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Mousa WK, Abu-Izneid T, Salah-Tantawy A. High-throughput sequencing reveals the structure and metabolic resilience of desert microbiome confronting climate change. FRONTIERS IN PLANT SCIENCE 2024; 15:1294173. [PMID: 38510442 PMCID: PMC10953687 DOI: 10.3389/fpls.2024.1294173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 02/06/2024] [Indexed: 03/22/2024]
Abstract
Introduction Desert ecosystems harbor a unique microbial diversity that is crucial for ecological stability and biogeochemical cycles. An in-depth understanding of the biodiversity, compositions, and functions of these microbial communities is imperative to navigate global changes and confront potential threats and opportunities applicable to agricultural ecosystems amid climate change. Methods This study explores microbial communities in the rhizosphere and endosphere of desert plants native to the Arabian Peninsula using next-generation sequencing of the 16S rRNA gene (V3-V4 hypervariable region). Results Our results reveal that each microbial community has a diverse and unique microbial composition. Based on alpha and beta diversity indices, the rhizosphere microbiome is significantly diverse and richer in microbial taxa compared to the endosphere. The data reveals a shift towards fast-growing microbes with active metabolism, involvement in nutrient cycling, nitrogen fixation, and defense pathways. Our data reveals the presence of habitat-specific microbial communities in the desert, highlighting their remarkable resilience and adaptability to extreme environmental conditions. Notably, we observed the existence of radiation-resistant microbes such as Deinococcus radiotolerans, Kocuria sp., and Rubrobacter radiotolerans which can tolerate high levels of ionizing radiation. Additionally, examples of microbes exhibiting tolerance to challenging conditions include Nocardioides halotolerans, thriving in high-salinity environments, and hyperthermophilic microbes such as Quasibacillus thermotolerans. Moreover, functional analysis reveals enrichment in chaperon biosynthesis pathways associated with correct protein folding under heat stress conditions. Discussion Our research sheds light on the unique diversity of desert microbes and underscores their potential applications to increase the resilience of agriculture ecosystems, offering a promising strategy to fortify crops against the challenges posed by climate change, ultimately supporting sustainable food production for our ever-expanding global population.
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Affiliation(s)
- Walaa K. Mousa
- College of Pharmacy, Al Ain University, Abu Dhabi, United Arab Emirates
- Al Ain University (AAU) Health and Biomedical Research Center, Al Ain University, Abu Dhabi, United Arab Emirates
- College of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Tareq Abu-Izneid
- College of Pharmacy, Al Ain University, Abu Dhabi, United Arab Emirates
- Al Ain University (AAU) Health and Biomedical Research Center, Al Ain University, Abu Dhabi, United Arab Emirates
| | - Ahmed Salah-Tantawy
- Institute of Analytical and Environmental Sciences, College of Nuclear Science, National Tsing Hua University, Hsinchu, Taiwan
- Department of Zoology, Marine Science Division, College of Science, Al-Azhar University, Assiut, Egypt
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Fullerton H, Smith L, Enriquez A, Butterfield D, Wheat CG, Moyer CL. Seafloor incubation experiments at deep-sea hydrothermal vents reveal distinct biogeographic signatures of autotrophic communities. FEMS Microbiol Ecol 2024; 100:fiae001. [PMID: 38200713 PMCID: PMC10808952 DOI: 10.1093/femsec/fiae001] [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: 05/23/2023] [Revised: 10/20/2023] [Accepted: 01/09/2024] [Indexed: 01/12/2024] Open
Abstract
The discharge of hydrothermal vents on the seafloor provides energy sources for dynamic and productive ecosystems, which are supported by chemosynthetic microbial populations. These populations use the energy gained by oxidizing the reduced chemicals contained within the vent fluids to fix carbon and support multiple trophic levels. Hydrothermal discharge is ephemeral and chemical composition of such fluids varies over space and time, which can result in geographically distinct microbial communities. To investigate the foundational members of the community, microbial growth chambers were placed within the hydrothermal discharge at Axial Seamount (Juan de Fuca Ridge), Magic Mountain Seamount (Explorer Ridge), and Kama'ehuakanaloa Seamount (Hawai'i hotspot). Campylobacteria were identified within the nascent communities, but different amplicon sequence variants were present at Axial and Kama'ehuakanaloa Seamounts, indicating that geography in addition to the composition of the vent effluent influences microbial community development. Across these vent locations, dissolved iron concentration was the strongest driver of community structure. These results provide insights into nascent microbial community structure and shed light on the development of diverse lithotrophic communities at hydrothermal vents.
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Affiliation(s)
- Heather Fullerton
- Department of Biology, College of Charleston, 66 George Street, Charleston, SC 29424, United States
| | - Lindsey Smith
- Department of Biology, Western Washington University, 516 High St, Bellingham, WA 98225, United States
| | - Alejandra Enriquez
- Department of Biology, College of Charleston, 66 George Street, Charleston, SC 29424, United States
| | - David Butterfield
- Cooperative Institute for Climate, Ocean, and Ecosystem Studies, University of Washington and NOAA/PMEL, John M. Wallace Hall, 3737 Brooklyn Ave NE, Seattle, WA 98105, United States
| | - C Geoffrey Wheat
- Institute of Marine Studies, College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, 2150 Koyukuk Drive, 245 O’Neill Building, PO Box 757220, Fairbanks, Alaska 99775-7220, United States
| | - Craig L Moyer
- Department of Biology, Western Washington University, 516 High St, Bellingham, WA 98225, United States
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Manners SH, Carere CR, Dhami MK, Dobson RCJ, Stott MB. Draft genome sequence of Thermococcus waiotapuensis WT1 T, a thermophilic sulfur-dependent archaeon from the order Thermococcales. Microbiol Resour Announc 2024; 13:e0081523. [PMID: 38095867 DOI: 10.1128/mra.00815-23] [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: 09/10/2023] [Accepted: 11/21/2023] [Indexed: 12/23/2023] Open
Abstract
Thermococcus waiotapuensis WT1T is a thermophilic, peptide, and amino acid-fermenting archaeon from the order Thermococcales. It was isolated from Waiotapu, Aotearoa-New Zealand, and has a genome size of 1.80 Mbp. The genome contains 2,000 total genes, of which 1,913 encode proteins and 46 encode tRNA.
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Affiliation(s)
- Sarah H Manners
- Te Kura Pūtaiao Koiora School of Biological Sciences, Te Whare Wānanga o Waitaha University of Canterbury , Christchurch, New Zealand
- Biomolecular Interaction Centre, Te Whare Wānanga o Waitaha, University of Canterbury , Christchurch, New Zealand
| | - Carlo R Carere
- Biomolecular Interaction Centre, Te Whare Wānanga o Waitaha, University of Canterbury , Christchurch, New Zealand
- Department of Chemical and Process Engineering, Te Tari Pūhanga Tukanga Matū, Te Whare Wānanga o Waitaha, University of Canterbury , Christchurch, New Zealand
| | - Manpreet K Dhami
- Biocontrol and Molecular Ecology, Manaaki Whenua Landcare Research , Lincoln, New Zealand
| | - Renwick C J Dobson
- Te Kura Pūtaiao Koiora School of Biological Sciences, Te Whare Wānanga o Waitaha University of Canterbury , Christchurch, New Zealand
- Biomolecular Interaction Centre, Te Whare Wānanga o Waitaha, University of Canterbury , Christchurch, New Zealand
| | - Matthew B Stott
- Te Kura Pūtaiao Koiora School of Biological Sciences, Te Whare Wānanga o Waitaha University of Canterbury , Christchurch, New Zealand
- Biomolecular Interaction Centre, Te Whare Wānanga o Waitaha, University of Canterbury , Christchurch, New Zealand
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Yang Y, Leng H, Fan Q, Xiao X, Zhao W. Thermococcus thermotolerans sp. nov., a hyperthermophilic archaeon isolated from a chimney in the Southwest Indian Ocean. Int J Syst Evol Microbiol 2023; 73. [PMID: 38038219 DOI: 10.1099/ijsem.0.005934] [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: 12/02/2023] Open
Abstract
An anaerobic hyperthermophilic archaeon was isolated from a black smoker chimney with a snail attachment at a water depth of 2 739 m in the Southwest Indian Ocean. The sample was taken from the chimney exterior wall. The enrichment was conducted under a continuous culture with temperature fluctuation of 80-130 °C over 24 h for 42 days at 28 MPa. The isolation was performed at 90 °C at 0.1 MPa. Cells of the isolated strain 813A4T were irregular cocci. Strain 813A4T grew at 60-94 °C (optimal growth at 85 °C) at 0.1 MPa, and growth was detected at up to 99 °C at 28 MPa. At 85 °C, the strain was able to grow at pressures ranging from 0.1 to 110 MPa (optimal pressure, 0.1-40 MPa). At 85 °C, the cells of 813A4T grew at pH 5.5-9 (optimal, pH 7.0) and a NaCl concentration of 1.0-4.0 % (w/v; optimum concentration, 2.5 % NaCl). Strain 813A4T utilized yeast extract, tryptone and peptone as single carbon sources for growth. Elemental sulphur stimulated its growth. The G+C content of the complete genome was 53.48 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 813A4T belonged to the genus Thermococcus, with the highest sequence similarity to Thermococcus barossii SHCK-94T (99.73 %). The average nucleotide identity between strains 813A4T and SHCK-94T was 82.56 %. All these data indicated that strain 813A4T should be classified as representing a novel species of the genus Thermococcus, for which Thermococcus thermotolerans sp. nov. is proposed. The type strain is 813A4T (=JCM 39367T=MCCC M28628T).
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Affiliation(s)
- Yi Yang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China
- International Center for Deep Life Investigation, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Hao Leng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China
- International Center for Deep Life Investigation, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Qilian Fan
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China
- International Center for Deep Life Investigation, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China
- International Center for Deep Life Investigation, Shanghai Jiao Tong University, Shanghai, 200240, PR China
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, PR China
- SJTU Yazhou Bay Institute of Deepsea Sci-Tech, Yongyou Industrial Park, Sanya, 572024, PR China
| | - Weishu Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China
- International Center for Deep Life Investigation, Shanghai Jiao Tong University, Shanghai, 200240, PR China
- SJTU Yazhou Bay Institute of Deepsea Sci-Tech, Yongyou Industrial Park, Sanya, 572024, PR China
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Fontana A, Falasconi I, Bellassi P, Fanfoni E, Puglisi E, Morelli L. Comparative Genomics of Halobacterium salinarum Strains Isolated from Salted Foods Reveals Protechnological Genes for Food Applications. Microorganisms 2023; 11:microorganisms11030587. [PMID: 36985161 PMCID: PMC10058572 DOI: 10.3390/microorganisms11030587] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/15/2023] [Accepted: 02/22/2023] [Indexed: 03/02/2023] Open
Abstract
Archaeal cell factories are becoming of great interest given their ability to produce a broad range of value-added compounds. Moreover, the Archaea domain often includes extremophilic microorganisms, facilitating their cultivation at the industrial level under nonsterile conditions. Halophilic archaea are studied for their ability to grow in environments with high NaCl concentrations. In this study, nine strains of Halobacterium salinarum were isolated from three different types of salted food, sausage casings, salted codfish, and bacon, and their genomes were sequenced along with the genome of the collection strain CECT 395. A comparative genomic analysis was performed on these newly sequenced genomes and the publicly available ones for a total of 19 H. salinarum strains. We elucidated the presence of unique gene clusters of the species in relation to the different ecological niches of isolation (salted foods, animal hides, and solar saltern sediments). Moreover, genome mining at the single-strain level highlighted the metabolic potential of H. salinarum UC4242, which revealed the presence of different protechnological genes (vitamins and myo-inositol biosynthetic pathways, aroma- and texture-related features, and antimicrobial compounds). Despite the presence of genes of potential concern (e.g., those involved in biogenic amine production), all the food isolates presented archaeocin-related genes (halocin-C8 and sactipeptides).
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Affiliation(s)
- Alessandra Fontana
- Department for Sustainable Food Process—DiSTAS, Università Cattolica del Sacro Cuore, Via Bissolati, 74, 26100 Cremona, Italy
- Correspondence: (A.F.); (L.M.)
| | - Irene Falasconi
- Department for Sustainable Food Process—DiSTAS, Università Cattolica del Sacro Cuore, Via Bissolati, 74, 26100 Cremona, Italy
| | - Paolo Bellassi
- Department for Sustainable Food Process—DiSTAS, Università Cattolica del Sacro Cuore, Via Bissolati, 74, 26100 Cremona, Italy
| | - Elisabetta Fanfoni
- Department for Sustainable Food Process—DiSTAS, Università Cattolica del Sacro Cuore, Via Bissolati, 74, 26100 Cremona, Italy
| | - Edoardo Puglisi
- Department for Sustainable Food Process—DiSTAS, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy
| | - Lorenzo Morelli
- Department for Sustainable Food Process—DiSTAS, Università Cattolica del Sacro Cuore, Via Bissolati, 74, 26100 Cremona, Italy
- Department for Sustainable Food Process—DiSTAS, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy
- Correspondence: (A.F.); (L.M.)
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Toshchakov SV, Izotova AO, Vinogradova EN, Kachmazov GS, Tuaeva AY, Abaev VT, Evteeva MA, Gunitseva NM, Korzhenkov AA, Elcheninov AG, Patrushev MV, Kublanov IV. Culture-Independent Survey of Thermophilic Microbial Communities of the North Caucasus. BIOLOGY 2021; 10:biology10121352. [PMID: 34943267 PMCID: PMC8698779 DOI: 10.3390/biology10121352] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/09/2021] [Accepted: 12/14/2021] [Indexed: 01/04/2023]
Abstract
Simple Summary The Republic of North Ossetia-Alania, located in the southern part of the North Caucasus, possess a number of hydrothermal habitats, including both subterranean thermal reservoirs and terrestrial hot springs. At the same time, reports on microbiology of numerous geothermal sites are rather scarce for the whole North Caucasus region. In this paper, we report on the first culture-independent metabarcoding study of thermal habitats in the North Caucasus, coupled with a chemical analysis of the elemental composition of water. The results of this work include the conclusions regarding key metabolic characteristics of these habitats as well as detection of few but abundant deep lineages of uncultivated microorganisms which could be regarded as endemic. This study may represent a first step in closing the knowledge gap in extremophilic microbial communities of the North Caucasus. Abstract The Greater Caucasus is a part of seismically active Alpine–Himalayan orogenic belt and has been a center of significant volcanic activity during the Quaternary period. That led to the formation of the number of hydrothermal habitats, including subterranean thermal aquifers and surface hot springs. However, there are only a limited number of scientific works reporting on the microbial communities of these habitats. Moreover, all these reports concern only studies of specific microbial taxa, carried out using classical cultivation approaches. In this work, we present first culture-independent study of hydrotherms in the Republic of North Ossetia-Alania, located in the southern part of the North Caucasus. Using 16S metabarcoding, we analyzed the composition of the microbial communities of two subterranean thermal aquifers and terrestrial hot springs of the Karmadon valley. Analysis of correlations between the chemical composition of water and the representation of key taxa allowed us to identify the key factors determining the formation of microbial communities. In addition, we were able to identify a significant number of highly abundant deep phylogenetic lineages. Our study represents a first glance on the thermophilic microbial communities of the North Caucasus and may serve as a basis for further microbiological studies of the extreme habitats of this region.
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Affiliation(s)
- Stepan V. Toshchakov
- Kurchatov Center for Genome Research, National Research Center “Kurchatov Institute”, Ac. Kurchatov Square, 1, Moscow 123098, Russia; (A.O.I.); (E.N.V.); (M.A.E.); (N.M.G.); (A.A.K.); (M.V.P.)
- Correspondence: ; Tel.: +7-911-481-1809
| | - Anna O. Izotova
- Kurchatov Center for Genome Research, National Research Center “Kurchatov Institute”, Ac. Kurchatov Square, 1, Moscow 123098, Russia; (A.O.I.); (E.N.V.); (M.A.E.); (N.M.G.); (A.A.K.); (M.V.P.)
| | - Elizaveta N. Vinogradova
- Kurchatov Center for Genome Research, National Research Center “Kurchatov Institute”, Ac. Kurchatov Square, 1, Moscow 123098, Russia; (A.O.I.); (E.N.V.); (M.A.E.); (N.M.G.); (A.A.K.); (M.V.P.)
- Faculty of Biology, Lomonosov Moscow State University, 1-12 Leninskie Gory, Moscow 119991, Russia
| | - Gennady S. Kachmazov
- Faculty of Chemistry, Biology and Biotechnology, North Ossetian State University Named after K.L. Khetagurov, Vatutina str., 44-46, Vladikavkaz 362025, Russia; (G.S.K.); (V.T.A.)
| | - Albina Y. Tuaeva
- National Research Center Kurchatov Institute-GOSNIIGENETIKA, 1st Dorozhny Pr., 1, Moscow 117545, Russia;
| | - Vladimir T. Abaev
- Faculty of Chemistry, Biology and Biotechnology, North Ossetian State University Named after K.L. Khetagurov, Vatutina str., 44-46, Vladikavkaz 362025, Russia; (G.S.K.); (V.T.A.)
| | - Martha A. Evteeva
- Kurchatov Center for Genome Research, National Research Center “Kurchatov Institute”, Ac. Kurchatov Square, 1, Moscow 123098, Russia; (A.O.I.); (E.N.V.); (M.A.E.); (N.M.G.); (A.A.K.); (M.V.P.)
| | - Natalia M. Gunitseva
- Kurchatov Center for Genome Research, National Research Center “Kurchatov Institute”, Ac. Kurchatov Square, 1, Moscow 123098, Russia; (A.O.I.); (E.N.V.); (M.A.E.); (N.M.G.); (A.A.K.); (M.V.P.)
| | - Aleksei A. Korzhenkov
- Kurchatov Center for Genome Research, National Research Center “Kurchatov Institute”, Ac. Kurchatov Square, 1, Moscow 123098, Russia; (A.O.I.); (E.N.V.); (M.A.E.); (N.M.G.); (A.A.K.); (M.V.P.)
| | - Alexander G. Elcheninov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology RAS, 60-let Oktyzbrya Av., 7/2, Moscow 119071, Russia; (A.G.E.); (I.V.K.)
| | - Maxim V. Patrushev
- Kurchatov Center for Genome Research, National Research Center “Kurchatov Institute”, Ac. Kurchatov Square, 1, Moscow 123098, Russia; (A.O.I.); (E.N.V.); (M.A.E.); (N.M.G.); (A.A.K.); (M.V.P.)
| | - Ilya V. Kublanov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology RAS, 60-let Oktyzbrya Av., 7/2, Moscow 119071, Russia; (A.G.E.); (I.V.K.)
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Le Guellec S, Leroy E, Courtine D, Godfroy A, Roussel EG. H 2-dependent formate production by hyperthermophilic Thermococcales: an alternative to sulfur reduction for reducing-equivalents disposal. THE ISME JOURNAL 2021; 15:3423-3436. [PMID: 34088977 PMCID: PMC8630068 DOI: 10.1038/s41396-021-01020-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 05/13/2021] [Accepted: 05/20/2021] [Indexed: 02/07/2023]
Abstract
Removal of reducing equivalents is an essential catabolic process for all microorganisms to maintain their internal redox balance. The electron disposal by chemoorganotrophic Thermococcales generates H2 by proton reduction or H2S in presence of S0. Although in the absence of S0 growth of these (hyper)thermopiles was previously described to be H2-limited, it remains unclear how Thermococcales could be present in H2-rich S0-depleted habitats. Here, we report that 12 of the 47 strains tested, distributed among all three orders of Thermococcales, could grow without S0 at 0.8 mM dissolved H2 and that tolerance to H2 was always associated with formate production. Two conserved gene clusters coding for a formate hydrogenlyase (FHL) and a putative formate dehydrogenase-NAD(P)H-oxidoreductase were only present in H2-dependent formate producers, and were both systematically associated with a formate dehydrogenase and a formate transporter. As the reaction involved in this alternative pathway for disposal of reducing equivalents was close to thermodynamic equilibrium, it was strongly controlled by the substrates-products concentration ratio even in the presence of S0. Moreover, experimental data and thermodynamic modelling also demonstrated that H2-dependent CO2 reduction to formate could occur within a large temperature range in contrasted hydrothermal systems, suggesting it could also provide an adaptive advantage.
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Affiliation(s)
- Sébastien Le Guellec
- Ifremer, Univ Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Elodie Leroy
- Ifremer, Univ Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Damien Courtine
- Ifremer, Univ Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Anne Godfroy
- Ifremer, Univ Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Erwan G. Roussel
- Ifremer, Univ Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
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He X, Guo Z, Lu J, Zhang P. Carbon-based conductive materials accelerated methane production in anaerobic digestion of waste fat, oil and grease. BIORESOURCE TECHNOLOGY 2021; 329:124871. [PMID: 33631454 DOI: 10.1016/j.biortech.2021.124871] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 02/10/2021] [Accepted: 02/12/2021] [Indexed: 06/12/2023]
Abstract
Little is known about the effect of carbon-based conductive material (CM) addition on the anaerobic co-digestion of fat, oil and grease (FOG) and waste activated sludge (WAS). In this study, three types of carbon-based CMs (nano-graphite (NG), granular activated carbon (GAC), and carbon cloth (CC)) and nine dosages were evaluated for their influences on co-digestion performance. The best dosage was achieved at 0.2 g/L NG, 10 g/L GAC, and 1 cm × 5 cm CC with 13-22% incremental methane production, 25-55% increased VS removal and 28-32% enhanced COD conversion efficiency compared to the control. The highest total amount of bacteria/archaea was found in CC (1 cm × 5 cm), followed by GAC at 10 g/L and NG at 0.2 g/L, which were all higher than those of the control. Microbial community analysis revealed that direct interspecies electron transfer (DIET)-mediated syntrophic acetate oxidation (SAO) enabling faster acetate conversion might be responsible for the enhancement of methane production.
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Affiliation(s)
- Xia He
- College of Environmental Science and Engineering, Guilin University of Technology, Guangxi 541006, China
| | - Zhenyu Guo
- College of Environmental Science and Engineering, Guilin University of Technology, Guangxi 541006, China
| | - Jian Lu
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai, Shandong 264003, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China.
| | - Ping Zhang
- College of Environmental Science and Engineering, Guilin University of Technology, Guangxi 541006, China
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Zhong C, Wang L, Ning K. Pan-genome study of Thermococcales reveals extensive genetic diversity and genetic evidence of thermophilic adaption. Environ Microbiol 2020; 23:3599-3613. [PMID: 32939951 DOI: 10.1111/1462-2920.15234] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 09/12/2020] [Indexed: 01/02/2023]
Abstract
Thermococcales has a strong adaptability to extreme environments, which is of profound interest in explaining how complex life forms emerge on earth. However, their gene composition, thermal stability and evolution in hyperthermal environments are still little known. Here, we characterized the pan-genome architecture of 30 Thermococcales species to gain insight into their genetic properties, evolutionary patterns and specific metabolisms adapted to niches. We revealed an open pan-genome of Thermococcales comprising 6070 gene families that tend to increase with the availability of additional genomes. The genome contents of Thermococcales were flexible, with a series of genes experienced gene duplication, progressive divergence, or gene gain and loss events exhibiting distinct functional features. These archaea had concise types of heat shock proteins, such as HSP20, HSP60 and prefoldin, which were constrained by strong purifying selection that governed their conservative evolution. Furthermore, purifying selection forced genes involved in enzyme, motility, secretion system, defence system and chaperones to differ in functional constraints and their disparity in the rate of evolution may be related to adaptation to specific niche. These results deepened our understanding of genetic diversity and adaptation patterns of Thermococcales, and provided valuable research models for studying the metabolic traits of early life forms.
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Affiliation(s)
- Chaofang Zhong
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China.,Department of Computer Science, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China
| | - Lusheng Wang
- Department of Computer Science, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China
| | - Kang Ning
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
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Moulana A, Anderson RE, Fortunato CS, Huber JA. Selection Is a Significant Driver of Gene Gain and Loss in the Pangenome of the Bacterial Genus Sulfurovum in Geographically Distinct Deep-Sea Hydrothermal Vents. mSystems 2020; 5:e00673-19. [PMID: 32291353 PMCID: PMC7159903 DOI: 10.1128/msystems.00673-19] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 03/30/2020] [Indexed: 12/20/2022] Open
Abstract
Microbial genomes have highly variable gene content, and the evolutionary history of microbial populations is shaped by gene gain and loss mediated by horizontal gene transfer and selection. To evaluate the influence of selection on gene content variation in hydrothermal vent microbial populations, we examined 22 metagenome-assembled genomes (MAGs) (70 to 97% complete) from the ubiquitous vent Epsilonbacteraeota genus Sulfurovum that were recovered from two deep-sea hydrothermal vent regions, Axial Seamount in the northeastern Pacific Ocean (13 MAGs) and the Mid-Cayman Rise in the Caribbean Sea (9 MAGs). Genes involved in housekeeping functions were highly conserved across Sulfurovum lineages. However, genes involved in environment-specific functions, and in particular phosphate regulation, were found mostly in Sulfurovum genomes from the Mid-Cayman Rise in the low-phosphate Atlantic Ocean environment, suggesting that nutrient limitation is an important selective pressure for these bacteria. Furthermore, genes that were rare within the pangenome were more likely to undergo positive selection than genes that were highly conserved in the pangenome, and they also appeared to have experienced gene-specific sweeps. Our results suggest that selection is a significant driver of gene gain and loss for dominant microbial lineages in hydrothermal vents and highlight the importance of factors like nutrient limitation in driving microbial adaptation and evolution.IMPORTANCE Microbes can alter their gene content through the gain and loss of genes. However, there is some debate as to whether natural selection or neutral processes play a stronger role in molding the gene content of microbial genomes. In this study, we examined variation in gene content for the Epsilonbacteraeota genus Sulfurovum from deep-sea hydrothermal vents, which are dynamic habitats known for extensive horizontal gene transfer within microbial populations. Our results show that natural selection is a strong driver of Sulfurovum gene content and that nutrient limitation in particular has shaped the Sulfurovum genome, leading to differences in gene content between ocean basins. Our results also suggest that recently acquired genes undergo stronger selection than genes that were acquired in the more distant past. Overall, our results highlight the importance of natural selection in driving the evolution of microbial populations in these dynamic habitats.
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Affiliation(s)
- Alief Moulana
- Biology Department, Carleton College, Northfield, Minnesota, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Rika E Anderson
- Biology Department, Carleton College, Northfield, Minnesota, USA
| | | | - Julie A Huber
- Marine Chemistry & Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
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11
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Duchinski K, Moyer CL, Hager K, Fullerton H. Fine-Scale Biogeography and the Inference of Ecological Interactions Among Neutrophilic Iron-Oxidizing Zetaproteobacteria as Determined by a Rule-Based Microbial Network. Front Microbiol 2019; 10:2389. [PMID: 31708884 PMCID: PMC6823593 DOI: 10.3389/fmicb.2019.02389] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Accepted: 10/02/2019] [Indexed: 12/16/2022] Open
Abstract
Hydrothermal vents, such as those at Lō‘ihi Seamount and the Mariana Arc and back-arc, release iron required to support life from the Earth’s crust. In these ecosystems, bacteria and archaea can oxidize the released iron and therefore play an important role in the biogeochemical cycles of essential nutrients. These organisms often form microbial mats, and the primary producers in these communities can support diverse higher trophic levels. One such class of bacteria are the Zetaproteobacteria. This class of bacteria oxidize iron and commonly produce extracellular iron oxyhydroxide matrices that provide architecture to the microbial mats, so they are considered foundational members of the community and ecosystem engineers. Zetaproteobacteria are responsible for the majority of iron-oxidation in circumneutral, marine, low-oxygen environments. To study the composition of these communities, microbial mats were collected using a biomat sampler, which allows for fine-scale collection of microbial mats. DNA was then extracted and amplified for analysis of the SSU rRNA gene. After quality control and filtering, the SSU rRNA genes from Mariana Arc and Lō‘ihi Seamount microbial mat communities were compared pairwise to determine which site exhibits a greater microbial diversity and how much community overlap exists between the two sites. In-depth analysis was performed with the rule-based microbial network (RMN) algorithm, which identified a possible competitive relationship across oligotypes of a cosmopolitan Zetaproteobacteria operational taxonomic unit (OTU). This result demonstrated the ecological relevance of oligotypes, or fine-scale OTU variants. The oligotype distributions of the cosmopolitan ZetaOTUs varied greatly across the Pacific Ocean. The competitive relationship between dominant oligotypes at Lō‘ihi Seamount and the Mariana Arc and back-arc may be driving their differential distributions across the two regions and may result in species divergence within a cosmopolitan ZetaOTU. This implementation of the RMN algorithm can both predict directional relationships within a community and provide insight to the level at which evolution is occurring across ecosystems.
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Affiliation(s)
| | - Craig L Moyer
- Department of Biology, Western Washington University, Bellingham, WA, United States
| | - Kevin Hager
- Department of Biology, Western Washington University, Bellingham, WA, United States
| | - Heather Fullerton
- Department of Biology, College of Charleston, Charleston, SC, United States
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12
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A series of new E. coli-Thermococcus shuttle vectors compatible with previously existing vectors. Extremophiles 2018; 22:591-598. [PMID: 29497842 PMCID: PMC5988781 DOI: 10.1007/s00792-018-1019-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 02/21/2018] [Indexed: 11/04/2022]
Abstract
Hyperthermophilic microorganisms are an important asset in the toolkits of biotechnologists, biochemists and evolutionary biologists. The anaerobic archaeon, Thermococcus kodakarensis, has become one of the most useful hyperthermophilic model species, not least due to its natural competence and genetic tractability. Despite this, the range of genetic tools available for T. kodakarensis remains limited. Using sequencing and phylogenetic analyses, we determined that the rolling-circle replication origin of the cryptic mini-plasmid pTP2 from T. prieurii is suitable for plasmid replication in T. kodakarensis. Based on this replication origin, we present a novel series of replicative E. coli–T. kodakarensis shuttle vectors. These shuttle vectors have been constructed with three different selectable markers, allowing selection in a range of T. kodakarensis backgrounds. Moreover, these pTP2-derived plasmids are compatible with the single-existing E. coli–T. kodakarensis shuttle vector, pLC70. We show that both pTP2-derived and pLC70-derived plasmids replicate faithfully while cohabitating in T. kodakarensis cells. These plasmids open the door for new areas of research in plasmid segregation, DNA replication and gene expression.
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13
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Topçuoğlu BD, Meydan C, Orellana R, Holden JF. Formate hydrogenlyase and formate secretion ameliorate H
2
inhibition in the hyperthermophilic archaeon
Thermococcus paralvinellae. Environ Microbiol 2017; 20:949-957. [DOI: 10.1111/1462-2920.14022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 11/06/2017] [Accepted: 11/06/2017] [Indexed: 11/26/2022]
Affiliation(s)
- Begüm D. Topçuoğlu
- Department of MicrobiologyUniversity of MassachusettsAmherst MA 01003 USA
| | - Cem Meydan
- Institute for Computational Biomedicine, Weill Cornell Medical CollegeNew York NY 10021 USA
| | - Roberto Orellana
- Centro de Biotecnología, Universidad Técnica Federico Santa MaríaValparaíso Chile
| | - James F. Holden
- Department of MicrobiologyUniversity of MassachusettsAmherst MA 01003 USA
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14
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Mino S, Nakagawa S, Makita H, Toki T, Miyazaki J, Sievert SM, Polz MF, Inagaki F, Godfroy A, Kato S, Watanabe H, Nunoura T, Nakamura K, Imachi H, Watsuji TO, Kojima S, Takai K, Sawabe T. Endemicity of the cosmopolitan mesophilic chemolithoautotroph Sulfurimonas at deep-sea hydrothermal vents. ISME JOURNAL 2017; 11:909-919. [PMID: 28045457 DOI: 10.1038/ismej.2016.178] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 10/21/2016] [Accepted: 10/31/2016] [Indexed: 11/09/2022]
Abstract
Rich animal and microbial communities have been found at deep-sea hydrothermal vents. Although the biogeography of vent macrofauna is well understood, the corresponding knowledge about vent microbial biogeography is lacking. Here, we apply the multilocus sequence analysis (MLSA) to assess the genetic variation of 109 Sulfurimonas strains with ⩾98% 16S rRNA gene sequence similarity, which were isolated from four different geographical regions (Okinawa Trough (OT), Mariana Volcanic Arc and Trough (MVAT), Central Indian Ridge (CIR) and Mid-Atlantic Ridge (MAR)). Sequence typing based on 11 protein-coding genes revealed high genetic variation, including some allele types that are widespread within regions, resulting in 102 nucleotide sequence types (STs). This genetic variation was predominantly due to mutation rather than recombination. Phylogenetic analysis of the 11 concatenated genes showed a clear geographical isolation corresponding to the hydrothermal regions they originated from, suggesting limited dispersal. Genetic differentiation among Sulfurimonas populations was primarily influenced by geographical distance rather than gas composition of vent fluid or habitat, although in situ environmental conditions of each microhabitat could not be examined. Nevertheless, Sulfurimonas may possess a higher dispersal capability compared with deep-sea hydrothermal vent thermophiles. This is the first report on MLSA of deep-sea hydrothermal vent Epsilonproteobacteria, which is indicative of allopatric speciation.
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Affiliation(s)
- Sayaka Mino
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Satoshi Nakagawa
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan.,Department of Subsurface Geobiology Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Hiroko Makita
- Department of Subsurface Geobiology Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Tomohiro Toki
- Department of Chemistry, Biology, and Marine Science, Faculty of Science, University of the Ryukyus, Nishihara, Japan
| | - Junichi Miyazaki
- Department of Subsurface Geobiology Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Stefan M Sievert
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Martin F Polz
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Fumio Inagaki
- Kochi Institute for Core Sample Research, JAMSTEC, Nankoku, Japan.,Research and Development Center for Ocean Drilling Science (ODS), JAMSTEC, Yokohama, Japan
| | - Anne Godfroy
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Shingo Kato
- Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Japan
| | - Hiromi Watanabe
- Department of Marine Biodiversity Research, JAMSTEC, Yokosuka, Japan
| | - Takuro Nunoura
- Research and Development Center for Marine Biosciences, JAMSTEC, Yokosuka, Japan
| | - Koichi Nakamura
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Hiroyuki Imachi
- Department of Subsurface Geobiology Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Tomo-O Watsuji
- Department of Subsurface Geobiology Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Shigeaki Kojima
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Japan
| | - Ken Takai
- Department of Subsurface Geobiology Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Tomoo Sawabe
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
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15
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Meier DV, Bach W, Girguis PR, Gruber-Vodicka HR, Reeves EP, Richter M, Vidoudez C, Amann R, Meyerdierks A. HeterotrophicProteobacteriain the vicinity of diffuse hydrothermal venting. Environ Microbiol 2016; 18:4348-4368. [DOI: 10.1111/1462-2920.13304] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 03/13/2016] [Indexed: 11/27/2022]
Affiliation(s)
- Dimitri V. Meier
- Max Planck Institute for Marine Microbiology; Celsiusstrasse 1 D-28359 Bremen Germany
| | - Wolfgang Bach
- University of Bremen, MARUM - Center for Marine Environmental Sciences, Petrology of the Ocean Crust group; Leobener Str. D-28359 Bremen Germany
| | - Peter R. Girguis
- Harvard University, Department of Organismic & Evolutionary Biology; 16 Divinity Avenue Cambridge MA 02138-2020 USA
| | | | - Eoghan P. Reeves
- University of Bremen, MARUM - Center for Marine Environmental Sciences, Petrology of the Ocean Crust group; Leobener Str. D-28359 Bremen Germany
- University of Bergen, Department of Earth Science and Centre for Geobiology; Postboks 7803 N-5020 Bergen Norway
| | - Michael Richter
- Max Planck Institute for Marine Microbiology; Celsiusstrasse 1 D-28359 Bremen Germany
| | - Charles Vidoudez
- Harvard University, Department of Organismic & Evolutionary Biology; 16 Divinity Avenue Cambridge MA 02138-2020 USA
| | - Rudolf Amann
- Max Planck Institute for Marine Microbiology; Celsiusstrasse 1 D-28359 Bremen Germany
| | - Anke Meyerdierks
- Max Planck Institute for Marine Microbiology; Celsiusstrasse 1 D-28359 Bremen Germany
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