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Chaudhari NM, Pérez-Carrascal OM, Overholt WA, Totsche KU, Küsel K. Genome streamlining in Parcubacteria transitioning from soil to groundwater. ENVIRONMENTAL MICROBIOME 2024; 19:41. [PMID: 38902796 PMCID: PMC11188291 DOI: 10.1186/s40793-024-00581-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 06/03/2024] [Indexed: 06/22/2024]
Abstract
BACKGROUND To better understand the influence of habitat on the genetic content of bacteria, with a focus on members of Candidate Phyla Radiation (CPR) bacteria, we studied the effects of transitioning from soil via seepage waters to groundwater on genomic composition of ultra-small Parcubacteria, the dominating CPR class in seepage waters, using genome resolved metagenomics. RESULTS Bacterial metagenome-assembled genomes (MAGs), (318 total, 32 of Parcubacteria) were generated from seepage waters and compared directly to groundwater counterparts. The estimated average genome sizes of members of major phyla Proteobacteria, Bacteroidota and Cand. Patescibacteria (Candidate Phyla Radiation - CPR bacteria) were significantly higher in soil-seepage water as compared to their groundwater counterparts. Seepage water Parcubacteria (Paceibacteria) exhibited 1.18-fold greater mean genome size and 2-fold lower mean proportion of pseudogenes than those in groundwater. Bacteroidota and Proteobacteria also showed a similar trend of reduced genomes in groundwater compared to seepage. While exploring gene loss and adaptive gains in closely related CPR lineages in groundwater, we identified a membrane protein, and a lipoglycopeptide resistance gene unique to a seepage Parcubacterium genome. A nitrite reductase gene was also identified and was unique to the groundwater Parcubacteria genomes, likely acquired from other planktonic microbes via horizontal gene transfer. CONCLUSIONS Overall, our data suggest that bacteria in seepage waters, including ultra-small Parcubacteria, have significantly larger genomes and higher metabolic enrichment than their groundwater counterparts, highlighting possible genome streamlining of the latter in response to habitat selection in an oligotrophic environment.
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Affiliation(s)
- Narendrakumar M Chaudhari
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Friedrich-Schiller-Universität, Leipzig, Germany
| | - Olga M Pérez-Carrascal
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
| | - Will A Overholt
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany
| | - Kai U Totsche
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
- Hydrogeology, Institute of Geowissenschaften, Friedrich-Schiller-Universität Jena, Burgweg 11, 07749, Jena, Germany
| | - Kirsten Küsel
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany.
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Friedrich-Schiller-Universität, Leipzig, Germany.
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany.
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2
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Felipe Benites L, Stephens TG, Van Etten J, James T, Christian WC, Barry K, Grigoriev IV, McDermott TR, Bhattacharya D. Hot springs viruses at Yellowstone National Park have ancient origins and are adapted to thermophilic hosts. Commun Biol 2024; 7:312. [PMID: 38594478 PMCID: PMC11003980 DOI: 10.1038/s42003-024-05931-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 02/16/2024] [Indexed: 04/11/2024] Open
Abstract
Geothermal springs house unicellular red algae in the class Cyanidiophyceae that dominate the microbial biomass at these sites. Little is known about host-virus interactions in these environments. We analyzed the virus community associated with red algal mats in three neighboring habitats (creek, endolithic, soil) at Lemonade Creek, Yellowstone National Park (YNP), USA. We find that despite proximity, each habitat houses a unique collection of viruses, with the giant viruses, Megaviricetes, dominant in all three. The early branching phylogenetic position of genes encoded on metagenome assembled virus genomes (vMAGs) suggests that the YNP lineages are of ancient origin and not due to multiple invasions from mesophilic habitats. The existence of genomic footprints of adaptation to thermophily in the vMAGs is consistent with this idea. The Cyanidiophyceae at geothermal sites originated ca. 1.5 Bya and are therefore relevant to understanding biotic interactions on the early Earth.
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Affiliation(s)
- L Felipe Benites
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Timothy G Stephens
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Julia Van Etten
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
- Graduate Program in Ecology and Evolution, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Timeeka James
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - William C Christian
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, Montana, USA
| | - Kerrie Barry
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Timothy R McDermott
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA.
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3
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Xu S, Shao S, Feng X, Li S, Zhang L, Wu W, Liu M, Tracy ME, Zhong C, Guo Z, Wu CI, Shi S, He Z. Adaptation in Unstable Environments and Global Gene Losses: Small but Stable Gene Networks by the May-Wigner Theory. Mol Biol Evol 2024; 41:msae059. [PMID: 38507653 PMCID: PMC10991078 DOI: 10.1093/molbev/msae059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 03/07/2024] [Accepted: 03/15/2024] [Indexed: 03/22/2024] Open
Abstract
Although gene loss is common in evolution, it remains unclear whether it is an adaptive process. In a survey of seven major mangrove clades that are woody plants in the intertidal zones of daily environmental perturbations, we noticed that they generally evolved reduced gene numbers. We then focused on the largest clade of Rhizophoreae and observed the continual gene set reduction in each of the eight species. A great majority of gene losses are concentrated on environmental interaction processes, presumably to cope with the constant fluctuations in the tidal environments. Genes of the general processes for woody plants are largely retained. In particular, fewer gene losses are found in physiological traits such as viviparous seeds, high salinity, and high tannin content. Given the broad and continual genome reductions, we propose the May-Wigner theory (MWT) of system stability as a possible mechanism. In MWT, the most effective solution for buffering continual perturbations is to reduce the size of the system (or to weaken the total genic interactions). Mangroves are unique as immovable inhabitants of the compound environments in the land-sea interface, where environmental gradients (such as salinity) fluctuate constantly, often drastically. Extending MWT to gene regulatory network (GRN), computer simulations and transcriptome analyses support the stabilizing effects of smaller gene sets in mangroves vis-à-vis inland plants. In summary, we show the adaptive significance of gene losses in mangrove plants, including the specific role of promoting phenotype innovation and a general role in stabilizing GRN in unstable environments as predicted by MWT.
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Affiliation(s)
- Shaohua Xu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
- School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Shao Shao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Xiao Feng
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Sen Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Lingjie Zhang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Weihong Wu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Min Liu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Miles E Tracy
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Cairong Zhong
- Institute of Wetland Research, Hainan Academy of Forestry (Hainan Academy of Mangrove), Haikou, China
| | - Zixiao Guo
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Chung-I Wu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Suhua Shi
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Ziwen He
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
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Bureš P, Elliott TL, Veselý P, Šmarda P, Forest F, Leitch IJ, Nic Lughadha E, Soto Gomez M, Pironon S, Brown MJM, Šmerda J, Zedek F. The global distribution of angiosperm genome size is shaped by climate. THE NEW PHYTOLOGIST 2024; 242:744-759. [PMID: 38264772 DOI: 10.1111/nph.19544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 01/03/2024] [Indexed: 01/25/2024]
Abstract
Angiosperms, which inhabit diverse environments across all continents, exhibit significant variation in genome sizes, making them an excellent model system for examining hypotheses about the global distribution of genome size. These include the previously proposed large genome constraint, mutational hazard, polyploidy-mediated, and climate-mediated hypotheses. We compiled the largest genome size dataset to date, encompassing 16 017 (> 5% of known) angiosperm species, and analyzed genome size distribution using a comprehensive geographic distribution dataset for all angiosperms. We observed that angiosperms with large range sizes generally had small genomes, supporting the large genome constraint hypothesis. Climate was shown to exert a strong influence on genome size distribution along the global latitudinal gradient, while the frequency of polyploidy and the type of growth form had negligible effects. In contrast to the unimodal patterns along the global latitudinal gradient shown by plant size traits and polyploid proportions, the increase in angiosperm genome size from the equator to 40-50°N/S is probably mediated by different (mostly climatic) mechanisms than the decrease in genome sizes observed from 40 to 50°N northward. Our analysis suggests that the global distribution of genome sizes in angiosperms is mainly shaped by climatically mediated purifying selection, genetic drift, relaxed selection, and environmental filtering.
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Affiliation(s)
- Petr Bureš
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlarska 2, 611 37, Brno, Czech Republic
| | - Tammy L Elliott
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlarska 2, 611 37, Brno, Czech Republic
- Department of Biological Sciences, University of Cape Town, Cape Town, 7700, South Africa
| | - Pavel Veselý
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlarska 2, 611 37, Brno, Czech Republic
| | - Petr Šmarda
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlarska 2, 611 37, Brno, Czech Republic
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, TW9 3AE, UK
| | | | | | | | - Samuel Pironon
- Royal Botanic Gardens, Kew, Richmond, TW9 3AE, UK
- UN Environment Programme World Conservation Monitoring Centre (UNEP-WCMC), Cambridge, CB3 0DL, UK
| | | | - Jakub Šmerda
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlarska 2, 611 37, Brno, Czech Republic
| | - František Zedek
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlarska 2, 611 37, Brno, Czech Republic
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5
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Takemata N. How Do Thermophiles Organize Their Genomes? Microbes Environ 2024; 39:n/a. [PMID: 38839371 DOI: 10.1264/jsme2.me23087] [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] [Indexed: 06/07/2024] Open
Abstract
All cells must maintain the structural and functional integrity of the genome under a wide range of environments. High temperatures pose a formidable challenge to cells by denaturing the DNA double helix, causing chemical damage to DNA, and increasing the random thermal motion of chromosomes. Thermophiles, predominantly classified as bacteria or archaea, exhibit an exceptional capacity to mitigate these detrimental effects and prosper under extreme thermal conditions, with some species tolerating temperatures higher than 100°C. Their genomes are mainly characterized by the presence of reverse gyrase, a unique topoisomerase that introduces positive supercoils into DNA. This enzyme has been suggested to maintain the genome integrity of thermophiles by limiting DNA melting and mediating DNA repair. Previous studies provided significant insights into the mechanisms by which NAPs, histones, SMC superfamily proteins, and polyamines affect the 3D genomes of thermophiles across different scales. Here, I discuss current knowledge of the genome organization in thermophiles and pertinent research questions for future investigations.
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Affiliation(s)
- Naomichi Takemata
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University
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6
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Chi B, Huang Y, Xiong Z, Tan J, Zhou W, Yang Z, Zhou K, Duan X, Chen A, Zha R, Gui K. Investigation of lysing excess sludge slurry using hydrolase secreting thermophilic bacterial communities. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 349:119562. [PMID: 37952379 DOI: 10.1016/j.jenvman.2023.119562] [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: 05/12/2023] [Revised: 10/22/2023] [Accepted: 11/04/2023] [Indexed: 11/14/2023]
Abstract
Sludge reduction is a critical challenge in biological wastewater treatment. Combining excess sludge slurry lysis technology with traditional activated sludge processes is a promising approach for in-situ sludge reduction. Here, a strategy for excess sludge slurry lysis based on thermophilic bacterial communities (LTBC) was proposed. This investigation focused on the process of excess sludge slurry lysis dominated by thermophilic bacterial communities domesticated at different temperatures (55-75 °C). The evolution of sludge lysate was analyzed, and the mechanism of excess sludge slurry lysis under the action of thermophilic bacterial communities was elucidated through amplicon sequencing analysis. The results demonstrated that the aerobic thermophilic bacterial communities adapted to 75 °C exhibit the highest efficiency in sludge slurry lysis. During LTBC process, the removal efficiency of volatile suspended solids reached 53.9 ± 1.8% within 2 h, and 97.0 ± 1.0% of the protein and 96.0 ± 1.0% of the polysaccharide in the extracellular polymers was solubilized, and bacterial cell walls in sludge were disrupted. Fourier transform infrared spectroscopy and excitation-emission matrix spectroscopy of the sludge lysate demonstrated that the LTBC process was accompanied by humification process. The accumulation of humic acid primarily occurred at 55 °C and 65 °C, while fulvic acid occurred at 75 °C. The thermophilic bacterial communities adapted to 75 °C were dominated by Thermus and Thermaerobacter. Phylogenetic studies showed that the LTBC hydrolase system comprises enzymes related to protein hydrolysis, carbohydrate hydrolysis, and peptidoglycan hydrolysis, including metalopeptidase MepB, neutral α-glucosidase C, N-acetyl Muramyl-L-alanine amidase, and others enzymes. These results provide a theoretical basis for the application of LTBC technology in the reduction of sludge which generated in traditional waste water activated sludge processes.
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Affiliation(s)
- Baoyan Chi
- Solid Waste Treatment and Resource Recycle Research Laboratory, Department of Environmental Science and Technology, School of Energy and Environment, Southeast University, Nanjing, 210096, PR China; Key Laboratory of Energy Thermal Conversion and Control of Ministry of Education, Southeast University, Nanjing, 210096, PR China
| | - Ying Huang
- Solid Waste Treatment and Resource Recycle Research Laboratory, Department of Environmental Science and Technology, School of Energy and Environment, Southeast University, Nanjing, 210096, PR China; Key Laboratory of Energy Thermal Conversion and Control of Ministry of Education, Southeast University, Nanjing, 210096, PR China.
| | - Zhenfeng Xiong
- Solid Waste Treatment and Resource Recycle Research Laboratory, Department of Environmental Science and Technology, School of Energy and Environment, Southeast University, Nanjing, 210096, PR China; Key Laboratory of Energy Thermal Conversion and Control of Ministry of Education, Southeast University, Nanjing, 210096, PR China
| | - Jiali Tan
- Solid Waste Treatment and Resource Recycle Research Laboratory, Department of Environmental Science and Technology, School of Energy and Environment, Southeast University, Nanjing, 210096, PR China; Key Laboratory of Energy Thermal Conversion and Control of Ministry of Education, Southeast University, Nanjing, 210096, PR China
| | - Weidong Zhou
- Nanjing Water Group Co., Ltd., Nanjing, 210002, PR China
| | - Zhuo Yang
- Central & South China Municipal Engineering Design and Research Institute Co., Ltd., Wuhan, 430010, PR China
| | - Kemei Zhou
- Nanjing Water Group Co., Ltd., Nanjing, 210002, PR China
| | - Xinxin Duan
- Solid Waste Treatment and Resource Recycle Research Laboratory, Department of Environmental Science and Technology, School of Energy and Environment, Southeast University, Nanjing, 210096, PR China
| | - Ao Chen
- Solid Waste Treatment and Resource Recycle Research Laboratory, Department of Environmental Science and Technology, School of Energy and Environment, Southeast University, Nanjing, 210096, PR China
| | - Rong Zha
- Zhenjiang Esther Environment Protection Technology Co., Ltd., Jurong City, 212400, PR China
| | - Keting Gui
- Solid Waste Treatment and Resource Recycle Research Laboratory, Department of Environmental Science and Technology, School of Energy and Environment, Southeast University, Nanjing, 210096, PR China
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7
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Mara P, Geller-McGrath D, Edgcomb V, Beaudoin D, Morono Y, Teske A. Metagenomic profiles of archaea and bacteria within thermal and geochemical gradients of the Guaymas Basin deep subsurface. Nat Commun 2023; 14:7768. [PMID: 38012208 PMCID: PMC10681998 DOI: 10.1038/s41467-023-43296-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 11/02/2023] [Indexed: 11/29/2023] Open
Abstract
Previous studies of microbial communities in subseafloor sediments reported that microbial abundance and diversity decrease with sediment depth and age, and microbes dominating at depth tend to be a subset of the local seafloor community. However, the existence of geographically widespread, subsurface-adapted specialists is also possible. Here, we use metagenomic and metatranscriptomic analyses of the hydrothermally heated, sediment layers of Guaymas Basin (Gulf of California, Mexico) to examine the distribution and activity patterns of bacteria and archaea along thermal, geochemical and cell count gradients. We find that the composition and distribution of metagenome-assembled genomes (MAGs), dominated by numerous lineages of Chloroflexota and Thermoproteota, correlate with biogeochemical parameters as long as temperatures remain moderate, but downcore increasing temperatures beyond ca. 45 ºC override other factors. Consistently, MAG size and diversity decrease with increasing temperature, indicating a downcore winnowing of the subsurface biosphere. By contrast, specific archaeal MAGs within the Thermoproteota and Hadarchaeota increase in relative abundance and in recruitment of transcriptome reads towards deeper, hotter sediments, marking the transition towards a specialized deep, hot biosphere.
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Affiliation(s)
- Paraskevi Mara
- Geology and Geophysics Department, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - David Geller-McGrath
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Virginia Edgcomb
- Geology and Geophysics Department, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - David Beaudoin
- Geology and Geophysics Department, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Yuki Morono
- Kochi Institute for Core Sample Research, Institute for Extra-cutting-edge Science and Technology Avantgarde Research (X-STAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Monobe, Nankoku, Kochi, Japan
| | - Andreas Teske
- Department of Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
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Mino S, Fukazawa S, Tsuchiya J, McNichol JC, Sievert SM, Yamaki S, Ando Y, Sawabe T. Hydrogenimonas cancrithermarum sp. nov., a hydrogen- and thiosulfate-oxidizing mesophilic chemolithoautotroph isolated from diffuse-flow fluids on the East Pacific Rise, and an emended description of the genus Hydrogenimonas. Int J Syst Evol Microbiol 2023; 73. [PMID: 37921642 DOI: 10.1099/ijsem.0.006132] [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] [Indexed: 11/04/2023] Open
Abstract
A novel mesophilic, hydrogen- and thiosulfate-oxidizing bacterium, strain ISO32T, was isolated from diffuse-flow hydrothermal fluids from the Crab Spa vent on the East Pacific Rise. Cells of ISO32T were rods, being motile by means of a single polar flagellum. The isolate grew at a temperature range between 30 and 55 °C (optimum, 43 °C), at a pH range between 5.3 and 7.6 (optimum, pH 5.8) and in the presence of 2.0-4.0 % NaCl (optimum, 2.5 %). The isolate was able to grow chemolithoautotrophically with molecular hydrogen, thiosulfate or elemental sulfur as the sole electron donor. Thiosulfate, elemental sulfur, nitrate and molecular oxygen were each used as a sole electron acceptor. Phylogenetic analysis of 16S rRNA gene sequences placed ISO32T in the genus Hydrogenimonas of the class Epsilonproteobacteria, with Hydrogenimonas thermophila EP1-55-1 %T as its closest relative (95.95 % similarity). On the basis of the phylogenetic, physiological and genomic characteristics, it is proposed that the organism represents a novel species within the genus Hydrogenimonas, Hydrogenimonas cancrithermarum sp. nov. The type strain is ISO32T (=JCM 39185T =KCTC 25252T). Furthermore, the genomic properties of members of the genus Hydrogenimonas are distinguished from those of members of other thermophilic genera in the orders Campylobacterales (Nitratiruptor and Nitrosophilus) and Nautiliales (Caminibacter, Nautilia and Lebetimonas), with larger genome sizes and lower 16S rRNA G+C content values. Comprehensive metabolic comparisons based on genomes revealed that genes responsible for the Pta-AckA pathway were observed exclusively in members of mesophilic genera in the order Campylobacterales and of the genus Hydrogenimonas. Our results indicate that the genus Hydrogenimonas contributes to elucidating the evolutionary history of Epsilonproteobacteria in terms of metabolism and transition from a thermophilic to a mesophilic lifestyle.
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Affiliation(s)
- Sayaka Mino
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - So Fukazawa
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Jiro Tsuchiya
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Jesse C McNichol
- Biology Department, Woods Hole Oceanographic Institution, MA, USA
- Department of Biology, St. Francis Xavier University, NS, Canada
| | - Stefan M Sievert
- Biology Department, Woods Hole Oceanographic Institution, MA, USA
| | - Shogo Yamaki
- Laboratory of Marine Food Science and Technology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Yasuhiro Ando
- Laboratory of Marine Bioresources Chemistry, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Tomoo Sawabe
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
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9
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Sriaporn C, Campbell KA, Van Kranendonk MJ, Handley KM. Bacterial and archaeal community distributions and cosmopolitanism across physicochemically diverse hot springs. ISME COMMUNICATIONS 2023; 3:80. [PMID: 37596308 PMCID: PMC10439147 DOI: 10.1038/s43705-023-00291-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 08/01/2023] [Accepted: 08/04/2023] [Indexed: 08/20/2023]
Abstract
Terrestrial hot springs harbor diverse microbial communities whose compositions are shaped by the wide-ranging physico-chemistries of individual springs. The effect of enormous physico-chemical differences on bacterial and archaeal distributions and population structures is little understood. We therefore analysed the prevalence and relative abundance of bacteria and archaea in the sediments (n = 76) of hot spring features, in the Taupō Volcanic Zone (New Zealand), spanning large differences in major anion water chemistry, pH (2.0-7.5), and temperature (17.5-92.9 °C). Community composition, based on 16S rRNA amplicon sequence variants (ASVs) was strongly influenced by both temperature and pH. However, certain lineages characterized diverse hot springs. At the domain level, bacteria and archaea shared broadly equivalent community abundances across physico-chemically diverse springs, despite slightly lower bacteria-to-archaea ratios and microbial 16S rRNA gene concentrations at higher temperatures. Communities were almost exclusively dominated by Proteobacteria, Euryarchaeota or Crenarchaeota. Eight archaeal and bacterial ASVs from Thermoplasmatales, Desulfurellaceae, Mesoaciditogaceae and Acidithiobacillaceae were unusually prevalent (present in 57.9-84.2% of samples) and abundant (1.7-12.0% sample relative abundance), and together comprised 44% of overall community abundance. Metagenomic analyses generated multiple populations associated with dominant ASVs, and showed characteristic traits of each lineage for sulfur, nitrogen and hydrogen metabolism. Differences in metabolic gene composition and genome-specific metabolism delineated populations from relatives. Genome coverage calculations showed that populations associated with each lineage were distributed across a physicochemically broad range of hot springs. Results imply that certain bacterial and archaeal lineages harbor different population structures and metabolic potentials for colonizing diverse hot spring environments.
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Affiliation(s)
- Chanenath Sriaporn
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Kathleen A Campbell
- School of Environment & Te Ao Mārama - Centre for Fundamental Inquiry, The University of Auckland, Auckland, New Zealand
| | - Martin J Van Kranendonk
- Australian Centre for Astrobiology, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Kim M Handley
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand.
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10
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He Q, Wang S, Feng K, Michaletz ST, Hou W, Zhang W, Li F, Zhang Y, Wang D, Peng X, Yang X, Deng Y. High speciation rate of niche specialists in hot springs. THE ISME JOURNAL 2023:10.1038/s41396-023-01447-4. [PMID: 37286739 DOI: 10.1038/s41396-023-01447-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 05/24/2023] [Accepted: 05/26/2023] [Indexed: 06/09/2023]
Abstract
Ecological and evolutionary processes simultaneously regulate microbial diversity, but the evolutionary processes and their driving forces remain largely unexplored. Here we investigated the ecological and evolutionary characteristics of microbiota in hot springs spanning a broad temperature range (54.8-80 °C) by sequencing the 16S rRNA genes. Our results demonstrated that niche specialists and niche generalists are embedded in a complex interaction of ecological and evolutionary dynamics. On the thermal tolerance niche axis, thermal (T) sensitive (at a specific temperature) versus T-resistant (at least in five temperatures) species were characterized by different niche breadth, community abundance and dispersal potential, consequently differing in potential evolutionary trajectory. The niche-specialized T-sensitive species experienced strong temperature barriers, leading to completely species shift and high fitness but low abundant communities at each temperature ("home niche"), and such trade-offs thus reinforced peak performance, as evidenced by high speciation across temperatures and increasing diversification potential with temperature. In contrast, T-resistant species are advantageous of niche expansion but with poor local performance, as shown by wide niche breadth with high extinction, indicating these niche generalists are "jack-of-all-trades, master-of-none". Despite of such differences, the T-sensitive and T-resistant species are evolutionarily interacted. Specifically, the continuous transition from T-sensitive to T-resistant species insured the exclusion probability of T-resistant species at a relatively constant level across temperatures. The co-evolution and co-adaptation of T-sensitive and T-resistant species were in line with the red queen theory. Collectively, our findings demonstrate that high speciation of niche specialists could alleviate the environmental-filtering-induced negative effect on diversity.
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Affiliation(s)
- Qing He
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100190, China
| | - Shang Wang
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China.
| | - Kai Feng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
| | - Sean T Michaletz
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Weiguo Hou
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China
| | - Wenhui Zhang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China
| | - Fangru Li
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China
| | - Yidi Zhang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China
| | - Danrui Wang
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100190, China
| | - Xi Peng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100190, China
| | - Xingsheng Yang
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100190, China
| | - Ye Deng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China.
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100190, China.
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11
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Eme L, Tamarit D, Caceres EF, Stairs CW, De Anda V, Schön ME, Seitz KW, Dombrowski N, Lewis WH, Homa F, Saw JH, Lombard J, Nunoura T, Li WJ, Hua ZS, Chen LX, Banfield JF, John ES, Reysenbach AL, Stott MB, Schramm A, Kjeldsen KU, Teske AP, Baker BJ, Ettema TJG. Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes. Nature 2023; 618:992-999. [PMID: 37316666 PMCID: PMC10307638 DOI: 10.1038/s41586-023-06186-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 05/10/2023] [Indexed: 06/16/2023]
Abstract
In the ongoing debates about eukaryogenesis-the series of evolutionary events leading to the emergence of the eukaryotic cell from prokaryotic ancestors-members of the Asgard archaea play a key part as the closest archaeal relatives of eukaryotes1. However, the nature and phylogenetic identity of the last common ancestor of Asgard archaea and eukaryotes remain unresolved2-4. Here we analyse distinct phylogenetic marker datasets of an expanded genomic sampling of Asgard archaea and evaluate competing evolutionary scenarios using state-of-the-art phylogenomic approaches. We find that eukaryotes are placed, with high confidence, as a well-nested clade within Asgard archaea and as a sister lineage to Hodarchaeales, a newly proposed order within Heimdallarchaeia. Using sophisticated gene tree and species tree reconciliation approaches, we show that analogous to the evolution of eukaryotic genomes, genome evolution in Asgard archaea involved significantly more gene duplication and fewer gene loss events compared with other archaea. Finally, we infer that the last common ancestor of Asgard archaea was probably a thermophilic chemolithotroph and that the lineage from which eukaryotes evolved adapted to mesophilic conditions and acquired the genetic potential to support a heterotrophic lifestyle. Our work provides key insights into the prokaryote-to-eukaryote transition and a platform for better understanding the emergence of cellular complexity in eukaryotic cells.
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Affiliation(s)
- Laura Eme
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Laboratoire Écologie, Systématique, Évolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
| | - Daniel Tamarit
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Theoretical Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Eva F Caceres
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Courtney W Stairs
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Department of Biology, Lund University, Lund, Sweden
| | - Valerie De Anda
- Department of Marine Science, Marine Science Institute, University of Texas Austin, Port Aransas, TX, USA
- Department of Integrative Biology, University of Texas Austin, Austin, TX, USA
| | - Max E Schön
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Kiley W Seitz
- Department of Marine Science, Marine Science Institute, University of Texas Austin, Port Aransas, TX, USA
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Nina Dombrowski
- Department of Marine Science, Marine Science Institute, University of Texas Austin, Port Aransas, TX, USA
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, AB Den Burg, The Netherlands
| | - William H Lewis
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Felix Homa
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Jimmy H Saw
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Department of Biological Sciences, The George Washington University, Washington, DC, USA
| | - Jonathan Lombard
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Zheng-Shuang Hua
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, PR China
| | - Lin-Xing Chen
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA, USA
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
| | - Emily St John
- Department of Biology, Portland State University, Portland, OR, USA
| | | | - Matthew B Stott
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Andreas Schramm
- Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Kasper U Kjeldsen
- Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Andreas P Teske
- Department of Earth, Marine and Environmental Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Brett J Baker
- Department of Marine Science, Marine Science Institute, University of Texas Austin, Port Aransas, TX, USA
- Department of Integrative Biology, University of Texas Austin, Austin, TX, USA
| | - Thijs J G Ettema
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands.
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12
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Nguyen TV, Viver T, Smets I, Bernaerts K, Faust K, Lavigne R, Poughon L, Dussap CG, Springael D. Thermocaproicibacter melissae gen. nov., sp. nov., a thermophilic chain-elongating bacterium, producing n-caproate from polymeric carbohydrates. Int J Syst Evol Microbiol 2023; 73. [PMID: 37200213 DOI: 10.1099/ijsem.0.005893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023] Open
Abstract
Strain MDTJ8T is a chain-elongating thermophilic bacterium isolated from a thermophilic acidogenic anaerobic digestor treating human waste while producing the high commodity chemical n-caproate. The strain grows and produces formate, acetate, n-butyrate, n-caproate and lactate from mono-, di- and polymeric saccharides at 37-60 °C (optimum, 50-55 °C) and at pH 5.0-7.0 (optimum, pH 6.5). The organism is an obligate anaerobe, is motile and its cells form rods (0.3-0.5×1.0-3.0 µm) that stain Gram-positive and occur primarily as chains. Phylogenetic analysis of both the 16S rRNA gene and full genome sequence shows that strain MDTJ8T belongs to a group that consists of mesophylic chain-elongating bacteria within the family Oscillospiraceae, being nearest to Caproicibacter fermentans EA1T (94.8 %) and Caproiciproducens galactitolivorans BS-1T (93.7 %). Its genome (1.96 Mbp) with a G+C content of 49.6 mol% is remarkably smaller than those of other chain-elongating bacteria of the family Oscillospiraceae. Pairwise average nucleotide identity and DNA-DNA hybridization values between strain MDJT8T and its mesophilic family members are less than 70 and 35 %, respectively, while pairwise average amino acid identity values are less than 68 %. In addition, strain MDJT8T uses far less carbohydrate and non-carbohydrate substrates compared to its nearest family members. The predominant cellular fatty acids of strain MDTJ8T are C14 : 0, C14 : 0 DMA (dimethyl acetal) and C16 : 0, while its polar lipid profile shows three unidentified glycophospholipids, 11 glycolipids, 13 phospholipids and six unidentified lipids. No respiratory quinones and polyamines are detected. Based on its phylogenetic, genotypic, morphological, physiological, biochemical and chemotaxonomic characteristics, strain MDTJ8T represents a novel species and novel genus of the family Oscillospiraceae and Thermocaproicibacter melissae gen. nov., sp. nov. is proposed as its name. The type strain is MDTJ8T (=DSM 114174T=LMG 32615T=NCCB 100883T).
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Affiliation(s)
- Tinh Van Nguyen
- Division of Soil and Water Management, KU Leuven, Kasteelpark Arenberg 20, B-3001 Heverlee, Belgium
- Institut Pascal, Université Clermont Auvergne, Avenue Blaise Pascal 4, F-63178 Aubiére cedex, France
| | - Tomeu Viver
- Marine Microbiology Group, Mediterranean Institute of Advanced Studies (CSIC-UIB), C/Miquel Marquès 21, 07190 Esporles, Spain
| | - Ilse Smets
- Chemical Reactor Engineering and Safety, KU Leuven, Celestijnenlaan 200F, B-3001, Heverlee, Belgium
| | - Kristel Bernaerts
- Chemical Reactor Engineering and Safety, KU Leuven, Celestijnenlaan 200F, B-3001, Heverlee, Belgium
| | - Karoline Faust
- Laboratory of Molecular Bacteriology (Rega Institute), KU Leuven, Herestraat 49, B-3000 Leuven, Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21, B-3001 Heverlee, Belgium
| | - Laurent Poughon
- Institut Pascal, Université Clermont Auvergne, Avenue Blaise Pascal 4, F-63178 Aubiére cedex, France
| | - Claude-Gilles Dussap
- Institut Pascal, Université Clermont Auvergne, Avenue Blaise Pascal 4, F-63178 Aubiére cedex, France
| | - Dirk Springael
- Division of Soil and Water Management, KU Leuven, Kasteelpark Arenberg 20, B-3001 Heverlee, Belgium
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13
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Zhang Y, Liu T, Li MM, Hua ZS, Evans P, Qu Y, Tan S, Zheng M, Lu H, Jiao JY, Lücker S, Daims H, Li WJ, Guo J. Hot spring distribution and survival mechanisms of thermophilic comammox Nitrospira. THE ISME JOURNAL 2023:10.1038/s41396-023-01409-w. [PMID: 37069235 DOI: 10.1038/s41396-023-01409-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 03/29/2023] [Accepted: 03/31/2023] [Indexed: 04/19/2023]
Abstract
The recent discovery of Nitrospira species capable of complete ammonia oxidation (comammox) in non-marine natural and engineered ecosystems under mesothermal conditions has changed our understanding of microbial nitrification. However, little is known about the occurrence of comammox bacteria or their ability to survive in moderately thermal and/or hyperthermal habitats. Here, we report the wide distribution of comammox Nitrospira in five terrestrial hot springs at temperatures ranging from 36 to 80°C and provide metagenome-assembled genomes of 11 new comammox strains. Interestingly, the identification of dissimilatory nitrate reduction to ammonium (DNRA) in thermophilic comammox Nitrospira lineages suggests that they have versatile ecological functions as both sinks and sources of ammonia, in contrast to the described mesophilic comammox lineages, which lack the DNRA pathway. Furthermore, the in situ expression of key genes associated with nitrogen metabolism, thermal adaptation, and oxidative stress confirmed their ability to survive in the studied hot springs and their contribution to nitrification in these environments. Additionally, the smaller genome size and higher GC content, less polar and more charged amino acids in usage profiles, and the expression of a large number of heat shock proteins compared to mesophilic comammox strains presumably confer tolerance to thermal stress. These novel insights into the occurrence, metabolic activity, and adaptation of comammox Nitrospira in thermal habitats further expand our understanding of the global distribution of comammox Nitrospira and have significant implications for how these unique microorganisms have evolved thermal tolerance strategies.
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Affiliation(s)
- Yan Zhang
- School of Environmental and Chemical Engineering, Foshan University, Foshan, China
| | - Tao Liu
- Australian Centre for Water and Environmental Biotechnology, Faculty of Engineering, Architecture and Information Technology, The University of Queensland, St Lucia, QLD, Australia
| | - Meng-Meng Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zheng-Shuang Hua
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, China.
| | - Paul Evans
- The Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
| | - Yanni Qu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Sha Tan
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Min Zheng
- Australian Centre for Water and Environmental Biotechnology, Faculty of Engineering, Architecture and Information Technology, The University of Queensland, St Lucia, QLD, Australia
| | - Hui Lu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, China
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Sebastian Lücker
- Department of Microbiology, RIBES, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Holger Daims
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
- The Comammox Research Platform, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China.
| | - Jianhua Guo
- Australian Centre for Water and Environmental Biotechnology, Faculty of Engineering, Architecture and Information Technology, The University of Queensland, St Lucia, QLD, Australia.
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14
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Rao YZ, Li YX, Li ZW, Qu YN, Qi YL, Jiao JY, Shu WS, Hua ZS, Li WJ. Metagenomic Discovery of " Candidatus Parvarchaeales"-Related Lineages Sheds Light on Adaptation and Diversification from Neutral-Thermal to Acidic-Mesothermal Environments. mSystems 2023; 8:e0125222. [PMID: 36943058 PMCID: PMC10134863 DOI: 10.1128/msystems.01252-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023] Open
Abstract
"Candidatus Parvarchaeales" microbes, representing a DPANN archaeal group with limited metabolic potential and reliance on hosts for their growth, were initially found in acid mine drainage (AMD). Due to the lack of representatives, however, their ecological roles and adaptation to extreme habitats such as AMD as well as how they diverge across the lineage remain largely unexplored. By applying genome-resolved metagenomics, 28 Parvarchaeales-associated metagenome-assembled genomes (MAGs) representing two orders and five genera were recovered. Among them, we identified three new genera and proposed the names "Candidatus Jingweiarchaeum," "Candidatus Haiyanarchaeum," and "Candidatus Rehaiarchaeum," with the former two belonging to a new order, "Candidatus Jingweiarchaeales." Further analyses of the metabolic potentials revealed substantial niche differentiation between Jingweiarchaeales and Parvarchaeales. Jingweiarchaeales may rely on fermentation, salvage pathways, partial glycolysis, and the pentose phosphate pathway (PPP) for energy conservation reservation, while the metabolic potentials of Parvarchaeales might be more versatile. Comparative genomic analyses suggested that Jingweiarchaeales favor habitats with higher temperatures and that Parvarchaeales are better adapted to acidic environments. We further revealed that the thermal adaptation of these lineages, especially Haiyanarchaeum, might rely on genomic features such as the usage of specific amino acids, genome streamlining, and hyperthermophile featured genes such as rgy. Notably, the adaptation of Parvarchaeales to acidic environments was possibly driven by horizontal gene transfer (HGT). The reconstruction of ancestral states demonstrated that both may have originated from thermal and neutral environments and later spread to mesothermal and acidic environments. These evolutionary processes may also be accompanied by adaptation to oxygen-rich environments via HGT. IMPORTANCE "Candidatus Parvarchaeales" microbes may represent a lineage uniquely distributed in extreme environments such as AMD and hot springs. However, little is known about the strategies and processes of how they adapted to these extreme environments. By the discovery of potential new order-level lineages, "Ca. Jingweiarchaeales," and in-depth comparative genomic analysis, we unveiled the functional differentiation of these lineages. Furthermore, we show that the adaptation of these lineages to high-temperature and acidic environments was driven by different strategies, with the former relying more on genomic characteristics such as genome streamlining and amino acid compositions and the latter relying more on the acquisition of genes associated with acid tolerance. Finally, by the reconstruction of the ancestral states of the optimal growth temperature (OGT) and isoelectric point (pI), we showed the potential evolutionary process of Parvarchaeales-related lineages with regard to the shift from the high-temperature environment of their common ancestors to low-temperature (potentially acidic) environments.
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Affiliation(s)
- Yang-Zhi Rao
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China
- Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Yu-Xian Li
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, People's Republic of China
| | - Ze-Wei Li
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, People's Republic of China
| | - Yan-Ni Qu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China
- Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Yan-Ling Qi
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, People's Republic of China
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China
- Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Wen-Sheng Shu
- School of Life Sciences, South China Normal University, Guangzhou, People's Republic of China
| | - Zheng-Shuang Hua
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, People's Republic of China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China
- Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, People's Republic of China
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15
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Ngugi DK, Acinas SG, Sánchez P, Gasol JM, Agusti S, Karl DM, Duarte CM. Abiotic selection of microbial genome size in the global ocean. Nat Commun 2023; 14:1384. [PMID: 36914646 PMCID: PMC10011403 DOI: 10.1038/s41467-023-36988-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 02/27/2023] [Indexed: 03/14/2023] Open
Abstract
Strong purifying selection is considered a major evolutionary force behind small microbial genomes in the resource-poor photic ocean. However, very little is currently known about how the size of prokaryotic genomes evolves in the global ocean and whether patterns reflect shifts in resource availability in the epipelagic and relatively stable deep-sea environmental conditions. Using 364 marine microbial metagenomes, we investigate how the average genome size of uncultured planktonic prokaryotes varies across the tropical and polar oceans to the hadal realm. We find that genome size is highest in the perennially cold polar ocean, reflecting elongation of coding genes and gene dosage effects due to duplications in the interior ocean microbiome. Moreover, the rate of change in genome size due to temperature is 16-fold higher than with depth up to 200 m. Our results demonstrate how environmental factors can influence marine microbial genome size selection and ecological strategies of the microbiome.
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Affiliation(s)
- David K Ngugi
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, CSIC, Barcelona, Spain
| | - Pablo Sánchez
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, CSIC, Barcelona, Spain
| | - Josep M Gasol
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, CSIC, Barcelona, Spain
| | - Susana Agusti
- King Abdullah University of Science and Technology, Red Sea Research Center, Thuwal, Saudi Arabia
| | - David M Karl
- Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawaií at Mãnoa, Honolulu, USA
| | - Carlos M Duarte
- King Abdullah University of Science and Technology, Red Sea Research Center, Thuwal, Saudi Arabia
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16
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Liu H, Zhang H, Powell J, Delgado‐Baquerizo M, Wang J, Singh B. Warmer and drier ecosystems select for smaller bacterial genomes in global soils. IMETA 2023; 2:e70. [PMID: 38868347 PMCID: PMC10989973 DOI: 10.1002/imt2.70] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 11/01/2022] [Accepted: 11/28/2022] [Indexed: 06/14/2024]
Abstract
Bacterial genome size reflects bacterial evolutionary processes and metabolic lifestyles, with implications for microbial community assembly and ecosystem functions. However, to understand the extent of genome-mediated microbial responses to environmental selections, we require studies that observe genome size distributions along environmental gradients representing different conditions that soil bacteria normally encounter. In this study, we used surface soils collected from 237 sites across the globe and analyzed how environmental conditions (e.g., soil carbon and nutrients, aridity, pH, and temperature) affect soil bacterial occurrences and genome size at the community level using bacterial community profiling. We used a joint species distribution model to quantify the effects of environments on species occurrences and found that aridity was a major regulator of genome size with warmer and drier environments selecting bacteria with smaller genomes. Drought-induced physiological constraints on bacterial growth (e.g., water scarcity for cell metabolisms) may have led to these correlations. This finding suggests that increasing cover by warmer and drier ecosystems may result in bacterial genome simplifications by a reduction of genome size.
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Affiliation(s)
- Hongwei Liu
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityPenrithNew South WalesAustralia
| | - Haiyang Zhang
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityPenrithNew South WalesAustralia
- College of Life SciencesHebei UniversityBaodingChina
| | - Jeff Powell
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityPenrithNew South WalesAustralia
| | - Manuel Delgado‐Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento EcosistemicoInstituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSICSevillaSpain
- Unidad Asociada CSIC‐UPO (BioFun)Universidad Pablo de OlavideSevillaSpain
| | - Juntao Wang
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityPenrithNew South WalesAustralia
- Global Centre for Land‐Based InnovationWestern Sydney UniversityPenrithNew South WalesAustralia
| | - Brajesh Singh
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityPenrithNew South WalesAustralia
- Global Centre for Land‐Based InnovationWestern Sydney UniversityPenrithNew South WalesAustralia
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17
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Laso-Pérez R, Wu F, Crémière A, Speth DR, Magyar JS, Zhao K, Krupovic M, Orphan VJ. Evolutionary diversification of methanotrophic ANME-1 archaea and their expansive virome. Nat Microbiol 2023; 8:231-245. [PMID: 36658397 PMCID: PMC9894754 DOI: 10.1038/s41564-022-01297-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 11/29/2022] [Indexed: 01/21/2023]
Abstract
'Candidatus Methanophagales' (ANME-1) is an order-level clade of archaea responsible for anaerobic methane oxidation in deep-sea sediments. The diversity, ecology and evolution of ANME-1 remain poorly understood. In this study, we use metagenomics on deep-sea hydrothermal samples to expand ANME-1 diversity and uncover the effect of virus-host dynamics. Phylogenetic analyses reveal a deep-branching, thermophilic family, 'Candidatus Methanospirareceae', closely related to short-chain alkane oxidizers. Global phylogeny and near-complete genomes show that hydrogen metabolism within ANME-1 is an ancient trait that was vertically inherited but differentially lost during lineage diversification. Metagenomics also uncovered 16 undescribed virus families so far exclusively targeting ANME-1 archaea, showing unique structural and replicative signatures. The expansive ANME-1 virome contains a metabolic gene repertoire that can influence host ecology and evolution through virus-mediated gene displacement. Our results suggest an evolutionary continuum between anaerobic methane and short-chain alkane oxidizers and underscore the effects of viruses on the dynamics and evolution of methane-driven ecosystems.
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Affiliation(s)
- Rafael Laso-Pérez
- MARUM, Center for Marine Environmental Science, and Department of Geosciences, University of Bremen, Bremen, Germany.
- Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain.
| | - Fabai Wu
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, China.
- Ocean College, Zhejiang University, Zhoushan, China.
- Donghai Laboratory, Zhoushan, China.
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA.
| | - Antoine Crémière
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - Daan R Speth
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Max-Planck Institute for Marine Microbiology, Bremen, Germany
| | - John S Magyar
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - Kehan Zhao
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, China
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris, France.
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA.
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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18
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Van Nguyen T, Viver T, Mortier J, Liu B, Smets I, Bernaerts K, Faust K, Lavigne R, Poughon L, Dussap CG, Springael D. Isolation and characterization of a thermophilic chain elongating bacterium that produces the high commodity chemical n-caproate from polymeric carbohydrates. BIORESOURCE TECHNOLOGY 2023; 367:128170. [PMID: 36283667 DOI: 10.1016/j.biortech.2022.128170] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/15/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
A thermophilic chain elongating bacterium, strain MDTJ8, was isolated from a thermophilic acidogenic anaerobic digestor producing n-caproate from human waste, growing optimally at 50-55 °C and pH 6.5. 16S rRNA gene analysis suggests that MDTJ8 represents a new species/genus within a group currently composed of mesophilic chain elongators of the Oscillospiraceae family. Genome analysis showed that strain MDTJ8 contains homologues of genes encoding for chain elongation and energy conservation but also indicated n-caproate production from carbohydrates including polymeric substances. This was confirmed by culturing experiments in which MDTJ8 converted, at pH 6.5 and 55 °C, mono-, di- and polymeric carbohydrates (starch and hemicellulose) to n-caproate reaching concentrations up to 283 mg/L and accounting for up to 10 % of the measured fermentation products. MDTJ8 is the first axenic organism that thermophilically performs chain elongation, opening doors to understand and intensify thermophilic bioprocesses targeting anaerobic digestion towards the production of the value-added chemical n-caproate.
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Affiliation(s)
- Tinh Van Nguyen
- Division of Soil and Water Management, KU Leuven, Kasteelpark Arenberg 20, B-3001 Heverlee, Belgium; Institut Pascal, Université Clermont Auvergne, Avenue Blaise Pascal 4, F-63178 Aubiére cedex, France
| | - Tomeu Viver
- Marine Microbiology Group, Mediterranean Institute of Advanced Studies (CSIC-UIB), C/Miquel Marqués 21, 07190 Esporles, Spain
| | - Jonah Mortier
- Division of Soil and Water Management, KU Leuven, Kasteelpark Arenberg 20, B-3001 Heverlee, Belgium
| | - Bin Liu
- Laboratory of Molecular Bacteriology (Rega Institute), KU Leuven, Herestraat 49, B-3000 Leuven, Belgium
| | - Ilse Smets
- Chemical Reactor Engineering and Safety, KU Leuven, Celestijnenlaan 200F, B-3001 Heverlee, Belgium
| | - Kristel Bernaerts
- Chemical Reactor Engineering and Safety, KU Leuven, Celestijnenlaan 200F, B-3001 Heverlee, Belgium
| | - Karoline Faust
- Laboratory of Molecular Bacteriology (Rega Institute), KU Leuven, Herestraat 49, B-3000 Leuven, Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21, B-3001 Heverlee, Belgium
| | - Laurent Poughon
- Institut Pascal, Université Clermont Auvergne, Avenue Blaise Pascal 4, F-63178 Aubiére cedex, France
| | - Claude-Gilles Dussap
- Institut Pascal, Université Clermont Auvergne, Avenue Blaise Pascal 4, F-63178 Aubiére cedex, France
| | - Dirk Springael
- Division of Soil and Water Management, KU Leuven, Kasteelpark Arenberg 20, B-3001 Heverlee, Belgium.
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19
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Matsui Y, Nagai M, Ying BW. Growth rate-associated transcriptome reorganization in response to genomic, environmental, and evolutionary interruptions. Front Microbiol 2023; 14:1145673. [PMID: 37032868 PMCID: PMC10073601 DOI: 10.3389/fmicb.2023.1145673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 03/02/2023] [Indexed: 04/11/2023] Open
Abstract
The genomic, environmental, and evolutionary interruptions caused the changes in bacterial growth, which were stringently associated with changes in gene expression. The growth and gene expression changes remained unclear in response to these interruptions that occurred combinative. As a pilot study, whether and how bacterial growth was affected by the individual and dual interruptions of genome reduction, environmental stress, and adaptive evolution were investigated. Growth assay showed that the presence of the environmental stressors, i.e., threonine and chloramphenicol, significantly decreased the growth rate of the wild-type Escherichia coli, whereas not that of the reduced genome. It indicated a canceling effect in bacterial growth due to the dual interruption of the genomic and environmental changes. Experimental evolution of the reduced genome released the canceling effect by improving growth fitness. Intriguingly, the transcriptome architecture maintained a homeostatic chromosomal periodicity regardless of the genomic, environmental, and evolutionary interruptions. Negative epistasis in transcriptome reorganization was commonly observed in response to the dual interruptions, which might contribute to the canceling effect. It was supported by the changes in the numbers of differentially expressed genes (DEGs) and the enriched regulons and functions. Gene network analysis newly constructed 11 gene modules, one out of which was correlated to the growth rate. Enrichment of DEGs in these modules successfully categorized them into three types, i.e., conserved, responsive, and epistatic. Taken together, homeostasis in transcriptome architecture was essential to being alive, and it might be attributed to the negative epistasis in transcriptome reorganization and the functional differentiation in gene modules. The present study directly connected bacterial growth fitness with transcriptome reorganization and provided a global view of how microorganisms responded to genomic, environmental, and evolutionary interruptions for survival from wild nature.
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Vergara-Barros P, Alcorta J, Casanova-Katny A, Nürnberg DJ, Díez B. Compensatory Transcriptional Response of Fischerella thermalis to Thermal Damage of the Photosynthetic Electron Transfer Chain. Molecules 2022; 27:8515. [PMID: 36500606 PMCID: PMC9740203 DOI: 10.3390/molecules27238515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 11/29/2022] [Accepted: 11/29/2022] [Indexed: 12/11/2022] Open
Abstract
Key organisms in the environment, such as oxygenic photosynthetic primary producers (photosynthetic eukaryotes and cyanobacteria), are responsible for fixing most of the carbon globally. However, they are affected by environmental conditions, such as temperature, which in turn affect their distribution. Globally, the cyanobacterium Fischerella thermalis is one of the main primary producers in terrestrial hot springs with thermal gradients up to 60 °C, but the mechanisms by which F. thermalis maintains its photosynthetic activity at these high temperatures are not known. In this study, we used molecular approaches and bioinformatics, in addition to photophysiological analyses, to determine the genetic activity associated with the energy metabolism of F. thermalis both in situ and in high-temperature (40 °C to 65 °C) cultures. Our results show that photosynthesis of F. thermalis decays with temperature, while increased transcriptional activity of genes encoding photosystem II reaction center proteins, such as PsbA (D1), could help overcome thermal damage at up to 60 °C. We observed that F. thermalis tends to lose copies of the standard G4 D1 isoform while maintaining the recently described D1INT isoform, suggesting a preference for photoresistant isoforms in response to the thermal gradient. The transcriptional activity and metabolic characteristics of F. thermalis, as measured by metatranscriptomics, further suggest that carbon metabolism occurs in parallel with photosynthesis, thereby assisting in energy acquisition under high temperatures at which other photosynthetic organisms cannot survive. This study reveals that, to cope with the harsh conditions of hot springs, F. thermalis has several compensatory adaptations, and provides emerging evidence for mixotrophic metabolism as being potentially relevant to the thermotolerance of this species. Ultimately, this work increases our knowledge about thermal adaptation strategies of cyanobacteria.
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Affiliation(s)
- Pablo Vergara-Barros
- Department of Molecular Genetics and Microbiology, Biological Sciences Faculty, Pontifical Catholic University of Chile, Santiago 8331150, Chile
- Millennium Institute Center for Genome Regulation (CGR), Santiago 8370186, Chile
| | - Jaime Alcorta
- Department of Molecular Genetics and Microbiology, Biological Sciences Faculty, Pontifical Catholic University of Chile, Santiago 8331150, Chile
| | - Angélica Casanova-Katny
- Laboratory of Plant Ecophysiology, Faculty of Natural Resources, Campus Luis Rivas del Canto, Catholic University of Temuco, Temuco 4780000, Chile
| | - Dennis J. Nürnberg
- Institute of Experimental Physics, Freie Universität Berlin, 14195 Berlin, Germany
- Dahlem Centre of Plant Sciences, Freie Universität Berlin, 14195 Berlin, Germany
| | - Beatriz Díez
- Department of Molecular Genetics and Microbiology, Biological Sciences Faculty, Pontifical Catholic University of Chile, Santiago 8331150, Chile
- Millennium Institute Center for Genome Regulation (CGR), Santiago 8370186, Chile
- Center for Climate and Resilience Research (CR)2, Santiago 8370449, Chile
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21
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Somayaji A, Dhanjal CR, Lingamsetty R, Vinayagam R, Selvaraj R, Varadavenkatesan T, Govarthanan M. An insight into the mechanisms of homeostasis in extremophiles. Microbiol Res 2022; 263:127115. [PMID: 35868258 DOI: 10.1016/j.micres.2022.127115] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 07/07/2022] [Accepted: 07/07/2022] [Indexed: 01/10/2023]
Abstract
The homeostasis of extremophiles is one that is a diamond hidden in the rough. The way extremophiles adapt to their extreme environments gives a clue into the true extent of what is possible when it comes to life. The discovery of new extremophiles is ever-expanding and an explosion of knowledge surrounding their successful existence in extreme environments is obviously perceived in scientific literature. The present review paper aims to provide a comprehensive view on the different mechanisms governing the extreme adaptations of extremophiles, along with insights and discussions on what the limits of life can possibly be. The membrane adaptations that are vital for survival are discussed in detail. It was found that there are many alterations in the genetic makeup of such extremophiles when compared to their mesophilic counterparts. Apart from the several proteins involved, the significance of chaperones, efflux systems, DNA repair proteins and a host of other enzymes that adapt to maintain functionality, are enlisted, and explained. A deeper understanding of the underlying mechanisms could have a plethora of applications in the industry. There are cases when certain microbes can withstand extreme doses of antibiotics. Such microbes accumulate numerous genetic elements (or plasmids) that possess genes for multiple drug resistance (MDR). A deeper understanding of such mechanisms helps in the development of potential approaches and therapeutic schemes for treating pathogen-mediated outbreaks. An in-depth analysis of the parameters - radiation, pressure, temperature, pH value and metal resistance - are discussed in this review, and the key to survival in these precarious niches is described.
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Affiliation(s)
- Adithi Somayaji
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India; Manipal Biomachines, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Chetan Roger Dhanjal
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India; Manipal Biomachines, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Rathnamegha Lingamsetty
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India; Manipal Biomachines, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Ramesh Vinayagam
- Department of Chemical Engineering, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Raja Selvaraj
- Department of Chemical Engineering, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Thivaharan Varadavenkatesan
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India.
| | - Muthusamy Govarthanan
- Department of Environmental Engineering, Kyungpook National University, Daegu, South Korea; Department of Biomaterials, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences, Chennai 600077, India.
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22
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Genomic attributes of thermophilic and hyperthermophilic bacteria and archaea. World J Microbiol Biotechnol 2022; 38:135. [PMID: 35695998 DOI: 10.1007/s11274-022-03327-z] [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: 03/07/2022] [Accepted: 05/31/2022] [Indexed: 10/18/2022]
Abstract
Thermophiles and hyperthermophiles are immensely useful in understanding the evolution of life, besides their utility in environmental and industrial biotechnology. Advancements in sequencing technologies have revolutionized the field of microbial genomics. The massive generation of data enhances the sequencing coverage multi-fold and allows to analyse the entire genomic features of microbes efficiently and accurately. The mandate of a pure isolate can also be bypassed where whole metagenome-assembled genomes and single cell-based sequencing have fulfilled the majority of the criteria to decode various attributes of microbial genomes. A boom has, therefore, been seen in analysing the extremophilic bacteria and archaea using sequence-based approaches. Due to extensive sequence analysis, it becomes easier to understand the gene flow and their evolution among the members of bacteria and archaea. For instance, sequencing unveiled that Thermotoga maritima shares around 24% of genes of archaeal origin. Comparative and functional genomics provide an analytical view to understanding the microbial diversity of thermophilic bacteria and archaea, their interactions with other microbes, their adaptations, gene flow, and evolution over time. In this review, the genomic features of thermophilic bacteria and archaea are dealt with comprehensively.
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23
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Bourquin M, Busi SB, Fodelianakis S, Peter H, Washburne A, Kohler TJ, Ezzat L, Michoud G, Wilmes P, Battin TJ. The microbiome of cryospheric ecosystems. Nat Commun 2022; 13:3087. [PMID: 35655063 PMCID: PMC9163120 DOI: 10.1038/s41467-022-30816-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 05/20/2022] [Indexed: 01/03/2023] Open
Abstract
The melting of the cryosphere is among the most conspicuous consequences of climate change, with impacts on microbial life and related biogeochemistry. However, we are missing a systematic understanding of microbiome structure and function across cryospheric ecosystems. Here, we present a global inventory of the microbiome from snow, ice, permafrost soils, and both coastal and freshwater ecosystems under glacier influence. Combining phylogenetic and taxonomic approaches, we find that these cryospheric ecosystems, despite their particularities, share a microbiome with representatives across the bacterial tree of life and apparent signatures of early and constrained radiation. In addition, we use metagenomic analyses to define the genetic repertoire of cryospheric bacteria. Our work provides a reference resource for future studies on climate change microbiology. The cryosphere includes those parts of Earth where water or soil is frozen, such as snow, ice, glaciers and permafrost soils. Here, the authors present a global inventory of cryospheric microbial communities and their genetic repertoires.
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Affiliation(s)
- Massimo Bourquin
- River Ecosystems Laboratory, Centre for Alpine and Polar Environmental Research (ALPOLE), École Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland.
| | - Susheel Bhanu Busi
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, 7, avenue des Hauts-Fourneaux, L-4362, Esch-sur-Alzette, Luxembourg
| | - Stilianos Fodelianakis
- River Ecosystems Laboratory, Centre for Alpine and Polar Environmental Research (ALPOLE), École Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland
| | - Hannes Peter
- River Ecosystems Laboratory, Centre for Alpine and Polar Environmental Research (ALPOLE), École Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland
| | | | - Tyler J Kohler
- River Ecosystems Laboratory, Centre for Alpine and Polar Environmental Research (ALPOLE), École Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland
| | - Leïla Ezzat
- River Ecosystems Laboratory, Centre for Alpine and Polar Environmental Research (ALPOLE), École Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland
| | - Grégoire Michoud
- River Ecosystems Laboratory, Centre for Alpine and Polar Environmental Research (ALPOLE), École Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, 7, avenue des Hauts-Fourneaux, L-4362, Esch-sur-Alzette, Luxembourg.,Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, 7, avenue des Hauts-Fourneaux, L-4362, Esch-sur-Alzette, Luxembourg
| | - Tom J Battin
- River Ecosystems Laboratory, Centre for Alpine and Polar Environmental Research (ALPOLE), École Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland.
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24
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Jiao J, Lian Z, Li M, Salam N, Zhou E, Liu L, Ming H, Nie G, Shu W, Zhao G, Hedlund BP, Li W. Comparative genomic analysis of Thermus provides insights into the evolutionary history of an incomplete denitrification pathway. MLIFE 2022; 1:198-209. [PMID: 38817678 PMCID: PMC10989939 DOI: 10.1002/mlf2.12009] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 12/25/2021] [Accepted: 01/08/2022] [Indexed: 06/01/2024]
Abstract
Biological denitrification is a crucial process in the nitrogen biogeochemical cycle, and Thermus has been reported to be a significant heterotrophic denitrifier in terrestrial geothermal environments. However, neither the denitrification potential nor the evolutionary history of denitrification genes in the genus Thermus or phylum Deinococcota is well understood. Here, we performed a comparative analysis of 23 Thermus genomes and identified denitrification genes in 15 Thermus strains. We confirmed that Thermus harbors an incomplete denitrification pathway as none of the strains contain the nosZ gene. Ancestral character state reconstructions and phylogenetic analyses showed that narG, nirS, and norB genes were acquired by the last common ancestor of Thermales and were inherited vertically. In contrast, nirK of Thermales was acquired via two distinct horizontal gene transfers from Proteobacteria to the genus Caldithermus and from an unknown donor to the common ancestor of all known Thermus species except Thermus filiformis. This study expands our understanding of the genomic potential for incomplete denitrification in Thermus, revealing a largely vertical evolutionary history of the denitrification pathway in the Thermaceae, and supporting the important role for Thermus as an important heterotrophic denitrifier in geothermal environments.
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Affiliation(s)
- Jian‐Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - Zheng‐Han Lian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - Meng‐Meng Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - Nimaichand Salam
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - En‐Min Zhou
- International Joint Research Center for Karstology, School of Earth SciencesYunnan UniversityKunmingChina
| | - Lan Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - Hong Ming
- Synthetic Biology Engineering Laboratory of Henan Province, College of Life Sciences and TechnologyXinxiang Medical UniversityXinxiangChina
| | - Guoxing Nie
- College of FisheriesHenan Normal UniversityXinxiangChina
| | - Wensheng Shu
- Institute of Ecological Science, School of Life ScienceSouth China Normal UniversityGuangzhouChina
| | - Guoping Zhao
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhenChina
| | - Brian P. Hedlund
- School of Life SciencesUniversity of NevadaLas VegasNevadaUSA
- Nevada Institute of Personalized MedicineUniversity of NevadaLas VegasNevadaUSA
| | - Wen‐Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
- State Key Laboratory of Desert and Oasis EcologyXinjiang Institute of Ecology and Geography, Chinese Academy of SciencesUrumqiChina.
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25
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Translation stalling proline motifs are enriched in slow-growing, thermophilic, and multicellular bacteria. THE ISME JOURNAL 2022; 16:1065-1073. [PMID: 34824398 DOI: 10.1038/s41396-021-01154-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 11/09/2021] [Accepted: 11/10/2021] [Indexed: 12/17/2022]
Abstract
Rapid bacterial growth depends on the speed at which ribosomes can translate mRNA into proteins. mRNAs that encode successive stretches of proline can cause ribosomes to stall, substantially reducing translation speed. Such stalling is especially detrimental for species that must grow and divide rapidly. Here, we focus on di-prolyl motifs (XXPPX) and ask whether their prevalence varies with growth rate. To find out we conducted a broad survey of such motifs in >3000 bacterial genomes across 35 phyla. Indeed, fast-growing species encode fewer motifs than slow-growing species, especially in highly expressed proteins. We also found many di-prolyl motifs within thermophiles, where prolines can help maintain proteome stability. Moreover, bacteria with complex, multicellular lifecycles also encode many di-prolyl motifs. This is especially evident in the slow-growing phylum Myxococcota. Bacteria in this phylum encode many serine-threonine kinases, and many di-prolyl motifs at potential phosphorylation sites within these kinases. Serine-threonine kinases are involved in cell signaling and help regulate developmental processes linked to multicellularity in the Myxococcota. Altogether, our observations suggest that weakened selection on translational rate, whether due to slow or thermophilic growth, may allow di-prolyl motifs to take on new roles in biological processes that are unrelated to translational rate.
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26
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Cortez D, Neira G, González C, Vergara E, Holmes DS. A Large-Scale Genome-Based Survey of Acidophilic Bacteria Suggests That Genome Streamlining Is an Adaption for Life at Low pH. Front Microbiol 2022; 13:803241. [PMID: 35387071 PMCID: PMC8978632 DOI: 10.3389/fmicb.2022.803241] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 02/07/2022] [Indexed: 01/04/2023] Open
Abstract
The genome streamlining theory suggests that reduction of microbial genome size optimizes energy utilization in stressful environments. Although this hypothesis has been explored in several cases of low-nutrient (oligotrophic) and high-temperature environments, little work has been carried out on microorganisms from low-pH environments, and what has been reported is inconclusive. In this study, we performed a large-scale comparative genomics investigation of more than 260 bacterial high-quality genome sequences of acidophiles, together with genomes of their closest phylogenetic relatives that live at circum-neutral pH. A statistically supported correlation is reported between reduction of genome size and decreasing pH that we demonstrate is due to gene loss and reduced gene sizes. This trend is independent from other genome size constraints such as temperature and G + C content. Genome streamlining in the evolution of acidophilic bacteria is thus supported by our results. The analyses of predicted Clusters of Orthologous Genes (COG) categories and subcellular location predictions indicate that acidophiles have a lower representation of genes encoding extracellular proteins, signal transduction mechanisms, and proteins with unknown function but are enriched in inner membrane proteins, chaperones, basic metabolism, and core cellular functions. Contrary to other reports for genome streamlining, there was no significant change in paralog frequencies across pH. However, a detailed analysis of COG categories revealed a higher proportion of genes in acidophiles in the following categories: "replication and repair," "amino acid transport," and "intracellular trafficking". This study brings increasing clarity regarding the genomic adaptations of acidophiles to life at low pH while putting elements, such as the reduction of average gene size, under the spotlight of streamlining theory.
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Affiliation(s)
- Diego Cortez
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
| | - Gonzalo Neira
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
| | - Carolina González
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
| | - Eva Vergara
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
| | - David S. Holmes
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastian, Santiago, Chile
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Liu YF, Yang L, Liu ZL, Chen J, Fang B, Zhou L, Liu JF, Yang SZ, Gu JD, Mu BZ. Discovery of the non-cosmopolitan lineages in Candidatus Thermoprofundales. Environ Microbiol 2022; 24:3063-3080. [PMID: 35254697 DOI: 10.1111/1462-2920.15965] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 02/28/2022] [Accepted: 03/02/2022] [Indexed: 11/27/2022]
Abstract
The recently proposed order Candidatus Thermoprofundales, currently containing only one family-level lineage Marine Benthic Group-D (MBG-D), is distributed in global subsurface ecosystems and ecologically important, but its diversity, evolution and metabolism remain largely unknown. Here we described two novel family-level specialized lineages in Ca. Thermoprofundales, JdFR-43 and HyVt, which are restricted to specific biotopes (primarily in marine hydrothermal vents and occasionally in oil reservoirs and hot springs) in contrast to the cosmopolitan lineage MBG-D. The comparative genomics revealed that the specialized lineages have streamlined genomes, higher GC contents, enriched genes associated with nucleotide biosynthesis, ribosome biogenesis and DNA repair and additional thermostable aminopeptidases, enabling them to adapt to high-temperature habitats such as marine hydrothermal vents, deep subsurface oil reservoirs and hot springs. On the contrary, the unique metabolic traits of the cosmopolitan MBG-D, motility, glycolysis, butanoate metabolism, secondary metabolites production and additional genes for specific peptides and carbohydrates degradation potentially enhance its response to environmental change. Substrate preference is found for most MAGs across all lineages with the ability to utilize both polysaccharides (chitin and starch) and proteinaceous substances, whereas JdFR-43 members from oil reservoirs can only utilize proteins. These results expand the diversity of Ca. Thermoprofundales significantly and further improve our understandings of the adaptations of Ca. Thermoprofundales to various environments. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Yi-Fan Liu
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P.R. China.,Engineering Research Center of MEOR, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P.R. China.,Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, P.R. China
| | - Liu Yang
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P.R. China.,Engineering Research Center of MEOR, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P.R. China
| | - Zhong-Lin Liu
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P.R. China.,Engineering Research Center of MEOR, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P.R. China
| | - Jing Chen
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P.R. China.,Engineering Research Center of MEOR, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P.R. China
| | - Bo Fang
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P.R. China.,Engineering Research Center of MEOR, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P.R. China
| | - Lei Zhou
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P.R. China.,Engineering Research Center of MEOR, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P.R. China
| | - Jin-Feng Liu
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P.R. China.,Engineering Research Center of MEOR, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P.R. China
| | - Shi-Zhong Yang
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P.R. China.,Engineering Research Center of MEOR, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P.R. China
| | - Ji-Dong Gu
- Environmental Science and Engineering Group, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong, 515063, P.R. China
| | - Bo-Zhong Mu
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P.R. China.,Engineering Research Center of MEOR, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P.R. China
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Environmental stress leads to genome streamlining in a widely distributed species of soil bacteria. THE ISME JOURNAL 2022; 16:423-434. [PMID: 34408268 PMCID: PMC8776746 DOI: 10.1038/s41396-021-01082-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 07/14/2021] [Accepted: 07/28/2021] [Indexed: 02/07/2023]
Abstract
Bacteria have highly flexible pangenomes, which are thought to facilitate evolutionary responses to environmental change, but the impacts of environmental stress on pangenome evolution remain unclear. Using a landscape pangenomics approach, I demonstrate that environmental stress leads to consistent, continuous reduction in genome content along four environmental stress gradients (acidity, aridity, heat, salinity) in naturally occurring populations of Bradyrhizobium diazoefficiens (widespread soil-dwelling plant mutualists). Using gene-level network and duplication functional traits to predict accessory gene distributions across environments, genes predicted to be superfluous are more likely lost in high stress, while genes with multi-functional roles are more likely retained. Genes with higher probabilities of being lost with stress contain significantly higher proportions of codons under strong purifying and positive selection. Gene loss is widespread across the entire genome, with high gene-retention hotspots in close spatial proximity to core genes, suggesting Bradyrhizobium has evolved to cluster essential-function genes (accessory genes with multifunctional roles and core genes) in discrete genomic regions, which may stabilise viability during genomic decay. In conclusion, pangenome evolution through genome streamlining are important evolutionary responses to environmental change. This raises questions about impacts of genome streamlining on the adaptive capacity of bacterial populations facing rapid environmental change.
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Abstract
Modern genome-scale methods that identify new genes, such as proteogenomics and ribosome profiling, have revealed, to the surprise of many, that overlap in genes, open reading frames and even coding sequences is widespread and functionally integrated into prokaryotic, eukaryotic and viral genomes. In parallel, the constraints that overlapping regions place on genome sequences and their evolution can be harnessed in bioengineering to build more robust synthetic strains and constructs. With a focus on overlapping protein-coding and RNA-coding genes, this Review examines their discovery, topology and biogenesis in the context of their genome biology. We highlight exciting new uses for sequence overlap to control translation, compress synthetic genetic constructs, and protect against mutation.
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Chuckran PF, Hungate BA, Schwartz E, Dijkstra P. Variation in genomic traits of microbial communities among ecosystems. FEMS MICROBES 2021. [DOI: 10.1093/femsmc/xtab020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
ABSTRACT
Free-living bacteria in nutrient limited environments often exhibit traits which may reduce the cost of reproduction, such as smaller genome size, low GC content and fewer sigma (σ) factor and 16S rRNA gene copies. Despite the potential utility of these traits to detect relationships between microbial communities and ecosystem-scale properties, few studies have assessed these traits on a community-scale. Here, we analysed these traits from publicly available metagenomes derived from marine, soil, host-associated and thermophilic communities. In marine and thermophilic communities, genome size and GC content declined in parallel, consistent with genomic streamlining, with GC content in thermophilic communities generally higher than in marine systems. In contrast, soil communities averaging smaller genomes featured higher GC content and were often from low-carbon environments, suggesting unique selection pressures in soil bacteria. The abundance of specific σ-factors varied with average genome size and ecosystem type. In oceans, abundance of fliA, a σ-factor controlling flagella biosynthesis, was positively correlated with community average genome size—reflecting known trade-offs between nutrient conservation and chemotaxis. In soils, a high abundance of the stress response σ-factor gene rpoS was associated with smaller average genome size and often located in harsh and/or carbon-limited environments—a result which tracks features observed in culture and indicates an increased capacity for stress response in nutrient-poor soils. This work shows how ecosystem-specific constraints are associated with trade-offs which are embedded in the genomic features of bacteria in microbial communities, and which can be detected at the community level, highlighting the importance of genomic features in microbial community analysis.
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Affiliation(s)
- Peter F Chuckran
- Center for Ecosystem Science and Society (ECOSS) and Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Bruce A Hungate
- Center for Ecosystem Science and Society (ECOSS) and Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Egbert Schwartz
- Center for Ecosystem Science and Society (ECOSS) and Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Paul Dijkstra
- Center for Ecosystem Science and Society (ECOSS) and Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
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Li YX, Rao YZ, Qi YL, Qu YN, Chen YT, Jiao JY, Shu WS, Jiang H, Hedlund BP, Hua ZS, Li WJ. Deciphering Symbiotic Interactions of " Candidatus Aenigmarchaeota" with Inferred Horizontal Gene Transfers and Co-occurrence Networks. mSystems 2021; 6:e0060621. [PMID: 34313464 PMCID: PMC8407114 DOI: 10.1128/msystems.00606-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 07/09/2021] [Indexed: 11/30/2022] Open
Abstract
"Candidatus Aenigmarchaeota" ("Ca. Aenigmarchaeota") represents one of the earliest proposed evolutionary branches within the Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota (DPANN) superphylum. However, their ecological roles and potential host-symbiont interactions are still poorly understood. Here, eight metagenome-assembled genomes (MAGs) were reconstructed from hot spring ecosystems, and further in-depth comparative and evolutionary genomic analyses were conducted on these MAGs and other genomes downloaded from public databases. Although with limited metabolic capacities, we reported that "Ca. Aenigmarchaeota" in thermal environments harbor more genes related to carbohydrate metabolism than "Ca. Aenigmarchaeota" in nonthermal environments. Evolutionary analyses suggested that members from the Thaumarchaeota, Aigarchaeota, Crenarchaeota, and Korarchaeota (TACK) superphylum and Euryarchaeota contribute substantially to the niche expansion of "Ca. Aenigmarchaeota" via horizontal gene transfer (HGT), especially genes related to virus defense and stress responses. Based on co-occurrence network results and recent genetic exchanges among community members, we conjectured that "Ca. Aenigmarchaeota" may be symbionts associated with one MAG affiliated with the genus Pyrobaculum, though host specificity might be wide and variable across different "Ca. Aenigmarchaeota" organisms. This study provides significant insight into possible DPANN-host interactions and ecological roles of "Ca. Aenigmarchaeota." IMPORTANCE Recent advances in sequencing technology promoted the blowout discovery of super tiny microbes in the Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota (DPANN) superphylum. However, the unculturable properties of the majority of microbes impeded our investigation of their behavior and symbiotic lifestyle in the corresponding community. By integrating horizontal gene transfer (HGT) detection and co-occurrence network analysis on "Candidatus Aenigmarchaeota" ("Ca. Aenigmarchaeota"), we made one of the first attempts to infer their putative interaction partners and further decipher the potential functional and genetic interactions between the symbionts. We revealed that HGTs contributed by members from the Thaumarchaeota, Aigarchaeota, Crenarchaeota, and Korarchaeota (TACK) superphylum and Euryarchaeota conferred "Ca. Aenigmarchaeota" with the ability to survive under different environmental stresses, such as virus infection, high temperature, and oxidative stress. This study demonstrates that the interaction partners might be inferable by applying informatics analyses on metagenomic sequencing data.
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Affiliation(s)
- Yu-Xian Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, People’s Republic of China
| | - Yang-Zhi Rao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, People’s Republic of China
| | - Yan-Ling Qi
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, People’s Republic of China
| | - Yan-Ni Qu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, People’s Republic of China
| | - Ya-Ting Chen
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, People’s Republic of China
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, People’s Republic of China
| | - Wen-Sheng Shu
- School of Life Sciences, South China Normal University, Guangzhou, People’s Republic of China
| | - Hongchen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, People’s Republic of China
| | - Brian P. Hedlund
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, USA
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, Nevada, USA
| | - Zheng-Shuang Hua
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, People’s Republic of China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, People’s Republic of China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, People’s Republic of China
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Comparative Genomics Reveals Thermal Adaptation and a High Metabolic Diversity in " Candidatus Bathyarchaeia". mSystems 2021; 6:e0025221. [PMID: 34282939 PMCID: PMC8407382 DOI: 10.1128/msystems.00252-21] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
"Candidatus Bathyarchaeia" is a phylogenetically diverse and widely distributed lineage often in high abundance in anoxic submarine sediments; however, their evolution and ecological roles in terrestrial geothermal habitats are poorly understood. In the present study, 35 Ca. Bathyarchaeia metagenome-assembled genomes (MAGs) were recovered from hot spring sediments in Tibet and Yunnan, China. Phylogenetic analysis revealed all MAGs of Ca. Bathyarchaeia can be classified into 7 orders and 15 families. Among them, 4 families have been first discovered in the present study, significantly expanding the known diversity of Ca. Bathyarchaeia. Comparative genomics demonstrated Ca. Bathyarchaeia MAGs from thermal habitats to encode a large variety of genes related to carbohydrate degradation, which are likely a metabolic adaptation of these organisms to a lifestyle at high temperatures. At least two families are potential methanogens/alkanotrophs, indicating a potential for the catalysis of short-chain hydrocarbons. Three MAGs from Family-7.3 are identified as alkanotrophs due to the detection of an Mcr complex. Family-2 contains the largest number of genes relevant to alkyl-CoM transformation, indicating the potential for methylotrophic methanogenesis, although their evolutionary history suggests the ancestor of Ca. Bathyarchaeia was unable to metabolize alkanes. Subsequent lineages have acquired the ability via horizontal gene transfer. Overall, our study significantly expands our knowledge and understanding of the metabolic capabilities, habitat adaptations, and evolution of Ca. Bathyarchaeia in thermal environments. IMPORTANCE Ca. Bathyarchaeia MAGs from terrestrial hot spring habitats are poorly revealed, though they have been studied extensively in marine ecosystems. In this study, we uncovered the metabolic capabilities and ecological role of Ca. Bathyarchaeia in hot springs and give a comprehensive comparative analysis between thermal and nonthermal habitats to reveal the thermal adaptability of Ca. Bathyarchaeia. Also, we attempt to determine the evolutionary history of methane/alkane metabolism in Ca. Bathyarchaeia, since it appears to be the first archaea beyond Euryarchaeota which contains the mcrABG genes. The reclassification of Ca. Bathyarchaeia and significant genomic differences among different lineages largely expand our knowledge on these cosmopolitan archaea, which will be beneficial in guiding the future studies.
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Abstract
DPANN is known as highly diverse, globally widespread, and mostly ectosymbiotic archaeal superphylum. However, this group of archaea was overlooked for a long time, and there were limited in-depth studies reported. In this investigation, 41 metagenome-assembled genomes (MAGs) belonging to the DPANN superphylum were recovered (18 MAGs had average nucleotide identity [ANI] values of <95% and a percentage of conserved proteins [POCP] of >50%, while 14 MAGs showed a POCP of <50%), which were analyzed comparatively with 515 other published DPANN genomes. Mismatches to known 16S rRNA gene primers were identified among 16S rRNA genes of DPANN archaea. Numbers of gene families lost (mostly related to energy and amino acid metabolism) were over three times greater than those gained in the evolution of DPANN archaea. Lateral gene transfer (LGT; ∼45.5% was cross-domain) had facilitated niche adaption of the DPANN archaea, ensuring a delicate equilibrium of streamlined genomes with efficient niche-adaptive strategies. For instance, LGT-derived cytochrome bd ubiquinol oxidase and arginine deiminase in the genomes of “Candidatus Micrarchaeota” could help them better adapt to aerobic acidic mine drainage habitats. In addition, most DPANN archaea acquired enzymes for biosynthesis of extracellular polymeric substances (EPS) and transketolase/transaldolase for the pentose phosphate pathway from Bacteria. IMPORTANCE The domain Archaea is a key research model for gaining insights into the origin and evolution of life, as well as the relevant biogeochemical processes. The discovery of nanosized DPANN archaea has overthrown many aspects of microbiology. However, the DPANN superphylum still contains a vast genetic novelty and diversity that need to be explored. Comprehensively comparative genomic analysis on the DPANN superphylum was performed in this study, with an attempt to illuminate its metabolic potential, ecological distribution and evolutionary history. Many interphylum differences within the DPANN superphylum were found. For example, Altiarchaeota had the biggest genome among DPANN phyla, possessing many pathways missing in other phyla, such as formaldehyde assimilation and the Wood-Ljungdahl pathway. In addition, LGT acted as an important force to provide DPANN archaeal genetic flexibility that permitted the occupation of diverse niches. This study has advanced our understanding of the diversity and genome evolution of archaea.
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Dong W, Song A, Yin H, Liu X, Li J, Fan F. Decomposition of Microbial Necromass Is Divergent at the Individual Taxonomic Level in Soil. Front Microbiol 2021; 12:679793. [PMID: 34276613 PMCID: PMC8283313 DOI: 10.3389/fmicb.2021.679793] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 05/31/2021] [Indexed: 11/13/2022] Open
Abstract
The turnover of microbial biomass plays an important part in providing a significant source of carbon (C) to soil organic C. However, whether the decomposition of microbial necromass (non-living microbial biomass) in the soil varies at the individual taxa level remains largely unknown. To fill up these gaps, we compared the necromass decomposition of bacterial and archaeal taxa by separating live microbial biomass with 18O-stable isotope probing from dead microbial biomass in soil. Our results showed that most of the microbial necromass at the operational taxonomic unit level (88.51%), which mainly belong to Acidobacteria, Actinobacteria, Gemmatimonadetes, and Proteobacteria, decomposed significantly after 30 days. In addition, there were great variations in necromass decomposition within each phylum, such as the decomposition of operational taxonomic units in Proteobacteria that ranged from 51% (Beijerinckia) to 92% (Nitrosospira). More importantly, the necromass decomposition was not related to the chemical composition of the cell wall but might positively correlate with the guanine-cytosine content of DNA and negatively correlated with genome size. This study provided a new insight that the decomposition of microbial necromass in soil was divergent at the individual taxonomic level and could not be fully explained by previously proposed mechanisms.
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Affiliation(s)
- Weiling Dong
- Key Laboratory of Biometallurgy of Ministry of Education, School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Alin Song
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huaqun Yin
- Key Laboratory of Biometallurgy of Ministry of Education, School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Xueduan Liu
- Key Laboratory of Biometallurgy of Ministry of Education, School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Jianwei Li
- Department of Agricultural and Environmental Sciences, Tennessee State University, Nashville, TN, United States
| | - Fenliang Fan
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
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Sriaporn C, Campbell KA, Van Kranendonk MJ, Handley KM. Genomic adaptations enabling Acidithiobacillus distribution across wide-ranging hot spring temperatures and pHs. MICROBIOME 2021; 9:135. [PMID: 34116726 PMCID: PMC8196465 DOI: 10.1186/s40168-021-01090-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 05/09/2021] [Indexed: 05/09/2023]
Abstract
BACKGROUND Terrestrial hot spring settings span a broad spectrum of physicochemistries. Physicochemical parameters, such as pH and temperature, are key factors influencing differences in microbial composition across diverse geothermal areas. Nonetheless, analysis of hot spring pools from the Taupo Volcanic Zone (TVZ), New Zealand, revealed that some members of the bacterial genus, Acidithiobacillus, are prevalent across wide ranges of hot spring pHs and temperatures. To determine the genomic attributes of Acidithiobacillus that inhabit such diverse conditions, we assembled the genomes of 19 uncultivated hot spring Acidithiobacillus strains from six geothermal areas and compared these to 37 publicly available Acidithiobacillus genomes from various habitats. RESULTS Analysis of 16S rRNA gene amplicons from 138 samples revealed that Acidithiobacillus comprised on average 11.4 ± 16.8% of hot spring prokaryotic communities, with three Acidithiobacillus amplicon sequence variants (ASVs) (TVZ_G1, TVZ_G2, TVZ_G3) accounting for > 90% of Acidithiobacillus in terms of relative abundance, and occurring in 126 out of 138 samples across wide ranges of temperature (17.5-92.9 °C) and pH (1.0-7.5). We recovered 19 environmental genomes belonging to each of these three ASVs, as well as a fourth related group (TVZ_G4). Based on genome average nucleotide identities, the four groups (TVZ_G1-TVZ_G4) constitute distinct species (ANI < 96.5%) of which three are novel Acidithiobacillus species (TVZ_G2-TVZ_G4) and one belongs to Acidithiobacillus caldus (TVZ_G1). All four TVZ Acidithiobacillus groups were found in hot springs with temperatures above the previously known limit for the genus (up to 40 °C higher), likely due to significantly higher proline and GC contents than other Acidithiobacillus species, which are known to increase thermostability. Results also indicate hot spring-associated Acidithiobacillus have undergone genome streamlining, likely due to thermal adaptation. Moreover, our data suggest that Acidithiobacillus prevalence across varied hot spring pHs is supported by distinct strategies, whereby TVZ_G2-TVZ_G4 regulate pH homeostasis mostly through Na+/H+ antiporters and proton-efflux ATPases, whereas TVZ_G1 mainly relies on amino acid decarboxylases. CONCLUSIONS This study provides insights into the distribution of Acidithiobacillus species across diverse hot spring physichochemistries and determines genomic features and adaptations that potentially enable Acidithiobacillus species to colonize a broad range of temperatures and pHs in geothermal environments. Video Abstract.
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Affiliation(s)
- Chanenath Sriaporn
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Kathleen A. Campbell
- School of Environment & Te Ao Mārama – Centre for Fundamental Inquiry, The University of Auckland, Auckland, New Zealand
| | - Martin J. Van Kranendonk
- Australian Centre for Astrobiology & School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Kim M. Handley
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
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Unexpectedly high mutation rate of a deep-sea hyperthermophilic anaerobic archaeon. THE ISME JOURNAL 2021; 15:1862-1869. [PMID: 33452477 PMCID: PMC8163891 DOI: 10.1038/s41396-020-00888-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 12/14/2020] [Accepted: 12/16/2020] [Indexed: 01/29/2023]
Abstract
Deep-sea hydrothermal vents resemble the early Earth, and thus the dominant Thermococcaceae inhabitants, which occupy an evolutionarily basal position of the archaeal tree and take an obligate anaerobic hyperthermophilic free-living lifestyle, are likely excellent models to study the evolution of early life. Here, we determined that unbiased mutation rate of a representative species, Thermococcus eurythermalis, exceeded that of all known free-living prokaryotes by 1-2 orders of magnitude, and thus rejected the long-standing hypothesis that low mutation rates were selectively favored in hyperthermophiles. We further sequenced multiple and diverse isolates of this species and calculated that T. eurythermalis has a lower effective population size than other free-living prokaryotes by 1-2 orders of magnitude. These data collectively indicate that the high mutation rate of this species is not selectively favored but instead driven by random genetic drift. The availability of these unusual data also helps explore mechanisms underlying microbial genome size evolution. We showed that genome size is negatively correlated with mutation rate and positively correlated with effective population size across 30 bacterial and archaeal lineages, suggesting that increased mutation rate and random genetic drift are likely two important mechanisms driving microbial genome reduction. Future determinations of the unbiased mutation rate of more representative lineages with highly reduced genomes such as Prochlorococcus and Pelagibacterales that dominate marine microbial communities are essential to test these hypotheses.
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Westoby M, Nielsen DA, Gillings MR, Litchman E, Madin JS, Paulsen IT, Tetu SG. Cell size, genome size, and maximum growth rate are near-independent dimensions of ecological variation across bacteria and archaea. Ecol Evol 2021; 11:3956-3976. [PMID: 33976787 PMCID: PMC8093753 DOI: 10.1002/ece3.7290] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/18/2021] [Accepted: 01/22/2021] [Indexed: 02/06/2023] Open
Abstract
Among bacteria and archaea, maximum relative growth rate, cell diameter, and genome size are widely regarded as important influences on ecological strategy. Via the most extensive data compilation so far for these traits across all clades and habitats, we ask whether they are correlated and if so how. Overall, we found little correlation among them, indicating they should be considered as independent dimensions of ecological variation. Nor was correlation evident within particular habitat types. A weak nonlinearity (6% of variance) was found whereby high maximum growth rates (temperature-adjusted) tended to occur in the midrange of cell diameters. Species identified in the literature as oligotrophs or copiotrophs were clearly separated on the dimension of maximum growth rate, but not on the dimensions of genome size or cell diameter.
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Affiliation(s)
- Mark Westoby
- Department of Biological SciencesMacquarie UniversitySydneyNSWAustralia
| | | | | | - Elena Litchman
- Kellogg Biological StationMichigan State UniversityHickory CornersMIUSA
| | - Joshua S. Madin
- Hawaii Institute of Marine BiologyUniversity of HawaiiKaneoheHIUSA
| | - Ian T. Paulsen
- Department of Molecular SciencesMacquarie UniversitySydneyNSWAustralia
| | - Sasha G. Tetu
- Department of Molecular SciencesMacquarie UniversitySydneyNSWAustralia
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Westoby M, Gillings MR, Madin JS, Nielsen DA, Paulsen IT, Tetu SG. Trait dimensions in bacteria and archaea compared to vascular plants. Ecol Lett 2021; 24:1487-1504. [PMID: 33896087 DOI: 10.1111/ele.13742] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 02/25/2021] [Accepted: 03/04/2021] [Indexed: 01/04/2023]
Abstract
Bacteria and archaea have very different ecology compared to plants. One similarity, though, is that much discussion of their ecological strategies has invoked concepts such as oligotrophy or stress tolerance. For plants, so-called 'trait ecology'-strategy description reframed along measurable trait dimensions-has made global syntheses possible. Among widely measured trait dimensions for bacteria and archaea three main axes are evident. Maximum growth rate in association with rRNA operon copy number expresses a rate-yield trade-off that is analogous to the acquisitive-conservative spectrum in plants, though underpinned by different trade-offs. Genome size in association with signal transduction expresses versatility. Cell size has influence on diffusive uptake and on relative wall costs. These trait dimensions, and potentially others, offer promise for interpreting ecology. At the same time, there are very substantial differences from plant trait ecology. Traits and their underpinning trade-offs are different. Also, bacteria and archaea use a variety of different substrates. Bacterial strategies can be viewed both through the facet of substrate-use pathways, and also through the facet of quantitative traits such as maximum growth rate. Preliminary evidence shows the quantitative traits vary widely within substrate-use pathways. This indicates they convey information complementary to substrate use.
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Affiliation(s)
- Mark Westoby
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia
| | - Michael R Gillings
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia
| | - Joshua S Madin
- Hawaii Institute of Marine Biology, University of Hawaii, Kaneohe, HI, USA
| | - Daniel A Nielsen
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia
| | - Ian T Paulsen
- Dept of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Sasha G Tetu
- Dept of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
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Glazier DS. Genome Size Covaries More Positively with Propagule Size than Adult Size: New Insights into an Old Problem. BIOLOGY 2021; 10:270. [PMID: 33810583 PMCID: PMC8067107 DOI: 10.3390/biology10040270] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/18/2021] [Accepted: 03/23/2021] [Indexed: 12/17/2022]
Abstract
The body size and (or) complexity of organisms is not uniformly related to the amount of genetic material (DNA) contained in each of their cell nuclei ('genome size'). This surprising mismatch between the physical structure of organisms and their underlying genetic information appears to relate to variable accumulation of repetitive DNA sequences, but why this variation has evolved is little understood. Here, I show that genome size correlates more positively with egg size than adult size in crustaceans. I explain this and comparable patterns observed in other kinds of animals and plants as resulting from genome size relating strongly to cell size in most organisms, which should also apply to single-celled eggs and other reproductive propagules with relatively few cells that are pivotal first steps in their lives. However, since body size results from growth in cell size or number or both, it relates to genome size in diverse ways. Relationships between genome size and body size should be especially weak in large organisms whose size relates more to cell multiplication than to cell enlargement, as is generally observed. The ubiquitous single-cell 'bottleneck' of life cycles may affect both genome size and composition, and via both informational (genotypic) and non-informational (nucleotypic) effects, many other properties of multicellular organisms (e.g., rates of growth and metabolism) that have both theoretical and practical significance.
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Mol V, Bennett M, Sánchez BJ, Lisowska BK, Herrgård MJ, Nielsen AT, Leak DJ, Sonnenschein N. Genome-scale metabolic modeling of P. thermoglucosidasius NCIMB 11955 reveals metabolic bottlenecks in anaerobic metabolism. Metab Eng 2021; 65:123-134. [PMID: 33753231 DOI: 10.1016/j.ymben.2021.03.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 03/01/2021] [Indexed: 12/27/2022]
Abstract
Parageobacillus thermoglucosidasius represents a thermophilic, facultative anaerobic bacterial chassis, with several desirable traits for metabolic engineering and industrial production. To further optimize strain productivity, a systems level understanding of its metabolism is needed, which can be facilitated by a genome-scale metabolic model. Here, we present p-thermo, the most complete, curated and validated genome-scale model (to date) of Parageobacillus thermoglucosidasius NCIMB 11955. It spans a total of 890 metabolites, 1175 reactions and 917 metabolic genes, forming an extensive knowledge base for P. thermoglucosidasius NCIMB 11955 metabolism. The model accurately predicts aerobic utilization of 22 carbon sources, and the predictive quality of internal fluxes was validated with previously published 13C-fluxomics data. In an application case, p-thermo was used to facilitate more in-depth analysis of reported metabolic engineering efforts, giving additional insight into fermentative metabolism. Finally, p-thermo was used to resolve a previously uncharacterised bottleneck in anaerobic metabolism, by identifying the minimal required supplemented nutrients (thiamin, biotin and iron(III)) needed to sustain anaerobic growth. This highlights the usefulness of p-thermo for guiding the generation of experimental hypotheses and for facilitating data-driven metabolic engineering, expanding the use of P. thermoglucosidasius as a high yield production platform.
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Affiliation(s)
- Viviënne Mol
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Martyn Bennett
- The Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, United Kingdom; The Centre for Sustainable Chemical Technologies (CSCT), University of Bath, Claverton Down, Bath, BA2 7AY, United Kingdom
| | - Benjamín J Sánchez
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark; Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Beata K Lisowska
- The Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, United Kingdom
| | - Markus J Herrgård
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark; BioInnovation Institute, Copenhagen N, Denmark
| | - Alex Toftgaard Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark.
| | - David J Leak
- The Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, United Kingdom; The Centre for Sustainable Chemical Technologies (CSCT), University of Bath, Claverton Down, Bath, BA2 7AY, United Kingdom.
| | - Nikolaus Sonnenschein
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark.
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Sato Y, Okano K, Kimura H, Honda K. TEMPURA: Database of Growth TEMPeratures of Usual and RAre Prokaryotes. Microbes Environ 2021; 35. [PMID: 32727974 PMCID: PMC7511790 DOI: 10.1264/jsme2.me20074] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Growth temperature is one of the most representative biological parameters for characterizing living organisms. Prokaryotes have been isolated from various temperature environments and show wide diversity in their growth temperatures. We herein constructed a database of growth TEMPeratures of Usual and RAre prokaryotes (TEMPURA, http://togodb.org/db/tempura), which contains the minimum, optimum, and maximum growth temperatures of 8,639 prokaryotic strains. Growth temperature information is linked with taxonomy IDs, phylogenies, and genomic information. TEMPURA provides useful information to researchers working on biotechnological applications of extremophiles and their biomolecules as well as those performing fundamental studies on the physiological diversity of prokaryotes.
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Affiliation(s)
- Yu Sato
- International Center for Biotechnology, Osaka University
| | - Kenji Okano
- International Center for Biotechnology, Osaka University
| | - Hiroyuki Kimura
- Research Institute of Green Science and Technology, Shizuoka University.,Department of Geosciences, Faculty of Science, Shizuoka University
| | - Kohsuke Honda
- International Center for Biotechnology, Osaka University
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Berger D, Stångberg J, Baur J, Walters RJ. Elevated temperature increases genome-wide selection on de novo mutations. Proc Biol Sci 2021; 288:20203094. [PMID: 33529558 DOI: 10.1098/rspb.2020.3094] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Adaptation in new environments depends on the amount of genetic variation available for evolution, and the efficacy by which natural selection discriminates among this variation. However, whether some ecological factors reveal more genetic variation, or impose stronger selection pressures than others, is typically not known. Here, we apply the enzyme kinetic theory to show that rising global temperatures are predicted to intensify natural selection throughout the genome by increasing the effects of DNA sequence variation on protein stability. We test this prediction by (i) estimating temperature-dependent fitness effects of induced mutations in seed beetles adapted to ancestral or elevated temperature, and (ii) calculate 100 paired selection estimates on mutations in benign versus stressful environments from unicellular and multicellular organisms. Environmental stress per se did not increase mean selection on de novo mutation, suggesting that the cost of adaptation does not generally increase in new ecological settings to which the organism is maladapted. However, elevated temperature increased the mean strength of selection on genome-wide polymorphism, signified by increases in both mutation load and mutational variance in fitness. These results have important implications for genetic diversity gradients and the rate and repeatability of evolution under climate change.
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Affiliation(s)
- David Berger
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Josefine Stångberg
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Julian Baur
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Richard J Walters
- Centre for Environmental and Climate Research, Lund University, Sölvegatan 37, 223 62 Lund, Sweden
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Nielsen DA, Fierer N, Geoghegan JL, Gillings MR, Gumerov V, Madin JS, Moore L, Paulsen IT, Reddy TBK, Tetu SG, Westoby M. Aerobic bacteria and archaea tend to have larger and more versatile genomes. OIKOS 2021. [DOI: 10.1111/oik.07912] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
| | - Noah Fierer
- Dept of Ecology and Evolutionary Biology, Cooperative Inst. for Research in Environmental Sciences, Univ. of Colorado Boulder CO USA
| | - Jemma L. Geoghegan
- Dept of Biological Sciences, Macquarie Univ. Sydney NSW Australia
- Dept of Microbiology and Immunology, Univ. of Otago New Zealand
| | | | - Vadim Gumerov
- Dept of Microbiology, Ohio State Univ. Columbus Ohio USA
| | - Joshua S. Madin
- Hawaii Inst. of Marine Biology, Univ. of Hawaii Kaneohe HI USA
| | - Lisa Moore
- Dept of Molecular Sciences, Macquarie Univ. Sydney NSW Australia
| | | | - T. B. K. Reddy
- Dept of Molecular Sciences, Macquarie Univ. Sydney NSW Australia
| | - Sasha G. Tetu
- Dept of Molecular Sciences, Macquarie Univ. Sydney NSW Australia
| | - Mark Westoby
- Dept of Biological Sciences, Macquarie Univ. Sydney NSW Australia
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Marguerite NT, Bernard J, Harrison DA, Harris D, Cooper RL. Effect of Temperature on Heart Rate for Phaenicia sericata and Drosophila melanogaster with Altered Expression of the TrpA1 Receptors. INSECTS 2021; 12:38. [PMID: 33418937 PMCID: PMC7825143 DOI: 10.3390/insects12010038] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 12/24/2020] [Accepted: 01/02/2021] [Indexed: 11/29/2022]
Abstract
The transient receptor potential (TrpA-ankyrin) receptor has been linked to pathological conditions in cardiac function in mammals. To better understand the function of the TrpA1 in regulation of the heart, a Drosophila melanogaster model was used to express TrpA1 in heart and body wall muscles. Heartbeat of in intact larvae as well as hearts in situ, devoid of hormonal and neural input, indicate that strong over-expression of TrpA1 in larvae at 30 or 37 °C stopped the heart from beating, but in a diastolic state. Cardiac function recovered upon cooling after short exposure to high temperature. Parental control larvae (UAS-TrpA1) increased heart rate transiently at 30 and 37 °C but slowed at 37 °C within 3 min for in-situ preparations, while in-vivo larvae maintained a constant heart rate. The in-situ preparations maintained an elevated rate at 30 °C. The heartbeat in the TrpA1-expressing strains could not be revived at 37 °C with serotonin. Thus, TrpA1 activation may have allowed enough Ca2+ influx to activate K(Ca) channels into a form of diastolic stasis. TrpA1 activation in body wall muscle confirmed a depolarization of membrane. In contrast, blowfly Phaenicia sericata larvae increased heartbeat at 30 and 37 °C, demonstrating greater cardiac thermotolerance.
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Affiliation(s)
- Nicole T. Marguerite
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA; (N.T.M.); (J.B.); (D.A.H.)
| | - Jate Bernard
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA; (N.T.M.); (J.B.); (D.A.H.)
| | - Douglas A. Harrison
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA; (N.T.M.); (J.B.); (D.A.H.)
| | | | - Robin L. Cooper
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA; (N.T.M.); (J.B.); (D.A.H.)
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Elcheninov AG, Podosokorskaya OA, Kovaleva OL, Novikov AA, Toshchakov SV, Bonch-Osmolovskaya EA, Kublanov IV. Thermogemmata fonticola gen. nov., sp. nov., the first thermophilic planctomycete of the order Gemmatales from a Kamchatka hot spring. Syst Appl Microbiol 2020; 44:126157. [PMID: 33220635 DOI: 10.1016/j.syapm.2020.126157] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 10/21/2020] [Accepted: 11/02/2020] [Indexed: 01/08/2023]
Abstract
A novel aerobic moderately thermophilic bacterium, designated strain 2918T, was isolated from a terrestrial hot spring of Kamchatka, Russian Federation. Gram-negative, motile, spherical cells were present singly, in pairs, or aggregates, and reproduced by budding. The strain grew at 25-60°C and within a pH range of 5.0-8.0 with an optimum at 54-60°C and pH 7.5. Strain 2918T did not require sodium chloride or yeast extract for growth. It was a chemoorganoheterotroph, growing on mono-, di- and polysaccharides (starch, lichenan, galactan, arabinan, xanthan gum, beta-glucan). No growth was observed under anaerobic conditions neither in the presence of sulfur, nitrate, or thiosulfate nor without adding any electron acceptor. Major cellular fatty acids were C18:0 and C20:0. The respiratory quinone was MK-6. The size of the genome of strain 2918T was 4.81 Mb. Genomic DNA G+C content was 60.4mol%. According to the 16S rRNA gene sequence and conserved protein sequences phylogenies, strain 2918T represented a distinct lineage of the order Gemmatales within Planctomycetes. Based on phylogenetic analysis and phenotypic features, the novel isolate was assigned to a novel genus in the Gemmatales for which the name Thermogemmata gen. nov. is proposed. Strain 2918T (=KCTC 72012T =VKM B-3161T) represents its first species Thermogemmata fonticola sp. nov.
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Affiliation(s)
- Alexander G Elcheninov
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology RAS, 7/2 Prospekt 60-letiya Oktyabrya, 117312 Moscow, Russia.
| | - Olga A Podosokorskaya
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology RAS, 7/2 Prospekt 60-letiya Oktyabrya, 117312 Moscow, Russia
| | - Olga L Kovaleva
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology RAS, 7/2 Prospekt 60-letiya Oktyabrya, 117312 Moscow, Russia
| | - Andrei A Novikov
- Gubkin Russian State University of Oil and Gas, Leninskiy Prospect 65, 119991 Moscow, Russia
| | - Stepan V Toshchakov
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology RAS, 7/2 Prospekt 60-letiya Oktyabrya, 117312 Moscow, Russia
| | - Elizaveta A Bonch-Osmolovskaya
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology RAS, 7/2 Prospekt 60-letiya Oktyabrya, 117312 Moscow, Russia; Lomonosov State University, Leninskie Gory 1 Bldg 12, Moscow, Russia
| | - Ilya V Kublanov
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology RAS, 7/2 Prospekt 60-letiya Oktyabrya, 117312 Moscow, Russia
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46
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Alcorta J, Alarcón-Schumacher T, Salgado O, Díez B. Taxonomic Novelty and Distinctive Genomic Features of Hot Spring Cyanobacteria. Front Genet 2020; 11:568223. [PMID: 33250920 PMCID: PMC7674949 DOI: 10.3389/fgene.2020.568223] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 10/15/2020] [Indexed: 01/06/2023] Open
Abstract
Several cyanobacterial species are dominant primary producers in hot spring microbial mats. To date, hot spring cyanobacterial taxonomy, as well as the evolution of their genomic adaptations to high temperatures, are poorly understood, with genomic information currently available for only a few dominant genera, including Fischerella and Synechococcus. To address this knowledge gap, the present study expands the genomic landscape of hot spring cyanobacteria and traces the phylum-wide genomic consequences of evolution in high temperature environments. From 21 globally distributed hot spring metagenomes, with temperatures between 32 and 75°C, 57 medium- and high-quality cyanobacterial metagenome-assembled genomes were recovered, representing taxonomic novelty for 1 order, 3 families, 15 genera and 36 species. Comparative genomics of 93 hot spring genomes (including the 57 metagenome-assembled genomes) and 66 non-thermal genomes, showed that the former have smaller genomes and a higher GC content, as well as shorter proteins that are more hydrophilic and basic, when compared to the non-thermal genomes. Additionally, the core accessory orthogroups from the hot spring genomes of some genera had a greater abundance of functional categories, such as inorganic ion metabolism, translation and post-translational modifications. Moreover, hot spring genomes showed increased abundances of inorganic ion transport and amino acid metabolism, as well as less replication and transcription functions in the protein coding sequences. Furthermore, they showed a higher dependence on the CRISPR-Cas defense system against exogenous nucleic acids, and a reduction in secondary metabolism biosynthetic gene clusters. This suggests differences in the cyanobacterial response to environment-specific microbial communities. This phylum-wide study provides new insights into cyanobacterial genomic adaptations to a specific niche where they are dominant, which could be essential to trace bacterial evolution pathways in a warmer world, such as the current global warming scenario.
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Affiliation(s)
- Jaime Alcorta
- Department of Molecular Genetics and Microbiology, Biological Sciences Faculty, Pontifical Catholic University of Chile, Santiago, Chile
| | - Tomás Alarcón-Schumacher
- Department of Molecular Genetics and Microbiology, Biological Sciences Faculty, Pontifical Catholic University of Chile, Santiago, Chile
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Oscar Salgado
- Department of Molecular Genetics and Microbiology, Biological Sciences Faculty, Pontifical Catholic University of Chile, Santiago, Chile
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Laboratorio de Bioinformática, Facultad de Educación, Universidad Adventista de Chile, Chillán, Chile
| | - Beatriz Díez
- Department of Molecular Genetics and Microbiology, Biological Sciences Faculty, Pontifical Catholic University of Chile, Santiago, Chile
- Center for Climate and Resilience Research (CR)2, University of Chile, Santiago, Chile
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47
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Messer LF, Ostrowski M, Doblin MA, Petrou K, Baird ME, Ingleton T, Bissett A, Van de Kamp J, Nelson T, Paulsen I, Bodrossy L, Fuhrman JA, Seymour JR, Brown MV. Microbial tropicalization driven by a strengthening western ocean boundary current. GLOBAL CHANGE BIOLOGY 2020; 26:5613-5629. [PMID: 32715608 DOI: 10.1111/gcb.15257] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 04/22/2020] [Accepted: 06/09/2020] [Indexed: 06/11/2023]
Abstract
Western boundary currents (WBCs) redistribute heat and oligotrophic seawater from the tropics to temperate latitudes, with several displaying substantial climate change-driven intensification over the last century. Strengthening WBCs have been implicated in the poleward range expansion of marine macroflora and fauna, however, the impacts on the structure and function of temperate microbial communities are largely unknown. Here we show that the major subtropical WBC of the South Pacific Ocean, the East Australian Current (EAC), transports microbial assemblages that maintain tropical and oligotrophic (k-strategist) signatures, to seasonally displace more copiotrophic (r-strategist) temperate microbial populations within temperate latitudes of the Tasman Sea. We identified specific characteristics of EAC microbial assemblages compared with non-EAC assemblages, including strain transitions within the SAR11 clade, enrichment of Prochlorococcus, predicted smaller genome sizes and shifts in the importance of several functional genes, including those associated with cyanobacterial photosynthesis, secondary metabolism and fatty acid and lipid transport. At a temperate time-series site in the Tasman Sea, we observed significant reductions in standing stocks of total carbon and chlorophyll a, and a shift towards smaller phytoplankton and carnivorous copepods, associated with the seasonal impact of the EAC microbial assemblage. In light of the substantial shifts in microbial assemblage structure and function associated with the EAC, we conclude that climate-driven expansions of WBCs will expand the range of tropical oligotrophic microbes, and potentially profoundly impact the trophic status of temperate waters.
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Affiliation(s)
- Lauren F Messer
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Qld, Australia
| | - Martin Ostrowski
- Climate Change Cluster, University of Technology, Sydney, Sydney, Australia
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Martina A Doblin
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Katherina Petrou
- School of Life Sciences, University of Technology, Sydney, Sydney, NSW, Australia
| | - Mark E Baird
- CSIRO Oceans and Atmosphere, Hobart, Tas., Australia
| | | | | | | | - Tiffanie Nelson
- Geelong Centre for Emerging Infectious Diseases, Deakin University, Melbourne, Vic., Australia
| | - Ian Paulsen
- Climate Change Cluster, University of Technology, Sydney, Sydney, Australia
| | | | - Jed A Fuhrman
- University of Southern California, Los Angeles, CA, USA
| | - Justin R Seymour
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Mark V Brown
- School of Environmental and Life Sciences, University of Newcastle Australia, Callaghan, NSW, Australia
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48
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Hassler G, Tolkoff MR, Allen WL, Ho LST, Lemey P, Suchard MA. Inferring Phenotypic Trait Evolution on Large Trees With Many Incomplete Measurements. J Am Stat Assoc 2020; 117:678-692. [PMID: 36060555 PMCID: PMC9438787 DOI: 10.1080/01621459.2020.1799812] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 05/27/2020] [Accepted: 07/15/2020] [Indexed: 01/03/2023]
Abstract
Comparative biologists are often interested in inferring covariation between multiple biological traits sampled across numerous related taxa. To properly study these relationships, we must control for the shared evolutionary history of the taxa to avoid spurious inference. An additional challenge arises as obtaining a full suite of measurements becomes increasingly difficult with increasing taxa. This generally necessitates data imputation or integration, and existing control techniques typically scale poorly as the number of taxa increases. We propose an inference technique that integrates out missing measurements analytically and scales linearly with the number of taxa by using a post-order traversal algorithm under a multivariate Brownian diffusion (MBD) model to characterize trait evolution. We further exploit this technique to extend the MBD model to account for sampling error or non-heritable residual variance. We test these methods to examine mammalian life history traits, prokaryotic genomic and phenotypic traits, and HIV infection traits. We find computational efficiency increases that top two orders-of-magnitude over current best practices. While we focus on the utility of this algorithm in phylogenetic comparative methods, our approach generalizes to solve long-standing challenges in computing the likelihood for matrix-normal and multivariate normal distributions with missing data at scale.
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Affiliation(s)
- Gabriel Hassler
- Department of Biomathematics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, United States
| | - Max R Tolkoff
- Department of Biostatistics, Jonathan and Karin Fielding School of Public Health, University of California, Los Angeles, United States
| | - William L Allen
- Department of Biosciences, Swansea University, Swansea, United Kingdom
| | - Lam Si Tung Ho
- Department of Mathematics and Statistics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Philippe Lemey
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Marc A Suchard
- Department of Biomathematics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, United States
- Department of Biostatistics, Jonathan and Karin Fielding School of Public Health, University of California, Los Angeles, United States
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Universtiy of California, Los Angeles, United States
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49
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The whale shark genome reveals how genomic and physiological properties scale with body size. Proc Natl Acad Sci U S A 2020; 117:20662-20671. [PMID: 32753383 DOI: 10.1073/pnas.1922576117] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The endangered whale shark (Rhincodon typus) is the largest fish on Earth and a long-lived member of the ancient Elasmobranchii clade. To characterize the relationship between genome features and biological traits, we sequenced and assembled the genome of the whale shark and compared its genomic and physiological features to those of 83 animals and yeast. We examined the scaling relationships between body size, temperature, metabolic rates, and genomic features and found both general correlations across the animal kingdom and features specific to the whale shark genome. Among animals, increased lifespan is positively correlated to body size and metabolic rate. Several genomic traits also significantly correlated with body size, including intron and gene length. Our large-scale comparative genomic analysis uncovered general features of metazoan genome architecture: Guanine and cytosine (GC) content and codon adaptation index are negatively correlated, and neural connectivity genes are longer than average genes in most genomes. Focusing on the whale shark genome, we identified multiple features that significantly correlate with lifespan. Among these were very long gene length, due to introns being highly enriched in repetitive elements such as CR1-like long interspersed nuclear elements, and considerably longer neural genes of several types, including connectivity, activity, and neurodegeneration genes. The whale shark genome also has the second slowest evolutionary rate observed in vertebrates to date. Our comparative genomics approach uncovered multiple genetic features associated with body size, metabolic rate, and lifespan and showed that the whale shark is a promising model for studies of neural architecture and lifespan.
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50
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Wang P, Li LZ, Qin YL, Liang ZL, Li XT, Yin HQ, Liu LJ, Liu SJ, Jiang CY. Comparative Genomic Analysis Reveals the Metabolism and Evolution of the Thermophilic Archaeal Genus Metallosphaera. Front Microbiol 2020; 11:1192. [PMID: 32655516 PMCID: PMC7325606 DOI: 10.3389/fmicb.2020.01192] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 05/11/2020] [Indexed: 01/15/2023] Open
Abstract
Members of the genus Metallosphaera are widely found in sulfur-rich and metal-laden environments, but their physiological and ecological roles remain poorly understood. Here, we sequenced Metallosphaera tengchongensis Ric-A, a strain isolated from the Tengchong hot spring in Yunnan Province, China, and performed a comparative genome analysis with other Metallosphaera genomes. The genome of M. tengchongensis had an average nucleotide identity (ANI) of approximately 70% to that of Metallosphaera cuprina. Genes sqr, tth, sir, tqo, hdr, tst, soe, and sdo associated with sulfur oxidation, and gene clusters fox and cbs involved in iron oxidation existed in all Metallosphaera genomes. However, the adenosine-5'-phosphosulfate (APS) pathway was only detected in Metallosphaera sedula and Metallosphaera yellowstonensis, and several subunits of fox cluster were lost in M. cuprina. The complete 3-hydroxypropionate/4-hydroxybutyrate cycle and dicarboxylate/4-hydroxybutyrate cycle involved in carbon fixation were found in all Metallosphaera genomes. A large number of gene family gain events occurred in M. yellowstonensis and M. sedula, whereas gene family loss events occurred frequently in M. cuprina. Pervasive strong purifying selection was found acting on the gene families of Metallosphaera, of which transcription-related genes underwent the strongest purifying selection. In contrast, genes related to prophages, transposons, and defense mechanisms were under weaker purifying pressure. Taken together, this study expands knowledge of the genomic traits of Metallosphaera species and sheds light on their evolution.
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Affiliation(s)
- Pei Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Liang Zhi Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Ya Ling Qin
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zong Lin Liang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xiu Tong Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Hua Qun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Li Jun Liu
- Department of Pathogen Biology, School of Basic Medical Science, Xi’an Medical University, Xi’an, China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Cheng-Ying Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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