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Aplakidou E, Vergoulidis N, Chasapi M, Venetsianou NK, Kokoli M, Panagiotopoulou E, Iliopoulos I, Karatzas E, Pafilis E, Georgakopoulos-Soares I, Kyrpides NC, Pavlopoulos GA, Baltoumas FA. Visualizing metagenomic and metatranscriptomic data: A comprehensive review. Comput Struct Biotechnol J 2024; 23:2011-2033. [PMID: 38765606 PMCID: PMC11101950 DOI: 10.1016/j.csbj.2024.04.060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 04/25/2024] [Accepted: 04/25/2024] [Indexed: 05/22/2024] Open
Abstract
The fields of Metagenomics and Metatranscriptomics involve the examination of complete nucleotide sequences, gene identification, and analysis of potential biological functions within diverse organisms or environmental samples. Despite the vast opportunities for discovery in metagenomics, the sheer volume and complexity of sequence data often present challenges in processing analysis and visualization. This article highlights the critical role of advanced visualization tools in enabling effective exploration, querying, and analysis of these complex datasets. Emphasizing the importance of accessibility, the article categorizes various visualizers based on their intended applications and highlights their utility in empowering bioinformaticians and non-bioinformaticians to interpret and derive insights from meta-omics data effectively.
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Affiliation(s)
- Eleni Aplakidou
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
- Department of Informatics and Telecommunications, Data Science and Information Technologies program, University of Athens, 15784 Athens, Greece
| | - Nikolaos Vergoulidis
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
| | - Maria Chasapi
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
- Department of Informatics and Telecommunications, Data Science and Information Technologies program, University of Athens, 15784 Athens, Greece
| | - Nefeli K. Venetsianou
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
| | - Maria Kokoli
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
| | - Eleni Panagiotopoulou
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
- Department of Informatics and Telecommunications, Data Science and Information Technologies program, University of Athens, 15784 Athens, Greece
| | - Ioannis Iliopoulos
- Department of Basic Sciences, School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - Evangelos Karatzas
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Evangelos Pafilis
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Greece
| | - Ilias Georgakopoulos-Soares
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Nikos C. Kyrpides
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Georgios A. Pavlopoulos
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
- Center of New Biotechnologies & Precision Medicine, Department of Medicine, School of Health Sciences, National and Kapodistrian University of Athens, Greece
- Hellenic Army Academy, 16673 Vari, Greece
| | - Fotis A. Baltoumas
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
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Xiao JZ, Nesbø CL, Molenda O, Toth CRA, Edwards EA. Metagenomic and genomic sequences from a nitrate-reducing benzene-degrading enrichment culture. Microbiol Resour Announc 2024; 13:e0029424. [PMID: 39248562 PMCID: PMC11465867 DOI: 10.1128/mra.00294-24] [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: 03/24/2024] [Accepted: 07/27/2024] [Indexed: 09/10/2024] Open
Abstract
Metagenome-assembled genomes (MAGs) were recovered from metagenomic assemblies from a nitrate-reducing benzene-degrading enrichment culture. Ten MAGs of high quality or functional interest to benzene degradation are reported, seven of which are single contig genomes.
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Affiliation(s)
- Johnny Z. Xiao
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Camilla L. Nesbø
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Olivia Molenda
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Courtney R. A. Toth
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Elizabeth A. Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
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Dyksma S, Pester M. Growth of sulfate-reducing Desulfobacterota and Bacillota at periodic oxygen stress of 50% air-O 2 saturation. MICROBIOME 2024; 12:191. [PMID: 39367500 PMCID: PMC11451228 DOI: 10.1186/s40168-024-01909-7] [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: 02/13/2024] [Accepted: 08/16/2024] [Indexed: 10/06/2024]
Abstract
BACKGROUND Sulfate-reducing bacteria (SRB) are frequently encountered in anoxic-to-oxic transition zones, where they are transiently exposed to microoxic or even oxic conditions on a regular basis. This can be marine tidal sediments, microbial mats, and freshwater wetlands like peatlands. In the latter, a cryptic but highly active sulfur cycle supports their anaerobic activity. Here, we aimed for a better understanding of how SRB responds to periodically fluctuating redox regimes. RESULTS To mimic these fluctuating redox conditions, a bioreactor was inoculated with peat soil supporting cryptic sulfur cycling and consecutively exposed to oxic (one week) and anoxic (four weeks) phases over a period of > 200 days. SRB affiliated to the genus Desulfosporosinus (Bacillota) and the families Syntrophobacteraceae, Desulfomonilaceae, Desulfocapsaceae, and Desulfovibrionaceae (Desulfobacterota) successively established growing populations (up to 2.9% relative abundance) despite weekly periods of oxygen exposures at 133 µM (50% air saturation). Adaptation mechanisms were analyzed by genome-centric metatranscriptomics. Despite a global drop in gene expression during oxic phases, the perpetuation of gene expression for energy metabolism was observed for all SRBs. The transcriptional response pattern for oxygen resistance was differentiated across individual SRBs, indicating different adaptation strategies. Most SRB transcribed differing sets of genes for oxygen consumption, reactive oxygen species detoxification, and repair of oxidized proteins as a response to the periodical redox switch from anoxic to oxic conditions. Noteworthy, a Desulfosporosinus, a Desulfovibrionaceaea, and a Desulfocapsaceaea representative maintained high transcript levels of genes encoding oxygen defense proteins even under anoxic conditions, while representing dominant SRB populations after half a year of bioreactor operation. CONCLUSIONS In situ-relevant peatland SRB established large populations despite periodic one-week oxygen levels that are one order of magnitude higher than known to be tolerated by pure cultures of SRB. The observed decrease in gene expression regulation may be key to withstand periodically occurring changes in redox regimes in these otherwise strictly anaerobic microorganisms. Our study provides important insights into the stress response of SRB that drives sulfur cycling at oxic-anoxic interphases. Video Abstract.
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Affiliation(s)
- Stefan Dyksma
- Department of Microorganisms, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
| | - Michael Pester
- Department of Microorganisms, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
- Technical University of Braunschweig, Institute of Microbiology, Braunschweig, Germany.
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Phillips E, Picott K, Kümmel S, Bulka O, Edwards E, Wang P, Gehre M, Nijenhuis I, Lollar BS. Vitamin B 12 as a source of variability in isotope effects for chloroform biotransformation by Dehalobacter. Microbiologyopen 2024; 13:e1433. [PMID: 39190020 PMCID: PMC11348799 DOI: 10.1002/mbo3.1433] [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: 05/03/2024] [Revised: 07/03/2024] [Accepted: 08/01/2024] [Indexed: 08/28/2024] Open
Abstract
Carbon and chlorine isotope effects for biotransformation of chloroform by different microbes show significant variability. Reductive dehalogenases (RDase) enzymes contain different cobamides, affecting substrate preferences, growth yields, and dechlorination rates and extent. We investigate the role of cobamide type on carbon and chlorine isotopic signals observed during reductive dechlorination of chloroform by the RDase CfrA. Microcosm experiments with two subcultures of a Dehalobacter-containing culture expressing CfrA-one with exogenous cobamide (Vitamin B12, B12+) and one without (to drive native cobamide production)-resulted in a markedly smaller carbon isotope enrichment factor (εC, bulk) for B12- (-22.1 ± 1.9‰) compared to B12+ (-26.8 ± 3.2‰). Both cultures exhibited significant chlorine isotope fractionation, and although a lower εCl, bulk was observed for B12- (-6.17 ± 0.72‰) compared to B12+ (-6.86 ± 0.77‰) cultures, these values are not statistically different. Importantly, dual-isotope plots produced identical slopes of ΛCl/C (ΛCl/C, B12+ = 3.41 ± 0.15, ΛCl/C, B12- = 3.39 ± 0.15), suggesting the same reaction mechanism is involved in both experiments, independent of the lower cobamide bases. A nonisotopically fractionating masking effect may explain the smaller fractionations observed for the B12- containing culture.
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Affiliation(s)
- Elizabeth Phillips
- Department of Earth SciencesUniversity of TorontoTorontoOntarioCanada
- Present address:
Inorganic Chemistry LaboratoryUniversity of OxfordOxfordUK
| | - Katherine Picott
- Department of Chemical Engineering and Applied ChemistryUniversity of TorontoTorontoOntarioCanada
| | - Steffen Kümmel
- Department of Technical BiogeochemistryHelmholtz Centre for Environmental Research—UFZLeipzigGermany
| | - Olivia Bulka
- Department of Chemical Engineering and Applied ChemistryUniversity of TorontoTorontoOntarioCanada
| | - Elizabeth Edwards
- Department of Chemical Engineering and Applied ChemistryUniversity of TorontoTorontoOntarioCanada
| | - Po‐Hsiang Wang
- Department of Chemical Engineering and Applied ChemistryUniversity of TorontoTorontoOntarioCanada
- Present address:
Graduate Institute of Environmental EngineeringNational Central UniversityTaoyuan CityTaiwan
| | - Matthias Gehre
- Department of Technical BiogeochemistryHelmholtz Centre for Environmental Research—UFZLeipzigGermany
| | - Ivonne Nijenhuis
- Department of Technical BiogeochemistryHelmholtz Centre for Environmental Research—UFZLeipzigGermany
| | - Barbara S. Lollar
- Department of Earth SciencesUniversity of TorontoTorontoOntarioCanada
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Yi L, Solanki R, Strous M. In search of the pH limit of growth in halo-alkaliphilic cyanobacteria. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13323. [PMID: 39128846 PMCID: PMC11317126 DOI: 10.1111/1758-2229.13323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 07/12/2024] [Indexed: 08/13/2024]
Abstract
Cyanobacteria have many biotechnological applications. Increasing their cultivation pH can assist in capturing carbon dioxide and avoiding invasion by other organisms. However, alkaline media may have adverse effects on cyanobacteria, such as reducing the Carbon-Concentrating Mechanism's efficiency. Here, we cultivated two halo-alkaliphilic cyanobacteria consortia in chemostats at pH 10.2-11.4. One consortium was dominated by Ca. Sodalinema alkaliphilum, the other by a species of Nodosilinea. These two cyanobacteria dominate natural communities in Canadian and Asian alkaline soda lakes. We show that increasing the pH decreased biomass yield. This decrease was caused, in part, by a dramatic increase in carbon transfer to heterotrophs. At pH 11.4, cyanobacterial growth became limited by bicarbonate uptake, which was mainly ATP dependent. In parallel, the higher the pH, the more sensitive cyanobacteria became to light, resulting in photoinhibition and upregulation of DNA repair systems.
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Affiliation(s)
- Lianchun Yi
- Department of Earth, Energy, and EnvironmentUniversity of CalgaryCalgaryAlbertaCanada
| | - Ruchita Solanki
- Department of Earth, Energy, and EnvironmentUniversity of CalgaryCalgaryAlbertaCanada
| | - Marc Strous
- Department of Earth, Energy, and EnvironmentUniversity of CalgaryCalgaryAlbertaCanada
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6
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Bulka O, Picott K, Mahadevan R, Edwards EA. From mec cassette to rdhA: a key Dehalobacter genomic neighborhood in a chloroform and dichloromethane-transforming microbial consortium. Appl Environ Microbiol 2024; 90:e0073224. [PMID: 38819127 PMCID: PMC11218628 DOI: 10.1128/aem.00732-24] [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: 04/16/2024] [Accepted: 05/20/2024] [Indexed: 06/01/2024] Open
Abstract
Chloroform (CF) and dichloromethane (DCM) are groundwater contaminants of concern due to their high toxicity and inhibition of important biogeochemical processes such as methanogenesis. Anaerobic biotransformation of CF and DCM has been well documented but typically independently of one another. CF is the electron acceptor for certain organohalide-respiring bacteria that use reductive dehalogenases (RDases) to dechlorinate CF to DCM. In contrast, known DCM degraders use DCM as their electron donor, which is oxidized using a series of methyltransferases and associated proteins encoded by the mec cassette to facilitate the entry of DCM to the Wood-Ljungdahl pathway. The SC05 culture is an enrichment culture sold commercially for bioaugmentation, which transforms CF via DCM to CO2. This culture has the unique ability to dechlorinate CF to DCM using electron equivalents provided by the oxidation of DCM to CO2. Here, we use metagenomic and metaproteomic analyses to identify the functional genes involved in each of these transformations. Though 91 metagenome-assembled genomes were assembled, the genes for an RDase-named acdA-and a complete mec cassette were found to be encoded on a single contig belonging to Dehalobacter. AcdA and critical Mec proteins were also highly expressed by the culture. Heterologously expressed AcdA dechlorinated CF and other chloroalkanes but had 100-fold lower activity on DCM. Overall, the high expression of Mec proteins and the activity of AcdA suggest a Dehalobacter capable of dechlorination of CF to DCM and subsequent mineralization of DCM using the mec cassette. IMPORTANCE Chloroform (CF) and dichloromethane (DCM) are regulated groundwater contaminants. A cost-effective approach to remove these pollutants from contaminated groundwater is to employ microbes that transform CF and DCM as part of their metabolism, thus depleting the contamination as the microbes continue to grow. In this work, we investigate bioaugmentation culture SC05, a mixed microbial consortium that effectively and simultaneously degrades both CF and DCM coupled to the growth of Dehalobacter. We identified the functional genes responsible for the transformation of CF and DCM in SC05. These genetic biomarkers provide a means to monitor the remediation process in the field.
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Affiliation(s)
- Olivia Bulka
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Katherine Picott
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Elizabeth A. Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
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Lirette AO, Chen YJ, Freyria NJ, Góngora E, Greer CW, Whyte LG. Characterization of hydrocarbon degraders from Northwest Passage beach sediments and assessment of their ability for bioremediation. Can J Microbiol 2024; 70:163-177. [PMID: 38350082 DOI: 10.1139/cjm-2023-0093] [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: 02/15/2024]
Abstract
Global warming-induced sea ice loss in the Canadian Northwest Passage (NWP) will result in more shipping traffic, increasing the risk of oil spills. Microorganisms inhabiting NWP beach sediments may degrade hydrocarbons, offering a potential bioremediation strategy. In this study, the characterization and genomic analyses of 22 hydrocarbon-biodegradative bacterial isolates revealed that they contained a diverse range of key alkane and aromatic hydrocarbon-degradative genes, as well as cold and salt tolerance genes indicating they are highly adapted to the extreme Arctic environment. Some isolates successfully degraded Ultra Low Sulfur Fuel Oil (ULSFO) at temperatures as low as -5 °C and high salinities (3%-10%). Three isolates were grown in liquid medium containing ULSFO as sole carbon source over 3 months and variation of hydrocarbon concentration was measured at three time points to determine their rate of hydrocarbon biodegradation. Our results demonstrate that two isolates (Rhodococcus sp. R1B_2T and Pseudarthrobacter sp. R2D_1T) possess complete degradation pathways and can grow on alkane and aromatic components of ULSFO under Arctic conditions. Overall, these results demonstrate that diverse hydrocarbon-degrading microorganisms exist in the NWP beach sediments, offering a potential bioremediation strategy in the events of a marine fuel spill reaching the shores of the NWP.
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Affiliation(s)
- Antoine-O Lirette
- Department of Natural Resource Sciences, McGill University, QC, Canada
| | - Ya-Jou Chen
- Department of Natural Resource Sciences, McGill University, QC, Canada
| | | | - Esteban Góngora
- Department of Natural Resource Sciences, McGill University, QC, Canada
| | - Charles W Greer
- Department of Natural Resource Sciences, McGill University, QC, Canada
| | - Lyle G Whyte
- Department of Natural Resource Sciences, McGill University, QC, Canada
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Yao X, Wang J, He M, Liu Z, Zhao Y, Li Y, Chi T, Zhu L, Zheng P, Jetten MSM, Hu B. Methane-dependent complete denitrification by a single Methylomirabilis bacterium. Nat Microbiol 2024; 9:464-476. [PMID: 38228857 DOI: 10.1038/s41564-023-01578-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 12/08/2023] [Indexed: 01/18/2024]
Abstract
Methane-dependent nitrate and nitrite removal in anoxic environments is thought to rely on syntrophy between ANME-2d archaea and bacteria in the genus 'Candidatus Methylomirabilis'. Here we enriched and purified a single Methylomirabilis from paddy soil fed with nitrate and methane, which is capable of coupling methane oxidation to nitrate reduction via nitrite to dinitrogen independently. Isotope labelling showed that this bacterium we name 'Ca. Methylomirabilis sinica' stoichiometrically performed methane-dependent complete nitrate reduction to dinitrogen gas. Multi-omics analyses collectively demonstrated that 'M. sinica' actively expressed a well-established pathway for this process, especially including nitrate reductase Nap. Furthermore, 'M. sinica' exhibited a higher nitrate affinity than most denitrifiers, implying its competitive fitness under oligotrophic nitrogen-limited conditions. Our findings revise the paradigm of methane-dependent denitrification performed by two organisms, and the widespread presence of 'M. sinica' in public databases suggests that the coupling of methane oxidation and complete denitrification in single cells substantially contributes to global methane and nitrogen budgets.
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Affiliation(s)
- Xiangwu Yao
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, China
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Jiaqi Wang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Mingyue He
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Zishu Liu
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, China
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Yuxiang Zhao
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Yufen Li
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Taolve Chi
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Lin Zhu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Ping Zheng
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, China
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Mike S M Jetten
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences (RIBES), Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Baolan Hu
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, China.
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China.
- Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, China.
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9
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Kim C, Pongpanich M, Porntaveetus T. Unraveling metagenomics through long-read sequencing: a comprehensive review. J Transl Med 2024; 22:111. [PMID: 38282030 PMCID: PMC10823668 DOI: 10.1186/s12967-024-04917-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 01/21/2024] [Indexed: 01/30/2024] Open
Abstract
The study of microbial communities has undergone significant advancements, starting from the initial use of 16S rRNA sequencing to the adoption of shotgun metagenomics. However, a new era has emerged with the advent of long-read sequencing (LRS), which offers substantial improvements over its predecessor, short-read sequencing (SRS). LRS produces reads that are several kilobases long, enabling researchers to obtain more complete and contiguous genomic information, characterize structural variations, and study epigenetic modifications. The current leaders in LRS technologies are Pacific Biotechnologies (PacBio) and Oxford Nanopore Technologies (ONT), each offering a distinct set of advantages. This review covers the workflow of long-read metagenomics sequencing, including sample preparation (sample collection, sample extraction, and library preparation), sequencing, processing (quality control, assembly, and binning), and analysis (taxonomic annotation and functional annotation). Each section provides a concise outline of the key concept of the methodology, presenting the original concept as well as how it is challenged or modified in the context of LRS. Additionally, the section introduces a range of tools that are compatible with LRS and can be utilized to execute the LRS process. This review aims to present the workflow of metagenomics, highlight the transformative impact of LRS, and provide researchers with a selection of tools suitable for this task.
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Affiliation(s)
- Chankyung Kim
- Center of Excellence in Genomics and Precision Dentistry, Department of Physiology, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand
- Graduate Program in Bioinformatics and Computational Biology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Monnat Pongpanich
- Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence for Cancer and Inflammation, Chulalongkorn University, Bangkok, Thailand
| | - Thantrira Porntaveetus
- Center of Excellence in Genomics and Precision Dentistry, Department of Physiology, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand.
- Graduate Program in Geriatric and Special Patients Care, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand.
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10
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Roothans N, Gabriëls M, Abeel T, Pabst M, van Loosdrecht MCM, Laureni M. Aerobic denitrification as an N2O source from microbial communities. THE ISME JOURNAL 2024; 18:wrae116. [PMID: 38913498 PMCID: PMC11272060 DOI: 10.1093/ismejo/wrae116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 04/26/2024] [Accepted: 06/21/2024] [Indexed: 06/26/2024]
Abstract
Nitrous oxide (N2O) is a potent greenhouse gas of primarily microbial origin. Oxic and anoxic emissions are commonly ascribed to autotrophic nitrification and heterotrophic denitrification, respectively. Beyond this established dichotomy, we quantitatively show that heterotrophic denitrification can significantly contribute to aerobic nitrogen turnover and N2O emissions in complex microbiomes exposed to frequent oxic/anoxic transitions. Two planktonic, nitrification-inhibited enrichment cultures were established under continuous organic carbon and nitrate feeding, and cyclic oxygen availability. Over a third of the influent organic substrate was respired with nitrate as electron acceptor at high oxygen concentrations (>6.5 mg/L). N2O accounted for up to one-quarter of the nitrate reduced under oxic conditions. The enriched microorganisms maintained a constitutive abundance of denitrifying enzymes due to the oxic/anoxic frequencies exceeding their protein turnover-a common scenario in natural and engineered ecosystems. The aerobic denitrification rates are ascribed primarily to the residual activity of anaerobically synthesised enzymes. From an ecological perspective, the selection of organisms capable of sustaining significant denitrifying activity during aeration shows their competitive advantage over other heterotrophs under varying oxygen availabilities. Ultimately, we propose that the contribution of heterotrophic denitrification to aerobic nitrogen turnover and N2O emissions is currently underestimated in dynamic environments.
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Affiliation(s)
- Nina Roothans
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Minke Gabriëls
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Thomas Abeel
- Delft Bioinformatics Lab, Delft University of Technology, van Mourik Broekmanweg 6, Delft 2628 XE, the Netherlands
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, United States
| | - Martin Pabst
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Mark C M van Loosdrecht
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Michele Laureni
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, the Netherlands
- Department of Water Management, Delft University of Technology, Stevinweg 1, 2628 CN Delft, the Netherlands
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11
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Khot V, Strous M, Dong X, Kiesser AK. Viral diversity and dynamics and CRISPR-Cas-mediated immunity in a robust alkaliphilic cyanobacterial consortium. Microbiol Spectr 2023; 11:e0221723. [PMID: 37819096 PMCID: PMC10715143 DOI: 10.1128/spectrum.02217-23] [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: 07/31/2023] [Accepted: 08/25/2023] [Indexed: 10/13/2023] Open
Abstract
IMPORTANCE Biotechnology applications utilizing the function of microbial communities have become increasingly important solutions as we strive for sustainable applications. Although viral infections are known to have a significant impact on microbial turnover and nutrient cycling, viral dynamics have remained largely overlooked in these engineered communities. Predatory perturbations to the functional stability of these microbial biotechnology applications must be investigated in order to design more robust applications. In this study, we closely examine virus-microbe dynamics in a model microbial community used in a biotechnology application. Our findings suggest that viral dynamics change significantly with environmental conditions and that microbial immunity may play an important role in maintaining functional stability. We present this study as a comprehensive template for other researchers interested in exploring predatory dynamics in engineered microbial communities.
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Affiliation(s)
- Varada Khot
- Department of Geoscience, University of Calgary, Calgary, Alberta, Canada
| | - Marc Strous
- Department of Geoscience, University of Calgary, Calgary, Alberta, Canada
| | - Xiaoli Dong
- Department of Geoscience, University of Calgary, Calgary, Alberta, Canada
- Public Health Laboratory, Alberta Precision Laboratories, Foothills Medical Centre, Calgary, Alberta, Canada
| | - Alyse K. Kiesser
- School of Engineering, University of British Columbia Okanagan, Kelowna, British Columbia, Canada
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12
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Zorz J, Paquette AJ, Gillis T, Kouris A, Khot V, Demirkaya C, De La Hoz Siegler H, Strous M, Vadlamani A. Coordinated proteome change precedes cell lysis and death in a mat-forming cyanobacterium. THE ISME JOURNAL 2023; 17:2403-2414. [PMID: 37914776 PMCID: PMC10689466 DOI: 10.1038/s41396-023-01545-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 10/12/2023] [Accepted: 10/16/2023] [Indexed: 11/03/2023]
Abstract
Cyanobacteria form dense multicellular communities that experience transient conditions in terms of access to light and oxygen. These systems are productive but also undergo substantial biomass turnover through cell death, supplementing heightened heterotrophic respiration. Here we use metagenomics and metaproteomics to survey the molecular response of a mat-forming cyanobacterium undergoing mass cell lysis after exposure to dark and anoxic conditions. A lack of evidence for viral, bacterial, or eukaryotic antagonism contradicts commonly held beliefs on the causative agent for cyanobacterial death during dense growth. Instead, proteogenomics data indicated that lysis likely resulted from a genetically programmed response triggered by a failure to maintain osmotic pressure in the wake of severe energy limitation. Cyanobacterial DNA was rapidly degraded, yet cyanobacterial proteins remained abundant. A subset of proteins, including enzymes involved in amino acid metabolism, peptidases, toxin-antitoxin systems, and a potentially self-targeting CRISPR-Cas system, were upregulated upon lysis, indicating possible involvement in the programmed cell death response. We propose this natural form of cell death could provide new pathways for controlling harmful algal blooms and for sustainable bioproduct production.
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Affiliation(s)
- Jackie Zorz
- Department of Earth, Energy, and Environment, University of Calgary, Calgary, AB, Canada.
| | - Alexandre J Paquette
- Department of Earth, Energy, and Environment, University of Calgary, Calgary, AB, Canada
| | - Timber Gillis
- Department of Earth, Energy, and Environment, University of Calgary, Calgary, AB, Canada
| | - Angela Kouris
- Department of Earth, Energy, and Environment, University of Calgary, Calgary, AB, Canada
- Synergia Biotech Inc., Calgary, AB, Canada
| | - Varada Khot
- Department of Earth, Energy, and Environment, University of Calgary, Calgary, AB, Canada
| | - Cigdem Demirkaya
- Department of Chemical and Petroleum Engineering, University of Calgary, Calgary, AB, Canada
| | | | - Marc Strous
- Department of Earth, Energy, and Environment, University of Calgary, Calgary, AB, Canada
| | - Agasteswar Vadlamani
- Department of Earth, Energy, and Environment, University of Calgary, Calgary, AB, Canada
- Synergia Biotech Inc., Calgary, AB, Canada
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13
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Li S, Luo Z, Wang S, Nan Q, Ji G. Denitrification fractionates N and O isotopes of nitrate following a ratio independent of carbon sources in freshwaters. Environ Microbiol 2023; 25:2404-2415. [PMID: 37503781 DOI: 10.1111/1462-2920.16468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 07/10/2023] [Indexed: 07/29/2023]
Abstract
The stable isotope technique has been used in tracking nitrogen cycling processes, but the isotopic characteristics are influenced by environmental conditions. To better understand the variability of nitrate isotopes in nature, we investigated the influence of organic carbon sources on isotope fractionation characteristics during microbial denitrification. Denitrifying cultures were inoculated with freshwater samples and enriched with five forms of organic compounds, that is, acetate, citrate, glucose, cellobiose, and leucine. Though the isotope enrichment factors of nitrogen and oxygen (15 ε and 18 ε) changed with carbon sources, 18 ε/15 ε always followed a proportionality near 1. Genome-centred metagenomics revealed the enrichment of a few populations, such as Pseudomonas, Enterobacter, and Atlantibacter, most of which contained both NapA- and NarG-type nitrate reductases. Metatranscriptome showed that both NapA and NarG were expressed but to different extents in the enrichments. Furthermore, isotopic data collected from a deep reservoir was analysed. The results showed δ18 O- and δ15 N-nitrate did not correlate in the surface water where nitrification was active, but 18 ε/15 ε followed a proportionality of 1.05 ± 011 in deeper waters (≥ 12 m) where denitrification controlled the nitrate isotope. The independence of 18 ε/15 ε from carbon sources provides an opportunity to determine heterotrophic denitrification and helps the interpretation of nitrate isotopes in freshwaters.
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Affiliation(s)
- Shengjie Li
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing, China
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Zhongxin Luo
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing, China
- China Institute of Water Resources and Hydropower Research, Beijing, China
- National Research Center for Sustainable Hydropower Development, Beijing, China
| | - Shuo Wang
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing, China
| | - Qiong Nan
- Institute of Environment Pollution Control and Treatment, College of Environment and Resource Science, Zhejiang University, Hangzhou, China
| | - Guodong Ji
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing, China
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14
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Li S, Mosier D, Dong X, Kouris A, Ji G, Strous M, Diao M. Frequency of change determines effectiveness of microbial response strategies. THE ISME JOURNAL 2023; 17:2047-2057. [PMID: 37723339 PMCID: PMC10579261 DOI: 10.1038/s41396-023-01515-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 09/04/2023] [Accepted: 09/06/2023] [Indexed: 09/20/2023]
Abstract
Nature challenges microbes with change at different frequencies and demands an effective response for survival. Here, we used controlled laboratory experiments to investigate the effectiveness of different response strategies, such as post-translational modification, transcriptional regulation, and specialized versus adaptable metabolisms. For this, we inoculated replicated chemostats with an enrichment culture obtained from sulfidic stream microbiomes 16 weeks prior. The chemostats were submitted to alternatingly oxic and anoxic conditions at three frequencies, with periods of 1, 4 and 16 days. The microbial response was recorded with 16S rRNA gene amplicon sequencing, shotgun metagenomics, transcriptomics and proteomics. Metagenomics resolved provisional genomes of all abundant bacterial populations, mainly affiliated with Proteobacteria and Bacteroidetes. Almost all these populations maintained a steady growth rate under both redox conditions at all three frequencies of change. Our results supported three conclusions: (1) Oscillating oxic/anoxic conditions selected for generalistic species, rather than species specializing in only a single condition. (2) A high frequency of change selected for strong codon usage bias. (3) Alignment of transcriptomes and proteomes required multiple generations and was dependent on a low frequency of change.
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Affiliation(s)
- Shengjie Li
- Department of Geoscience, University of Calgary, Calgary, AB, T2N 1N4, Canada
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, 100871, Beijing, China
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany
| | - Damon Mosier
- Department of Geoscience, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Xiaoli Dong
- Department of Geoscience, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Angela Kouris
- Department of Geoscience, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Guodong Ji
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, 100871, Beijing, China
| | - Marc Strous
- Department of Geoscience, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Muhe Diao
- Department of Geoscience, University of Calgary, Calgary, AB, T2N 1N4, Canada.
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15
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Walsh LH, Coakley M, Walsh AM, O'Toole PW, Cotter PD. Bioinformatic approaches for studying the microbiome of fermented food. Crit Rev Microbiol 2023; 49:693-725. [PMID: 36287644 DOI: 10.1080/1040841x.2022.2132850] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 08/11/2022] [Accepted: 09/28/2022] [Indexed: 11/03/2022]
Abstract
High-throughput DNA sequencing-based approaches continue to revolutionise our understanding of microbial ecosystems, including those associated with fermented foods. Metagenomic and metatranscriptomic approaches are state-of-the-art biological profiling methods and are employed to investigate a wide variety of characteristics of microbial communities, such as taxonomic membership, gene content and the range and level at which these genes are expressed. Individual groups and consortia of researchers are utilising these approaches to produce increasingly large and complex datasets, representing vast populations of microorganisms. There is a corresponding requirement for the development and application of appropriate bioinformatic tools and pipelines to interpret this data. This review critically analyses the tools and pipelines that have been used or that could be applied to the analysis of metagenomic and metatranscriptomic data from fermented foods. In addition, we critically analyse a number of studies of fermented foods in which these tools have previously been applied, to highlight the insights that these approaches can provide.
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Affiliation(s)
- Liam H Walsh
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
- School of Microbiology, University College Cork, Ireland
| | - Mairéad Coakley
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - Aaron M Walsh
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - Paul W O'Toole
- School of Microbiology, University College Cork, Ireland
- APC Microbiome Ireland, University College Cork, Ireland
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Ireland
- VistaMilk SFI Research Centre, Teagasc, Moorepark, Fermoy, Cork, Ireland
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16
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Dyksma S, Pester M. Oxygen respiration and polysaccharide degradation by a sulfate-reducing acidobacterium. Nat Commun 2023; 14:6337. [PMID: 37816749 PMCID: PMC10564751 DOI: 10.1038/s41467-023-42074-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 09/25/2023] [Indexed: 10/12/2023] Open
Abstract
Sulfate-reducing microorganisms represent a globally important link between the sulfur and carbon cycles. Recent metagenomic surveys expanded the diversity of microorganisms putatively involved in sulfate reduction underscoring our incomplete understanding of this functional guild. Here, we use genome-centric metatranscriptomics to study the energy metabolism of Acidobacteriota that carry genes for dissimilation of sulfur compounds in a long-term continuous culture running under alternating anoxic and oxic conditions. Differential gene expression analysis reveals the unique metabolic flexibility of a pectin-degrading acidobacterium to switch from sulfate to oxygen reduction when shifting from anoxic to oxic conditions. The combination of facultative anaerobiosis and polysaccharide degradation expands the metabolic versatility among sulfate-reducing microorganisms. Our results highlight that sulfate reduction and aerobic respiration are not mutually exclusive in the same organism, sulfate reducers can mineralize organic polymers, and anaerobic mineralization of complex organic matter is not necessarily a multi-step process involving different microbial guilds but can be bypassed by a single microbial species.
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Affiliation(s)
- Stefan Dyksma
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Department of Microorganisms, Braunschweig, Germany.
| | - Michael Pester
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Department of Microorganisms, Braunschweig, Germany.
- Technical University of Braunschweig, Institute of Microbiology, Braunschweig, Germany.
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17
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Hartmann M, Herzog C, Brunner I, Stierli B, Meyer F, Buchmann N, Frey B. Long-term mitigation of drought changes the functional potential and life-strategies of the forest soil microbiome involved in organic matter decomposition. Front Microbiol 2023; 14:1267270. [PMID: 37840720 PMCID: PMC10570739 DOI: 10.3389/fmicb.2023.1267270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 09/14/2023] [Indexed: 10/17/2023] Open
Abstract
Climate change can alter the flow of nutrients and energy through terrestrial ecosystems. Using an inverse climate change field experiment in the central European Alps, we explored how long-term irrigation of a naturally drought-stressed pine forest altered the metabolic potential of the soil microbiome and its ability to decompose lignocellulolytic compounds as a critical ecosystem function. Drought mitigation by a decade of irrigation stimulated profound changes in the functional capacity encoded in the soil microbiome, revealing alterations in carbon and nitrogen metabolism as well as regulatory processes protecting microorganisms from starvation and desiccation. Despite the structural and functional shifts from oligotrophic to copiotrophic microbial lifestyles under irrigation and the observation that different microbial taxa were involved in the degradation of cellulose and lignin as determined by a time-series stable-isotope probing incubation experiment with 13C-labeled substrates, degradation rates of these compounds were not affected by different water availabilities. These findings provide new insights into the impact of precipitation changes on the soil microbiome and associated ecosystem functioning in a drought-prone pine forest and will help to improve our understanding of alterations in biogeochemical cycling under a changing climate.
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Affiliation(s)
- Martin Hartmann
- Department of Environmental Systems Science, Sustainable Agroecosystems, Institute of Agricultural Sciences, ETH Zürich, Zürich, Switzerland
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Claude Herzog
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
- Department of Environmental Systems Science, Grassland Sciences, Institute of Agricultural Sciences, ETH Zürich, Zürich, Switzerland
| | - Ivano Brunner
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Beat Stierli
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Folker Meyer
- Data Science, Institute for AI in Medicine, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Argonne National Laboratory, Argonne, IL, United States
- Computation Institute, University of Chicago, Chicago, IL, United States
- Department of Medicine, University of Chicago, Chicago, IL, United States
| | - Nina Buchmann
- Department of Environmental Systems Science, Grassland Sciences, Institute of Agricultural Sciences, ETH Zürich, Zürich, Switzerland
| | - Beat Frey
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
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18
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Kumari S, Leon Magdaleno JS, Grewal RK, Narsing Rao MP, Rajjak Shaikh A, Cavallo L, Chawla M, Kumar M. High potential for biomass-degrading CAZymes revealed by pine forest soil metagenomics. J Biomol Struct Dyn 2023:1-12. [PMID: 37768075 DOI: 10.1080/07391102.2023.2262600] [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: 05/13/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023]
Abstract
The undisturbed environment in Netarhat, with its high levels of accumulated lignocellulosic biomass, presents an opportunity to identify microbes for biomass digestion. This study focuses on the bioprospecting of native soil microbes from the Netarhat forest in Jharkhand, India, with the potential for lignocellulosic substrate digestion. These biocatalysts could help overcome the bottleneck of biomass saccharification and reduce the overall cost of biofuel production, replacing harmful fossil fuels. The study used metagenomic analysis of pine forest soil via whole genome shotgun sequencing, revealing that most of the reads matched with the bacterial species, very low percentage of reads (0.1%) belongs to fungal species, with 13% of unclassified reads. Actinobacteria were found to be predominant among the bacterial species. MetaErg annotation identified 11,830 protein family genes and 2 metabolic marker genes in the soil samples. Based on the Carbohydrate Active EnZyme (CAZy) database, 3,996 carbohydrate enzyme families were identified, with family Glycosyl hydrolase (GH) dominating with 1,704 genes. Most observed GH families in the study were GH0, 3, 5, 6. 9, 12. 13, 15, 16, 39, 43, 57, and 97. Modelling analysis of a representative GH 43 gene suggested a strong affinity for cellulose than xylan. This study highlights the lignocellulosic digestion potential of the native microfauna of the lesser-known pine forest of Netarhat.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sonam Kumari
- Department of Life Sciences, School of Natural Sciences, Central University of Jharkhand, Ranchi, Jharkhand, India
| | - Jorge S Leon Magdaleno
- Physical Sciences and Engineering Division, Kaust Catalysis Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Ravneet Kaur Grewal
- Department of Research and Innovation, STEMskills Research and Education Lab Private Limited, Faridabad, Haryana, India
| | - Manik Prabhu Narsing Rao
- Instituto de Ciencias Aplicadas, Facultad de Ingeniería, Universidad Autónoma de Chile, Sede Talca, Talca, Chile
| | - Abdul Rajjak Shaikh
- Department of Research and Innovation, STEMskills Research and Education Lab Private Limited, Faridabad, Haryana, India
| | - Luigi Cavallo
- Physical Sciences and Engineering Division, Kaust Catalysis Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Mohit Chawla
- Physical Sciences and Engineering Division, Kaust Catalysis Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Manoj Kumar
- Department of Life Sciences, School of Natural Sciences, Central University of Jharkhand, Ranchi, Jharkhand, India
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19
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Liang X, Zhang J, Kim Y, Ho J, Liu K, Keenum I, Gupta S, Davis B, Hepp SL, Zhang L, Xia K, Knowlton KF, Liao J, Vikesland PJ, Pruden A, Heath LS. ARGem: a new metagenomics pipeline for antibiotic resistance genes: metadata, analysis, and visualization. Front Genet 2023; 14:1219297. [PMID: 37811141 PMCID: PMC10558085 DOI: 10.3389/fgene.2023.1219297] [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: 05/08/2023] [Accepted: 09/01/2023] [Indexed: 10/10/2023] Open
Abstract
Antibiotic resistance is of crucial interest to both human and animal medicine. It has been recognized that increased environmental monitoring of antibiotic resistance is needed. Metagenomic DNA sequencing is becoming an attractive method to profile antibiotic resistance genes (ARGs), including a special focus on pathogens. A number of computational pipelines are available and under development to support environmental ARG monitoring; the pipeline we present here is promising for general adoption for the purpose of harmonized global monitoring. Specifically, ARGem is a user-friendly pipeline that provides full-service analysis, from the initial DNA short reads to the final visualization of results. The capture of extensive metadata is also facilitated to support comparability across projects and broader monitoring goals. The ARGem pipeline offers efficient analysis of a modest number of samples along with affordable computational components, though the throughput could be increased through cloud resources, based on the user's configuration. The pipeline components were carefully assessed and selected to satisfy tradeoffs, balancing efficiency and flexibility. It was essential to provide a step to perform short read assembly in a reasonable time frame to ensure accurate annotation of identified ARGs. Comprehensive ARG and mobile genetic element databases are included in ARGem for annotation support. ARGem further includes an expandable set of analysis tools that include statistical and network analysis and supports various useful visualization techniques, including Cytoscape visualization of co-occurrence and correlation networks. The performance and flexibility of the ARGem pipeline is demonstrated with analysis of aquatic metagenomes. The pipeline is freely available at https://github.com/xlxlxlx/ARGem.
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Affiliation(s)
- Xiao Liang
- Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Jingyi Zhang
- Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Yoonjin Kim
- Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Josh Ho
- Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Kevin Liu
- Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Ishi Keenum
- Department of Civil and Environmental Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Suraj Gupta
- Interdisciplinary PhD Program in Genetics, Bioinformatics, and Computational Biology, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Benjamin Davis
- Department of Civil and Environmental Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Shannon L. Hepp
- Department of Civil and Environmental Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Liqing Zhang
- Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Kang Xia
- School of Plant and Environmental Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Katharine F. Knowlton
- Department of Dairy Science, Virginia Polytechnic Institute and State University, Blacksburg, VaA, United States
| | - Jingqiu Liao
- Department of Civil and Environmental Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Peter J. Vikesland
- Department of Civil and Environmental Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Amy Pruden
- Department of Civil and Environmental Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Lenwood S. Heath
- Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
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20
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Durand M, Touchette D, Chen YJ, Magnuson E, Wasserscheid J, Greer CW, Whyte LG, Altshuler I. Effects of marine diesel on microbial diversity and activity in high Arctic beach sediments. MARINE POLLUTION BULLETIN 2023; 194:115226. [PMID: 37442053 DOI: 10.1016/j.marpolbul.2023.115226] [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: 03/22/2023] [Revised: 06/22/2023] [Accepted: 06/25/2023] [Indexed: 07/15/2023]
Abstract
Global warming induced sea ice loss increases Arctic maritime traffic, enhancing the risk of ecosystem contamination from fuel spills and nutrient loading. The impact of marine diesel on bacterial metabolic activity and diversity, assessed by colorimetric assay, 16S rRNA and metagenomic sequencing, of Northwest Passage (Arctic Ocean) beach sediments was assessed with nutrient amendment at environmentally relevant temperatures (5 and 15 °C). Higher temperature and nutrients stimulated microbial activity, while diesel reduced it, with metabolism inhibited at and above 0.01 % (without nutrients) and at 1 % (with nutrients) diesel inclusions. Diesel exposure significantly decreased microbial diversity and selected for Psychrobacter genus. Microbial hydrocarbon degradation, organic compound metabolism, and exopolysaccharide production gene abundances increased under higher diesel concentrations. Metagenomic binning recovered nine MAGs/bins with hydrocarbon degradation genes. We demonstrate a nutrients' rescue-type effect in diesel contaminated microbial communities via enrichment of microorganisms with stress response, aromatic compound, and ammonia assimilation metabolisms.
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Affiliation(s)
- Margaux Durand
- Natural Resource Sciences, McGill University, 21111 Lakeshore, Ste Anne-de-Bellevue, Quebec, Canada; Energy, Mining and Environment Research Centre, National Research Council Canada (NRC), Montreal, Quebec, Canada; Université Paris-Saclay, INRAE, AgroParisTech, Paris-Saclay Applied Economics, 91120 Palaiseau, France
| | - David Touchette
- Natural Resource Sciences, McGill University, 21111 Lakeshore, Ste Anne-de-Bellevue, Quebec, Canada; River Ecosystems Laboratory, ALPOLE, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Ya-Jou Chen
- Natural Resource Sciences, McGill University, 21111 Lakeshore, Ste Anne-de-Bellevue, Quebec, Canada
| | - Elisse Magnuson
- Natural Resource Sciences, McGill University, 21111 Lakeshore, Ste Anne-de-Bellevue, Quebec, Canada
| | - Jessica Wasserscheid
- Energy, Mining and Environment Research Centre, National Research Council Canada (NRC), Montreal, Quebec, Canada
| | - Charles W Greer
- Energy, Mining and Environment Research Centre, National Research Council Canada (NRC), Montreal, Quebec, Canada
| | - Lyle G Whyte
- Natural Resource Sciences, McGill University, 21111 Lakeshore, Ste Anne-de-Bellevue, Quebec, Canada
| | - Ianina Altshuler
- Natural Resource Sciences, McGill University, 21111 Lakeshore, Ste Anne-de-Bellevue, Quebec, Canada; Energy, Mining and Environment Research Centre, National Research Council Canada (NRC), Montreal, Quebec, Canada; MACE Laboratory, ALPOLE, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
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21
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Samanta B, Sharma S, Budhwar R. Metagenome Analysis of Speleothem Microbiome from Subterranean Cave Reveals Insight into Community Structure, Metabolic Potential, and BGCs Diversity. Curr Microbiol 2023; 80:317. [PMID: 37561193 DOI: 10.1007/s00284-023-03431-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 07/26/2023] [Indexed: 08/11/2023]
Abstract
The Borra caves, the second largest subterranean karst cave ecosystem in the Indian sub-continent, are located at the Ananthagiri hills of Araku Valley in the Alluri district of Andhra Pradesh, India. The present investigation applied a shotgun metagenomic approach to gain insights into the microbial community structure, metabolic potential, and biosynthetic gene cluster (BGC) diversity of the microbes colonizing the surface of the speleothems from the aphotic zone of Borra caves. The taxonomic analysis of the metagenome data illustrated that the speleothem-colonizing core microbial community was dominated mainly by Alpha-, Beta-, and Gamma-Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes. The key energy metabolic pathways analysis provides strong evidence of chemolithoautotrophic and chemoheterotrophic modes of nutrition in the speleothem-colonizing microbial community. Metagenome data suggests that sulfur reducers and sulfur-disproportionating microbes might play a vital role in energy generation in this ecosystem. Our metagenome data also suggest that the dissimilatory nitrifiers and nitrifying denitrifiers might play an essential role in conserving nitrogen pools in the ecosystem. Furthermore, metagenome-wide BGCs mining retrieved 451 putative BGCs; NRPS was the most abundant (24%). Phylogenetic analysis of the C domain of NRPS showed that sequences were distributed across all six function categories of the known C domain, including several novel subclades. For example, a novel subclade had been recovered within the LCL domain clade as a sister subclade of immunosuppressant cyclosporin encoding C domain sequences. Our result suggested that subterranean cave microbiomes might be a potential reservoir of novel microbial metabolites.
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Affiliation(s)
- Brajogopal Samanta
- Department of Microbiology and FST, GITAM School of Science, GITAM (Deemed to Be University), Rushikonda, Visakhapatnam, Andhra Pradesh, 530045, India.
| | - Shivasmi Sharma
- Bionivid Technology Private Limited, Bengaluru, Karnataka, 560043, India
| | - Roli Budhwar
- Bionivid Technology Private Limited, Bengaluru, Karnataka, 560043, India
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22
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Ruff SE, Humez P, de Angelis IH, Diao M, Nightingale M, Cho S, Connors L, Kuloyo OO, Seltzer A, Bowman S, Wankel SD, McClain CN, Mayer B, Strous M. Hydrogen and dark oxygen drive microbial productivity in diverse groundwater ecosystems. Nat Commun 2023; 14:3194. [PMID: 37311764 DOI: 10.1038/s41467-023-38523-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 05/05/2023] [Indexed: 06/15/2023] Open
Abstract
Around 50% of humankind relies on groundwater as a source of drinking water. Here we investigate the age, geochemistry, and microbiology of 138 groundwater samples from 95 monitoring wells (<250 m depth) located in 14 aquifers in Canada. The geochemistry and microbiology show consistent trends suggesting large-scale aerobic and anaerobic hydrogen, methane, nitrogen, and sulfur cycling carried out by diverse microbial communities. Older groundwaters, especially in aquifers with organic carbon-rich strata, contain on average more cells (up to 1.4 × 107 mL-1) than younger groundwaters, challenging current estimates of subsurface cell abundances. We observe substantial concentrations of dissolved oxygen (0.52 ± 0.12 mg L-1 [mean ± SE]; n = 57) in older groundwaters that seem to support aerobic metabolisms in subsurface ecosystems at an unprecedented scale. Metagenomics, oxygen isotope analyses and mixing models indicate that dark oxygen is produced in situ via microbial dismutation. We show that ancient groundwaters sustain productive communities and highlight an overlooked oxygen source in present and past subsurface ecosystems of Earth.
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Affiliation(s)
- S Emil Ruff
- Department of Geoscience, University of Calgary, Calgary, Canada.
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA.
- Ecosystems Center, Marine Biological Laboratory, Woods Hole, MA, USA.
| | - Pauline Humez
- Department of Geoscience, University of Calgary, Calgary, Canada
| | - Isabella Hrabe de Angelis
- Department of Geoscience, University of Calgary, Calgary, Canada
- Multiphase Chemistry Department, Max Planck Institute for Chemistry, Mainz, Germany
| | - Muhe Diao
- Department of Geoscience, University of Calgary, Calgary, Canada
| | | | - Sara Cho
- Department of Geoscience, University of Calgary, Calgary, Canada
| | - Liam Connors
- Department of Geoscience, University of Calgary, Calgary, Canada
| | | | - Alan Seltzer
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Samuel Bowman
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Scott D Wankel
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Cynthia N McClain
- Department of Geoscience, University of Calgary, Calgary, Canada
- Alberta Environment and Protected Areas, Calgary, Canada
- Alberta Biodiversity Monitoring Institute, Edmonton, Canada
| | - Bernhard Mayer
- Department of Geoscience, University of Calgary, Calgary, Canada
| | - Marc Strous
- Department of Geoscience, University of Calgary, Calgary, Canada
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23
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Das R, Tamang B, Najar IN, Thakur N, Mondal K. First report on metagenomics and their predictive functional analysis of fermented bamboo shoot food of Tripura, North East India. Front Microbiol 2023; 14:1158411. [PMID: 37125168 PMCID: PMC10130461 DOI: 10.3389/fmicb.2023.1158411] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 03/27/2023] [Indexed: 05/02/2023] Open
Abstract
Moiya pansung, mileye amileye, moiya koshak, and midukeye are naturally fermented bamboo shoot foods of Tripura. The present study aimed to reveal the whole microbial community structure of naturally fermented moiya pangsung, mileye amileye, moiya koshak, and midukeye along with the prediction of microbial functional profiles by shotgun metagenomic sequence analysis. The metataxonomic profile of moiya pangsung, mileye amileye, moiya koshak, and midukeye samples showed different domains, viz., bacteria (97.70%) followed by the virus (0.76%), unclassified (0.09%), eukaryotes (1.46%) and archaea (0.05%). Overall, 49 phyla, 409 families, 841 genera, and 1,799 species were found in all the fermented bamboo shoot samples collected from different places of Tripura. Firmicutes was the most abundant phylum (89.28%) followed by Proteobacteria (5.13%), Bacteroidetes (4.38%), Actinobacteria (1.02%), and Fusobacteria (0.17%). Lactiplantibacillus plantarum was the most abundant species in moiya pangsung, mileye amileye, moiya koshak, and midukeye followed by Lactococcus lactis, Levilactobacillus brevis, Leuconostoc mesenteroides, Weissella paramesenteroides, Leuconostoc kimchii, Pediococcus pentosaceus, Leuconostoc gasicomitatum, and Lacticaseibacillus casei. A few phyla of fungus were found, viz., Ascomycota, Basidiomycota, and Glomeromycota, where Ascomycota was present in high abundance. Functional analysis of moiya pangsung, mileye amileye, moiya koshak, and midukeye metagenome revealed the genes for the synthesis and metabolism of a wide range of bioactive compounds including, various essential amino acids, and conjugated amino acids. The abundance profile and predictive analysis of fermented bamboo shoots revealed a huge plethora of essential microorganisms and KEGG analysis revealed genes for amino acid metabolism, pectin degradation, lipid metabolism, and many other essential pathways that can be essential for the improvement of nutritional and sensory qualities of the fermented bamboo shoot products.
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Affiliation(s)
- Rohit Das
- Department of Microbiology, Sikkim University, Gangtok, India
| | | | | | - Nagendra Thakur
- Department of Microbiology, Sikkim University, Gangtok, India
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24
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Shaffer M, Borton MA, Bolduc B, Faria JP, Flynn RM, Ghadermazi P, Edirisinghe JN, Wood-Charlson EM, Miller CS, Chan SHJ, Sullivan MB, Henry CS, Wrighton KC. kb_DRAM: annotation and metabolic profiling of genomes with DRAM in KBase. Bioinformatics 2023; 39:btad110. [PMID: 36857575 PMCID: PMC10068739 DOI: 10.1093/bioinformatics/btad110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 12/30/2022] [Accepted: 02/28/2023] [Indexed: 03/03/2023] Open
Abstract
Microbial genome annotation is the process of identifying structural and functional elements in DNA sequences and subsequently attaching biological information to those elements. DRAM is a tool developed to annotate bacterial, archaeal, and viral genomes derived from pure cultures or metagenomes. DRAM goes beyond traditional annotation tools by distilling multiple gene annotations to genome level summaries of functional potential. Despite these benefits, a downside of DRAM is the requirement of large computational resources, which limits its accessibility. Further, it did not integrate with downstream metabolic modeling tools that require genome annotation. To alleviate these constraints, DRAM and the viral counterpart, DRAM-v, are now available and integrated with the freely accessible KBase cyberinfrastructure. With kb_DRAM users can generate DRAM annotations and functional summaries from microbial or viral genomes in a point-and-click interface, as well as generate genome-scale metabolic models from DRAM annotations. AVAILABILITY AND IMPLEMENTATION For kb_DRAM users, the kb_DRAM apps on KBase can be found in the catalog at https://narrative.kbase.us/#catalog/modules/kb_DRAM. For kb_DRAM users, a tutorial workflow with all documentation is available at https://narrative.kbase.us/narrative/129480. For kb_DRAM developers, software is available at https://github.com/shafferm/kb_DRAM.
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Affiliation(s)
| | | | - Ben Bolduc
- The Ohio State University, Columbus, OH, USA
| | | | - Rory M Flynn
- Colorado State University, Fort Collins, CO, USA
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25
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Rohrer SD, Jiménez-Uzcátegui G, Parker PG, Chubiz LM. Composition and function of the Galapagos penguin gut microbiome vary with age, location, and a putative bacterial pathogen. Sci Rep 2023; 13:5358. [PMID: 37005428 PMCID: PMC10067942 DOI: 10.1038/s41598-023-31826-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 03/17/2023] [Indexed: 04/04/2023] Open
Abstract
Microbial colonization plays a direct role in host health. Understanding the ecology of the resident microbial community for a given host species is thus an important step for detecting population vulnerabilities like disease. However, the idea of integrating microbiome research into conservation is still relatively new, and wild birds have received less attention in this field than mammals or domesticated animals. Here we examine the composition and function of the gut microbiome of the endangered Galapagos penguin (Spheniscus mendiculus) with the goals of characterizing the normal microbial community and resistome, identifying likely pathogens, and testing hypotheses of structuring forces for this community based on demographics, location, and infection status. We collected fecal samples from wild penguins in 2018 and performed 16S rRNA gene sequencing and whole genome sequencing (WGS) on extracted DNA. 16S sequencing revealed that the bacterial phyla Fusobacteria, Epsilonbacteraeota, Firmicutes, and Proteobacteria dominate the community. Functional pathways were computed from WGS data, showing genetic functional potential primarily focused on metabolism-amino acid metabolism, carbohydrate metabolism, and energy metabolism are the most well-represented functional groups. WGS samples were each screened for antimicrobial resistance, characterizing a resistome made up of nine antibiotic resistance genes. Samples were screened for potential enteric pathogens using virulence factors as indicators; Clostridium perfringens was revealed as a likely pathogen. Overall, three factors appear to be shaping the alpha and beta diversity of the microbial community: penguin developmental stage, sampling location, and C. perfringens. We found that juvenile penguins have significantly lower alpha diversity than adults based on three metrics, as well as significantly different beta diversity. Location effects are minimal, but one site has significantly lower Shannon diversity than the other primary sites. Finally, when samples were grouped by C. perfringens virulence factors, we found dramatic changes in beta diversity based on operational taxonomic units, protein families, and functional pathways. This study provides a baseline microbiome for an endangered species, implicates both penguin age and the presence of a potential bacterial pathogen as primary factors associated with microbial community variance, and reveals widespread antibiotic resistance genes across the population.
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Affiliation(s)
- Sage D Rohrer
- Department of Biology and Whitney R. Harris World Ecology Center, University of Missouri-St. Louis, One University Blvd., St. Louis, MO, 63121, USA.
| | | | - Patricia G Parker
- Department of Biology and Whitney R. Harris World Ecology Center, University of Missouri-St. Louis, One University Blvd., St. Louis, MO, 63121, USA
- WildCare Institute, Saint Louis Zoo, One Government Drive, St. Louis, MO, 63110, USA
| | - Lon M Chubiz
- Department of Biology and Whitney R. Harris World Ecology Center, University of Missouri-St. Louis, One University Blvd., St. Louis, MO, 63121, USA
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26
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Baltoumas FA, Karatzas E, Paez-Espino D, Venetsianou NK, Aplakidou E, Oulas A, Finn RD, Ovchinnikov S, Pafilis E, Kyrpides NC, Pavlopoulos GA. Exploring microbial functional biodiversity at the protein family level-From metagenomic sequence reads to annotated protein clusters. FRONTIERS IN BIOINFORMATICS 2023; 3:1157956. [PMID: 36959975 PMCID: PMC10029925 DOI: 10.3389/fbinf.2023.1157956] [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: 02/07/2023] [Accepted: 02/21/2023] [Indexed: 03/06/2023] Open
Abstract
Metagenomics has enabled accessing the genetic repertoire of natural microbial communities. Metagenome shotgun sequencing has become the method of choice for studying and classifying microorganisms from various environments. To this end, several methods have been developed to process and analyze the sequence data from raw reads to end-products such as predicted protein sequences or families. In this article, we provide a thorough review to simplify such processes and discuss the alternative methodologies that can be followed in order to explore biodiversity at the protein family level. We provide details for analysis tools and we comment on their scalability as well as their advantages and disadvantages. Finally, we report the available data repositories and recommend various approaches for protein family annotation related to phylogenetic distribution, structure prediction and metadata enrichment.
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Affiliation(s)
- Fotis A. Baltoumas
- Institute for Fundamental Biomedical Research, BSRC “Alexander Fleming”, Vari, Greece
| | - Evangelos Karatzas
- Institute for Fundamental Biomedical Research, BSRC “Alexander Fleming”, Vari, Greece
| | - David Paez-Espino
- Lawrence Berkeley National Laboratory, DOE Joint Genome Institute, Berkeley, CA, United States
| | - Nefeli K. Venetsianou
- Institute for Fundamental Biomedical Research, BSRC “Alexander Fleming”, Vari, Greece
| | - Eleni Aplakidou
- Institute for Fundamental Biomedical Research, BSRC “Alexander Fleming”, Vari, Greece
| | - Anastasis Oulas
- The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Robert D. Finn
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, United Kingdom
| | - Sergey Ovchinnikov
- John Harvard Distinguished Science Fellowship Program, Harvard University, Cambridge, MA, United States
| | - Evangelos Pafilis
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Greece
| | - Nikos C. Kyrpides
- Lawrence Berkeley National Laboratory, DOE Joint Genome Institute, Berkeley, CA, United States
| | - Georgios A. Pavlopoulos
- Institute for Fundamental Biomedical Research, BSRC “Alexander Fleming”, Vari, Greece
- Center of New Biotechnologies and Precision Medicine, Department of Medicine, School of Health Sciences, National and Kapodistrian University of Athens, Athens, Greece
- Hellenic Army Academy, Vari, Greece
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27
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Dong X, Lan H, Huang L, Zhang H, Lin X, Weng S, Peng Y, Lin J, Wang JH, Peng J, Yang Y. Metagenomic Views of Microbial Communities in Sand Sediments Associated with Coral Reefs. MICROBIAL ECOLOGY 2023; 85:465-477. [PMID: 35113183 DOI: 10.1007/s00248-021-01957-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 12/29/2021] [Indexed: 06/14/2023]
Abstract
Reef sediments, the home for microbes with high abundances, provide an important source of carbonates and nutrients for the growth and maintenance of coral reefs. However, there is a lack of systematic research on the composition of microbial community in sediments of different geographic sites and their potential effect on nutrient recycling and health of the coral reef ecosystem. In combination of biogeochemical measurements with gene- and genome-centric metagenomics, we assessed microbial community compositions and functional diversity, as well as profiles of antibiotic resistance genes in surface sediments of 16 coral reef sites at different depths from the Xisha islands in the South China Sea. Reef sediment microbiomes are diverse and novel at lower taxonomic ranks, dominated by Proteobacteria and Planctomycetota. Most reef sediment bacteria potentially participate in biogeochemical cycling via oxidizing various organic and inorganic compounds as energy sources. High abundances of Proteobacteria (mostly Rhizobiales and Woeseiales) are metabolically flexible and contain rhodopsin genes. Various classes of antibiotic resistance genes, hosted by diverse bacterial lineages, were identified to confer resistance to multidrug, aminoglycoside, and other antibiotics. Overall, our findings expanded the understanding of reef sediment microbial ecology and provided insights for their link to the coral reef ecosystem health.
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Affiliation(s)
- Xiyang Dong
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China.
| | - Haoyu Lan
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Liangtian Huang
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Haikun Zhang
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
| | - Xianbiao Lin
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Shengze Weng
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Yongyi Peng
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Jia Lin
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Jiang-Hai Wang
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Juan Peng
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Ying Yang
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China.
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28
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Complete Genome Sequence of Vibrio natriegens Strain PWH3a. Microbiol Resour Announc 2023; 12:e0110822. [PMID: 36598262 PMCID: PMC9872580 DOI: 10.1128/mra.01108-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Vibrio natriegens strain PWH3a, isolated from the Texas Gulf Coast, is used as a model organism in marine microbiology. Here, we report the complete genome sequence of strain PWH3a, which has two circular chromosomes, 4,650 coding sequences, 34 rRNA, 4 noncoding RNA (ncRNA), 131 tRNA genes, and one Mu-like prophage sequence.
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29
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Xu Y, You G, Yin J, Zhang M, Peng D, Xu J, Yang S, Hou J. Salt tolerance evolution facilitates antibiotic resistome in soil microbiota: Evidences from dissemination evaluation, hosts identification and co-occurrence exploration. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 317:120830. [PMID: 36481466 DOI: 10.1016/j.envpol.2022.120830] [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: 08/10/2022] [Revised: 11/26/2022] [Accepted: 12/04/2022] [Indexed: 06/17/2023]
Abstract
Salinity is considered as one of the vital factors affecting the profiles of antibiotic resistance genes (ARGs) in soils, whereby its roles in shaping the antibiotic resistome were still poorly understood. Here, metagenomic analysis was conducted to track the ARGs distributions and dissemination in soils during salt accumulation and desalinization processes. Neutral-salt accumulation for 45 and 90 days significantly increased the relative abundances of ARGs and mobile genetic elements (MGEs) carrying antibiotic resistance contigs (ARCs). The ARGs within antibiotic efflux and target protection families primarily carried by Streptomyces, Nocardioides, Rhodanobacter and Monashia were largely enriched by salinity. The ARGs subtypes of the resistance-nodulation-division (RND) family, ATP-binding cassette (ABC) family, rRNA methyltransferase and other efflux were closely associated with MGEs, contributing to the enrichment of ARGs. Moreover, the ARGs subtypes and transposons were genetically linked with the salt-tolerance mechanisms of organic osmolyte transporters and K+ uptake proteins on the same ARC, demonstrating the coselection of ARGs and halotolerant genes. Furthermore, the antibiotic resistome could recover to a normal state after the prolonged incubation by alleviating salt stress. Nevertheless, the acquisition of ARGs by opportunistic pathogens after salt treatment was increased, serving to prioritize further efforts on the health risks correlated with resistance propagation and human exposure in saline soils.
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Affiliation(s)
- Yi Xu
- College of Agricultural Science and Engineering, Hohai University, Nanjing, People's Republic of China, 210098.
| | - Guoxiang You
- Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing, People's Republic of China, 210098
| | - Jinbao Yin
- Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing, People's Republic of China, 210098
| | - Mairan Zhang
- College of Agricultural Science and Engineering, Hohai University, Nanjing, People's Republic of China, 210098
| | - Dengyun Peng
- College of Agricultural Science and Engineering, Hohai University, Nanjing, People's Republic of China, 210098
| | - Junzeng Xu
- College of Agricultural Science and Engineering, Hohai University, Nanjing, People's Republic of China, 210098; State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing 210098, PR China
| | - Shihong Yang
- College of Agricultural Science and Engineering, Hohai University, Nanjing, People's Republic of China, 210098; State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing 210098, PR China.
| | - Jun Hou
- Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing, People's Republic of China, 210098
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30
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Shi LD, Gao TY, Wei XW, Shapleigh JP, Zhao HP. pH-Dependent Hydrogenotrophic Denitratation Based on Self-Alkalization. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:685-696. [PMID: 36408861 DOI: 10.1021/acs.est.2c05559] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Producing stable nitrite is a necessity for anaerobic ammonium oxidation (anammox) but remains a huge challenge. Here, we describe the design and operation of a hydrogenotrophic denitratation system that stably reduced >90% nitrate to nitrite under self-alkaline conditions of pH up to 10.80. Manually lowering the pH to a range of 9.00-10.00 dramatically decreased the nitrate-to-nitrite transformation ratio to <20%, showing a significant role of high pH in denitratation. Metagenomics combined with metatranscriptomics indicated that six microorganisms, including a Thauera member, dominated the community and encoded the various genes responsible for hydrogen oxidation and the complete denitrification process. During denitratation at high pH, transcription of periplasmic genes napA, nirS, and nirK, whose products perform nitrate and nitrite reduction, decreased sharply compared to that under neutral conditions, while narG, encoding a membrane-associated nitrate reductase, remained transcriptionally active, as were genes involved in intracellular proton homeostasis. Together with no reduction in only nitrite-amended samples, these results disproved the electron competition between reductions of nitrate and nitrite but highlighted a lack of protons outside cells constraining biological nitrite reduction. Overall, our study presents a stably efficient strategy for nitrite production and provides a major advance in the understanding of denitratation.
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Affiliation(s)
- Ling-Dong Shi
- MOE Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou310058, Zhejiang, China
| | - Tian-Yu Gao
- MOE Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou310058, Zhejiang, China
| | - Xiao-Wen Wei
- MOE Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou310058, Zhejiang, China
| | - James P Shapleigh
- Department of Microbiology, Cornell University, Ithaca, New York14853, United States
| | - He-Ping Zhao
- MOE Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou310058, Zhejiang, China
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31
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Li S, Wang S, Ji G. Influences of carbon sources on N 2O production during denitrification in freshwaters: Activity, isotopes and functional microbes. WATER RESEARCH 2022; 226:119315. [PMID: 36369690 DOI: 10.1016/j.watres.2022.119315] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 08/15/2022] [Accepted: 10/29/2022] [Indexed: 06/16/2023]
Abstract
Denitrification is one of the major sources of N2O in freshwaters. Diverse forms of organic compounds act as the electron donors for microbial denitrification. However, the influences of carbon sources on N2O production, N2O reduction, isotope fractionation and functional microbes during denitrification were largely unknown. In this study, five forms of carbon sources (i.e. acetate, citrate, glucose, cellobiose and leucine) were used to enrich denitrifiers in freshwater sediments. N2O conversion in the enrichments was investigated by a combination of inhibition technique, natural stable isotope method and metagenomics. Acetylene was effective in inhibiting N2O reduction without influencing the isotopic characteristics during N2O production. Glucose led to the least N2O production and reduction, in accordance with the lowest abundance of both NO and N2O reductases in this enrichment. δ18O and site preference value (SP, =δ15Nα-δ15Nβ) of N2O were sensitive to discriminate the five carbon sources, except when comparing acetate and leucine. Isotopic values of N2O were not significantly different in these two enrichments due to the similarity of NO reductases - Pseudomonas-type cNorB. Specifically, the enrichment with cellobiose produced N2O with the lowest δ18O values (39.4‰±1.1‰), due to Alicycliphilus with both cNorB and qNorB. The enrichment with glucose led to the highest SP values (8.9‰±8.6‰), caused by Thiobacillus-type cNorB. Our results demonstrated the link between carbon sources, N2O production and reduction, isotopic signatures, microbial populations and enzymes during denitrification in freshwaters.
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Affiliation(s)
- Shengjie Li
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing 100871, China
| | - Shuo Wang
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing 100871, China
| | - Guodong Ji
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing 100871, China.
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32
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Ong CT, Ross EM, Boe-Hansen G, Turni C, Hayes BJ, Fordyce G, Tabor AE. Adaptive sampling during sequencing reveals the origins of the bovine reproductive tract microbiome across reproductive stages and sexes. Sci Rep 2022; 12:15075. [PMID: 36065055 PMCID: PMC9445037 DOI: 10.1038/s41598-022-19022-w] [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] [Received: 03/18/2022] [Accepted: 08/23/2022] [Indexed: 11/30/2022] Open
Abstract
Cattle enterprises are one of the major livestock production systems globally and are forecasted to have stable growth in the next decade. To facilitate sustainable live weight production, optimal reproductive performance is essential. Microbial colonisation in the reproductive tract has been demonstrated as one of the factors contributing to bovine reproductive performance. Studies also implied that reproductive metagenomes are different at each stage of the estrous cycle. This study applied Oxford Nanopore Technologies’ adaptive long-read sequencing to profile the bovine reproductive microbiome collected from tropical cattle in northern Queensland, Australia. The microbiome samples were collected from cattle of different sexes, reproductive status and locations to provide a comprehensive view of the bovine reproductive microbiome in northern Australian cattle. Ascomycota, Firmicutes and Proteobacteria were abundant phyla identified in the bovine reproductive metagenomes of Australian cattle regardless of sexes, reproductive status and location. The species level taxonomical investigation suggested that gastrointestinal metagenome and the surrounding environment were potentially the origins of the bovine reproductive metagenome. Functional profiles further affirmed this implication, revealing that the reproductive metagenomes of the prepubertal and postpartum animals were dominated by microorganisms that catabolise dietary polysaccharides as an energy substrate while that of the pregnant animals had the function of harvesting energy from aromatic compounds. Bovine reproductive metagenome investigations can be employed to trace the origins of abnormal metagenomes, which is beneficial for disease prevention and control. Additionally, our results demonstrated different reproductive metagenome diversities between cattle from two different locations. The variation in diversity within one location can serve as the indicator of abnormal reproductive metagenome, but between locations inferences cannot be made. We suggest establishing localised metagenomic indices that can be used to infer abnormal reproductive metagenomes which contribute to abortion or sub-fertility.
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Affiliation(s)
- Chian Teng Ong
- Queensland Alliance for Agriculture and Food Innovation, Centre for Animal Science, The University of Queensland, Brisbane, QLD, 4072, Australia.
| | - Elizabeth M Ross
- Queensland Alliance for Agriculture and Food Innovation, Centre for Animal Science, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Gry Boe-Hansen
- Faculty of Science, School of Veterinary Science, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Conny Turni
- Queensland Alliance for Agriculture and Food Innovation, Centre for Animal Science, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Ben J Hayes
- Queensland Alliance for Agriculture and Food Innovation, Centre for Animal Science, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Geoffry Fordyce
- Queensland Alliance for Agriculture and Food Innovation, Centre for Animal Science, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Ala E Tabor
- Queensland Alliance for Agriculture and Food Innovation, Centre for Animal Science, The University of Queensland, Brisbane, QLD, 4072, Australia. .,Faculty of Science, School of Chemistry and Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.
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Gittins DA, Desiage PA, Morrison N, Rattray JE, Bhatnagar S, Chakraborty A, Zorz J, Li C, Horanszky O, Cramm MA, Bisiach F, Bennett R, Webb J, MacDonald A, Fowler M, Campbell DC, Hubert CRJ. Geological processes mediate a microbial dispersal loop in the deep biosphere. SCIENCE ADVANCES 2022; 8:eabn3485. [PMID: 36026445 PMCID: PMC9417182 DOI: 10.1126/sciadv.abn3485] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The deep biosphere is the largest microbial habitat on Earth and features abundant bacterial endospores. Whereas dormancy and survival at theoretical energy minima are hallmarks of microbial physiology in the subsurface, ecological processes such as dispersal and selection in the deep biosphere remain poorly understood. We investigated the biogeography of dispersing bacteria in the deep sea where upward hydrocarbon seepage was confirmed by acoustic imagery and geochemistry. Thermophilic endospores in the permanently cold seabed correlated with underlying seep conduits reveal geofluid-facilitated cell migration pathways originating in deep petroleum-bearing sediments. Endospore genomes highlight adaptations to life in anoxic petroleum systems and bear close resemblance to oil reservoir microbiomes globally. Upon transport out of the subsurface, viable thermophilic endospores reenter the geosphere by sediment burial, enabling germination and environmental selection at depth where new petroleum systems establish. This microbial dispersal loop circulates living biomass in and out of the deep biosphere.
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Affiliation(s)
- Daniel A. Gittins
- Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, Canada
- Corresponding author.
| | | | - Natasha Morrison
- Department of Natural Resources and Renewables, Government of Nova Scotia, Halifax, Canada
| | - Jayne E. Rattray
- Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Srijak Bhatnagar
- Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, Canada
| | | | - Jackie Zorz
- Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Carmen Li
- Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Oliver Horanszky
- Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Margaret A. Cramm
- Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Francesco Bisiach
- Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Robbie Bennett
- Natural Resources Canada, Geological Survey of Canada-Atlantic, Dartmouth, Canada
| | - Jamie Webb
- Applied Petroleum Technology, Calgary, Canada
| | - Adam MacDonald
- Department of Natural Resources and Renewables, Government of Nova Scotia, Halifax, Canada
| | | | - D. Calvin Campbell
- Natural Resources Canada, Geological Survey of Canada-Atlantic, Dartmouth, Canada
| | - Casey R. J. Hubert
- Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, Canada
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Dong X, Zhang C, Peng Y, Zhang HX, Shi LD, Wei G, Hubert CRJ, Wang Y, Greening C. Phylogenetically and catabolically diverse diazotrophs reside in deep-sea cold seep sediments. Nat Commun 2022; 13:4885. [PMID: 35985998 PMCID: PMC9391474 DOI: 10.1038/s41467-022-32503-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 08/03/2022] [Indexed: 11/16/2022] Open
Abstract
Microbially mediated nitrogen cycling in carbon-dominated cold seep environments remains poorly understood. So far anaerobic methanotrophic archaea (ANME-2) and their sulfate-reducing bacterial partners (SEEP-SRB1 clade) have been identified as diazotrophs in deep sea cold seep sediments. However, it is unclear whether other microbial groups can perform nitrogen fixation in such ecosystems. To fill this gap, we analyzed 61 metagenomes, 1428 metagenome-assembled genomes, and six metatranscriptomes derived from 11 globally distributed cold seeps. These sediments contain phylogenetically diverse nitrogenase genes corresponding to an expanded diversity of diazotrophic lineages. Diverse catabolic pathways were predicted to provide ATP for nitrogen fixation, suggesting diazotrophy in cold seeps is not necessarily associated with sulfate-dependent anaerobic oxidation of methane. Nitrogen fixation genes among various diazotrophic groups in cold seeps were inferred to be genetically mobile and subject to purifying selection. Our findings extend the capacity for diazotrophy to five candidate phyla (Altarchaeia, Omnitrophota, FCPU426, Caldatribacteriota and UBA6262), and suggest that cold seep diazotrophs might contribute substantially to the global nitrogen balance.
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Affiliation(s)
- Xiyang Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China.
| | - Chuwen Zhang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China
| | - Yongyi Peng
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China
| | - Hong-Xi Zhang
- Institute for Marine Engineering, Shenzhen International Graduate School, Tsinghua University, University Town, Shenzhen, China
- Department of Life Science, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Ling-Dong Shi
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Guangshan Wei
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Casey R J Hubert
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Yong Wang
- Institute for Marine Engineering, Shenzhen International Graduate School, Tsinghua University, University Town, Shenzhen, China.
- Department of Life Science, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Clayton, VIC, Australia
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Shi LD, Zhou YJ, Tang XJ, Kappler A, Chistoserdova L, Zhu LZ, Zhao HP. Coupled Aerobic Methane Oxidation and Arsenate Reduction Contributes to Soil-Arsenic Mobilization in Agricultural Fields. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:11845-11856. [PMID: 35920083 DOI: 10.1021/acs.est.2c01878] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Microbial oxidation of organic compounds can promote arsenic release by reducing soil-associated arsenate to the more mobile form arsenite. While anaerobic oxidation of methane has been demonstrated to reduce arsenate, it remains elusive whether and to what extent aerobic methane oxidation (aeMO) can contribute to reductive arsenic mobilization. To fill this knowledge gap, we performed incubations of both microbial laboratory cultures and soil samples from arsenic-contaminated agricultural fields in China. Incubations with laboratory cultures showed that aeMO could couple to arsenate reduction, wherein the former bioprocess was carried out by aerobic methanotrophs and the latter by a non-methanotrophic bacterium belonging to a novel and uncultivated representative of Burkholderiaceae. Metagenomic analyses combined with metabolite measurements suggested that formate served as the interspecies electron carrier linking aeMO to arsenate reduction. Such coupled bioprocesses also take place in the real world, supported by a similar stoichiometry and gene activity in the incubations with natural paddy soils, and contribute up to 76.2% of soil-arsenic mobilization into pore waters in the top layer of the soils where oxygen was present. Overall, this study reveals a previously overlooked yet significant contribution of aeMO to reductive arsenic mobilization.
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Affiliation(s)
- Ling-Dong Shi
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yu-Jie Zhou
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xian-Jin Tang
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Andreas Kappler
- Center for Applied Geosciences, University of Tübingen, Tübingen 72074, Germany
| | - Ludmila Chistoserdova
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195-0005, United States
| | - Li-Zhong Zhu
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - He-Ping Zhao
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
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Dyksma S, Gallert C. Effect of magnetite addition on transcriptional profiles of syntrophic Bacteria and Archaea during anaerobic digestion of propionate in wastewater sludge. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:664-678. [PMID: 35615789 DOI: 10.1111/1758-2229.13080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/20/2022] [Accepted: 04/24/2022] [Indexed: 05/23/2023]
Abstract
Anaerobic digestion (AD) is an important technology for the effective conversion of waste and wastewater to methane. Here, syntrophic bacteria transfer molecular hydrogen (H2 ), formate, or directly supply electrons (direct interspecies electron transfer, DIET) to the methanogens. Evidence is accumulating that the methanation of short-chain fatty acids can be enhanced by the addition of conductive material to the anaerobic digester, which has often been attributed to the stimulation of DIET. Since little is known about the transcriptional response of a complex AD microbial community to the addition of conductive material, we added magnetite to propionate-fed laboratory-scale reactors that were inoculated with wastewater sludge. Compared to the control reactors, the magnetite-amended reactors showed improved methanation of propionate. A genome-centric metatranscriptomics approach identified the active SCFA-oxidizing bacteria that affiliated with Firmicutes, Desulfobacterota and Cloacimonadota. The transcriptional profiles revealed that the syntrophic bacteria transferred acetate, H2 and formate to acetoclastic and hydrogenotrophic methanogens, whereas transcription of potential determinants for DIET such as conductive pili and outer-membrane cytochromes did not significantly change with magnetite addition. Overall, changes in the transcriptional profiles of syntrophic Bacteria and Archaea in propionate-fed lab-scale reactors amended with magnetite refute a major role of DIET in the studied system.
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Affiliation(s)
- Stefan Dyksma
- Faculty of Technology, Microbiology - Biotechnology, University of Applied Sciences Emden/Leer, Emden, Germany
| | - Claudia Gallert
- Faculty of Technology, Microbiology - Biotechnology, University of Applied Sciences Emden/Leer, Emden, Germany
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37
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Shi LD, Dong X, Liu Z, Yang Y, Lin JG, Li M, Gu JD, Zhu LZ, Zhao HP. A mixed blessing of viruses in wastewater treatment plants. WATER RESEARCH 2022; 215:118237. [PMID: 35245718 DOI: 10.1016/j.watres.2022.118237] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/23/2022] [Accepted: 02/24/2022] [Indexed: 06/14/2023]
Abstract
Activated sludge of wastewater treatment plants harbors a very high diversity of both microorganisms and viruses, wherein the latter control microbial dynamics and metabolisms by infection and lysis of cells. However, it remains poorly understood how viruses impact the biochemical processes of activated sludge, for example in terms of treatment efficiency and pollutant removal. Using metagenomic and metatranscriptomic deep sequencing, the present study recovered thousands of viral sequences from activated sludge samples of three conventional wastewater treatment plants. Gene-sharing network indicated that most of viruses could not be assigned to known viral genera, implying activated sludge as an underexplored reservoir for new viruses and viral diversity. In silico predictions of virus-host linkages demonstrated that infected microbial hosts, mostly belonging to bacteria, were transcriptionally active and able to hydrolyze polymers including starches, celluloses, and proteins. Some viruses encode auxiliary metabolic genes (AMGs) involved in carbon, nitrogen, and sulfur cycling, and antibiotic resistance genes (ARGs) for resistance to multiple drugs. The virus-encoded AMGs may enhance the biodegradation of contaminants like starches and celluloses, suggesting a positive role for viruses in strengthening the performance of activated sludge. However, ARGs would be disseminated to different microorganisms using viruses as gene shuttles, demonstrating the possibility for viruses to facilitate the spread of antibiotic resistance in the environment. Collectively, this study highlights the mixed blessing of viruses in wastewater treatment plants, and deciphers how they manipulate the biochemical processes in the activated sludge, with implications for both environmental protection and ecosystem security.
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Affiliation(s)
- Ling-Dong Shi
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiyang Dong
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Zongbao Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Yuchun Yang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou 510275, China
| | - Jih-Gaw Lin
- Institute of Environmental Engineering, National Yang Ming Chiao Tung University, 1001 University Road, Hsinchu 30010, Taiwan
| | - 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
| | - Ji-Dong Gu
- Environmental Science and Engineering Program, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, China
| | - Li-Zhong Zhu
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - He-Ping Zhao
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, China.
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38
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Liu S, Moon CD, Zheng N, Huws S, Zhao S, Wang J. Opportunities and challenges of using metagenomic data to bring uncultured microbes into cultivation. MICROBIOME 2022; 10:76. [PMID: 35546409 PMCID: PMC9097414 DOI: 10.1186/s40168-022-01272-5] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 04/10/2022] [Indexed: 05/12/2023]
Abstract
Although there is now an extensive understanding of the diversity of microbial life on earth through culture-independent metagenomic DNA sequence analyses, the isolation and cultivation of microbes remains critical to directly study them and confirm their metabolic and physiological functions, and their ecological roles. The majority of environmental microbes are as yet uncultured however; therefore, bringing these rare or poorly characterized groups into culture is a priority to further understand microbiome functions. Moreover, cultivated isolates may find utility in a range of applications, such as new probiotics, biocontrol agents, and agents for industrial processes. The growing abundance of metagenomic and meta-transcriptomic sequence information from a wide range of environments provides more opportunities to guide the isolation and cultivation of microbes of interest. In this paper, we discuss a range of successful methodologies and applications that have underpinned recent metagenome-guided isolation and cultivation of microbe efforts. These approaches include determining specific culture conditions to enrich for taxa of interest, to more complex strategies that specifically target the capture of microbial species through antibody engineering and genome editing strategies. With the greater degree of genomic information now available from uncultivated members, such as via metagenome-assembled genomes, the theoretical understanding of their cultivation requirements will enable greater possibilities to capture these and ultimately gain a more comprehensive understanding of the microbiomes. Video Abstract.
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Affiliation(s)
- Sijia Liu
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Christina D Moon
- AgResearch Ltd., Grasslands Research Centre, Palmerston North, New Zealand
| | - Nan Zheng
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China
| | - Sharon Huws
- School of Biological Sciences and Institute for Global Food Security, 19 Chlorine Gardens, Queen's University Belfast, Belfast, UK
| | - Shengguo Zhao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China.
| | - Jiaqi Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China.
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39
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Karp PD, Paley S, Krummenacker M, Kothari A, Wannemuehler MJ, Phillips GJ. Pathway Tools Management of Pathway/Genome Data for Microbial Communities. FRONTIERS IN BIOINFORMATICS 2022; 2:869150. [PMID: 36304298 PMCID: PMC9580912 DOI: 10.3389/fbinf.2022.869150] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 04/05/2022] [Indexed: 11/14/2022] Open
Abstract
The Pathway Tools (PTools) software provides a suite of capabilities for storing and analyzing integrated collections of genomic and metabolic information in the form of organism-specific Pathway/Genome Databases (PGDBs). A microbial community is represented in PTools by generating a PGDB from each metagenome-assembled genome (MAG). PTools computes a metabolic reconstruction for each organism, and predicts its operons. The properties of individual MAGs can be investigated using the many search and visualization operations within PTools. PTools also enables the user to investigate the properties of the microbial community by issuing searches across the full community, and by performing comparative operations across genome and pathway information. The software can generate a metabolic network diagram for the community, and it can overlay community omics datasets on that network diagram. PTools also provides a tool for searching for metabolic transformation routes across an organism community.
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Affiliation(s)
- Peter D. Karp
- Bioinformatics Research Group, Artificial Intelligence Center, SRI International, Menlo Park, CA, United States,*Correspondence: Peter D. Karp,
| | - Suzanne Paley
- Bioinformatics Research Group, Artificial Intelligence Center, SRI International, Menlo Park, CA, United States
| | - Markus Krummenacker
- Bioinformatics Research Group, Artificial Intelligence Center, SRI International, Menlo Park, CA, United States
| | - Anamika Kothari
- Bioinformatics Research Group, Artificial Intelligence Center, SRI International, Menlo Park, CA, United States
| | | | - Gregory J. Phillips
- Department of Veterinary Microbiology, Iowa State University, Ames, IA, United States
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40
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Zhong C, Nesbø CL, von Gunten K, Zhang Y, Shao X, Jin R, Konhauser KO, Goss GG, Martin JW, He Y, Qian PY, Lanoil BD, Alessi DS. Complex impacts of hydraulic fracturing return fluids on soil microbial community respiration, structure, and functional potentials. Environ Microbiol 2022; 24:4108-4123. [PMID: 35416402 DOI: 10.1111/1462-2920.16009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 04/07/2022] [Indexed: 11/27/2022]
Abstract
The consequences of soils exposed to hydraulic fracturing (HF) return fluid, often collectively termed flowback and produced water (FPW), are poorly understood, even though soils are a common receptor of FPW spills. Here, we investigate the impacts on soil microbiota exposed to FPW collected from the Montney Formation of western Canada. We measured soil respiration, microbial community structure, and functional potentials under FPW exposure across a range of concentrations, exposure time, and soil types (luvisol and chernozem). We find that soil type governs microbial community response upon FPW exposure. Within each soil, FPW exposure led to reduced biotic soil respiration, and shifted microbial community structure and functional potentials. We detect substantially higher species richness and more unique functional genes in FPW-exposed soils than in FPW-unexposed soils, with metagenome-assembled genomes (e.g., Marinobacter persicus) from luvisol soil exposed to concentrated FPW being most similar to genomes from HF/FPW sites. Our data demonstrate the complex impacts of microbial communities following FPW exposure, and highlight the site-specific effects in evaluation of spills and agricultural reuse of FPW on the normal soil functions. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Cheng Zhong
- Department of Earth and Atmospheric Sciences, Faculty of Science, University of Alberta, Edmonton, Alberta, T6G 2E3, Canada.,Department of Ocean Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China.,Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, Guangzhou, China
| | - Camilla L Nesbø
- Department of Biological Sciences, Faculty of Science, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada
| | - Konstantin von Gunten
- Department of Earth and Atmospheric Sciences, Faculty of Science, University of Alberta, Edmonton, Alberta, T6G 2E3, Canada
| | - Yifeng Zhang
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Xiaoqing Shao
- Department of Physical and Environmental Sciences, University of Toronto, Toronto, Ontario, M1C 1A4, Canada
| | - Rong Jin
- Department of Earth and Atmospheric Sciences, Faculty of Science, University of Alberta, Edmonton, Alberta, T6G 2E3, Canada
| | - Kurt O Konhauser
- Department of Earth and Atmospheric Sciences, Faculty of Science, University of Alberta, Edmonton, Alberta, T6G 2E3, Canada
| | - Greg G Goss
- Department of Biological Sciences, Faculty of Science, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada
| | - Jonathan W Martin
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Yuhe He
- School of Energy and Environment and State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong, China
| | - Pei-Yuan Qian
- Department of Ocean Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China.,Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, Guangzhou, China
| | - Brian D Lanoil
- Department of Biological Sciences, Faculty of Science, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada
| | - Daniel S Alessi
- Department of Earth and Atmospheric Sciences, Faculty of Science, University of Alberta, Edmonton, Alberta, T6G 2E3, Canada
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Evaluation of Host Depletion and Extraction Methods for Shotgun Metagenomic Analysis of Bovine Vaginal Samples. Microbiol Spectr 2022; 10:e0041221. [PMID: 35404108 PMCID: PMC9045270 DOI: 10.1128/spectrum.00412-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The reproductive tract metagenome plays a significant role in the various reproductive system functions, including reproductive cycles, health, and fertility. One of the major challenges in bovine vaginal metagenome studies is host DNA contamination, which limits the sequencing capacity for metagenomic content and reduces the accuracy of untargeted shotgun metagenomic profiling. This is the first study comparing the effectiveness of different host depletion and DNA extraction methods for bovine vaginal metagenomic samples. The host depletion methods evaluated were slow centrifugation (Soft-spin), NEBNext Microbiome DNA Enrichment kit (NEBNext), and propidium monoazide (PMA) treatment, while the extraction methods were DNeasy Blood and Tissue extraction (DNeasy) and QIAamp DNA Microbiome extraction (QIAamp). Soft-spin and QIAamp were the most effective host depletion method and extraction methods, respectively, in reducing the number of cattle genomic content in bovine vaginal samples. The reduced host-to-microbe ratio in the extracted DNA increased the sequencing depth for microbial reads in untargeted shotgun sequencing. Bovine vaginal samples extracted with QIAamp presented taxonomical profiles which closely resembled the mock microbial composition, especially for the recovery of Gram-positive bacteria. Additionally, samples extracted with QIAamp presented extensive functional profiles with deep coverage. Overall, a combination of Soft-spin and QIAamp provided the most robust representation of the vaginal microbial community in cattle while minimizing host DNA contamination. IMPORTANCE In addition to the host tissue collected during the sampling process, bovine vaginal samples are saturated with large amounts of extracellular DNA and secreted proteins that are essential for physiological purposes, including the reproductive cycle and immune defense. Due to the high host-to-microbe genome ratio, which hampers the sequencing efficacy for metagenome samples and the recovery of the actual metagenomic profiles, bovine vaginal samples cannot benefit from the full potential of shotgun sequencing. This is the first investigation on the most effective host depletion and extraction methods for bovine vaginal metagenomic samples. This study demonstrated an effective combination of host depletion and extraction methods, which harvested higher percentages of 16S rRNA genes and microbial reads, which subsequently led to a taxonomical profile that resembled the actual community and a functional profile with deeper coverage. A representative metagenomic profile is essential for investigating the role of the bovine vaginal metagenome for both reproductive function and susceptibility to infections.
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Zhang H, Wang Y, Liu P, Sun Y, Dong X, Hu X. Unveiling the occurrence, hosts and mobility potential of antibiotic resistance genes in the deep ocean. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 816:151539. [PMID: 34762954 DOI: 10.1016/j.scitotenv.2021.151539] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 10/20/2021] [Accepted: 11/04/2021] [Indexed: 06/13/2023]
Abstract
As emerging microbial contaminants, antibiotic resistance genes (ARGs) are widely reported in the neritic zone. However, the profiles of ARGs in the deep ocean have not yet been fully resolved. In this study, the distribution, hosts, and mobility potential of ARGs at different water depths in the Western Pacific (WP) were investigated and compared to those in Bohai Sea (BH) waters using environmental parameter measurements, amplicon sequencing, metagenomic assembly and binning approaches. Our results showed that the top eight most abundant known ARG types in WP and BH waters were multidrug (39.85%), peptide (14.98%), aminoglycoside (11.33%), macrolide-lincosamide-streptogramin (MLS, 4.06%), tetracycline (3.74%), beta-lactam (3.12%), fluoroquinolone (1.79%) and rifamycin (1.24%). The ARGs observed in mesopelagic and bathypelagic waters were abundant and diverse as those observed in neritic waters, indicating that deep-sea water could be another environmental reservoir for ARGs. For deep-sea ARGs, members from classes Gammaproteobacteria (70%) and Alphaproteobacteria (21.1%) were the most important potential hosts. In addition, mobile genetic element analysis suggested that the ARG migration potential in dee sea water (> 1000 m) was relatively high. Overall, our findings expanded the understanding of ARGs in deep seawater and provided guidance for ARG pollution control and risk prediction.
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Affiliation(s)
- Haikun Zhang
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Yibo Wang
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Pengyuan Liu
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China; University of Chinese Academy of Sciences, Beijing, China
| | - Yanyu Sun
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China; University of Chinese Academy of Sciences, Beijing, China
| | - Xiyang Dong
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China.
| | - Xiaoke Hu
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.
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Vuong P, Moreira-Grez B, Wise MJ, Whiteley AS, Kumaresan D, Kaur P. From Rags to Enriched: Metagenomic Insights into Ammonia-oxidizing Archaea Following Ammonia Enrichment of a Denuded Oligotrophic Soil Ecosystem. Environ Microbiol 2022; 24:3097-3110. [PMID: 35384236 PMCID: PMC9545067 DOI: 10.1111/1462-2920.15994] [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] [Received: 11/26/2021] [Accepted: 03/28/2022] [Indexed: 11/29/2022]
Abstract
Stored topsoil acts as a microbial inoculant for ecological restoration of land after disturbance, but the altered circumstances frequently create unfavorable conditions for microbial survival. Nitrogen cycling is a critical indicator for ecological success and this study aimed to investigate the cornerstone taxa driving the process. Previous in-silico studies investigating stored topsoil discovered persistent archaeal taxa with the potential for re-establishing ecological activity. Ammonia oxidization is the limiting step in nitrification and as such, ammonia oxidizing archaea (AOA) can be considered as the one of the gatekeepers for the re-establishment of the nitrogen cycle in disturbed soils. Semi-arid soil samples were enriched with ammonium sulfate to promote the selective enrichment of ammonia oxidizers for targeted genomic recovery, and to investigate the microbial response of the microcosm to nitrogen input. Ammonia addition produced an increase in AOA population, particularly within the genus Candidatus Nitrosotalea, from which metagenome-assembled genomes (MAGs) were successfully recovered. The Ca. Nitrosotalea archaeon candidates' ability to survive in extreme conditions and rapidly respond to ammonia input makes it a potential bioprospecting target for application in ecological restoration of semi-arid soils and the recovered MAGs provide a metabolic blueprint for developing potential strategies towards isolation of these acclimated candidates. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Paton Vuong
- UWA School of Agriculture & Environment, University of Western Australia, Perth, Australia
| | - Benjamin Moreira-Grez
- UWA School of Agriculture & Environment, University of Western Australia, Perth, Australia
| | - Michael J Wise
- School of Physics, Mathematics and Computing, University of Western Australia, Perth, Australia.,The Marshall Centre of Infectious Diseases, School of Biological Sciences, The University of Western Australia, Perth, Australia
| | - Andrew S Whiteley
- Centre for Environment & Life Sciences, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Floreat, Australia
| | - Deepak Kumaresan
- School of Biological Sciences, Queen's University of Belfast, Belfast, UK
| | - Parwinder Kaur
- UWA School of Agriculture & Environment, University of Western Australia, Perth, Australia
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Morais DAA, Cavalcante JVF, Monteiro SS, Pasquali MAB, Dalmolin RJS. MEDUSA: A Pipeline for Sensitive Taxonomic Classification and Flexible Functional Annotation of Metagenomic Shotgun Sequences. Front Genet 2022; 13:814437. [PMID: 35330728 PMCID: PMC8940201 DOI: 10.3389/fgene.2022.814437] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 02/09/2022] [Indexed: 11/24/2022] Open
Abstract
Metagenomic studies unravel details about the taxonomic composition and the functions performed by microbial communities. As a complete metagenomic analysis requires different tools for different purposes, the selection and setup of these tools remain challenging. Furthermore, the chosen toolset will affect the accuracy, the formatting, and the functional identifiers reported in the results, impacting the results interpretation and the biological answer obtained. Thus, we surveyed state-of-the-art tools available in the literature, created simulated datasets, and performed benchmarks to design a sensitive and flexible metagenomic analysis pipeline. Here we present MEDUSA, an efficient pipeline to conduct comprehensive metagenomic analyses. It performs preprocessing, assembly, alignment, taxonomic classification, and functional annotation on shotgun data, supporting user-built dictionaries to transfer annotations to any functional identifier. MEDUSA includes several tools, as fastp, Bowtie2, DIAMOND, Kaiju, MEGAHIT, and a novel tool implemented in Python to transfer annotations to BLAST/DIAMOND alignment results. These tools are installed via Conda, and the workflow is managed by Snakemake, easing the setup and execution. Compared with MEGAN 6 Community Edition, MEDUSA correctly identifies more species, especially the less abundant, and is more suited for functional analysis using Gene Ontology identifiers.
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Affiliation(s)
- Diego A. A. Morais
- Bioinformatics Multidisciplinary Environment, Federal University of Rio Grande do Norte, Natal, Brazil
| | - João V. F. Cavalcante
- Bioinformatics Multidisciplinary Environment, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Shênia S. Monteiro
- Graduate Program in Engineering and Natural Resources Management, Federal University of Campina Grande, Campina Grande, Brazil
| | - Matheus A. B. Pasquali
- Graduate Program in Engineering and Natural Resources Management, Federal University of Campina Grande, Campina Grande, Brazil
- Academic Food Engineering Unit, Federal University of Campina Grande, Campina Grande, Brazil
| | - Rodrigo J. S. Dalmolin
- Bioinformatics Multidisciplinary Environment, Federal University of Rio Grande do Norte, Natal, Brazil
- Department of Biochemistry, Federal University of Rio Grande do Norte, Natal, Brazil
- *Correspondence: Rodrigo J. S. Dalmolin,
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Ataeian M, Liu Y, Kouris A, Hawley AK, Strous M. Ecological Interactions of Cyanobacteria and Heterotrophs Enhances the Robustness of Cyanobacterial Consortium for Carbon Sequestration. Front Microbiol 2022; 13:780346. [PMID: 35222325 PMCID: PMC8880816 DOI: 10.3389/fmicb.2022.780346] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 01/19/2022] [Indexed: 12/21/2022] Open
Abstract
Lack of robustness is a major barrier to foster a sustainable cyanobacterial biotechnology. Use of cyanobacterial consortium increases biodiversity, which provides functional redundancy and prevents invading species from disrupting the production ecosystem. Here we characterized a cyanobacterial consortium enriched from microbial mats of alkaline soda lakes in BC, Canada, at high pH and alkalinity. This consortium has been grown in open laboratory culture for 4 years without crashes. Using shotgun metagenomic sequencing, 29 heterotrophic metagenome-assembled-genomes (MAGs) were retrieved and were assigned to Bacteroidota, Alphaproteobacteria, Gammaproteobacteria, Verrucomicrobiota, Patescibacteria, Planctomycetota, and Archaea. In combination with metaproteomics, the overall stability of the consortium was determined under different cultivation conditions. Genome information from each heterotrophic population was investigated for six ecological niches created by cyanobacterial metabolism and one niche for phototrophy. Genome-resolved metaproteomics with stable isotope probing using 13C-bicarbonate (protein/SIP) showed tight coupling of carbon transfer from cyanobacteria to the heterotrophic populations, specially Wenzhouxiangella. The community structure was compared to a previously described consortium of a closely related cyanobacteria, which indicated that the results may be generalized. Productivity losses associated with heterotrophic metabolism were relatively small compared to other losses during photosynthesis.
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Affiliation(s)
- Maryam Ataeian
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Yihua Liu
- Department Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Angela Kouris
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Alyse K. Hawley
- School of Engineering, University of British Columbia Okanagan, Kelowna, BC, Canada
| | - Marc Strous
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
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46
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Li S, Liao Y, Pang Y, Dong X, Strous M, Ji G. Denitrification and dissimilatory nitrate reduction to ammonia in long-term lake sediment microcosms with iron(II). THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 807:150835. [PMID: 34627917 DOI: 10.1016/j.scitotenv.2021.150835] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 09/19/2021] [Accepted: 10/02/2021] [Indexed: 06/13/2023]
Abstract
Nitrate is an abundant pollutant in aquatic environments. Competition between the nitrate reduction processes, denitrification, which converts nitrate into nitrogen gas, and dissimilatory nitrate reduction to ammonia (DNRA), which converts nitrate into ammonia, decides whether an ecosystem removes or retains nitrogen. The presence of iron was previously reported to stimulate DNRA while sometimes inhibiting denitrification in in-situ studies, but long-term effect of iron(II) inputs on the competition is unknown. Here we inoculated long-term microcosms with sediments from two freshwater lakes. During 540 days of incubations, the microcosms with nitrate and Fe(II) additions of both lakes were able to sustain high nitrate reduction rates. Lepidocrocite was produced as a product of iron oxidation. We found both denitrification and DNRA were stimulated by nitrate and iron in the absence of external organic carbon addition. Phylogenetic analysis of denitrification genes, nirK and nirS, and DNRA genes, nirB and nrfA, was performed with metagenomic sequencing results. Enrichment was shown for reported Fe(II)-dependent nitrate reducers associated with nirS and nirB. Most of these bacteria are affiliated with Betaproteobacteria. From 16S rRNA gene analysis, Betaproteobacteria was enriched as well. In parallel, heterotrophic denitrifiers and methanotrophic DNRA archaea increased in abundance. Our results suggested heterotrophic and Fe(II)-dependent nitrate reducers both contributed to denitrification and DNRA in long-term microcosm incubations provided with iron.
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Affiliation(s)
- Shengjie Li
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing 100871, China; Department of Geoscience, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Yinhao Liao
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing 100871, China
| | - Yunmeng Pang
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing 100871, China; Collaborative Innovation Center for Advanced Nuclear Energy Technology, INET, Tsinghua University, Beijing 100084, China
| | - Xiaoli Dong
- Department of Geoscience, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Marc Strous
- Department of Geoscience, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Guodong Ji
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing 100871, China.
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Loza A, García-Guevara F, Segovia L, Escobar-Zepeda A, Sanchez-Olmos MDC, Merino E, Sanchez-Flores A, Pardo-Lopez L, Juarez K, Gutierrez-Rios RM. Definition of the Metagenomic Profile of Ocean Water Samples From the Gulf of Mexico Based on Comparison With Reference Samples From Sites Worldwide. Front Microbiol 2022; 12:781497. [PMID: 35178038 PMCID: PMC8846951 DOI: 10.3389/fmicb.2021.781497] [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] [Received: 09/22/2021] [Accepted: 12/23/2021] [Indexed: 11/13/2022] Open
Abstract
Computational and statistical analysis of shotgun metagenomes can predict gene abundance and is helpful for elucidating the functional and taxonomic compositions of environmental samples. Gene products are compared against physicochemical conditions or perturbations to shed light on the functions performed by the microbial community of an environmental sample; however, this information is not always available. The present study proposes a method for inferring the metabolic potential of metagenome samples by constructing a reference based on determining the probability distribution of the counts of each enzyme annotated. To test the methodology, we used marine water samples distributed worldwide as references. Then, the references were utilized to compare the annotated enzymes of two different water samples extracted from the Gulf of Mexico (GoM) to distinguish those enzymes with atypical behavior. The enzymes whose annotation counts presented frequencies significantly different from those of the reference were used to perform metabolic reconstruction, which naturally identified pathways. We found that several of the enzymes were involved in the biodegradation of petroleum, which is consistent with the impact of human hydrocarbon extraction activity and its ubiquitous presence in the GoM. The examination of other reconstructed pathways revealed significant enzymes indicating the presence of microbial communities characterizing each ocean depth and ocean cycle, providing a fingerprint of each sampled site.
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Xu S, Chai W, Xiao R, Smets BF, Palomo A, Lu H. Survival strategy of comammox bacteria in a wastewater nutrient removal system with sludge fermentation liquid as additional carbon source. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 802:149862. [PMID: 34461473 DOI: 10.1016/j.scitotenv.2021.149862] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/19/2021] [Accepted: 08/19/2021] [Indexed: 06/13/2023]
Abstract
Complete ammonia oxidizing (comammox) bacteria are frequently detected in wastewater biological nutrient removal (BNR) systems. This study identified "Candidatus Nitrospira nitrosa"-like comammox bacteria as the predominant ammonia oxidizers (97.5-99.4%) in a lab-scale BNR system with acetate and sludge fermentation liquid as external carbon sources. The total nitrogen and phosphorus removals of the system were 75.9% and 86.9% with minimal N2O emission (0.27%). Low ammonia concentration, mixotrophic growth potentials and metabolic interactions with diverse heterotrophs collectively contributed to the survival of comammox bacteria in the system. The recovered draft genomes of comammox bacteria indicated their potentials in using acetate and propionate but not butyrate. Acetate and propionate indeed stimulated the transcription of comammox amoA genes (up-regulated by 4.1 folds compared with no organic addition), which was positively correlated with the ammonia oxidation rate of the community (r = 0.75, p < 0.05). Comammox bacteria could provide vitamins/cofactors (e.g., cobalamin and biotin) to heterotrophs (e.g., Burkholderiaceae), and in return receive amino acids (e.g., phenylalanine and tyrosine) from heterotrophs, which they cannot synthesize. Compared with comammox bacteria, ammonia oxidizing bacteria (AOB) exhibited lower metabolic versatility, and lacked more pathways for the synthesis of amino acids and vitamin/cofactors, leading to their washout in the studied system. BNRs with comammox bacteria as the major nitrifiers hold great potentials in achieving superior performance at low aeration cost and low N2O emission and at full-scale plants.
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Affiliation(s)
- Shaoyi Xu
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Wenbo Chai
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Rui Xiao
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Barth F Smets
- Department of Environmental Engineering, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Alejandro Palomo
- Department of Environmental Engineering, Technical University of Denmark, Kgs Lyngby, Denmark; State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Huijie Lu
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China.
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49
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Ong CT, Ross EM, Boe-Hansen GB, Turni C, Hayes BJ, Tabor AE. Technical note: overcoming host contamination in bovine vaginal metagenomic samples with nanopore adaptive sequencing. J Anim Sci 2022; 100:skab344. [PMID: 34791313 PMCID: PMC8722758 DOI: 10.1093/jas/skab344] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 11/10/2021] [Indexed: 12/11/2022] Open
Abstract
Animal metagenomic studies, in which host-associated microbiomes are profiled, are an increasingly important contribution to our understanding of the physiological functions, health and susceptibility to diseases of livestock. One of the major challenges in these studies is host DNA contamination, which limits the sequencing capacity for metagenomic content and reduces the accuracy of metagenomic profiling. This is the first study comparing the effectiveness of different sequencing methods for profiling bovine vaginal metagenomic samples. We compared the new method of Oxford Nanopore Technologies (ONT) adaptive sequencing, which can be used to target or eliminate defined genetic sequences, to standard ONT sequencing, Illumina 16S rDNA amplicon sequencing, and Illumina shotgun sequencing. The efficiency of each method in recovering the metagenomic data and recalling the metagenomic profiles was assessed. ONT adaptive sequencing yielded a higher amount of metagenomic data than the other methods per 1 Gb of sequence data. The increased sequencing efficiency of ONT adaptive sequencing consequently reduced the amount of raw data needed to provide sufficient coverage for the metagenomic samples with high host-to-microbe DNA ratio. Additionally, the long reads generated by ONT adaptive sequencing retained the continuity of read information, which benefited the in-depth annotations for both taxonomical and functional profiles of the metagenome. The different methods resulted in the identification of different taxa. Genera Clostridium, which was identified at low abundances and categorized under Order "Unclassified Clostridiales" when using the 16S rDNA amplicon sequencing method, was identified to be the dominant genera in the sample when sequenced with the three other methods. Additionally, higher numbers of annotated genes were identified with ONT adaptive sequencing, which also produced high coverage on most of the commonly annotated genes. This study illustrates the advantages of ONT adaptive sequencing in improving the amount of metagenomic data derived from microbiome samples with high host-to-microbe DNA ratio and the advantage of long reads in preserving intact information for accurate annotations.
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Affiliation(s)
- Chian Teng Ong
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Queensland 4072, Australia
| | - Elizabeth M Ross
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Queensland 4072, Australia
| | - Gry B Boe-Hansen
- Faculty of Science, School of Veterinary Science, The University of Queensland, Queensland 4072, Australia
| | - Conny Turni
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Queensland 4072, Australia
| | - Ben J Hayes
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Queensland 4072, Australia
| | - Ala E Tabor
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Queensland 4072, Australia
- Faculty of Science, School of Chemistry and Molecular Bioscience, The University of Queensland, Queensland 4072, Australia
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50
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Ellis M, Altshuler I, Schreiber L, Chen YJ, Okshevsky M, Lee K, Greer CW, Whyte LG. Hydrocarbon biodegradation potential of microbial communities from high Arctic beaches in Canada's Northwest Passage. MARINE POLLUTION BULLETIN 2022; 174:113288. [PMID: 35090274 DOI: 10.1016/j.marpolbul.2021.113288] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 12/12/2021] [Accepted: 12/20/2021] [Indexed: 06/14/2023]
Abstract
Sea ice loss is opening shipping routes in Canada's Northwest Passage, increasing the risk of an oil spill. Harnessing the capabilities of endemic microorganisms to degrade oil may be an effective remediation strategy for contaminated shorelines; however, limited data exists along Canada's Northwest Passage. In this study, hydrocarbon biodegradation potential of microbial communities from eight high Arctic beaches was assessed. Across high Arctic beaches, community composition was distinct, potential hydrocarbon-degrading genera were detected and microbial communities were able to degrade hydrocarbons (hexadecane, naphthalene, and alkanes) at low temperature (4 °C). Hexadecane and naphthalene biodegradation were stimulated by nutrients, but nutrients had little effect on Ultra Low Sulfur Fuel Oil biodegradation. Oiled microcosms showed a significant enrichment of Pseudomonas and Rhodococcus. Nutrient-amended microcosms showed increased abundances of key hydrocarbon biodegradation genes (alkB and CYP153). Ultimately, this work provides insight into hydrocarbon biodegradation on Arctic shorelines and oil-spill remediation in Canada's Northwest Passage.
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Affiliation(s)
- Madison Ellis
- Department of Natural Resource Sciences, McGill University, Quebec, Canada.
| | - Ianina Altshuler
- Department of Natural Resource Sciences, McGill University, Quebec, Canada; Faculty of Biosciences, Norwegian University of Life Sciences NMBU, Ås, Norway
| | - Lars Schreiber
- Energy, Mining and Environment Research Centre, National Research Council of Canada, Quebec, Canada
| | - Ya-Jou Chen
- Department of Natural Resource Sciences, McGill University, Quebec, Canada
| | - Mira Okshevsky
- Department of Natural Resource Sciences, McGill University, Quebec, Canada; Department of Human Health Therapeutics Research Centre, National Research Council of Canada, Quebec, Canada
| | - Kenneth Lee
- Ecosystem Science, Fisheries and Oceans Canada, Ottawa, Canada
| | - Charles W Greer
- Department of Natural Resource Sciences, McGill University, Quebec, Canada; Energy, Mining and Environment Research Centre, National Research Council of Canada, Quebec, Canada
| | - Lyle G Whyte
- Department of Natural Resource Sciences, McGill University, Quebec, Canada
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