1
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Zhang Y, Sun X, Wang F, Su T, Yang S, Ai S, Bian D, Huo H. Study on the effect and regularity of plating parts cleaning wastewater by enhanced aerobic process with high-density bacterial flora. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 357:120653. [PMID: 38574704 DOI: 10.1016/j.jenvman.2024.120653] [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: 10/05/2023] [Revised: 02/16/2024] [Accepted: 03/10/2024] [Indexed: 04/06/2024]
Abstract
In this research, we established an enhanced aerobic biological method utilizing a high-density bacterial flora for the treatment of low-biochemical plating parts washing wastewater. The elucidation of pollutant removal mechanisms was achieved through a comprehensive analysis of changes in sludge characteristics and bacterial community structure. The results demonstrated that throughout the operational period, the organic load remained stable within the range of 0.01-0.02 kgCOD/kgMLSS·d, the BOD5/COD ratio increased from 0.004 mg/L to 0.33 mg/L, and the average removal rates for key pollutants, including COD, NH4+-N, and TN, reached 98.13%, 99.86%, and 98.09%. MLSS concentration remained at 7627 mg/L, indicating a high-density flora. Notably, Proteobacteria, Bacteroidota, and Acidobacteriota, which have the ability to degrade large organic molecules, had been found in the system. This study affirms the efficacy of the intensive aerobic biological method for treating low-biochemical plating washing wastewater while ensuring system stability.
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Affiliation(s)
- Ying Zhang
- School of Environment, Northeast Normal University, Changchun, Jilin, 130117, China; Key Laboratory of Urban Wastewater Treatment in Jilin Province, Changchun College of Engineering, Changchun, 130012, Jilin, China
| | - Xuejian Sun
- School of Environment, Northeast Normal University, Changchun, Jilin, 130117, China; Key Laboratory of Urban Wastewater Treatment in Jilin Province, Changchun College of Engineering, Changchun, 130012, Jilin, China
| | - Fan Wang
- Key Laboratory of Urban Wastewater Treatment in Jilin Province, Changchun College of Engineering, Changchun, 130012, Jilin, China
| | - Ting Su
- School of Environment, Northeast Normal University, Changchun, Jilin, 130117, China
| | - Siwen Yang
- Key Laboratory of Urban Wastewater Treatment in Jilin Province, Changchun College of Engineering, Changchun, 130012, Jilin, China
| | - Shengshu Ai
- Key Laboratory of Urban Wastewater Treatment in Jilin Province, Changchun College of Engineering, Changchun, 130012, Jilin, China
| | - Dejun Bian
- Key Laboratory of Urban Wastewater Treatment in Jilin Province, Changchun College of Engineering, Changchun, 130012, Jilin, China.
| | - Hongliang Huo
- School of Environment, Northeast Normal University, Changchun, Jilin, 130117, China.
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2
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Keithley AE, Gomez-Alvarez V, Williams D, Ryu H, Lytle DA. Depth profiles of biological aerated contactors: Characterizing microbial activity treating reduced contaminants. JOURNAL OF WATER PROCESS ENGINEERING 2023; 56:1-11. [PMID: 38357328 PMCID: PMC10866302 DOI: 10.1016/j.jwpe.2023.104360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
The biological treatment process consisting of an aerated contactor and filter is effective for groundwaters containing elevated ammonia and other reduced contaminants, including iron, manganese, arsenic, and methane. Depth profiles characterizing microbial activity across aerated contactors are lacking. A 1-year pilot study comparing gravel- and ceramic-packed contactors was conducted, and media depth profile samples were collected at the conclusion of the study. Media and water samples also were collected from pilot-scale aerated contactors at 4 other water systems. Water quality, media surface metals concentrations, and a suite of biofilm parameters were analyzed. Media surface metals concentrations were greatest at the influent end. ATP concentrations, extracellular polymeric substances, and extracellular enzyme activities tended to be similar across depth. Bacteria and functional genes involved in contaminant oxidation co-occurred and tended to decrease across depth, but were not correlated to the media metals concentration. Microbial community composition changed with depth, and the diversity either decreased or remained similar. The microbial activity profiles through aerated contactors differed from what is typically reported for groundwater biofilters, suggesting that the different reactor flow and dissolved oxygen profiles impacted the microbial community.
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Affiliation(s)
- Asher E. Keithley
- U.S. Environmental Protection Agency, ORD, CESER, WID, Cincinnati, OH 45268, United States
| | - Vicente Gomez-Alvarez
- U.S. Environmental Protection Agency, ORD, CESER, WID, Cincinnati, OH 45268, United States
| | - Daniel Williams
- U.S. Environmental Protection Agency, ORD, CESER, WID, Cincinnati, OH 45268, United States
| | - Hodon Ryu
- U.S. Environmental Protection Agency, ORD, CESER, WID, Cincinnati, OH 45268, United States
| | - Darren A. Lytle
- U.S. Environmental Protection Agency, ORD, CESER, WID, Cincinnati, OH 45268, United States
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3
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Veloso M, Waldisperg A, Arros P, Berríos-Pastén C, Acosta J, Colque H, Varas MA, Allende ML, Orellana LH, Marcoleta AE. Diversity, Taxonomic Novelty, and Encoded Functions of Salar de Ascotán Microbiota, as Revealed by Metagenome-Assembled Genomes. Microorganisms 2023; 11:2819. [PMID: 38004830 PMCID: PMC10673233 DOI: 10.3390/microorganisms11112819] [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: 09/21/2023] [Revised: 11/12/2023] [Accepted: 11/15/2023] [Indexed: 11/26/2023] Open
Abstract
Salar de Ascotán is a high-altitude arsenic-rich salt flat exposed to high ultraviolet radiation in the Atacama Desert, Chile. It hosts unique endemic flora and fauna and is an essential habitat for migratory birds, making it an important site for conservation and protection. However, there is limited information on the resident microbiota's diversity, genomic features, metabolic potential, and molecular mechanisms that enable it to thrive in this extreme environment. We used long- and short-read metagenomics to investigate the microbial communities in Ascotán's water, sediment, and soil. Bacteria predominated, mainly Pseudomonadota, Acidobacteriota, and Bacteroidota, with a remarkable diversity of archaea in the soil. Following hybrid assembly, we recovered high-quality bacterial (101) and archaeal (6) metagenome-assembled genomes (MAGs), including representatives of two putative novel families of Patescibacteria and Pseudomonadota and two novel orders from the archaeal classes Halobacteriota and Thermoplasmata. We found different metabolic capabilities across distinct lineages and a widespread presence of genes related to stress response, DNA repair, and resistance to arsenic and other metals. These results highlight the remarkable diversity and taxonomic novelty of the Salar de Ascotán microbiota and its rich functional repertoire, making it able to resist different harsh conditions. The highly complete MAGs described here could serve future studies and bioprospection efforts focused on salt flat extremophiles, and contribute to enriching databases with microbial genome data from underrepresented regions of our planet.
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Affiliation(s)
- Marcelo Veloso
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Faculty of Science, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile; (M.V.); (A.W.); (P.A.); (C.B.-P.); (J.A.); (H.C.); (M.A.V.)
| | - Angie Waldisperg
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Faculty of Science, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile; (M.V.); (A.W.); (P.A.); (C.B.-P.); (J.A.); (H.C.); (M.A.V.)
| | - Patricio Arros
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Faculty of Science, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile; (M.V.); (A.W.); (P.A.); (C.B.-P.); (J.A.); (H.C.); (M.A.V.)
| | - Camilo Berríos-Pastén
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Faculty of Science, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile; (M.V.); (A.W.); (P.A.); (C.B.-P.); (J.A.); (H.C.); (M.A.V.)
| | - Joaquín Acosta
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Faculty of Science, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile; (M.V.); (A.W.); (P.A.); (C.B.-P.); (J.A.); (H.C.); (M.A.V.)
| | - Hazajem Colque
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Faculty of Science, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile; (M.V.); (A.W.); (P.A.); (C.B.-P.); (J.A.); (H.C.); (M.A.V.)
| | - Macarena A. Varas
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Faculty of Science, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile; (M.V.); (A.W.); (P.A.); (C.B.-P.); (J.A.); (H.C.); (M.A.V.)
- Millenium Institute Center for Genome Regulation, Faculty of Science, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile;
| | - Miguel L. Allende
- Millenium Institute Center for Genome Regulation, Faculty of Science, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile;
| | - Luis H. Orellana
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359 Bremen, Germany;
| | - Andrés E. Marcoleta
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Faculty of Science, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile; (M.V.); (A.W.); (P.A.); (C.B.-P.); (J.A.); (H.C.); (M.A.V.)
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4
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Oren A, Göker M. Candidatus List. Lists of names of prokaryotic Candidatus phyla. Int J Syst Evol Microbiol 2023; 73. [PMID: 37159402 DOI: 10.1099/ijsem.0.005821] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, 38124 Braunschweig, Germany
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5
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Zhang X, Liu Z, Xu W, Pan J, Huang Y, Cai M, Luo Z, Li M. Genomic insights into versatile lifestyle of three new bacterial candidate phyla. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1547-1562. [PMID: 35060074 DOI: 10.1007/s11427-021-2037-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 12/01/2021] [Indexed: 05/28/2023]
Abstract
Metagenomic explorations of the Earth's biosphere enable the discovery of previously unknown bacterial lineages of phylogenetic and ecological significance. Here, we retrieved 11 metagenomic-assembled genomes (MAGs) affiliated to three new monophyletic bacterial lineages from the seawater of the Yap Trench. Phylogenomic analysis revealed that each lineage is a new bacterial candidate phylum, subsequently named Candidatus Qinglongiota, Candidatus Heilongiota, and Candidatus Canglongiota. Metabolic reconstruction of genomes from the three phyla suggested that they adopt a versatile lifestyle, with the potential to utilize various types of sugars, proteins, and/or short-chain fatty acids through anaerobic pathways. This was further confirmed by a global distribution map of the three phyla, indicating a preference for oxygen-limited or particle-attached niches, such as anoxic sedimentary environments. Of note, Candidatus Canglongiota genomes harbor genes for the complete Wood- Ljungdahl pathway and sulfate reduction that are similar to those identified in some sulfate-reducing bacteria. Evolutionary analysis indicated that gene gain and loss events, and horizontal gene transfer (HGT) play important roles in shaping the genomic and metabolic features of the three new phyla. This study presents the genomic insight into the ecology, metabolism, and evolution of three new phyla, which broadens the phylum-level diversity within the domain Bacteria.
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Affiliation(s)
- Xinxu Zhang
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
| | - Zongbao Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
| | - Wei Xu
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China
| | - Jie Pan
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
| | - Yuhan Huang
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
| | - Mingwei Cai
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
| | - Zhuhua Luo
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China
- School of Marine Sciences, Nanjing University of Information Science & Technology, Nanjing, 210044, China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China.
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China.
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6
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Dalcin Martins P, de Jong A, Lenstra WK, van Helmond NAGM, Slomp CP, Jetten MSM, Welte CU, Rasigraf O. Enrichment of novel Verrucomicrobia, Bacteroidetes, and Krumholzibacteria in an oxygen-limited methane- and iron-fed bioreactor inoculated with Bothnian Sea sediments. Microbiologyopen 2021; 10:e1175. [PMID: 33650794 PMCID: PMC7914226 DOI: 10.1002/mbo3.1175] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 01/29/2021] [Accepted: 01/30/2021] [Indexed: 12/16/2022] Open
Abstract
Microbial methane oxidation is a major biofilter preventing larger emissions of this powerful greenhouse gas from marine coastal areas into the atmosphere. In these zones, various electron acceptors such as sulfate, metal oxides, nitrate, or oxygen can be used. However, the key microbial players and mechanisms of methane oxidation are poorly understood. In this study, we inoculated a bioreactor with methane‐ and iron‐rich sediments from the Bothnian Sea to investigate microbial methane and iron cycling under low oxygen concentrations. Using metagenomics, we investigated shifts in microbial community composition after approximately 2.5 years of bioreactor operation. Marker genes for methane and iron cycling, as well as respiratory and fermentative metabolism, were identified and used to infer putative microbial metabolism. Metagenome‐assembled genomes representing novel Verrucomicrobia, Bacteroidetes, and Krumholzibacteria were recovered and revealed a potential for methane oxidation, organic matter degradation, and iron cycling, respectively. This work brings new hypotheses on the identity and metabolic versatility of microorganisms that may be members of such functional guilds in coastal marine sediments and highlights that microorganisms potentially composing the methane biofilter in these sediments may be more diverse than previously appreciated.
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Affiliation(s)
- Paula Dalcin Martins
- Department of Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands.,Soehngen Institute of Anaerobic Microbiology (SIAM), Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Anniek de Jong
- Department of Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands.,Netherlands Earth System Science Centre (NESSC), Utrecht, The Netherlands
| | - Wytze K Lenstra
- Netherlands Earth System Science Centre (NESSC), Utrecht, The Netherlands.,Department of Earth Sciences, Utrecht University, Utrecht, The Netherlands
| | - Niels A G M van Helmond
- Netherlands Earth System Science Centre (NESSC), Utrecht, The Netherlands.,Department of Earth Sciences, Utrecht University, Utrecht, The Netherlands
| | - Caroline P Slomp
- Netherlands Earth System Science Centre (NESSC), Utrecht, The Netherlands.,Department of Earth Sciences, Utrecht University, Utrecht, The Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands.,Soehngen Institute of Anaerobic Microbiology (SIAM), Radboud University Nijmegen, Nijmegen, The Netherlands.,Netherlands Earth System Science Centre (NESSC), Utrecht, The Netherlands
| | - Cornelia U Welte
- Department of Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands.,Soehngen Institute of Anaerobic Microbiology (SIAM), Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Olivia Rasigraf
- Department of Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands.,Netherlands Earth System Science Centre (NESSC), Utrecht, The Netherlands.,Geomicrobiology, German Research Centre for Geosciences (GFZ), Potsdam, Germany
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7
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Jaffe AL, Thomas AD, He C, Keren R, Valentin-Alvarado LE, Munk P, Bouma-Gregson K, Farag IF, Amano Y, Sachdeva R, West PT, Banfield JF. Patterns of Gene Content and Co-occurrence Constrain the Evolutionary Path toward Animal Association in Candidate Phyla Radiation Bacteria. mBio 2021; 12:e0052121. [PMID: 34253055 PMCID: PMC8406219 DOI: 10.1128/mbio.00521-21] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 06/14/2021] [Indexed: 12/20/2022] Open
Abstract
Candidate Phyla Radiation (CPR) bacteria are small, likely episymbiotic organisms found across Earth's ecosystems. Despite their prevalence, the distribution of CPR lineages across habitats and the genomic signatures of transitions among these habitats remain unclear. Here, we expand the genome inventory for Absconditabacteria (SR1), Gracilibacteria, and Saccharibacteria (TM7), CPR bacteria known to occur in both animal-associated and environmental microbiomes, and investigate variation in gene content with habitat of origin. By overlaying phylogeny with habitat information, we show that bacteria from these three lineages have undergone multiple transitions from environmental habitats into animal microbiomes. Based on co-occurrence analyses of hundreds of metagenomes, we extend the prior suggestion that certain Saccharibacteria have broad bacterial host ranges and constrain possible host relationships for Absconditabacteria and Gracilibacteria. Full-proteome analyses show that animal-associated Saccharibacteria have smaller gene repertoires than their environmental counterparts and are enriched in numerous protein families, including those likely functioning in amino acid metabolism, phage defense, and detoxification of peroxide. In contrast, some freshwater Saccharibacteria encode a putative rhodopsin. For protein families exhibiting the clearest patterns of differential habitat distribution, we compared protein and species phylogenies to estimate the incidence of lateral gene transfer and genomic loss occurring over the species tree. These analyses suggest that habitat transitions were likely not accompanied by large transfer or loss events but rather were associated with continuous proteome remodeling. Thus, we speculate that CPR habitat transitions were driven largely by availability of suitable host taxa and were reinforced by acquisition and loss of some capacities. IMPORTANCE Studying the genetic differences between related microorganisms from different environment types can indicate factors associated with their movement among habitats. This is particularly interesting for bacteria from the Candidate Phyla Radiation because their minimal metabolic capabilities require associations with microbial hosts. We found that shifts of Absconditabacteria, Gracilibacteria, and Saccharibacteria between environmental ecosystems and mammalian mouths/guts probably did not involve major episodes of gene gain and loss; rather, gradual genomic change likely followed habitat migration. The results inform our understanding of how little-known microorganisms establish in the human microbiota where they may ultimately impact health.
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Affiliation(s)
- Alexander L Jaffe
- Department of Plant and Microbial Biology, University of California, Berkeleygrid.47840.3f, Berkeley, California, USA
| | - Alex D Thomas
- Department of Environmental Science, Policy, and Management, University of California, Berkeleygrid.47840.3f, Berkeley, California, USA
- Rocky Mountain Biological Laboratory, Crested Butte, Colorado, USA
| | - Christine He
- Innovative Genomics Institute, University of California, Berkeleygrid.47840.3f, Berkeley, California, USA
| | - Ray Keren
- Department of Civil and Environmental Engineering, University of California, Berkeleygrid.47840.3f, Berkeley, California, USA
| | - Luis E Valentin-Alvarado
- Department of Plant and Microbial Biology, University of California, Berkeleygrid.47840.3f, Berkeley, California, USA
- Innovative Genomics Institute, University of California, Berkeleygrid.47840.3f, Berkeley, California, USA
| | - Patrick Munk
- National Food Institute, Technical University of Denmarkgrid.5170.3, Kongens Lyngby, Denmark
| | - Keith Bouma-Gregson
- Department of Earth and Planetary Science, University of California, Berkeleygrid.47840.3f, Berkeley, California, USA
- Department of Integrative Biology, University of California, Berkeleygrid.47840.3f, Berkeley, California, USA
| | - Ibrahim F Farag
- School of Marine Science and Policy, University of Delaware, Lewes, Delaware, USA
| | - Yuki Amano
- Nuclear Fuel Cycle Engineering Laboratories, Japan Atomic Energy Agencygrid.20256.33, Ibaraki, Japan
- Horonobe Underground Research Center, Japan Atomic Energy Agencygrid.20256.33, Hokkaido, Japan
| | - Rohan Sachdeva
- Innovative Genomics Institute, University of California, Berkeleygrid.47840.3f, Berkeley, California, USA
- Department of Earth and Planetary Science, University of California, Berkeleygrid.47840.3f, Berkeley, California, USA
| | - Patrick T West
- Department of Medicine (Hematology & Blood and Marrow Transplantation), Stanford University, Stanford, California, USA
| | - Jillian F Banfield
- Department of Environmental Science, Policy, and Management, University of California, Berkeleygrid.47840.3f, Berkeley, California, USA
- Innovative Genomics Institute, University of California, Berkeleygrid.47840.3f, Berkeley, California, USA
- Department of Earth and Planetary Science, University of California, Berkeleygrid.47840.3f, Berkeley, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
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8
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Five Metagenome-Assembled Genomes of the Rare Phylum CSSED10-310 from Zodletone Spring (Oklahoma, USA). Microbiol Resour Announc 2021; 10:e0041421. [PMID: 34197190 PMCID: PMC8248873 DOI: 10.1128/mra.00414-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
We analyzed five metagenome-assembled genomes (MAGs) belonging to the rare, yet-uncultured phylum CSSED10-310 recovered from the anoxic sediments of Zodletone Spring (Oklahoma). Our analysis suggests their potential involvement in sulfite respiration.
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9
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Rezaei Somee M, Dastgheib SMM, Shavandi M, Ghanbari Maman L, Kavousi K, Amoozegar MA, Mehrshad M. Distinct microbial community along the chronic oil pollution continuum of the Persian Gulf converge with oil spill accidents. Sci Rep 2021; 11:11316. [PMID: 34059729 PMCID: PMC8166890 DOI: 10.1038/s41598-021-90735-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 05/17/2021] [Indexed: 02/04/2023] Open
Abstract
The Persian Gulf, hosting ca. 48% of the world's oil reserves, has been chronically exposed to natural oil seepage. Oil spill studies show a shift in microbial community composition in response to oil pollution; however, the influence of chronic oil exposure on the microbial community remains unknown. We performed genome-resolved comparative analyses of the water and sediment samples along Persian Gulf's pollution continuum (Strait of Hormuz, Asalouyeh, and Khark Island). Continuous exposure to trace amounts of pollution primed the intrinsic and rare marine oil-degrading microbes such as Oceanospirillales, Flavobacteriales, Alteromonadales, and Rhodobacterales to bloom in response to oil pollution in Asalouyeh and Khark samples. Comparative analysis of the Persian Gulf samples with 106 oil-polluted marine samples reveals that the hydrocarbon type, exposure time, and sediment depth are the main determinants of microbial response to pollution. High aliphatic content of the pollution enriched for Oceanospirillales, Alteromonadales, and Pseudomonadales whereas, Alteromonadales, Cellvibrionales, Flavobacteriales, and Rhodobacterales dominate polyaromatic polluted samples. In chronic exposure and oil spill events, the community composition converges towards higher dominance of oil-degrading constituents while promoting the division of labor for successful bioremediation.
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Affiliation(s)
- Maryam Rezaei Somee
- grid.46072.370000 0004 0612 7950Extremophiles Laboratory, Department of Microbiology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Seyed Mohammad Mehdi Dastgheib
- grid.419140.90000 0001 0690 0331Biotechnology and Microbiology Research Group, Research Institute of Petroleum Industry, Tehran, Iran
| | - Mahmoud Shavandi
- grid.419140.90000 0001 0690 0331Biotechnology and Microbiology Research Group, Research Institute of Petroleum Industry, Tehran, Iran
| | - Leila Ghanbari Maman
- grid.46072.370000 0004 0612 7950Laboratory of Complex Biological Systems and Bioinformatics (CBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Kaveh Kavousi
- grid.46072.370000 0004 0612 7950Laboratory of Complex Biological Systems and Bioinformatics (CBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Mohammad Ali Amoozegar
- grid.46072.370000 0004 0612 7950Extremophiles Laboratory, Department of Microbiology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Maliheh Mehrshad
- grid.8993.b0000 0004 1936 9457Department of Ecology and Genetics, Limnology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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10
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Oren A, Garrity GM. Candidatus List No. 2. Lists of names of prokaryotic Candidatus taxa. Int J Syst Evol Microbiol 2021; 71. [PMID: 33881984 DOI: 10.1099/ijsem.0.004671] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George M Garrity
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
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11
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Liu X, Wang Y, Gu JD. Ecological distribution and potential roles of Woesearchaeota in anaerobic biogeochemical cycling unveiled by genomic analysis. Comput Struct Biotechnol J 2021; 19:794-800. [PMID: 33552450 PMCID: PMC7844129 DOI: 10.1016/j.csbj.2021.01.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 01/06/2021] [Accepted: 01/08/2021] [Indexed: 12/21/2022] Open
Abstract
Woesearchaeota as a newly established member of the superphylum DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota and Nanohaloarchaea) are surprisingly abundant and diverse in a wide variety of environments, including deep oil reservoir, sulfuric springs and anoxic aquifers, indicating a high diversity of their roles in global biogeochemical cycles. However, ecological functions of them remain elusive. To fill up this gap, we analyzed and compared the global distribution patterns of Woesearchaeota using the genomes available publicly. As a result, both ecological distribution patterns and metabolic predictions support a key role of woesearchaeotal lineages in cycling of carbon, nitrogen, and sulfur. Multivariate regression analysis reveals that Woesearchaeota might function in consortium with methanogens in the cycling of carbon in anaerobic environments, particularly in soils or sediments. Moreover, comparative genomic analysis and ecological distribution suggest the potential roles of Woesearchaeota in the processes of denitrification, nitrogen fixation, and dissimilatory nitrite reduction, especially in the wastewater treatment systems; and also uncovered the potential capability of sulfate reduction, sulfide oxidation and thiosulfate oxidation in sulfuric or sulfidic-rich environments. Our findings add more information into the ecological roles of archaea in the anoxic environment.
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Affiliation(s)
- Xiaobo Liu
- Environmental Engineering Program, Guangdong Technion-Israel Institute of Technology (GTIIT), 241 Daxue Road, Shantou 515063, Guangdong, China
| | - Yali Wang
- Conservation Center, Guangdong Museum, 2 Zhujiang East Road, Tianhe District, Guangzhou 510623, Guangdong, China
| | - Ji-Dong Gu
- Environmental Engineering Program, Guangdong Technion-Israel Institute of Technology (GTIIT), 241 Daxue Road, Shantou 515063, Guangdong, China
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12
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Méheust R, Castelle CJ, Matheus Carnevali PB, Farag IF, He C, Chen LX, Amano Y, Hug LA, Banfield JF. Groundwater Elusimicrobia are metabolically diverse compared to gut microbiome Elusimicrobia and some have a novel nitrogenase paralog. ISME JOURNAL 2020; 14:2907-2922. [PMID: 32681159 DOI: 10.1038/s41396-020-0716-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 06/15/2020] [Accepted: 07/08/2020] [Indexed: 01/09/2023]
Abstract
Currently described members of Elusimicrobia, a relatively recently defined phylum, are animal-associated and rely on fermentation. However, free-living Elusimicrobia have been detected in sediments, soils and groundwater, raising questions regarding their metabolic capacities and evolutionary relationship to animal-associated species. Here, we analyzed 94 draft-quality, non-redundant genomes, including 30 newly reconstructed genomes, from diverse animal-associated and natural environments. Genomes group into 12 clades, 10 of which previously lacked reference genomes. Groundwater-associated Elusimicrobia are predicted to be capable of heterotrophic or autotrophic lifestyles, reliant on oxygen or nitrate/nitrite-dependent respiration, or a variety of organic compounds and Rhodobacter nitrogen fixation (Rnf) complex-dependent acetogenesis with hydrogen and carbon dioxide as the substrates. Genomes from two clades of groundwater-associated Elusimicrobia often encode a new group of nitrogenase paralogs that co-occur with an extensive suite of radical S-Adenosylmethionine (SAM) proteins. We identified similar genomic loci in genomes of bacteria from the Gracilibacteria phylum and the Myxococcales order and predict that the gene clusters reduce a tetrapyrrole, possibly to form a novel cofactor. The animal-associated Elusimicrobia clades nest phylogenetically within two free-living-associated clades. Thus, we propose an evolutionary trajectory in which some Elusimicrobia adapted to animal-associated lifestyles from free-living species via genome reduction.
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Affiliation(s)
- Raphaël Méheust
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, 94720, USA.,Innovative Genomics Institute, Berkeley, CA, 94720, USA
| | - Cindy J Castelle
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, 94720, USA.,Innovative Genomics Institute, Berkeley, CA, 94720, USA
| | - Paula B Matheus Carnevali
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, 94720, USA.,Innovative Genomics Institute, Berkeley, CA, 94720, USA
| | - Ibrahim F Farag
- School of Marine Science and Policy, University of Delaware, Lewes, DE, 19968, USA
| | - Christine He
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Lin-Xing Chen
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, 94720, USA.,Innovative Genomics Institute, Berkeley, CA, 94720, USA
| | - Yuki Amano
- Nuclear Fuel Cycle Engineering Laboratories, Japan Atomic Energy Agency, Tokai-mura, Ibaraki, Japan
| | - Laura A Hug
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, 94720, USA. .,Innovative Genomics Institute, Berkeley, CA, 94720, USA.
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13
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Youssef NH, Farag IF, Rudy S, Mulliner A, Walker K, Caldwell F, Miller M, Hoff W, Elshahed M. The Wood-Ljungdahl pathway as a key component of metabolic versatility in candidate phylum Bipolaricaulota (Acetothermia, OP1). ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:538-547. [PMID: 30888727 DOI: 10.1111/1758-2229.12753] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 03/15/2019] [Accepted: 03/18/2019] [Indexed: 06/09/2023]
Abstract
The Wood-Ljungdahl (WL) pathway is an important component of the metabolic machinery in multiple anaerobic prokaryotes, including numerous yet-uncultured bacterial phyla. The pathway can operate in the reductive and oxidative directions, enabling a wide range of metabolic processes. Here, we present a detailed analysis of 14 newly acquired, previously analysed, and publicly available genomic assemblies belonging to the candidate phylum Bipolaricaulota (candidate division OP1, and candidatus Acetothermia), where the occurrence of WL pathway appears to be universal. In silico analysis of predicted metabolic capabilities indicates that the pathway enables homoacetogenic fermentation of sugars and amino acids in all three Bipolaricaulota orders (RBG-16-55-9, UBA7950 and Bipolaricaulales). In addition, members of RBG-16-55-9 appear to possess the additional capacity for syntrophic acetate oxidation using the WL pathway; as well as for respiratory growth using oxygen or nitrate. Anabolically, all UBA7950, and the majority of the Bipolaricaulales genomes possess the capacity for autotrophic growth using the WL pathway. Our results highlight the WL-enabled metabolic versatility in the Bipolaricaulota, emphasize the need for examining the WL pathway in context of the overall metabolic circuitry in uncultured taxa, and demonstrate the value of comparative genomic analysis for providing a detailed overview of metabolic potential in a target microbial lineage and its potential functional niche in an ecosystem.
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Affiliation(s)
- Noha H Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74074, USA
| | - Ibrahim F Farag
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74074, USA
| | - Sydney Rudy
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74074, USA
| | - Ace Mulliner
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74074, USA
| | - Kara Walker
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74074, USA
| | - Ford Caldwell
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74074, USA
| | - Malik Miller
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74074, USA
| | - Wouter Hoff
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74074, USA
| | - Mostafa Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74074, USA
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14
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Genomic Characterization of Candidate Division LCP-89 Reveals an Atypical Cell Wall Structure, Microcompartment Production, and Dual Respiratory and Fermentative Capacities. Appl Environ Microbiol 2019; 85:AEM.00110-19. [PMID: 30902854 DOI: 10.1128/aem.00110-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 03/08/2019] [Indexed: 02/06/2023] Open
Abstract
Recent experimental and bioinformatic advances enable the recovery of genomes belonging to yet-uncultured microbial lineages directly from environmental samples. Here, we report on the recovery and characterization of single amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) representing candidate phylum LCP-89, previously defined based on 16S rRNA gene sequences. Analysis of LCP-89 genomes recovered from Zodletone Spring, an anoxic spring in Oklahoma, predicts slow-growing, rod-shaped organisms. LCP-89 genomes contain genes for cell wall lipopolysaccharide (LPS) production but lack the entire machinery for peptidoglycan biosynthesis, suggesting an atypical cell wall structure. The genomes, however, encode S-layer homology domain-containing proteins, as well as machinery for the biosynthesis of CMP-legionaminate, inferring the possession of an S-layer glycoprotein. A nearly complete chemotaxis machinery coupled to the absence of flagellar synthesis and assembly genes argues for the utilization of alternative types of motility. A strict anaerobic lifestyle is predicted, with dual respiratory (nitrite ammonification) and fermentative capacities. Predicted substrates include a wide range of sugars and sugar alcohols and a few amino acids. The capability of rhamnose metabolism is confirmed by the identification of bacterial microcompartment genes to sequester the toxic intermediates generated. Comparative genomic analysis identified differences in oxygen sensitivities, respiratory capabilities, substrate utilization preferences, and fermentation end products between LCP-89 genomes and those belonging to its four sister phyla (Calditrichota, SM32-31, AABM5-125-24, and KSB1) within the broader FCB (Fibrobacteres-Chlorobi-Bacteroidetes) superphylum. Our results provide a detailed characterization of members of the candidate division LCP-89 and highlight the importance of reconciling 16S rRNA-based and genome-based phylogenies.IMPORTANCE Our understanding of the metabolic capacities, physiological preferences, and ecological roles of yet-uncultured microbial phyla is expanding rapidly. Two distinct approaches are currently being utilized for characterizing microbial communities in nature: amplicon-based 16S rRNA gene surveys for community characterization and metagenomics/single-cell genomics for detailed metabolic reconstruction. The occurrence of multiple yet-uncultured bacterial phyla has been documented using 16S rRNA surveys, and obtaining genome representatives of these yet-uncultured lineages is critical to our understanding of the role of yet-uncultured organisms in nature. This study provides a genomics-based analysis highlighting the structural features and metabolic capacities of a yet-uncultured bacterial phylum (LCP-89) previously identified in 16S rRNA surveys for which no prior genomes have been described. Our analysis identifies several interesting structural features for members of this phylum, e.g., lack of peptidoglycan biosynthetic machinery and the ability to form bacterial microcompartments. Predicted metabolic capabilities include degradation of a wide range of sugars, anaerobic respiratory capacity, and fermentative capacities. In addition to the detailed structural and metabolic analysis provided for candidate division LCP-89, this effort represents an additional step toward a unified scheme for microbial taxonomy by reconciling 16S rRNA gene-based and genomics-based taxonomic outlines.
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15
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Konstantinidis KT, Rossello-Mora R, Amann R. Moving the cataloguing of the "uncultivated majority" forward. Syst Appl Microbiol 2018; 42:3-4. [PMID: 30558959 DOI: 10.1016/j.syapm.2018.12.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Konstantinos T Konstantinidis
- School of Civil and Environmental Engineering and School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
| | - Ramon Rossello-Mora
- Marine Microbiology Group, Department of Animal and Microbial Diversity, Institut Mediterrani d'Estudis Avançats (IMEDEA; CSIC-UIB), Esporles, Spain
| | - Rudolf Amann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
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