Geosciences, Wuhan, 430074, China
| | - Shuhai Xiao
- Department of Geosciences, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Jinnan Tong
- State Key Laboratory of Biogeology and Environmental Geology, School of Earth Science, China University of Geosciences, Wuhan, 430074, China
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21
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Brown MO, Olagunju BO, Giner JL, Welander PV. Sterol methyltransferases in uncultured bacteria complicate eukaryotic biomarker interpretations. Nat Commun 2023; 14:1859. [PMID: 37012227 PMCID: PMC10070321 DOI: 10.1038/s41467-023-37552-3] [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: 07/29/2022] [Accepted: 03/22/2023] [Indexed: 04/05/2023] Open
Abstract
Sterane molecular fossils are broadly interpreted as eukaryotic biomarkers, although diverse bacteria also produce sterols. Steranes with side-chain methylations can act as more specific biomarkers if their sterol precursors are limited to particular eukaryotes and are absent in bacteria. One such sterane, 24-isopropylcholestane, has been attributed to demosponges and potentially represents the earliest evidence for animals on Earth, but enzymes that methylate sterols to give the 24-isopropyl side-chain remain undiscovered. Here, we show that sterol methyltransferases from both sponges and yet-uncultured bacteria function in vitro and identify three methyltransferases from symbiotic bacteria each capable of sequential methylations resulting in the 24-isopropyl sterol side-chain. We demonstrate that bacteria have the genomic capacity to synthesize side-chain alkylated sterols, and that bacterial symbionts may contribute to 24-isopropyl sterol biosynthesis in demosponges. Together, our results suggest bacteria should not be dismissed as potential contributing sources of side-chain alkylated sterane biomarkers in the rock record.
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Affiliation(s)
- Malory O Brown
- Department of Earth System Science, Stanford University, Stanford, CA, 94305, USA
| | - Babatunde O Olagunju
- Department of Chemistry, State University of New York-Environmental Science and Forestry, Syracuse, NY, 13210, USA
| | - José-Luis Giner
- Department of Chemistry, State University of New York-Environmental Science and Forestry, Syracuse, NY, 13210, USA
| | - Paula V Welander
- Department of Earth System Science, Stanford University, Stanford, CA, 94305, USA.
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22
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Transfection of Sponge Cells and Intracellular Localization of Cancer-Related MYC, RRAS2, and DRG1 Proteins. Mar Drugs 2023; 21:md21020119. [PMID: 36827160 PMCID: PMC9964533 DOI: 10.3390/md21020119] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/08/2023] [Accepted: 02/08/2023] [Indexed: 02/15/2023] Open
Abstract
The determination of the protein's intracellular localization is essential for understanding its biological function. Protein localization studies are mainly performed on primary and secondary vertebrate cell lines for which most protocols have been optimized. In spite of experimental difficulties, studies on invertebrate cells, including basal Metazoa, have greatly advanced. In recent years, the interest in studying human diseases from an evolutionary perspective has significantly increased. Sponges, placed at the base of the animal tree, are simple animals without true tissues and organs but with a complex genome containing many genes whose human homologs have been implicated in human diseases, including cancer. Therefore, sponges are an innovative model for elucidating the fundamental role of the proteins involved in cancer. In this study, we overexpressed human cancer-related proteins and their sponge homologs in human cancer cells, human fibroblasts, and sponge cells. We demonstrated that human and sponge MYC proteins localize in the nucleus, the RRAS2 in the plasma membrane, the membranes of the endolysosomal vesicles, and the DRG1 in the cell's cytosol. Despite the very low transfection efficiency of sponge cells, we observed an identical localization of human proteins and their sponge homologs, indicating their similar cellular functions.
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23
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Manzuk RA, Maloof AC, Kaandorp JA, Webster M. Branching archaeocyaths as ecosystem engineers during the Cambrian radiation. GEOBIOLOGY 2023; 21:66-85. [PMID: 36017532 DOI: 10.1111/gbi.12521] [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: 04/27/2022] [Revised: 07/21/2022] [Accepted: 07/25/2022] [Indexed: 06/15/2023]
Abstract
The rapid origination and diversification of major animal body plans during the early Cambrian coincide with the rise of Earth's first animal-built framework reefs. Given the importance of scleractinian coral reefs as ecological facilitators in modern oceans, we investigate the impact of archaeocyathan (Class Archaeocyatha) reefs as engineered ecosystems during the Cambrian radiation. In this study, we present the first high-resolution, three-dimensional (3D) reconstructions of branching archaeocyathide (Order Archaeocyathida) individuals from three localities on the Laurentian paleocontinent. Because branched forms in sponges and corals display phenotypic plasticity that preserve the characteristics of the surrounding growth environment, we compare morphological measurements from our fossil specimens to those of modern corals to infer the surface conditions of Earth's first reefs. These data demonstrate that archaeocyaths could withstand and influence the flow of water, accommodate photosymbionts, and build topographically complex and stable structures much like corals today. We also recognize a stepwise increase in the roughness of reef environments in the lower Cambrian, which would have laid a foundation for more abundant and diverse coevolving fauna.
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Affiliation(s)
- Ryan A Manzuk
- Department of Geosciences, Princeton University, Princeton, New Jersey, USA
| | - Adam C Maloof
- Department of Geosciences, Princeton University, Princeton, New Jersey, USA
| | - Jaap A Kaandorp
- Computational Science Lab, University of Amsterdam, Amsterdam, The Netherlands
| | - Mark Webster
- Department of the Geophysical Sciences, University of Chicago, Chicago, Illinois, USA
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24
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de Menezes TA, de Freitas MAM, Lima MS, Soares AC, Leal C, Busch MDS, Tschoeke DA, de O Vidal L, Atella GC, Kruger RH, Setubal J, Vasconcelos AA, de Mahiques MM, Siegle E, Asp NE, Cosenza C, Hajdu E, de Rezende CE, Thompson CC, Thompson FL. Fluxes of the Amazon River plume nutrients and microbes into marine sponges. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 847:157474. [PMID: 35868367 DOI: 10.1016/j.scitotenv.2022.157474] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 06/14/2022] [Accepted: 07/14/2022] [Indexed: 06/15/2023]
Abstract
Sponges have co-evolved with microbes for over 400 myr. Previous studies have demonstrated that sponges can be classified according to the abundance of microbes in their tissues as Low Microbial Abundance (LMA) and High Microbial Abundance (HMA). While LMA sponges rely mainly on water column microbes, HMA appear to rely much more on symbiotic fermentative and autotrophic microbes maintained in their tissues. However, it is unclear if this pattern holds when comparing different species of tropical sponges under extreme nutrient conditions and sediment loads in the water column, such as the Great Amazon Reef System (GARS), which covers an area of ~56,000 km2 off the Amazon River mouth. Sponges are the major GARS benthic components. However, these sponges' microbiome across the GARS is still unknown. Here, we investigated water quality, isotopic values (δ13C and δ15N), metagenomic and lipidomic profiles of sponges obtained from different sectors throughout the GARS. >180 million shotgun metagenomic reads were annotated, covering 22 sponge species. Isotopic and lipidomic analyses suggested LMA sponges rely on the Amazon River Plume for nutrition. HMA sponges (N = 15) had higher Roseiflexus and Nitrospira abundance, whereas LMA sponges (N = 7) had higher Prochlorococcus and Pelagibacter abundance. Functional data revealed that the LMA sponge microbiomes had greater number of sequences related to phages and prophages as well as electron transport and photophosphorylation which may be related to photosynthetic processes associated with the Prochlorococcus and Synechococcus found in the LMA. The higher phages abundance in LMA sponges could be related to these holobionts' reduced defense towards phage infection. Meanwhile, HMA sponge microbiomes had higher Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR abundance, which may be involved in defense against phage infection. This study sheds light on the nutrient fluxes and microbes from the Amazon River plume into the sponge holobionts.
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Affiliation(s)
- Tatiane A de Menezes
- Laboratory of Microbiology, Biology Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Mayanne A M de Freitas
- Laboratory of Microbiology, Biology Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Michele S Lima
- Laboratory of Microbiology, Biology Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Ana Carolina Soares
- Bioinformatics Laboratory, Department of Biochemistry, Institute of Chemistry, University of São Paulo (USP), São Paulo, Brazil
| | - Camille Leal
- Laboratory of Microbiology, Biology Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Mileane de S Busch
- Laboratory of Lipids Biochemistry and Lipoprotein, Biochemistry Institute Leopoldo de Meis, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Diogo A Tschoeke
- Biomedical Engineering Program - COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Luciana de O Vidal
- Environmental Sciences Laboratory, Biosciences and Biotechnology Center, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, Rio de Janeiro, Brazil; Department of Ecology and Marine Resources, Institute of Biosciences, Universidade Federal do Estado do Rio de Janeiro (UNIRIO), Rio de Janeiro, Brazil
| | - Georgia C Atella
- Laboratory of Lipids Biochemistry and Lipoprotein, Biochemistry Institute Leopoldo de Meis, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Ricardo H Kruger
- Laboratory of Enzymology, University of Brasilia (UNB), Brasilia, Brazil
| | - João Setubal
- Bioinformatics Laboratory, Department of Biochemistry, Institute of Chemistry, University of São Paulo (USP), São Paulo, Brazil
| | | | | | - Eduardo Siegle
- Oceanographic Institute (IO), University of São Paulo (USP), São Paulo, Brazil
| | - Nils Edvin Asp
- Federal University of Pará, Institute of Coastal Studies (IECOS), Bragança Campus, Bragança, PA, Brazil
| | - Carlos Cosenza
- Center of Technology - CT2, SAGE-COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Eduardo Hajdu
- Department of Invertebrates, National Museum, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Carlos E de Rezende
- Environmental Sciences Laboratory, Biosciences and Biotechnology Center, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, Rio de Janeiro, Brazil.
| | - Cristiane C Thompson
- Laboratory of Microbiology, Biology Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
| | - Fabiano L Thompson
- Laboratory of Microbiology, Biology Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; Center of Technology - CT2, SAGE-COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
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25
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Kelly JB, Carlson DE, Low JS, Thacker RW. Novel trends of genome evolution in highly complex tropical sponge microbiomes. MICROBIOME 2022; 10:164. [PMID: 36195901 PMCID: PMC9531527 DOI: 10.1186/s40168-022-01359-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 08/03/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Tropical members of the sponge genus Ircinia possess highly complex microbiomes that perform a broad spectrum of chemical processes that influence host fitness. Despite the pervasive role of microbiomes in Ircinia biology, it is still unknown how they remain in stable association across tropical species. To address this question, we performed a comparative analysis of the microbiomes of 11 Ircinia species using whole-metagenomic shotgun sequencing data to investigate three aspects of bacterial symbiont genomes-the redundancy in metabolic pathways across taxa, the evolution of genes involved in pathogenesis, and the nature of selection acting on genes relevant to secondary metabolism. RESULTS A total of 424 new, high-quality bacterial metagenome-assembled genomes (MAGs) were produced for 10 Caribbean Ircinia species, which were evaluated alongside 113 publicly available MAGs sourced from the Pacific species Ircinia ramosa. Evidence of redundancy was discovered in that the core genes of several primary metabolic pathways could be found in the genomes of multiple bacterial taxa. Across hosts, the metagenomes were depleted in genes relevant to pathogenicity and enriched in eukaryotic-like proteins (ELPs) that likely mimic the hosts' molecular patterning. Finally, clusters of steroid biosynthesis genes (CSGs), which appear to be under purifying selection and undergo horizontal gene transfer, were found to be a defining feature of Ircinia metagenomes. CONCLUSIONS These results illustrate patterns of genome evolution within highly complex microbiomes that illuminate how associations with hosts are maintained. The metabolic redundancy within the microbiomes could help buffer the hosts from changes in the ambient chemical and physical regimes and from fluctuations in the population sizes of the individual microbial strains that make up the microbiome. Additionally, the enrichment of ELPs and depletion of LPS and cellular motility genes provide a model for how alternative strategies to virulence can evolve in microbiomes undergoing mixed-mode transmission that do not ultimately result in higher levels of damage (i.e., pathogenicity) to the host. Our last set of results provides evidence that sterol biosynthesis in Ircinia-associated bacteria is widespread and that these molecules are important for the survival of bacteria in highly complex Ircinia microbiomes. Video Abstract.
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Affiliation(s)
- Joseph B Kelly
- Aquatic Ecology and Evolution, Limnological Institute University Konstanz, Konstanz, Germany.
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA.
| | - David E Carlson
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA
| | - Jun Siong Low
- Institute of Microbiology,ETH Zürich, Zürich, Switzerland
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Robert W Thacker
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA
- Smithsonian Tropical Research Institute, Box 0843-03092, Balboa, Panama City, Republic of Panama
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26
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Atomic Details of Biomineralization Proteins Inspiring Protein Design and Reengineering for Functional Biominerals. CHEMISTRY 2022. [DOI: 10.3390/chemistry4030059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Biominerals are extraordinary materials that provide organisms with a variety of functions to support life. The synthesis of biominerals and organization at the macroscopic level is a consequence of the interactions of these materials with proteins. The association of biominerals and proteins is very ancient and has sparked a wealth of research across biological, medical and material sciences. Calcium carbonate, hydroxyapatite, and silica represent widespread natural biominerals. The atomic details of the interface between macromolecules and these biominerals is very intriguing from a chemical perspective, considering the association of chemical entities that are structurally different. With this review I provide an overview of the available structural studies of biomineralization proteins, explored from the Protein Data Bank (wwPDB) archive and scientific literature, and of how these studies are inspiring the design and engineering of proteins able to synthesize novel biominerals. The progression of this review from classical template proteins to silica polymerization seeks to benefit researchers involved in various interdisciplinary aspects of a biomineralization project, who need background information and a quick update on advances in the field. Lessons learned from structural studies are exemplary and will guide new projects for the imaging of new hybrid biomineral/protein superstructures at the atomic level.
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27
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Yun H, Luo C, Chang C, Li L, Reitner J, Zhang X. Adaptive specialization of a unique sponge body from the Cambrian Qingjiang biota. Proc Biol Sci 2022; 289:20220804. [PMID: 35703053 PMCID: PMC9198775 DOI: 10.1098/rspb.2022.0804] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Sponge fossils from the Cambrian black shales have attracted attention from both palaeontologists and geochemists for many years in terms of their high diversity, beautiful preservation and perplexing adaptation to inhospitable living environments. However, the body shape of these sponges, which contributes to deciphering adaptive evolution, has not been scrutinized. New complete specimens of the hexactinellid sponge Sanshapentella tentoriformis sp. nov. from the Qingjiang biota (black shale of the Cambrian Stage 3 Shuijingtuo Formation, ca 518 Ma) allow recognition of a unique dendriform body characterized by a columnar trunk with multiple conical high peaks and distinctive quadripod-shaped dermal spicules that frame each high peak. The body shape of this new sponge along with other early Cambrian hexactinellids, is classified into three morpho-groups that reflect different levels of adaptivity to the environment. The cylindrical and ovoid bodies generally adapted to a large spectrum of environments; however, the dendriform body of S. tentoriformis was restricted to the relatively deep-water, oxygen-deficient environment. From a hindsight view, the unique body shape represents a consequence of adaptation that helps maintain an effective use of oxygen and a low energy cost in hypoxic conditions.
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Affiliation(s)
- Hao Yun
- State Key Laboratory of Continental Dynamics and Shaanxi Key Laboratory of Early Life and Environments, Department of Geology, Northwest University, Xi'an 710069, People's Republic of China
| | - Cui Luo
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing 210008, People's Republic of China
| | - Chao Chang
- State Key Laboratory of Continental Dynamics and Shaanxi Key Laboratory of Early Life and Environments, Department of Geology, Northwest University, Xi'an 710069, People's Republic of China
| | - Luoyang Li
- Key Laboratory of Submarine Geosciences and Prospecting Techniques, Ministry of Education, and College of Marine Geosciences, Ocean University of China, Qingdao 266100, People's Republic of China
| | - Joachim Reitner
- Department of Geobiology, Centre of Geosciences of the University of Göttingen, Goldschmidtstraße 3, Göttingen 37077, Germany
| | - Xingliang Zhang
- State Key Laboratory of Continental Dynamics and Shaanxi Key Laboratory of Early Life and Environments, Department of Geology, Northwest University, Xi'an 710069, People's Republic of China,State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing 210008, People's Republic of China
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28
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Curdt F, Schupp PJ, Rohde S. Light Availability Affects the Symbiosis of Sponge Specific Cyanobacteria and the Common Blue Aquarium Sponge ( Lendenfeldia chondrodes). Animals (Basel) 2022; 12:1283. [PMID: 35625129 PMCID: PMC9137838 DOI: 10.3390/ani12101283] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 05/04/2022] [Accepted: 05/13/2022] [Indexed: 02/04/2023] Open
Abstract
Bacterial symbionts in marine sponges play a decisive role in the biological and ecological functioning of their hosts. Although this topic has been the focus of numerous studies, data from experiments under controlled conditions are rare. To analyze the ongoing metabolic processes, we investigated the symbiosis of the sponge specific cyanobacterium Synechococcus spongiarum and its sponge host Lendenfeldia chondrodes under varying light conditions in a defined aquarium setting for 68 days. Sponge clonal pieces were kept at four different light intensities, ranging from no light to higher intensities that were assumed to trigger light stress. Growth as a measure of host performance and photosynthetic yield as a proxy of symbiont photosynthetic activity were measured throughout the experiment. The lack of light prevented sponge growth and induced the expulsion of all cyanobacteria and related pigments by the end of the experiment. Higher light conditions allowed rapid sponge growth and high cyanobacteria densities. In addition, photosynthetically active radiation above a certain level triggered an increase in cyanobacteria's lutein levels, a UV absorbing protein, thus protecting itself and the host's cells from UV radiation damage. Thus, L. chondrodes seems to benefit strongly from hosting the cyanbacterium S. spongiarum and the relationship should be considered obligatory mutualistic.
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Affiliation(s)
- Franziska Curdt
- Department for Environmental Biochemistry, Institute for Chemistry and Biology of the Marine Environment Terramare, Carl-von-Ossietzky University Oldenburg, 26382 Wilhelmshaven, Germany; (F.C.); (P.J.S.)
| | - Peter J. Schupp
- Department for Environmental Biochemistry, Institute for Chemistry and Biology of the Marine Environment Terramare, Carl-von-Ossietzky University Oldenburg, 26382 Wilhelmshaven, Germany; (F.C.); (P.J.S.)
- Helmholtz Institute for Functional Marine Biodiversity, Carl-von-Ossietzky University of Oldenburg, 26129 Oldenburg, Germany
| | - Sven Rohde
- Department for Environmental Biochemistry, Institute for Chemistry and Biology of the Marine Environment Terramare, Carl-von-Ossietzky University Oldenburg, 26382 Wilhelmshaven, Germany; (F.C.); (P.J.S.)
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29
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Maria Costa-Paiva E, Mello B, Santos Bezerra B, Coates CJ, Halanych KM, Brown F, de Moraes Leme J, Trindade RIF. Molecular dating of the blood pigment hemocyanin provides new insight into the origin of animals. GEOBIOLOGY 2022; 20:333-345. [PMID: 34766436 DOI: 10.1111/gbi.12481] [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: 12/23/2020] [Revised: 10/14/2021] [Accepted: 10/26/2021] [Indexed: 06/13/2023]
Abstract
The Neoproterozoic included changes in oceanic redox conditions, the configuration of continents and climate, extreme ice ages (Sturtian and Marinoan), and the rise of complex life forms. A much-debated topic in geobiology concerns the influence of atmospheric oxygenation on Earth and the origin and diversification of animal lineages, with the most widely popularized hypotheses relying on causal links between oxygen levels and the rise of animals. The vast majority of extant animals use aerobic metabolism for growth and homeostasis; hence, the binding and transportation of oxygen represent a vital physiological task. Considering the blood pigment hemocyanin (Hc) is present in sponges and ctenophores, and likely to be present in the common ancestor of animals, we investigated the evolution and date of Hc emergence using bioinformatics approaches on both transcriptomic and genomic data. Bayesian molecular dating suggested that the ancestral animal Hc gene arose approximately 881 Ma during the Tonian Period (1000-720 Ma), prior to the extreme glaciation events of the Cryogenian Period (720-635 Ma). This result is corroborated by a recently discovered fossil of a putative sponge ~890 Ma and modern molecular dating for the origin of metazoans of ~1,000-650 Ma (but does contradict previous inferences regarding the origin of Hc ~700-600 Ma). Our data reveal that crown-group animals already possessed hemocyanin-like blood pigments, which may have enhanced the oxygen-carrying capacity of these animals in hypoxic environments at that time or acted in the transport of hormones, detoxification of heavy metals, and immunity pathways.
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Affiliation(s)
- Elisa Maria Costa-Paiva
- Zoology Department, Institute of Biosciences, University of Sao Paulo, Sao Paulo, Brazil
- Geophysics and Atmospheric Sciences, Institute of Astronomy, University of Sao Paulo, Sao Paulo, Brazil
| | - Beatriz Mello
- Genetics Department, Biology Institute, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Bruno Santos Bezerra
- Zoology Department, Institute of Biosciences, University of Sao Paulo, Sao Paulo, Brazil
| | - Christopher J Coates
- Department of Biosciences, Faculty of Science and Engineering, Swansea University, Swansea, UK
| | - Kenneth M Halanych
- Center for Marine Science, University of North Carolina Wilmington, Wilmington, NC, USA
| | - Federico Brown
- Zoology Department, Institute of Biosciences, University of Sao Paulo, Sao Paulo, Brazil
| | | | - Ricardo I F Trindade
- Geophysics and Atmospheric Sciences, Institute of Astronomy, University of Sao Paulo, Sao Paulo, Brazil
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Micaroni V, Strano F, McAllen R, Woods L, Turner J, Harman L, Bell JJ. Adaptive strategies of sponges to deoxygenated oceans. GLOBAL CHANGE BIOLOGY 2022; 28:1972-1989. [PMID: 34854178 DOI: 10.1111/gcb.16013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 11/08/2021] [Accepted: 11/13/2021] [Indexed: 06/13/2023]
Abstract
Ocean deoxygenation is one of the major consequences of climate change. In coastal waters, this process can be exacerbated by eutrophication, which is contributing to an alarming increase in the so-called 'dead zones' globally. Despite its severity, the effect of reduced dissolved oxygen has only been studied for a very limited number of organisms, compared to other climate change impacts such as ocean acidification and warming. Here, we experimentally assessed the response of sponges to moderate and severe simulated hypoxic events. We ran three laboratory experiments on four species from two different temperate oceans (NE Atlantic and SW Pacific). Sponges were exposed to a total of five hypoxic treatments, with increasing severity (3.3, 1.6, 0.5, 0.4 and 0.13 mg O2 L-1 , over 7-12-days). We found that sponges are generally very tolerant of hypoxia. All the sponges survived in the experimental conditions, except Polymastia crocea, which showed significant mortality at the lowest oxygen concentration (0.13 mg O2 L-1 , lethal median time: 286 h). In all species except Suberites carnosus, hypoxic conditions do not significantly affect respiration rate down to 0.4 mg O2 L-1 , showing that sponges can uptake oxygen at very low concentrations in the surrounding environment. Importantly, sponges displayed species-specific phenotypic modifications in response to the hypoxic treatments, including physiological, morphological and behavioural changes. This phenotypic plasticity likely represents an adaptive strategy to live in reduced or low oxygen water. Our results also show that a single sponge species (i.e., Suberites australiensis) can display different strategies at different oxygen concentrations. Compared to other sessile organisms, sponges generally showed higher tolerance to hypoxia, suggesting that sponges could be favoured and survive in future deoxygenated oceans.
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Affiliation(s)
- Valerio Micaroni
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Francesca Strano
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Rob McAllen
- School of Biological Earth and Environmental Sciences, University College Cork, Cork, Ireland
| | - Lisa Woods
- School of Mathematics and Statistics, Victoria University of Wellington, Wellington, New Zealand
| | - John Turner
- School of Ocean Sciences, Bangor University, Anglesey, UK
| | - Luke Harman
- School of Biological Earth and Environmental Sciences, University College Cork, Cork, Ireland
| | - James J Bell
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
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31
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Cohen PA, Kodner RB. The earliest history of eukaryotic life: uncovering an evolutionary story through the integration of biological and geological data. Trends Ecol Evol 2021; 37:246-256. [PMID: 34949483 DOI: 10.1016/j.tree.2021.11.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 10/29/2021] [Accepted: 11/01/2021] [Indexed: 11/17/2022]
Abstract
While there is significant data on eukaryogenesis and the early development of the eukaryotic lineage, major uncertainties regarding their origins and evolution remain, including questions of taxonomy, timing, and paleoecology. Here we examine the origin and diversification of the eukaryotes in the Proterozoic Eon as viewed through fossils, organic biomarkers, molecular clocks, phylogenies, and redox proxies. Our interpretation of the integration of these data suggest that eukaryotes were likely aerobic and established in Proterozoic ecosystems. We argue that we must closely examine and integrate both biological and geological evidence and examine points of agreement and contention to gain new insights into the true origin and early evolutionary history of this vastly important group.
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Affiliation(s)
- Phoebe A Cohen
- Williams College Department of Geosciences, Williamstown, MA, USA.
| | - Robin B Kodner
- Western Washington University Department of Environmental Sciences, Bellingham, WA, USA.
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32
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Koch MJ, Hesketh-Best PJ, Smerdon G, Warburton PJ, Howell K, Upton M. Impact of growth media and pressure on the diversity and antimicrobial activity of isolates from two species of hexactinellid sponge. MICROBIOLOGY (READING, ENGLAND) 2021; 167. [PMID: 34898418 PMCID: PMC8744994 DOI: 10.1099/mic.0.001123] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Access to deep-sea sponges brings with it the potential to discover novel antimicrobial candidates, as well as novel cold- and pressure-adapted bacteria with further potential clinical or industrial applications. In this study, we implemented a combination of different growth media, increased pressure and high-throughput techniques to optimize recovery of isolates from two deep-sea hexactinellid sponges, Pheronema carpenteri and Hertwigia sp., in the first culture-based microbial analysis of these two sponges. Using 16S rRNA gene sequencing for isolate identification, we found a similar number of cultivable taxa from each sponge species, as well as improved recovery of morphotypes from P. carpenteri at 22-25 °C compared to other temperatures, which allows a greater potential for screening for novel antimicrobial compounds. Bacteria recovered under conditions of increased pressure were from the phyla Proteobacteria, Actinobacteria and Firmicutes, except at 4 %O2/5 bar, when the phylum Firmicutes was not observed. Cultured isolates from both sponge species displayed antimicrobial activity against Micrococcus luteus, Staphylococcus aureus and Escherichia coli.
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Affiliation(s)
- Matthew J Koch
- School of Biomedical Sciences, University of Plymouth, Plymouth PL4 8AA, UK
| | - Poppy J Hesketh-Best
- School of Biological and Marine Sciences, University of Plymouth, Plymouth PL4 8AA, UK
| | - Gary Smerdon
- Diving Diseases Research Centre Healthcare, Plymouth Science Park, Research Way, Plymouth PL6 8BU, UK
| | - Philip J Warburton
- School of Biomedical Sciences, University of Plymouth, Plymouth PL4 8AA, UK
| | - Kerry Howell
- School of Biological and Marine Sciences, University of Plymouth, Plymouth PL4 8AA, UK
| | - Mathew Upton
- School of Biomedical Sciences, University of Plymouth, Plymouth PL4 8AA, UK
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33
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González-Castillo A, Carballo JL, Bautista-Guerrero E. Genomics and phylogeny of the proposed phylum 'Candidatus Poribacteria' associated with the excavating sponge Thoosa mismalolli. Antonie van Leeuwenhoek 2021; 114:2163-2174. [PMID: 34668097 DOI: 10.1007/s10482-021-01670-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 10/03/2021] [Indexed: 11/24/2022]
Abstract
Members of the proposed phylum 'Candidatus Poribacteria' are among the most abundant microorganisms in the highly diverse microbiome of the sponge mesohyl. Genomic and phylogenetic characteristics of this proposed phylum are barely known. In this study, we analyzed metagenome-assembled genomes (MAGs) obtained from the coral reef excavating sponge Thoosa mismalolli from the Mexican Pacific Ocean. Two MAGs were extracted and analyzed together with 32 MAGs and single-amplified genomes (SAGs) obtained from NCBI. The phylogenetic tree based on the sequences of 139 single-copy genes (SCG) showed two clades. Clade A (23 genomes) represented 67.7% of the total of the genomes, while clade B (11 genomes) comprised 32.3% of the genomes. The Average Nucleotide Identity (ANI) showed values between 66 and 99% for the genomes of the proposed phylum, and the pangenome of genomes revealed a total of 37,234 genes that included 1722 core gene. The number of genes used in the phylogenetic analysis increased from 28 (previous studies) to 139 (this study), which allowed a better resolution of the phylogeny of the proposed phylum. The results supported the two previously described classes, 'Candidatus Entoporibacteria' and 'Candidatus Pelagiporibacteria', and the genomes SB0101 and SB0202 obtained in this study belong to two new species of the class 'Candidatus Entoporibacteria'. This is the first comparative study that includes MAGs from a non-sponge host (Porites lutea) to elucidate the taxonomy of the poorly known Candidatus phylum in a polyphasic approach. Finally, our study also contributes to the sponge microbiome project by reporting the first MAGs of the proposed phylum 'Candidatus Poribacteria' isolated from the excavating sponge T. mismalolli.
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Affiliation(s)
- Adrián González-Castillo
- Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México (Unidad Académica Mazatlán), Mazatlán, México.
| | - José Luis Carballo
- Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México (Unidad Académica Mazatlán), Mazatlán, México.,Laboratorio de Biología Marina, Departamento de Zoología, Universidad de Sevilla, Avda. Reina Mercedes, 6, 41012, Sevilla, Spain
| | - Eric Bautista-Guerrero
- Laboratorio de Ecología Marina, Centro de Investigaciones Costeras, Centro Universitario de la Costa, Universidad de Guadalajara, Puerto Vallarta, México
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Abstract
AbstractAnimals, fungi, and algae with complex multicellular bodies all evolved independently from unicellular ancestors. The early history of these major eukaryotic multicellular clades, if not their origins, co-occur with an extreme phase of global glaciations known as the Snowball Earth. Here, I propose that the long-term loss of low-viscosity environments due to several rounds global glaciation drove the multiple origins of complex multicellularity in eukaryotes and the subsequent radiation of complex multicellular groups into previously unoccupied niches. In this scenario, life adapts to Snowball Earth oceans by evolving large size and faster speeds through multicellularity, which acts to compensate for high-viscosity seawater and achieve fluid flow at sufficient levels to satisfy metabolic needs. Warm, low-viscosity seawater returned with the melting of the Snowball glaciers, and with it, by virtue of large and fast multicellular bodies, new ways of life were unveiled.
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35
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Pehr K, Bisquera R, Bishop AN, Ossa Ossa F, Meredith W, Bekker A, Love GD. Preservation and Distributions of Covalently Bound Polyaromatic Hydrocarbons in Ancient Biogenic Kerogens and Insoluble Organic Macromolecules. ASTROBIOLOGY 2021; 21:1049-1075. [PMID: 34030461 DOI: 10.1089/ast.2020.2338] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The likelihood of finding pristine molecular biosignatures preserved in Earth's oldest rocks or on other planetary bodies is low, and new approaches are needed to assess the origins of highly altered and recalcitrant organic matter. In this study, we aim to understand the distributions and systematics of preservation of ancient polycyclic aromatic hydrocarbons (PAHs), as both free hydrocarbons and bound within insoluble macromolecules. We report the distributions of bound PAHs generated by catalytic hydropyrolysis from ancient biogenic kerogens and from insoluble organic matter (IOM) in high-temperature carbonaceous residues from pyrobitumens and synthetic coke. For biogenic kerogens, the degree of thermal maturity exerts the primary control on the preservation and distributions of the major five-ring and six-ring PAH compounds. This holds for both Precambrian and Phanerozoic rocks, thus source variation in primary biogenic organic matter inputs does not exert the major control on bound PAH. The IOM samples, predominantly residues from hydrocarbon cracking at high temperatures, preserve a bound PAH profile significantly distinct from ancient biogenic kerogens and characterized by an absence of perylene and higher abundance of large-ring condensed PAHs. Covalently bound PAH profiles offer promise as "last resort" molecular biosignatures for aiding the astrobiological search for ancient life.
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Affiliation(s)
- Kelden Pehr
- Department of Earth and Planetary Sciences, University of California-Riverside, Riverside, California, USA
| | - Rose Bisquera
- Department of Earth and Planetary Sciences, University of California-Riverside, Riverside, California, USA
| | | | - Frantz Ossa Ossa
- Department of Geosciences, University of Tübingen, Tübingen, Germany
| | - William Meredith
- Department of Chemical and Environmental Engineering, University of Nottingham, Nottingham, United Kingdom
| | - Andrey Bekker
- Department of Earth and Planetary Sciences, University of California-Riverside, Riverside, California, USA
| | - Gordon D Love
- Department of Earth and Planetary Sciences, University of California-Riverside, Riverside, California, USA
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36
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Lyons TW, Diamond CW, Planavsky NJ, Reinhard CT, Li C. Oxygenation, Life, and the Planetary System during Earth's Middle History: An Overview. ASTROBIOLOGY 2021; 21:906-923. [PMID: 34314605 PMCID: PMC8403206 DOI: 10.1089/ast.2020.2418] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The long history of life on Earth has unfolded as a cause-and-effect relationship with the evolving amount of oxygen (O2) in the oceans and atmosphere. Oxygen deficiency characterized our planet's first 2 billion years, yet evidence for biological O2 production and local enrichments in the surface ocean appear long before the first accumulations of O2 in the atmosphere roughly 2.4 to 2.3 billion years ago. Much has been written about this fundamental transition and the related balance between biological O2 production and sinks coupled to deep Earth processes that could buffer against the accumulation of biogenic O2. However, the relationship between complex life (eukaryotes, including animals) and later oxygenation is less clear. Some data suggest O2 was higher but still mostly low for another billion and a half years before increasing again around 800 million years ago, potentially setting a challenging course for complex life during its initial development and ecological expansion. The apparent rise in O2 around 800 million years ago is coincident with major developments in complex life. Multiple geochemical and paleontological records point to a major biogeochemical transition at that time, but whether rising and still dynamic biospheric oxygen triggered or merely followed from innovations in eukaryotic ecology, including the emergence of animals, is still debated. This paper focuses on the geochemical records of Earth's middle history, roughly 1.8 to 0.5 billion years ago, as a backdrop for exploring possible cause-and-effect relationships with biological evolution and the primary controls that may have set its pace, including solid Earth/tectonic processes, nutrient limitation, and their possible linkages. A richer mechanistic understanding of the interplay between coevolving life and Earth surface environments can provide a template for understanding and remotely searching for sustained habitability and even life on distant exoplanets.
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Affiliation(s)
- Timothy W. Lyons
- Department of Earth and Planetary Sciences, University of California, Riverside, California, USA
- Address correspondence to: Timothy W. Lyons, Department of Earth and Planetary Sciences, University of California, Riverside, CA 92521, USA
| | - Charles W. Diamond
- Department of Earth and Planetary Sciences, University of California, Riverside, California, USA
| | - Noah J. Planavsky
- Department of Earth and Planetary Sciences, Yale University, New Haven, Connecticut, USA
| | - Christopher T. Reinhard
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Chao Li
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
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Rivera-Valentín EG, Filiberto J, Lynch KL, Mamajanov I, Lyons TW, Schulte M, Méndez A. Introduction-First Billion Years: Habitability. ASTROBIOLOGY 2021; 21:893-905. [PMID: 34406807 PMCID: PMC8403211 DOI: 10.1089/ast.2020.2314] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 12/22/2020] [Indexed: 06/13/2023]
Abstract
The physical processes active during the first billion years (FBY) of Earth's history, such as accretion, differentiation, and impact cratering, provide constraints on the initial conditions that were conducive to the formation and establishment of life on Earth. This motivated the Lunar and Planetary Institute's FBY topical initiative, which was a four-part conference series intended to look at each of these physical processes to study the basic structure and composition of our Solar System that was set during the FBY. The FBY Habitability conference, held in September 2019, was the last in this series and was intended to synthesize the initiative; specifically, to further our understanding of the origins of life, planetary and environmental habitability, and the search for life beyond Earth. The conference included discussions of planetary habitability and the potential emergence of life on bodies within our Solar System, as well as extrasolar systems by applying our knowledge of the Solar System's FBY, and in particular Earth's early history. To introduce this Special Collection, which resulted from work discussed at the conference, we provide a review of the main themes and a synopsis of the FBY Habitability conference.
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Affiliation(s)
| | - Justin Filiberto
- Lunar and Planetary Institute, Universities Space Research Association, Houston, Texas, USA
| | - Kennda L. Lynch
- Lunar and Planetary Institute, Universities Space Research Association, Houston, Texas, USA
| | - Irena Mamajanov
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
| | - Timothy W. Lyons
- Department of Earth and Planetary Sciences, University of California Riverside, Riverside, California, USA
| | - Mitch Schulte
- Planetary Science Division, NASA Headquarters, Washington, District of Columbia, USA
| | - Abel Méndez
- Planetary Habitability Laboratory, University of Puerto Rico Arecibo, Arecibo, Puerto Rico
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Possible poriferan body fossils in early Neoproterozoic microbial reefs. Nature 2021; 596:87-91. [PMID: 34321662 PMCID: PMC8338550 DOI: 10.1038/s41586-021-03773-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 06/28/2021] [Indexed: 11/08/2022]
Abstract
Molecular phylogeny indicates that metazoans (animals) emerged early in the Neoproterozoic era1, but physical evidence is lacking. The search for animal fossils from the Proterozoic eon is hampered by uncertainty about what physical characteristics to expect. Sponges are the most basic known animal type2,3; it is possible that body fossils of hitherto-undiscovered Proterozoic metazoans might resemble aspect(s) of Phanerozoic fossil sponges. Vermiform microstructure4,5, a complex petrographic feature in Phanerozoic reefal and microbial carbonates, is now known to be the body fossil of nonspicular keratosan demosponges6-10. This Article presents petrographically identical vermiform microstructure from approximately 890-million-year-old reefs. The millimetric-to-centimetric vermiform-microstructured organism lived only on, in and immediately beside reefs built by calcifying cyanobacteria (photosynthesizers), and occupied microniches in which these calcimicrobes could not live. If vermiform microstructure is in fact the fossilized tissue of keratose sponges, the material described here would represent the oldest body-fossil evidence of animals known to date, and would provide the first physical evidence that animals emerged before the Neoproterozoic oxygenation event and survived through the glacial episodes of the Cryogenian period.
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Zilber-Rosenberg I, Rosenberg E. Microbial driven genetic variation in holobionts. FEMS Microbiol Rev 2021; 45:6261188. [PMID: 33930136 DOI: 10.1093/femsre/fuab022] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 04/11/2021] [Indexed: 12/11/2022] Open
Abstract
Genetic variation in holobionts, (host and microbiome), occurring by changes in both host and microbiome genomes, can be observed from two perspectives: observable variations and the processes that bring about the variation. The observable includes the enormous genetic diversity of prokaryotes, which gave rise to eukaryotic organisms. Holobionts then evolved a rich microbiome with a stable core containing essential genes, less so common taxa, and a more diverse non-core enabling considerable genetic variation. The result being that, the human gut microbiome, for example, contains 1,000 times more unique genes than are present in the human genome. Microbial driven genetic variation processes in holobionts include: (1) Acquisition of novel microbes from the environment, which bring in multiple genes in one step, (2) amplification/reduction of certain microbes in the microbiome, that contribute to holobiont` s adaptation to changing conditions, (3) horizontal gene transfer between microbes and between microbes and host, (4) mutation, which plays an important role in optimizing interactions between different microbiota and between microbiota and host. We suggest that invertebrates and plants, where microbes can live intracellularly, have a greater chance of genetic exchange between microbiota and host, thus a greater chance of vertical transmission and a greater effect of microbiome on evolution of host than vertebrates. However, even in vertebrates the microbiome can aid in environmental fluctuations by amplification/reduction and by acquisition of novel microorganisms.
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Affiliation(s)
- Ilana Zilber-Rosenberg
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv Israel
| | - Eugene Rosenberg
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv Israel
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40
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Strassert JFH, Irisarri I, Williams TA, Burki F. A molecular timescale for eukaryote evolution with implications for the origin of red algal-derived plastids. Nat Commun 2021; 12:1879. [PMID: 33767194 PMCID: PMC7994803 DOI: 10.1038/s41467-021-22044-z] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 02/25/2021] [Indexed: 01/31/2023] Open
Abstract
In modern oceans, eukaryotic phytoplankton is dominated by lineages with red algal-derived plastids such as diatoms, dinoflagellates, and coccolithophores. Despite the ecological importance of these groups and many others representing a huge diversity of forms and lifestyles, we still lack a comprehensive understanding of their evolution and how they obtained their plastids. New hypotheses have emerged to explain the acquisition of red algal-derived plastids by serial endosymbiosis, but the chronology of these putative independent plastid acquisitions remains untested. Here, we establish a timeframe for the origin of red algal-derived plastids under scenarios of serial endosymbiosis, using Bayesian molecular clock analyses applied on a phylogenomic dataset with broad sampling of eukaryote diversity. We find that the hypotheses of serial endosymbiosis are chronologically possible, as the stem lineages of all red plastid-containing groups overlap in time. This period in the Meso- and Neoproterozoic Eras set the stage for the later expansion to dominance of red algal-derived primary production in the contemporary oceans, which profoundly altered the global geochemical and ecological conditions of the Earth.
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Affiliation(s)
- Jürgen F H Strassert
- Department of Organismal Biology, Program in Systematic Biology, Uppsala University, Uppsala, Sweden
- Department of Ecosystem Research, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Iker Irisarri
- Department of Organismal Biology, Program in Systematic Biology, Uppsala University, Uppsala, Sweden
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid, Spain
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Göttingen, and Campus Institute Data Science (CIDAS), Göttingen, Germany
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, Life Sciences Building, Bristol, UK
| | - Fabien Burki
- Department of Organismal Biology, Program in Systematic Biology, Uppsala University, Uppsala, Sweden.
- Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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41
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Ammonia-oxidizing archaea in biological interactions. J Microbiol 2021; 59:298-310. [DOI: 10.1007/s12275-021-1005-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 01/28/2021] [Accepted: 01/29/2021] [Indexed: 10/22/2022]
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Vargas S, Leiva L, Wörheide G. Short-Term Exposure to High-Temperature Water Causes a Shift in the Microbiome of the Common Aquarium Sponge Lendenfeldia chondrodes. MICROBIAL ECOLOGY 2021; 81:213-222. [PMID: 32767091 PMCID: PMC7794106 DOI: 10.1007/s00248-020-01556-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 07/08/2020] [Indexed: 06/11/2023]
Abstract
Marine sponges harbor diverse microbiomes that contribute to their energetic and metabolic needs. Although numerous studies on sponge microbial diversity exist, relatively few focused on sponge microbial community changes under different sources of environmental stress. In this study, we assess the impact of elevated seawater temperature on the microbiome of cultured Lendenfeldia chondrodes, a coral reef sponge commonly found in marine aquaria. Lendenfeldia chondrodes exhibits high thermal tolerance showing no evidence of tissue damage or bleaching at 5 °C above control water temperature (26 °C). High-throughput sequencing of the bacterial 16S rRNA V4 region revealed a response of the microbiome of L. chondrodes to short-term exposure to elevated seawater temperature. Shifts in abundance and richness of the dominant bacterial phyla found in the microbiome of this species, namely Proteobacteria, Cyanobacteria, Planctomycetes, and Bacteroidetes, characterized this response. The observed resilience of L. chondrodes and the responsiveness of its microbiome to short-term increases in seawater temperature suggest that this holobiont may be capable of acclimating to anthropogenic-driven sublethal environmental stress via a re-accommodation of its associated bacterial community. This sheds a new light on the potential for resilience of some sponges to increasing surface seawater temperatures and associated projected regime shifts in coral reefs.
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Affiliation(s)
- Sergio Vargas
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333, Munich, Germany.
| | - Laura Leiva
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333, Munich, Germany
- Biologische Anstalt Helgoland, Shelf Sea System Ecology, Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, 27498, Helgoland, Germany
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333, Munich, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333, Munich, Germany
- SNSB - Bayerische Staatssammlung für Paläontologie und Geologie, Richard-Wagner-Str. 10, 80333, Munich, Germany
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43
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Li C, Shi W, Cheng M, Jin C, Algeo TJ. The redox structure of Ediacaran and early Cambrian oceans and its controls. Sci Bull (Beijing) 2020; 65:2141-2149. [PMID: 36732967 DOI: 10.1016/j.scib.2020.09.023] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/24/2020] [Accepted: 08/25/2020] [Indexed: 02/04/2023]
Abstract
The rapid diversification of early animals during the Ediacaran (635-541 Ma) and early Cambrian (ca. 541-509 Ma) has frequently been attributed to increasing oceanic oxygenation. However, the pattern of oceanic oxygenation and its relationship to early animal evolution remain in debate. In this review, we examine the redox structure of Ediacaran and early Cambrian oceans and its controls, offering new insights into contemporaneous oceanic oxygenation patterns and their role in the coevolution of environments and early animals. We review the development of marine redox models which, in combination with independent distal deep-ocean redox proxies, supports a highly redox-stratified shelf and an anoxia-dominated deep ocean during the Ediacaran and early Cambrian. Geochemical and modeling evidence indicates that the marine redox structure was likely controlled by low atmospheric O2 levels and low seawater vertical mixing rates on shelves at that time. Furthermore, theoretical analysis and increasing geochemical evidence, particularly from South China, show that limited sulfate availability was a primary control on the attenuation of mid-depth euxinia offshore, in contrast to the existing paradigm invoking decreased organic carbon fluxes distally. In light of our review, we infer that if oceanic oxygenation indeed triggered the rise of early animals, it must have done so through a shelf oxygenation which was probably driven by elevated oxidant availability. Our review calls for further studies on Ediacaran-Cambrian marine redox structure and its controls, particularly from regions outside of South China, in order to better understand the coevolutionary relationship between oceanic redox and early animals.
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Affiliation(s)
- Chao Li
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China.
| | - Wei Shi
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Meng Cheng
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Chengsheng Jin
- Yunnan Key Laboratory for Palaeobiology, Yunnan University, Kunming 650091, China
| | - Thomas J Algeo
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China; State Key Laboratory of Geological Process and Mineral Resources, China University of Geosciences, Wuhan 430074, China; Department of Geology, University of Cincinnati, Cincinnati OH45221, USA
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Abstract
Formation of highly symmetric skeletal elements in demosponges, called spicules, follows a unique biomineralization mechanism in which polycondensation of an inherently disordered amorphous silica is guided by a highly ordered proteinaceous scaffold, the axial filament. The enzymatically active proteins, silicateins, are assembled into a slender hybrid silica/protein crystalline superstructure that directs the morphogenesis of the spicules. Furthermore, silicateins are known to catalyze the formation of a large variety of other technologically relevant organic and inorganic materials. However, despite the biological and biotechnological importance of this macromolecule, its tertiary structure was never determined. Here we report the atomic structure of silicatein and the entire mineral/organic hybrid assembly with a resolution of 2.4 Å. In this work, the serial X-ray crystallography method was successfully adopted to probe the 2-µm-thick filaments in situ, being embedded inside the skeletal elements. In combination with imaging and chemical analysis using high-resolution transmission electron microscopy, we provide detailed information on the enzymatic activity of silicatein, its crystallization, and the emergence of a functional three-dimensional silica/protein superstructure in vivo. Ultimately, we describe a naturally occurring mineral/protein crystalline assembly at atomic resolution.
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van Maldegem LM, Nettersheim BJ, Leider A, Brocks JJ, Adam P, Schaeffer P, Hallmann C. Geological alteration of Precambrian steroids mimics early animal signatures. Nat Ecol Evol 2020; 5:169-173. [PMID: 33230255 DOI: 10.1038/s41559-020-01336-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 09/23/2020] [Indexed: 11/09/2022]
Abstract
The absence of unambiguous animal body fossils in rocks older than the late Ediacaran has rendered fossil lipids the most promising tracers of early organismic complexity. Yet much debate surrounds the various potential biological sources of putative metazoan steroids found in Precambrian rocks. Here we show that 26-methylated steranes-hydrocarbon structures currently attributed to the earliest animals-can form via geological alteration of common algal sterols, which carries important implications for palaeo-ecological interpretations and inhibits the use of such unconventional 'sponge' steranes for reconstructing early animal evolution.
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Affiliation(s)
- Lennart M van Maldegem
- Max Planck Institute for Biogeochemistry, Jena, Germany. .,MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany. .,The Australian National University, Canberra, Australian Capital Territory, Australia.
| | - Benjamin J Nettersheim
- Max Planck Institute for Biogeochemistry, Jena, Germany. .,MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.
| | - Arne Leider
- Max Planck Institute for Biogeochemistry, Jena, Germany.,MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Jochen J Brocks
- The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Pierre Adam
- University of Strasbourg, CNRS-UMR 7177, Strasbourg, France
| | | | - Christian Hallmann
- Max Planck Institute for Biogeochemistry, Jena, Germany. .,MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.
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46
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Algal origin of sponge sterane biomarkers negates the oldest evidence for animals in the rock record. Nat Ecol Evol 2020; 5:165-168. [PMID: 33230256 DOI: 10.1038/s41559-020-01334-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 09/23/2020] [Indexed: 12/18/2022]
Abstract
The earliest fossils of animal-like organisms occur in Ediacaran rocks that are approximately 571 million years old. Yet 24-isopropylcholestanes and other C30 fossil sterol molecules have been suggested to reflect an important ecological role of demosponges as the first abundant animals by the end of the Cryogenian period (>635 million years ago). Here, we demonstrate that C30 24-isopropylcholestane is not diagnostic for sponges and probably formed in Neoproterozoic sediments through the geological methylation of C29 sterols of chlorophyte algae, the dominant eukaryotes at that time. These findings reconcile biomarker evidence with the geological record and revert the oldest evidence for animals back into the latest Ediacaran.
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Plese B, Kenny NJ, Rossi ME, Cárdenas P, Schuster A, Taboada S, Koutsouveli V, Riesgo A. Mitochondrial evolution in the Demospongiae (Porifera): Phylogeny, divergence time, and genome biology. Mol Phylogenet Evol 2020; 155:107011. [PMID: 33217579 DOI: 10.1016/j.ympev.2020.107011] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 11/06/2020] [Accepted: 11/08/2020] [Indexed: 12/01/2022]
Abstract
The sponge class Demospongiae is the most speciose and morphologically diverse in the phylum Porifera, and the species within it are vital components of a range of ecosystems worldwide. Despite their ubiquity, a number of recalcitrant problems still remain to be solved regarding their phylogenetic inter-relationships, the timing of their appearance, and their mitochondrial biology, the latter of which is only beginning to be investigated. Here we generated 14 new demosponge mitochondrial genomes which, alongside previously published mitochondrial resources, were used to address these issues. In addition to phylogenomic analysis, we have used syntenic data and analysis of coding regions to forge a framework for understanding the inter-relationships between Demospongiae sub-classes and orders. We have also leveraged our new resources to study the mitochondrial biology of these clades in terms of codon usage, optimisation and gene expression, to understand how these vital cellular components may have contributed to the success of the Porifera. Our results strongly support a sister relationship between Keratosa and (Verongimorpha + Heteroscleromorpha), contradicting previous studies using nuclear markers. Our study includes one species of Clionaida, and show for the first time support for a grouping of Suberitida+(Clionaida+(Tethyida + Poecilosclerida). The findings of our phylogenetic analyses are supported by in-depth examination of structural and coding-level evidence from our mitochondrial data. A time-calibrated phylogeny estimated the origin of Demospongiae in the Cambrian (~529 Mya), and suggests that most demosponge order crown-groups emerged in the Mesozoic. This work therefore provides a robust basis for considering demosponge phylogenetic relationships, as well as essential mitochondrial data for understanding the biological basis for their success and diversity.
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Affiliation(s)
- Bruna Plese
- Life Sciences Department, The Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom.
| | - Nathan James Kenny
- Life Sciences Department, The Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom; Faculty of Health and Life Sciences, Oxford Brookes University, Headington Rd, Oxford OX3 0BP, United Kingdom(2).
| | - Maria Eleonora Rossi
- Life Sciences Department, The Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom; School of Earth Sciences, University of Bristol, Life Science Building, 24 Tyndall Ave, Bristol BS8 1TH, United Kingdom.
| | - Paco Cárdenas
- Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, Husargatan 3, Uppsala 751 23, Sweden.
| | - Astrid Schuster
- Department of Biology, University of Southern Denmark, Campusvej 55, Odense M 5230, Denmark; CIIMAR Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal.
| | - Sergi Taboada
- Life Sciences Department, The Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom; Department of Life Sciences, Universidad de Alcalá de Henares, 28871 Alcalá de Henares, Spain; Department of Biodiversity, Ecology and Evolution, Universidad Complutense de Madrid, C/ José Antonio Novais, 12, Ciudad Universitaria, 28040 Madrid, Spain.
| | - Vasiliki Koutsouveli
- Life Sciences Department, The Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom; Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, Husargatan 3, Uppsala 751 23, Sweden.
| | - Ana Riesgo
- Life Sciences Department, The Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom; Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales de Madrid (CSIC), c/ José Gutiérrez Abascal 2, 28006 Madrid, Spain.
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Roussel A, Cui X, Summons RE. Biomarker stratigraphy in the Athel Trough of the South Oman Salt Basin at the Ediacaran-Cambrian Boundary. GEOBIOLOGY 2020; 18:663-681. [PMID: 32643313 DOI: 10.1111/gbi.12407] [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: 01/13/2020] [Revised: 05/23/2020] [Accepted: 06/01/2020] [Indexed: 06/11/2023]
Abstract
The South Oman Salt Basin (SOSB) has been studied extensively for knowledge concerning the habitat of the enigmatic Ediacaran-Cambrian oils that are produced from that region. Geological, geochemical, geophysical, and geochronological investigations have all contributed to improved understanding of the range of late Neoproterozoic depositional environments recorded there. Of particular interest has been the deep Athel depocenter within the SOSB that features a silica-rich interval known as the Al Shomou Member or Athel Silicilyte and the co-eval A4 carbonate-evaporite sequence that straddles the Ediacaran-Cambrian boundary. The deep basin has been suggested to be anoxic and euxinic based on studies of sulfur isotopes, trace metal distributions and other proxies. Organic geochemistry has provided some clues concerning aspects of the depositional environments and microbial communities prevailing during this interval. However, ambiguities remain including a paucity of convincing molecular evidence for euxinia in the photic zone of the basin. Here, we present a comprehensive study of biomarker hydrocarbons, including steroids, triterpenoids, and carotenoids. Among the compounds detected is a distinctive array of aromatic carotenoids. Relatively low abundances of monoaromatic carotenoids, such as chlorobactane, okenane, and β-isorenieratane, suggest the possibility of transient photic zone euxinia with a shallow chemocline or, perhaps, exogenous inputs from microbial mats. However, it is the dominance of renieratane and renierapurpurane over isorenieratane in diaromatic carotenoids and their association with abundant C38 and C39 carotenoids that identifies cyanobacteria as major contributors to the inventory of carotenoids. Our results, based on multiple lines of molecular evidence and statistical analysis, also suggest that the Athel Silicilyte was biogeochemically distinct from the other units of the Ara Group. Overall, our study has important implications for understanding other late Neoproterozoic depositional environments.
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Affiliation(s)
- Anaïs Roussel
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Xingqian Cui
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Roger E Summons
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
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Duda JP, Love GD, Rogov VI, Melnik DS, Blumenberg M, Grazhdankin DV. Understanding the geobiology of the terminal Ediacaran Khatyspyt Lagerstätte (Arctic Siberia, Russia). GEOBIOLOGY 2020; 18:643-662. [PMID: 32881267 DOI: 10.1111/gbi.12412] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 06/16/2020] [Accepted: 07/30/2020] [Indexed: 06/11/2023]
Abstract
The Khatyspyt Lagerstätte (~544 Ma, Russia) provides a valuable window into late Ediacaran Avalon-type ecosystems with rangeomorphs, arboreomorphs, and mega-algae. Here, we tackle the geobiology of this Lagerstätte by the combined analysis of paleontological features, sedimentary facies, and lipid biomarkers. The Khatyspyt Formation was deposited in carbonate ramp environments. Organic matter (0.12-2.22 wt.% TOC) displays characteristic Ediacaran biomarker features (e.g., eukaryotic steranes dominated by the C29 stigmastane). Some samples contain a putative 2-methylgammacerane that was likely sourced by ciliates and/or bacteria. 24-isopropylcholestane and 26-methylstigmastane are consistently scarce (≤0.4% and ≤0.2% of ∑C27-30 regular steranes, respectively). Thus, Avalon-type organisms occupied different niches than organisms capable of directly synthesizing C30 sterane precursors among their major lipids. Relative abundances of eukaryotic steranes and bacterial hopanes (sterane/hopane ratios = 0.07-0.30) demonstrate oligotrophic and bacterially dominated marine environments, similar to findings from other successions with Ediacara-type fossils. Ediacara-type fossils occur in facies characterized by microbial mats and biomarkers indicative for a stratified marine environment with normal-moderate salinities (moderate-high gammacerane index of 2.3-5.7; low C35 homohopane index of 0.1-0.2). Mega-algae, in contrast, are abundant in facies that almost entirely consist of allochthonous event layers. Biomarkers in these samples indicate a non-stratified marine environment and normal salinities (low gammacerane index of 0.6-0.8; low C35 homohopane index of 0.1). Vertical burrowers occur in similar facies but with biomarker evidence for stratification in the water column or around the seafloor (high gammacerane index of 5.6). Thus, the distribution of macro-organisms and burrowers was controlled by various, dynamically changing environmental factors. It appears likely that dynamic settings like the Khatyspyt Lagerstätte provided metabolic challenges for sustenance and growth which primed eukaryotic organisms to cope with changing environmental habitats, allowing for a later diversification and expansion of complex macroscopic life in the marine realm.
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Affiliation(s)
- Jan-Peter Duda
- Department of Earth and Planetary Sciences, University of California, Riverside, CA, USA
- Geobiology Group, Geoscience Centre, University of Göttingen, Göttingen, Germany
| | - Gordon D Love
- Department of Earth and Planetary Sciences, University of California, Riverside, CA, USA
| | - Vladimir I Rogov
- Trofimuk Institute of Petroleum Geology and Geophysics, Siberian Branch Russian Academy of Sciences, Novosibirsk, Russia
| | - Dmitry S Melnik
- Trofimuk Institute of Petroleum Geology and Geophysics, Siberian Branch Russian Academy of Sciences, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Martin Blumenberg
- Federal Institute for Geosciences and Natural Resources (BGR), Hannover, Germany
| | - Dmitriy V Grazhdankin
- Trofimuk Institute of Petroleum Geology and Geophysics, Siberian Branch Russian Academy of Sciences, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
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50
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Beljan S, Herak Bosnar M, Ćetković H. Rho Family of Ras-Like GTPases in Early-Branching Animals. Cells 2020; 9:cells9102279. [PMID: 33066017 PMCID: PMC7600811 DOI: 10.3390/cells9102279] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/06/2020] [Accepted: 10/09/2020] [Indexed: 02/07/2023] Open
Abstract
Non-bilaterian animals consist of four phyla; Porifera, Cnidaria, Ctenophora, and Placozoa. These early-diverging animals are crucial for understanding the evolution of the entire animal lineage. The Rho family of proteins make up a major branch of the Ras superfamily of small GTPases, which function as key molecular switches that play important roles in converting and amplifying external signals into cellular responses. This review represents a compilation of the current knowledge on Rho-family GTPases in non-bilaterian animals, the available experimental data about their biochemical characteristics and functions, as well as original bioinformatics analysis, in order to gain a general insight into the evolutionary history of Rho-family GTPases in simple animals.
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Affiliation(s)
- Silvestar Beljan
- Division of Molecular Biology, Ruđer Bošković Institute, HR-10000 Zagreb, Croatia;
- Division of Molecular Biology, Faculty of Science, University of Zagreb, HR-10000 Zagreb, Croatia
| | - Maja Herak Bosnar
- Division of Molecular Medicine, Ruđer Bošković Institute, HR-10000 Zagreb, Croatia;
| | - Helena Ćetković
- Division of Molecular Biology, Ruđer Bošković Institute, HR-10000 Zagreb, Croatia;
- Correspondence: ; Tel.: +385-1-456-1115
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