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Freches A, Fradinho JC. The biotechnological potential of the Chloroflexota phylum. Appl Environ Microbiol 2024; 90:e0175623. [PMID: 38709098 DOI: 10.1128/aem.01756-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2024] Open
Abstract
In the next decades, the increasing material and energetic demand to support population growth and higher standards of living will amplify the current pressures on ecosystems and will call for greater investments in infrastructures and modern technologies. A valid approach to overcome such future challenges is the employment of sustainable bio-based technologies that explore the metabolic richness of microorganisms. Collectively, the metabolic capabilities of Chloroflexota, spanning aerobic and anaerobic conditions, thermophilic adaptability, anoxygenic photosynthesis, and utilization of toxic compounds as electron acceptors, underscore the phylum's resilience and ecological significance. These diverse metabolic strategies, driven by the interplay between temperature, oxygen availability, and energy metabolism, exemplify the complex adaptations that enabled Chloroflexota to colonize a wide range of ecological niches. In demonstrating the metabolic richness of the Chloroflexota phylum, specific members exemplify the diverse capabilities of these microorganisms: Chloroflexus aurantiacus showcases adaptability through its thermophilic and phototrophic growth, whereas members of the Anaerolineae class are known for their role in the degradation of complex organic compounds, contributing significantly to the carbon cycle in anaerobic environments, highlighting the phylum's potential for biotechnological exploitation in varying environmental conditions. In this context, the metabolic diversity of Chloroflexota must be considered a promising asset for a large range of applications. Currently, this bacterial phylum is organized into eight classes possessing different metabolic strategies to survive and thrive in a wide variety of extreme environments. This review correlates the ecological role of Chloroflexota in such environments with the potential application of their metabolisms in biotechnological approaches.
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Affiliation(s)
- André Freches
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University of Lisbon, Caparica, Portugal
- Department of Chemistry, UCIBIO - Applied Molecular Biosciences Unit, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
| | - Joana Costa Fradinho
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University of Lisbon, Caparica, Portugal
- Department of Chemistry, UCIBIO - Applied Molecular Biosciences Unit, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
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Nishihara A, Tsukatani Y, Azai C, Nobu MK. Illuminating the coevolution of photosynthesis and Bacteria. Proc Natl Acad Sci U S A 2024; 121:e2322120121. [PMID: 38875151 PMCID: PMC11194577 DOI: 10.1073/pnas.2322120121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 05/06/2024] [Indexed: 06/16/2024] Open
Abstract
Life harnessing light energy transformed the relationship between biology and Earth-bringing a massive flux of organic carbon and oxidants to Earth's surface that gave way to today's organotrophy- and respiration-dominated biosphere. However, our understanding of how life drove this transition has largely relied on the geological record; much remains unresolved due to the complexity and paucity of the genetic record tied to photosynthesis. Here, through holistic phylogenetic comparison of the bacterial domain and all photosynthetic machinery (totally spanning >10,000 genomes), we identify evolutionary congruence between three independent biological systems-bacteria, (bacterio)chlorophyll-mediated light metabolism (chlorophototrophy), and carbon fixation-and uncover their intertwined history. Our analyses uniformly mapped progenitors of extant light-metabolizing machinery (reaction centers, [bacterio]chlorophyll synthases, and magnesium-chelatases) and enzymes facilitating the Calvin-Benson-Bassham cycle (form I RuBisCO and phosphoribulokinase) to the same ancient Terrabacteria organism near the base of the bacterial domain. These phylogenies consistently showed that extant phototrophs ultimately derived light metabolism from this bacterium, the last phototroph common ancestor (LPCA). LPCA was a non-oxygen-generating (anoxygenic) phototroph that already possessed carbon fixation and two reaction centers, a type I analogous to extant forms and a primitive type II. Analyses also indicate chlorophototrophy originated before LPCA. We further reconstructed evolution of chlorophototrophs/chlorophototrophy post-LPCA, including vertical inheritance in Terrabacteria, the rise of oxygen-generating chlorophototrophy in one descendant branch near the Great Oxidation Event, and subsequent emergence of Cyanobacteria. These collectively unveil a detailed view of the coevolution of light metabolism and Bacteria having clear congruence with the geological record.
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Affiliation(s)
- Arisa Nishihara
- Department of Life Science and Biotechnology, The National Institute of Advanced Industrial Science and Technology, Ibaraki305-0817, Japan
| | - Yusuke Tsukatani
- Biogeochemistry Research Center, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Kanagawa237-0061, Japan
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Kanagawa237-0061, Japan
| | - Chihiro Azai
- College of Life Sciences, Ritsumeikan University, Shiga525-8577, Japan
- Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, Tokyo112-8551, Japan
| | - Masaru K. Nobu
- Department of Life Science and Biotechnology, The National Institute of Advanced Industrial Science and Technology, Ibaraki305-0817, Japan
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Kanagawa237-0061, Japan
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Blais MA, Vincent WF, Vigneron A, Labarre A, Matveev A, Coelho LF, Lovejoy C. Diverse winter communities and biogeochemical cycling potential in the under-ice microbial plankton of a subarctic river-to-sea continuum. Microbiol Spectr 2024; 12:e0416023. [PMID: 38511950 DOI: 10.1128/spectrum.04160-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 03/05/2024] [Indexed: 03/22/2024] Open
Abstract
Winter conditions greatly alter the limnological properties of lotic ecosystems and the availability of nutrients, carbon, and energy resources for microbial processes. However, the composition and metabolic capabilities of winter microbial communities are still largely uncharacterized. Here, we sampled the winter under-ice microbiome of the Great Whale River (Nunavik, Canada) and its discharge plume into Hudson Bay. We used a combination of 16S and 18S rRNA gene amplicon analysis and metagenomic sequencing to evaluate the size-fractionated composition and functional potential of the microbial plankton. These under-ice communities were diverse in taxonomic composition and metabolically versatile in terms of energy and carbon acquisition, including the capacity to carry out phototrophic processes and degrade aromatic organic matter. Limnological properties, community composition, and metabolic potential differed between shallow and deeper sites in the river, and between fresh and brackish water in the vertical profile of the plume. Community composition also varied by size fraction, with a greater richness of prokaryotes in the larger size fraction (>3 µm) and of microbial eukaryotes in the smaller size fraction (0.22-3 µm). The freshwater communities included cosmopolitan bacterial genera that were previously detected in the summer, indicating their persistence over time in a wide range of physico-chemical conditions. These observations imply that the microbial communities of subarctic rivers and their associated discharge plumes retain a broad taxonomic and functional diversity throughout the year and that microbial processing of complex terrestrial materials persists beneath the ice during the long winter season. IMPORTANCE Microbiomes vary over multiple timescales, with short- and long-term changes in the physico-chemical environment. However, there is a scarcity of data and understanding about the structure and functioning of aquatic ecosystems during winter relative to summer. This is especially the case for seasonally ice-covered rivers, limiting our understanding of these ecosystems that are common throughout the boreal, subpolar, and polar regions. Here, we examined the winter under-ice microbiome of a Canadian subarctic river and its entry to the sea to characterize the taxonomic and functional features of the microbial community. We found substantial diversity in both composition and functional capabilities, including the capacity to degrade complex terrestrial compounds, despite the constraints imposed by a prolonged seasonal ice-cover and near-freezing water temperatures. This study indicates the ecological complexity and importance of winter microbiomes in ice-covered rivers and the coastal marine environment that they discharge into.
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Affiliation(s)
- Marie-Amélie Blais
- Département de Biologie, Université Laval, Quebec City, Quebec, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
- Centre for Northern Studies (CEN), Université Laval, Quebec City, Quebec, Canada
- Takuvik Joint International Laboratory, Université Laval, Quebec City, Quebec, Canada
| | - Warwick F Vincent
- Département de Biologie, Université Laval, Quebec City, Quebec, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
- Centre for Northern Studies (CEN), Université Laval, Quebec City, Quebec, Canada
- Takuvik Joint International Laboratory, Université Laval, Quebec City, Quebec, Canada
| | - Adrien Vigneron
- Département de Biologie, Université Laval, Quebec City, Quebec, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
- Centre for Northern Studies (CEN), Université Laval, Quebec City, Quebec, Canada
- Takuvik Joint International Laboratory, Université Laval, Quebec City, Quebec, Canada
| | - Aurélie Labarre
- Département de Biologie, Université Laval, Quebec City, Quebec, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
- Takuvik Joint International Laboratory, Université Laval, Quebec City, Quebec, Canada
- Québec-Océan, Université Laval, Quebec City, Quebec, Canada
| | - Alex Matveev
- Département de Biologie, Université Laval, Quebec City, Quebec, Canada
- Centre for Northern Studies (CEN), Université Laval, Quebec City, Quebec, Canada
- Takuvik Joint International Laboratory, Université Laval, Quebec City, Quebec, Canada
| | - Lígia Fonseca Coelho
- Centro de Química Estrutural, Departamento de Engenharia Química, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
- Associate Laboratory i4HB-Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| | - Connie Lovejoy
- Département de Biologie, Université Laval, Quebec City, Quebec, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
- Takuvik Joint International Laboratory, Université Laval, Quebec City, Quebec, Canada
- Québec-Océan, Université Laval, Quebec City, Quebec, Canada
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Aguilar C, Alwali A, Mair M, Rodriguez-Orduña L, Contreras-Peruyero H, Modi R, Roberts C, Sélem-Mojica N, Licona-Cassani C, Parkinson EI. Actinomycetota bioprospecting from ore-forming environments. Microb Genom 2024; 10:001253. [PMID: 38743050 PMCID: PMC11165632 DOI: 10.1099/mgen.0.001253] [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: 11/21/2023] [Accepted: 04/26/2024] [Indexed: 05/16/2024] Open
Abstract
Natural products from Actinomycetota have served as inspiration for many clinically relevant therapeutics. Despite early triumphs in natural product discovery, the rate of unearthing new compounds has decreased, necessitating inventive approaches. One promising strategy is to explore environments where survival is challenging. These harsh environments are hypothesized to lead to bacteria developing chemical adaptations (e.g. natural products) to enable their survival. This investigation focuses on ore-forming environments, particularly fluoride mines, which typically have extreme pH, salinity and nutrient scarcity. Herein, we have utilized metagenomics, metabolomics and evolutionary genome mining to dissect the biodiversity and metabolism in these harsh environments. This work has unveiled the promising biosynthetic potential of these bacteria and has demonstrated their ability to produce bioactive secondary metabolites. This research constitutes a pioneering endeavour in bioprospection within fluoride mining regions, providing insights into uncharted microbial ecosystems and their previously unexplored natural products.
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Affiliation(s)
- César Aguilar
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Amir Alwali
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Madeline Mair
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | | | | | - Ramya Modi
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Carson Roberts
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | | | | | - Elizabeth Ivy Parkinson
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907, USA
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Liu B, Zheng Y, Wang X, Qi L, Zhou J, An Z, Wu L, Chen F, Lin Z, Yin G, Dong H, Li X, Liang X, Han P, Liu M, Hou L. Active dark carbon fixation evidenced by 14C isotope assimilation and metagenomic data across the estuarine-coastal continuum. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 914:169833. [PMID: 38190922 DOI: 10.1016/j.scitotenv.2023.169833] [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: 08/23/2023] [Revised: 12/24/2023] [Accepted: 12/30/2023] [Indexed: 01/10/2024]
Abstract
Estuaries, as important land-ocean transitional zones across the Earth's surface, are hotspots of microbially driven dark carbon fixation (DCF), yet understanding of DCF process remains limited across the estuarine-coastal continuum. This study explored DCF activities and associated chemoautotrophs along the estuarine and coastal environmental gradients, using radiocarbon labelling and molecular techniques. Significantly higher DCF rates were observed at middle- and high-salinity regions (0.65-2.31 and 0.66-2.82 mmol C m-2 d-1, respectively), compared to low-salinity zone (0.07-0.19 mmol C m-2 d-1). Metagenomic analysis revealed relatively stable DCF pathways along the estuarine-coastal continuum, primarily dominated by Calvin-Benson-Bassham (CBB) cycle and Wood-Ljungdahl (WL) pathway. Nevertheless, chemoautotrophic communities driving DCF exhibited significant spatial variations. It is worth noting that although CBB cycle played an important role in DCF in estuarine sediments, WL pathway might play a more significant role, which has not been previously recognized. Overall, this study highlights that DCF activities coincide with the genetic potential of chemoautotrophy and the availability of reductive substrates across the estuarine-coastal continuum, and provides an important scientific basis for accurate quantitative assessment of global estuarine carbon sink.
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Affiliation(s)
- Bolin Liu
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Yanling Zheng
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, 500 Dongchuan Road, Shanghai 200241, China.
| | - Xinyu Wang
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Lin Qi
- School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Jie Zhou
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Zhirui An
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Li Wu
- School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Feiyang Chen
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Zhuke Lin
- School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Guoyu Yin
- School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Hongpo Dong
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Xiaofei Li
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Xia Liang
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Ping Han
- School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Min Liu
- School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Lijun Hou
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China.
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Gwak JH, Rhee SK, Park JW. Bacteria involved in the sulfur cycle in tarballs collected from the Alabama Gulf Coast. FEMS Microbiol Lett 2024; 371:fnae003. [PMID: 38228401 DOI: 10.1093/femsle/fnae003] [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: 11/12/2023] [Revised: 01/04/2024] [Accepted: 01/15/2024] [Indexed: 01/18/2024] Open
Abstract
Tarballs are formed from released or discharged crude oil containing sulfur compounds. A considerable amount and variety of sulfate-reducing bacteria (SRB) and sulfur-oxidizing bacteria (SOB) were identified in tarballs collected from the intertidal and supratidal zones of Alabama's Gulf beaches. Amplicon sequencing of the bacterial 16S rRNA gene showed that SRB were more abundantly distributed in the core than on the surface of tarballs, while no significant differences were observed in the distribution of SOB. To our best knowledge, this is the first report on the spatial distribution of diverse SRB and SOB in tarballs.
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Affiliation(s)
- Joo-Han Gwak
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Seowon-Gu, Cheongju 28644, Republic of Korea
| | - Sung-Keun Rhee
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Seowon-Gu, Cheongju 28644, Republic of Korea
| | - Joong-Wook Park
- Department of Biological and Environmental Sciences, Troy University, Troy, AL 36082, United States
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Centurion VB, Rossi A, Orellana E, Ghiotto G, Kakuk B, Morlino MS, Basile A, Zampieri G, Treu L, Campanaro S. A unified compendium of prokaryotic and viral genomes from over 300 anaerobic digestion microbiomes. ENVIRONMENTAL MICROBIOME 2024; 19:1. [PMID: 38167520 PMCID: PMC10762816 DOI: 10.1186/s40793-023-00545-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 12/21/2023] [Indexed: 01/05/2024]
Abstract
BACKGROUND The anaerobic digestion process degrades organic matter into simpler compounds and occurs in strictly anaerobic and microaerophilic environments. The process is carried out by a diverse community of microorganisms where each species has a unique role and it has relevant biotechnological applications since it is used for biogas production. Some aspects of the microbiome, including its interaction with phages, remains still unclear: a better comprehension of the community composition and role of each species is crucial for a cured understanding of the carbon cycle in anaerobic systems and improving biogas production. RESULTS The primary objective of this study was to expand our understanding on the anaerobic digestion microbiome by jointly analyzing its prokaryotic and viral components. By integrating 192 additional datasets into a previous metagenomic database, the binning process generated 11,831 metagenome-assembled genomes from 314 metagenome samples published between 2014 and 2022, belonging to 4,568 non-redundant species based on ANI calculation and quality verification. CRISPR analysis on these genomes identified 76 archaeal genomes with active phage interactions. Moreover, single-nucleotide variants further pointed to archaea as the most critical members of the community. Among the MAGs, two methanogenic archaea, Methanothrix sp. 43zhSC_152 and Methanoculleus sp. 52maCN_3230, had the highest number of SNVs, with the latter having almost double the density of most other MAGs. CONCLUSIONS This study offers a more comprehensive understanding of microbial community structures that thrive at different temperatures. The findings revealed that the fraction of archaeal species characterized at the genome level and reported in public databases is higher than that of bacteria, although still quite limited. The identification of shared spacers between phages and microbes implies a history of phage-bacterial interactions, and specifically lysogenic infections. A significant number of SNVs were identified, primarily comprising synonymous and nonsynonymous variants. Together, the findings indicate that methanogenic archaea are subject to intense selective pressure and suggest that genomic variants play a critical role in the anaerobic digestion process. Overall, this study provides a more balanced and diverse representation of the anaerobic digestion microbiota in terms of geographic location, temperature range and feedstock utilization.
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Affiliation(s)
| | - Alessandro Rossi
- Department of Biology, University of Padua, Via U. Bassi 58/B, 35131, Padua, Italy
| | - Esteban Orellana
- Department of Biology, University of Padua, Via U. Bassi 58/B, 35131, Padua, Italy
| | - Gabriele Ghiotto
- Department of Biology, University of Padua, Via U. Bassi 58/B, 35131, Padua, Italy
| | - Balázs Kakuk
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, 12 Somogyi B. U. 4., Szeged, 6720, Hungary
| | - Maria Silvia Morlino
- Department of Biology, University of Padua, Via U. Bassi 58/B, 35131, Padua, Italy
| | - Arianna Basile
- MRC Toxicology Unit, University of Cambridge, Gleeson Building Tennis Court Road, Cambridge, UK
| | - Guido Zampieri
- Department of Biology, University of Padua, Via U. Bassi 58/B, 35131, Padua, Italy.
| | - Laura Treu
- Department of Biology, University of Padua, Via U. Bassi 58/B, 35131, Padua, Italy.
| | - Stefano Campanaro
- Department of Biology, University of Padua, Via U. Bassi 58/B, 35131, Padua, Italy
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Hribovšek P, Olesin Denny E, Dahle H, Mall A, Øfstegaard Viflot T, Boonnawa C, Reeves EP, Steen IH, Stokke R. Putative novel hydrogen- and iron-oxidizing sheath-producing Zetaproteobacteria thrive at the Fåvne deep-sea hydrothermal vent field. mSystems 2023; 8:e0054323. [PMID: 37921472 PMCID: PMC10734525 DOI: 10.1128/msystems.00543-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 10/02/2023] [Indexed: 11/04/2023] Open
Abstract
IMPORTANCE Knowledge on microbial iron oxidation is important for understanding the cycling of iron, carbon, nitrogen, nutrients, and metals. The current study yields important insights into the niche sharing, diversification, and Fe(III) oxyhydroxide morphology of Ghiorsea, an iron- and hydrogen-oxidizing Zetaproteobacteria representative belonging to Zetaproteobacteria operational taxonomic unit 9. The study proposes that Ghiorsea exhibits a more extensive morphology of Fe(III) oxyhydroxide than previously observed. Overall, the results increase our knowledge on potential drivers of Zetaproteobacteria diversity in iron microbial mats and can eventually be used to develop strategies for the cultivation of sheath-forming Zetaproteobacteria.
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Affiliation(s)
- Petra Hribovšek
- Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Earth Science, University of Bergen, Bergen, Norway
| | - Emily Olesin Denny
- Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
- Computational Biology Unit, University of Berge, Bergen, Norway
| | - Håkon Dahle
- Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
- Computational Biology Unit, University of Berge, Bergen, Norway
| | - Achim Mall
- Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Thomas Øfstegaard Viflot
- Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Earth Science, University of Bergen, Bergen, Norway
| | - Chanakan Boonnawa
- Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Earth Science, University of Bergen, Bergen, Norway
| | - Eoghan P. Reeves
- Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Earth Science, University of Bergen, Bergen, Norway
| | - Ida Helene Steen
- Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Runar Stokke
- Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
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Parsons RJ, Liu S, Longnecker K, Yongblah K, Johnson C, Bolaños LM, Comstock J, Opalk K, Kido Soule MC, Garley R, Carlson CA, Temperton B, Bates NR. Suboxic DOM is bioavailable to surface prokaryotes in a simulated overturn of an oxygen minimum zone, Devil's Hole, Bermuda. Front Microbiol 2023; 14:1287477. [PMID: 38179459 PMCID: PMC10765504 DOI: 10.3389/fmicb.2023.1287477] [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: 09/01/2023] [Accepted: 11/17/2023] [Indexed: 01/06/2024] Open
Abstract
Oxygen minimum zones (OMZs) are expanding due to increased sea surface temperatures, subsequent increased oxygen demand through respiration, reduced oxygen solubility, and thermal stratification driven in part by anthropogenic climate change. Devil's Hole, Bermuda is a model ecosystem to study OMZ microbial biogeochemistry because the formation and subsequent overturn of the suboxic zone occur annually. During thermally driven stratification, suboxic conditions develop, with organic matter and nutrients accumulating at depth. In this study, the bioavailability of the accumulated dissolved organic carbon (DOC) and the microbial community response to reoxygenation of suboxic waters was assessed using a simulated overturn experiment. The surface inoculated prokaryotic community responded to the deep (formerly suboxic) 0.2 μm filtrate with cell densities increasing 2.5-fold over 6 days while removing 5 μmol L-1 of DOC. After 12 days, the surface community began to shift, and DOC quality became less diagenetically altered along with an increase in SAR202, a Chloroflexi that can degrade recalcitrant dissolved organic matter (DOM). Labile DOC production after 12 days coincided with an increase of Nitrosopumilales, a chemoautotrophic ammonia oxidizing archaea (AOA) that converts ammonia to nitrite based on the ammonia monooxygenase (amoA) gene copy number and nutrient data. In comparison, the inoculation of the deep anaerobic prokaryotic community into surface 0.2 μm filtrate demonstrated a die-off of 25.5% of the initial inoculum community followed by a 1.5-fold increase in cell densities over 6 days. Within 2 days, the prokaryotic community shifted from a Chlorobiales dominated assemblage to a surface-like heterotrophic community devoid of Chlorobiales. The DOM quality changed to less diagenetically altered material and coincided with an increase in the ribulose-1,5-bisphosphate carboxylase/oxygenase form I (cbbL) gene number followed by an influx of labile DOM. Upon reoxygenation, the deep DOM that accumulated under suboxic conditions is bioavailable to surface prokaryotes that utilize the accumulated DOC initially before switching to a community that can both produce labile DOM via chemoautotrophy and degrade the more recalcitrant DOM.
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Affiliation(s)
- Rachel J. Parsons
- Microbial Ecology Laboratory, Bermuda Institute of Ocean Sciences, St. George’s, Bermuda
- Julie Ann Wrigley Global Futures Laboratory, School of Ocean Futures, Arizona State University, Tempe, AZ, United States
| | - Shuting Liu
- Department of Ecology, Evolution and Marine Biology, Marine Science Institute, University of California, Santa Barbara, California, CA, United States
- Department of Environmental and Sustainability Sciences, Kean University, Union, NJ, United States
| | - Krista Longnecker
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Kevin Yongblah
- Microbial Ecology Laboratory, Bermuda Institute of Ocean Sciences, St. George’s, Bermuda
- Department of Biology, University of Syracuse, Syracuse, NY, United States
| | - Carys Johnson
- Microbial Ecology Laboratory, Bermuda Institute of Ocean Sciences, St. George’s, Bermuda
| | - Luis M. Bolaños
- School of Biosciences, University of Exeter, Exeter, United Kingdom
| | - Jacqueline Comstock
- Department of Ecology, Evolution and Marine Biology, Marine Science Institute, University of California, Santa Barbara, California, CA, United States
| | - Keri Opalk
- Department of Ecology, Evolution and Marine Biology, Marine Science Institute, University of California, Santa Barbara, California, CA, United States
| | - Melissa C. Kido Soule
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Rebecca Garley
- Microbial Ecology Laboratory, Bermuda Institute of Ocean Sciences, St. George’s, Bermuda
- Julie Ann Wrigley Global Futures Laboratory, School of Ocean Futures, Arizona State University, Tempe, AZ, United States
| | - Craig A. Carlson
- Department of Ecology, Evolution and Marine Biology, Marine Science Institute, University of California, Santa Barbara, California, CA, United States
| | - Ben Temperton
- School of Biosciences, University of Exeter, Exeter, United Kingdom
| | - Nicholas R. Bates
- Microbial Ecology Laboratory, Bermuda Institute of Ocean Sciences, St. George’s, Bermuda
- Julie Ann Wrigley Global Futures Laboratory, School of Ocean Futures, Arizona State University, Tempe, AZ, United States
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10
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Moon J, Schubert A, Poehlein A, Daniel R, Müller V. A new metabolic trait in an acetogen: Mixed acid fermentation of fructose in a methylene-tetrahydrofolate reductase mutant of Acetobacterium woodii. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:339-351. [PMID: 37150590 PMCID: PMC10472528 DOI: 10.1111/1758-2229.13160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 04/20/2023] [Indexed: 05/09/2023]
Abstract
To inactivate the Wood-Ljungdahl pathway in the acetogenic model bacterium Acetobacterium woodii, the genes metVF encoding two of the subunits of the methylene-tetrahydrofolate reductase were deleted. As expected, the mutant did not grow on C1 compounds and also not on lactate, ethanol or butanediol. In contrast to a mutant in which the first enzyme of the pathway (hydrogen-dependent CO2 reductase) had been genetically deleted, cells were able to grow on fructose, albeit with lower rates and yields than the wild-type. Growth was restored by addition of an external electron sink, glycine betaine + CO2 or caffeate. Resting cells pre-grown on fructose plus an external electron acceptor fermented fructose to two acetate and four hydrogen, that is, performed hydrogenogenesis. Cells pre-grown under fermentative conditions on fructose alone redirected carbon and electrons to form lactate, formate, ethanol as well as hydrogen. Apparently, growth on fructose alone induced enzymes for mixed acid fermentation (MAF). Transcriptome analyses revealed enzymes potentially involved in MAF and a quantitative model for MAF from fructose in A. woodii is presented.
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Affiliation(s)
- Jimyung Moon
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular BiosciencesJohann Wolfgang Goethe UniversityFrankfurtGermany
| | - Anja Schubert
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular BiosciencesJohann Wolfgang Goethe UniversityFrankfurtGermany
| | - Anja Poehlein
- Göttingen Genomics Laboratory, Institute for Microbiology and GeneticsGeorg August UniversityGöttingenGermany
| | - Rolf Daniel
- Göttingen Genomics Laboratory, Institute for Microbiology and GeneticsGeorg August UniversityGöttingenGermany
| | - Volker Müller
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular BiosciencesJohann Wolfgang Goethe UniversityFrankfurtGermany
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11
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Popall RM, Postec A, Lecoeuvre A, Quéméneur M, Erauso G. Metabolic challenges and key players in serpentinite-hosted microbial ecosystems. Front Microbiol 2023; 14:1197823. [PMID: 37555067 PMCID: PMC10404738 DOI: 10.3389/fmicb.2023.1197823] [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: 03/31/2023] [Accepted: 06/29/2023] [Indexed: 08/10/2023] Open
Abstract
Serpentinite-hosted systems are amongst the most challenging environments for life on Earth. Serpentinization, a geochemical alteration of exposed ultramafic rock, produces hydrothermal fluids enriched in abiotically derived hydrogen (H2), methane (CH4), and small organic molecules. The hyperalkaline pH of these fluids poses a great challenge for metabolic energy and nutrient acquisition, curbing the cellular membrane potential and limiting electron acceptor, carbon, and phosphorous availability. Nevertheless, serpentinization supports the growth of diverse microbial communities whose metabolic make-up might shed light on the beginning of life on Earth and potentially elsewhere. Here, we outline current hypotheses on metabolic energy production, carbon fixation, and nutrient acquisition in serpentinizing environments. A taxonomic survey is performed for each important metabolic function, highlighting potential key players such as H2 and CH4 cycling Serpentinimonas, Hydrogenophaga, Methanobacteriales, Methanosarcinales, and novel candidate phyla. Methodological biases of the available data and future approaches are discussed.
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Affiliation(s)
| | | | | | | | - Gaël Erauso
- Aix-Marseille Univ, Univ Toulon, CNRS, IRD, MIO, Marseille, France
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12
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Xiang R, Tian Z, Zhang C, Zheng B, Jia H. Characterization of dissolved organic matter content, composition, and source during spring algal bloom in tributaries of the Three Gorges Reservoir. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 879:163139. [PMID: 36990236 DOI: 10.1016/j.scitotenv.2023.163139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 03/19/2023] [Accepted: 03/24/2023] [Indexed: 05/17/2023]
Abstract
Dissolved organic matter (DOM) is a key component of aquatic ecosystem function and biogeochemical processes. The characteristics of DOM in tributaries of the Three Gorges Reservoir (TGR) during the severe spring algal bloom period and their relationship with algal growth are unclear. In this study, the content, composition, and source of DOM in the Pengxi River (PXR) and Ruxi River (RXR) exhibiting typical TGR bloom problems were analyzed using various physicochemical indexes, carbon isotopes, fatty acids, and metagenomics. The results showed that chlorophyll a content increased with rising DOM concentration in the PXR and RXR. The dissolved organic carbon (DOC) and chromophoric dissolved organic matter (CDOM) contents in the two rivers were 4.656-16.560 mg/L and 14.373-50.848 μg/L, respectively, and increased during the bloom period. Four fluorescent components were identified, namely, two humic-like substances, and two protein-like substances. Proteobacteria, bacteroidetes, and actinobacteria were the greatest contributors to DOM content. The carbon fixation pathway of microorganisms increased the DOC concentration in both rivers during the bloom period. Physicochemical parameters (WT, pH, DO, and PAR) affected the DOM concentration by influencing microbial activity and DOM degradation. DOM in both rivers was derived from allochthonous and autogenous sources. Meanwhile, the DOC content was more strongly correlated with allochthonous sources. These findings might provide essential information for improving water environment management and algal bloom control in the TGR.
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Affiliation(s)
- Rong Xiang
- State Key Laboratory of Environmental Criteria and Risk Assessment, National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; School of Environment, Tsinghua University, Beijing 100084, China
| | - Zebin Tian
- State Key Laboratory of Environmental Criteria and Risk Assessment, National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Chuandong Zhang
- Yunyang County Ecology and Environment Bureau, Chongqing 404500, China
| | - Binghui Zheng
- State Key Laboratory of Environmental Criteria and Risk Assessment, National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
| | - Haifeng Jia
- School of Environment, Tsinghua University, Beijing 100084, China.
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13
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Zhao Y, Wu F, Liu Y, Wu M, Wang S, Sun HJ, Liu G, Zhang Y, Cui X, Zhang W, Chen T, Zhang G. The Distribution and Influencing Factors of Hypolithic Microbial Communities in the Hexi Corridor. Microorganisms 2023; 11:1212. [PMID: 37317185 DOI: 10.3390/microorganisms11051212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/26/2023] [Accepted: 04/28/2023] [Indexed: 06/16/2023] Open
Abstract
The Hexi Corridor is an arid region in northwestern China, where hypoliths are widely distributed, resulting from large amounts of translucent stone pavements. In this region, the water and heat distributions are uneven, with a descent gradient from east to west, which can affect the area's biological composition. The impact of environmental heterogeneity on the distribution of hypolithic microbial communities in this area is poorly understood, and this is an ideal location to investigate the factors that may influence the composition and structure of hypolithic microbial communities. An investigation of different sites with differences in precipitation between east and west revealed that the colonization rate decreased from 91.8% to 17.5% in the hypolithic community. Environmental heterogeneity influenced both the structure and function of the hypolithic community, especially total nitrogen (TN) and soil organic carbon (SOC). However, the effect on taxonomic composition was greater than that on ecological function. The dominant bacterial phyla in all sample sites were Cyanobacteria, Actinobacteria, Proteobacteria, and Deinococcus-Thermus, but the abundances varied significantly between the sampling sites. The eastern site had the highest relative abundance of Proteobacteria (18.43%) and Bacteroidetes (6.32%), while the western site had a higher relative abundance in the phyla Cyanobacteria (62%) and Firmicutes (1.45%); the middle site had a higher relative abundance of Chloroflexi (8.02%) and Gemmatimonadetes (1.87%). The dominant phylum in the fungal community is Ascomycota. Pearson correlation analysis showed that the soil's physicochemical properties were also associated with changes in community diversity at the sample sites. These results have important implications for better understanding the community assembly and ecological adaptations of hypolithic microorganisms.
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Affiliation(s)
- Yidan Zhao
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
| | - Fasi Wu
- National Research Center for Conservation of Ancient Wall Paintings and Earthen Sites, Department of Conservation Research, Dunhuang Academy, Dunhuang 736200, China
| | - Yang Liu
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
| | - Minghui Wu
- School of Ecology and Environmental Sciences, Yunnan University, Kunming 650091, China
| | - Shengjie Wang
- Faculty of Geographical Science, Beijing Normal University, No. 19, Xinjiekouwai Street, Haidian District, Beijing 100875, China
| | - Henry J Sun
- Desert Research Institute, Las Vegas, NV 89119, USA
| | - Guangxiu Liu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Yiyang Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Xiaowen Cui
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
| | - Wei Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Tuo Chen
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Gaosen Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
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