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Yan Y, Twible LE, Liu FYL, Arrey JLS, Colenbrander Nelson TE, Warren LA. Cascading sulfur cycling in simulated oil sands pit lake water cap mesocosms transitioning from oxic to euxinic conditions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 950:175272. [PMID: 39111438 DOI: 10.1016/j.scitotenv.2024.175272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 07/31/2024] [Accepted: 08/02/2024] [Indexed: 08/11/2024]
Abstract
Base Mine Lake (BML), the first full-scale demonstration of oil sands tailings pit lake reclamation technology, is experiencing expansive, episodic hypolimnetic euxinia resulting in greater sulfur biogeochemical cycling within the water cap. Here, Fluid Fine Tailings (FFT)-water mesocosm experiments simulating the in situ BML summer hypolimnetic oxic-euxinic transition determined sulfur biogeochemical processes and their controlling factors. While mesocosm water caps without FFT amendments experienced limited geochemical and microbial changes during the experimental period, FFT-amended mesocosm water caps evidenced three successive stages of S speciation in ∼30 days: (S1) rising expansion of water cap euxinia from FFT to water surface; enabling (S2) rapid sulfate (SO42-) reduction and sulfide production directly within the water column; fostering (S3) generation and subsequent consumption of sulfur oxidation intermediate compounds (SOI). Identified key SOI, elemental S and thiosulfate, support subsequent SOI oxidation, reduction, and/or disproportionation processes in the system. Dominant water cap microbes shifted from methanotrophs and denitrifying/iron-reducing bacteria to functionally versatile sulfur-reducing bacteria (SRB) comprising sulfate-reducing bacteria (Desulfovibrionales) and SOI-reducing/disproportionating bacteria (Campylobacterales and Desulfobulbales). The observed microbial shift is driven by decreasing [SO42-] and organic aromaticity, with putative hydrocarbon-degrading bacteria providing electron donors for SRB. Comparison between unsterile and sterile water treatments further underscores the biogeochemical readiness of the in situ water cap to enhance oxidant depletion, euxinia expansion and establishment of water cap SRB communities aided by FFT migration of anaerobes. Results here identify the collective influence of FFT and water cap microbial communities on water cap euxinia expansion associated with sequential S reactions that are controlled by concentrations of oxidants, labile organic substrates and S species. This emphasizes the necessity of understanding this complex S cycling in assessing BML water cap O2 persistence.
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Affiliation(s)
- Yunyun Yan
- Department of Civil and Mineral Engineering, University of Toronto, 35 St. George Street, Toronto, Ontario M5S 1A4, Canada
| | - Lauren E Twible
- Department of Civil and Mineral Engineering, University of Toronto, 35 St. George Street, Toronto, Ontario M5S 1A4, Canada
| | - Felicia Y L Liu
- Department of Civil and Mineral Engineering, University of Toronto, 35 St. George Street, Toronto, Ontario M5S 1A4, Canada
| | - James L S Arrey
- Department of Civil and Mineral Engineering, University of Toronto, 35 St. George Street, Toronto, Ontario M5S 1A4, Canada
| | - Tara E Colenbrander Nelson
- Department of Civil and Mineral Engineering, University of Toronto, 35 St. George Street, Toronto, Ontario M5S 1A4, Canada
| | - Lesley A Warren
- Department of Civil and Mineral Engineering, University of Toronto, 35 St. George Street, Toronto, Ontario M5S 1A4, Canada.
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Chen M, Grégoire DS, Bain JG, Blowes DW, Hug LA. Legacy copper/nickel mine tailings potentially harbor novel iron/sulfur cycling microorganisms within highly variable communities. Appl Environ Microbiol 2024; 90:e0014324. [PMID: 38814057 PMCID: PMC11218620 DOI: 10.1128/aem.00143-24] [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: 01/24/2024] [Accepted: 05/07/2024] [Indexed: 05/31/2024] Open
Abstract
The oxidation of sulfide-bearing mine tailings catalyzed by acidophilic iron and sulfur-oxidizing bacteria releases toxic metals and other contaminants into soil and groundwater as acid mine drainage. Understanding the environmental variables that control the community structure and metabolic activity of microbes indigenous to tailings (especially the abiotic stressors of low pH and high dissolved metal content) is crucial to developing sustainable bioremediation strategies. We determined the microbial community composition along two continuous vertical gradients of Cu/Ni mine tailings at each of two tailings impoundments near Sudbury, Ontario. 16S rRNA amplicon data showed high variability in community diversity and composition between locations, as well as at different depths within each location. A temporal comparison for one tailings location showed low fluctuation in microbial communities across 2 years. Differences in community composition correlated most strongly with pore-water pH, Eh, alkalinity, salinity, and the concentration of several dissolved metals (including iron, but not copper or nickel). The relative abundances of individual genera differed in their degrees of correlation with geochemical factors. Several abundant lineages present at these locations have not previously been associated with mine tailings environments, including novel species predicted to be involved in iron and sulfur cycling.IMPORTANCEMine tailings represent a significant threat to North American freshwater, with legacy tailings areas generating acid mine drainage (AMD) that contaminates rivers, lakes, and aquifers. Microbial activity accelerates AMD formation through oxidative metabolic processes but may also ameliorate acidic tailings by promoting secondary mineral precipitation and immobilizing dissolved metals. Tailings exhibit high geochemical variation within and between mine sites and may harbor many novel extremophiles adapted to high concentrations of toxic metals. Characterizing the unique microbiomes associated with tailing environments is key to identifying consortia that may be used as the foundation for innovative mine-waste bioremediation strategies. We provide an in-depth analysis of microbial diversity at four copper/nickel mine tailings impoundments, describe how communities (and individual lineages) differ based on geochemical gradients, predict organisms involved in AMD transformations, and identify taxonomically novel groups present that have not previously been observed in mine tailings.
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Affiliation(s)
- Molly Chen
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Daniel S. Grégoire
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
- Department of Chemistry, Carleton University, Ottawa, Ontario, Canada
| | - Jeffrey G. Bain
- Department of Earth and Environmental Sciences, University of Waterloo, Waterloo, Ontario, Canada
| | - David W. Blowes
- Department of Earth and Environmental Sciences, University of Waterloo, Waterloo, Ontario, Canada
| | - Laura A. Hug
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
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Wang J, Zhang Y, Ding Y, Zhang Y, Xu W, Zhang X, Wang Y, Li D. Adaptive characteristics of indigenous microflora in an organically contaminated high salinity groundwater. CHEMOSPHERE 2024; 349:140951. [PMID: 38101485 DOI: 10.1016/j.chemosphere.2023.140951] [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: 08/28/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 12/17/2023]
Abstract
Salinity, a critical factor, could directly or indirectly affect the microbial community structure and diversity. Changes in salinity levels act as environmental filters that influence the transformation of key microbial species. This study investigates the adaptive characteristics of indigenous microflora in groundwater in relation to external organic pollutants under high salinity stress. A highly mineralized shallow groundwater in Northwest China was conducted as the study area, and six representative sampling points were chosen to explore the response of groundwater hydrochemical parameters and microflora, as well as to identify the tolerance mechanisms of indigenous microflora to combined pollution. The results revealed that the dominant genera found in high salinity groundwater contaminated with organic pollutants possess the remarkable ability to degrade such pollutants even under challenging high salinity conditions, including Halomonas, Pseudomonas, Halothiobacillus, Sphingomonas, Lutibacter, Aquabacterium, Thiomicrospira, Aequorivita, etc. The hydrochemical factors, including total dissolved solids (TDS), sulfide, nitrite, nitrate, oxidation reduction potential (ORP), NH3-N, Na, Fe, benzene series, phenols, and halogenated hydrocarbons, demonstrated a significant influence on microflora. High levels of sulphate and sulfide in groundwater can exhibit dual effects on microflora. On one hand, these compounds can inhibit the growth and metabolism of microorganisms. On the other hand, they can also serve as effective electron donors/receptors during the microbial degradation of organic pollutants. Microorganisms exhibit resilience to the inhibitory effects of high salinity and organic pollutants via a series of tolerance mechanisms, such as strengthening the extracellular membrane barrier, enhancing the synthesis of relevant enzymes, initiating novel biochemical reactions, improving cellular self-healing capabilities, responding to unfavorable environmental conditions by migration, and enhancing the S cycle for the microbial metabolism of organic pollutants.
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Affiliation(s)
- Jili Wang
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun, 130021, China; College of New Energy and Environment, Jilin University, Changchun, 130021, China; Institute of Water Resources and Environment, Jilin University, Changchun, 130021, China
| | - Yuling Zhang
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun, 130021, China; College of New Energy and Environment, Jilin University, Changchun, 130021, China; Institute of Water Resources and Environment, Jilin University, Changchun, 130021, China.
| | - Yang Ding
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun, 130021, China; College of New Energy and Environment, Jilin University, Changchun, 130021, China; Institute of Water Resources and Environment, Jilin University, Changchun, 130021, China
| | - Yi Zhang
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun, 130021, China; College of New Energy and Environment, Jilin University, Changchun, 130021, China; Institute of Water Resources and Environment, Jilin University, Changchun, 130021, China
| | - Weiqing Xu
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun, 130021, China; College of New Energy and Environment, Jilin University, Changchun, 130021, China; Institute of Water Resources and Environment, Jilin University, Changchun, 130021, China
| | - Xinying Zhang
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun, 130021, China; College of New Energy and Environment, Jilin University, Changchun, 130021, China; Institute of Water Resources and Environment, Jilin University, Changchun, 130021, China
| | - Yiliang Wang
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun, 130021, China; College of New Energy and Environment, Jilin University, Changchun, 130021, China; Institute of Water Resources and Environment, Jilin University, Changchun, 130021, China
| | - Dong Li
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun, 130021, China; College of New Energy and Environment, Jilin University, Changchun, 130021, China; Institute of Water Resources and Environment, Jilin University, Changchun, 130021, China
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Gupta S, de Rink R, Klok JBM, Muyzer G, Plugge CM. Process conditions affect microbial diversity and activity in a haloalkaline biodesulfurization system. Appl Environ Microbiol 2024; 90:e0186423. [PMID: 38078763 PMCID: PMC10807427 DOI: 10.1128/aem.01864-23] [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: 10/19/2023] [Accepted: 10/30/2023] [Indexed: 01/25/2024] Open
Abstract
Biodesulfurization (BD) systems that treat sour gas employ mixtures of haloalkaliphilic sulfur-oxidizing bacteria to convert sulfide to elemental sulfur. In the past years, these systems have seen major technical innovations that have led to changes in microbial community composition. Different studies have identified and discussed the microbial communities in both traditional and improved systems. However, these studies do not identify metabolically active community members and merely focus on members' presence/absence. Therefore, their results cannot confirm the activity and role of certain bacteria in the BD system. To investigate the active community members, we determined the microbial communities of six different runs of a pilot-scale BD system. 16S rRNA gene-based amplicon sequencing was performed using both DNA and RNA. A comparison of the DNA- and RNA-based sequencing results identified the active microbes in the BD system. Statistical analyses indicated that not all the existing microbes were actively involved in the system and that microbial communities continuously evolved during the operation. At the end of the run, strains affiliated with Alkalilimnicola ehrlichii and Thioalkalivibrio sulfidiphilus were confirmed as the most active key bacteria in the BD system. This study determined that microbial communities were shaped predominantly by the combination of hydraulic retention time (HRT) and sulfide concentration in the anoxic reactor and, to a lesser extent, by other operational parameters.IMPORTANCEHaloalkaliphilic sulfur-oxidizing bacteria are integral to biodesulfurization (BD) systems and are responsible for converting sulfide to sulfur. To understand the cause of conversions occurring in the BD systems, knowing which bacteria are present and active in the systems is essential. So far, only a few studies have investigated the BD system's microbial composition, but none have identified the active microbial community. Here, we reveal the metabolically active community, their succession, and their influence on product formation.
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Affiliation(s)
- Suyash Gupta
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Leeuwarden, the Netherlands
- Microbial Systems Ecology, Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, the Netherlands
| | - Rieks de Rink
- Environmental Technology, Wageningen University & Research, Wageningen, the Netherlands
- Paqell B.V., Utrecht, the Netherlands
| | - Johannes B. M. Klok
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Leeuwarden, the Netherlands
| | - Gerard Muyzer
- Microbial Systems Ecology, Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, the Netherlands
| | - Caroline M. Plugge
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Leeuwarden, the Netherlands
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
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Yi Q, You F, Li Z, Wu S, Chan TS, Lu YR, Thomsen L, Wang J, Ma Y, Liu Y, Robertson L, Southam G, Huang L. Elemental Sulfur and Organic Matter Amendment Drive Alkaline pH Neutralization and Mineral Weathering in Iron Ore Tailings Through Inducing Sulfur Oxidizing Bacteria. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:21744-21756. [PMID: 38085882 DOI: 10.1021/acs.est.3c05749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Mineral weathering and alkaline pH neutralization are prerequisites to the ecoengineering of alkaline Fe-ore tailings into soil-like growth media (i.e., Technosols). These processes can be accelerated by the growth and physiological functions of tolerant sulfur oxidizing bacteria (SOB) in tailings. The present study characterized an indigenous SOB community enriched in the tailings, in response to the addition of elemental sulfur (S0) and organic matter (OM), as well as resultant S0oxidation, pH neutralization, and mineral weathering in a glasshouse experiment. The addition of S0 was found to have stimulated the growth of indigenous SOB, such as acidophilic Alicyclobacillaceae, Bacillaceae, and Hydrogenophilaceae in tailings. The OM amendment favored the growth of heterotrophic/mixotrophic SOB (e.g., class Alphaproteobacteria and Gammaproteobacteria). The resultant S0 oxidation neutralized the alkaline pH and enhanced the weathering of biotite-like minerals and formation of secondary minerals, such as ferrihydrite- and jarosite-like minerals. The improved physicochemical properties and secondary mineral formation facilitated organo-mineral associations that are critical to soil aggregate formation. From these findings, co-amendments of S0 and plant biomass (OM) can be applied to enhance the abundance of the indigenous SOB community in tailings and accelerate mineral weathering and geochemical changes for eco-engineered soil formation, as a sustainable option for rehabilitation of Fe ore tailings.
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Affiliation(s)
- Qing Yi
- Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, Brisbane 4072, Australia
- Fujian Provincial Key Laboratory of Water Cycling and Eco-Geological Processes, Xiamen 361021, China
- Institute of Hydrogeology and Environmental Geology, Chinese Academy of Geological Sciences, Shijiazhuang 050061, China
| | - Fang You
- Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, Brisbane 4072, Australia
| | - Zhen Li
- College of Land Science and Technology, China Agricultural University, Beijing 100193, China
| | - Songlin Wu
- Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, Brisbane 4072, Australia
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ting-Shan Chan
- National Synchrotron Radiation Research Center, Hsinchu Science Park, Hsinchu 30092, Taiwan
| | - Ying-Rui Lu
- National Synchrotron Radiation Research Center, Hsinchu Science Park, Hsinchu 30092, Taiwan
| | - Lars Thomsen
- Australian Synchrotron, ANSTO, Melbourne, Victoria 3168, Australia
| | - Jian Wang
- Canadian Light Source Inc., University of Saskatchewan, Saskatoon, Saskatchewan S7N 2 V3, Canada
| | - Yuanying Ma
- Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, Brisbane 4072, Australia
| | - Yunjia Liu
- Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, Brisbane 4072, Australia
- College of Land Science and Technology, China Agricultural University, Beijing 100193, China
| | - Lachlan Robertson
- Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, Brisbane 4072, Australia
| | - Gordon Southam
- School of the Environment, The University of Queensland, Brisbane 4072, Australia
| | - Longbin Huang
- Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, Brisbane 4072, Australia
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Faulkner M, Hoeven R, Kelly PP, Sun Y, Park H, Liu LN, Toogood HS, Scrutton NS. Chemoautotrophic production of gaseous hydrocarbons, bioplastics and osmolytes by a novel Halomonas species. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:152. [PMID: 37821908 PMCID: PMC10568851 DOI: 10.1186/s13068-023-02404-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 09/25/2023] [Indexed: 10/13/2023]
Abstract
BACKGROUND Production of relatively low value, bulk commodity chemicals and fuels by microbial species requires a step-change in approach to decrease the capital and operational costs associated with scaled fermentation. The utilisation of the robust and halophilic industrial host organisms of the genus Halomonas could dramatically decrease biomanufacturing costs owing to their ability to grow in seawater, using waste biogenic feedstocks, under non-sterile conditions. RESULTS We describe the isolation of Halomonas rowanensis, a novel facultative chemoautotrophic species of Halomonas from a natural brine spring. We investigated the ability of this species to produce ectoine, a compound of considerable industrial interest, under heterotrophic conditions. Fixation of radiolabelled NaH14CO3 by H. rowanensis was confirmed in mineral medium supplied with thiosulfate as an energy source. Genome sequencing suggested carbon fixation proceeds via a reductive tricarboxylic acid cycle, and not the Calvin-Bensen-Bassham cycle. The mechanism of energy generation to support chemoautotrophy is unknown owing to the absence of an annotated SOX-based thiosulfate-mediated energy conversion system. We investigated further the biotechnological potential of the isolated H. rowanensis by demonstrating production of the gaseous hydrocarbon (bio-propane), bioplastics (poly-3-hydroxybutyrate) and osmolytes (ectoine) under heterotrophic and autotrophic CO2 fixation growth conditions. CONCLUSIONS This proof-of-concept study illustrates the value of recruiting environmental isolates as industrial hosts for chemicals biomanufacturing, where CO2 utilisation could replace, or augment, the use of biogenic feedstocks in non-sterile, industrialised bioreactors.
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Affiliation(s)
- Matthew Faulkner
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Robin Hoeven
- C3 Biotechnologies Ltd, 20 Mannin Way, Caton Road, Lancaster, LA1 35W, Lancashire, UK
- Engineering Building A, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Paul P Kelly
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Yaqi Sun
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool, L69 7BE, UK
| | - Helen Park
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Lu-Ning Liu
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool, L69 7BE, UK
| | - Helen S Toogood
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
- C3 Biotechnologies Ltd, 20 Mannin Way, Caton Road, Lancaster, LA1 35W, Lancashire, UK.
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
- C3 Biotechnologies Ltd, 20 Mannin Way, Caton Road, Lancaster, LA1 35W, Lancashire, UK.
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Whaley-Martin KJ, Chen LX, Nelson TC, Gordon J, Kantor R, Twible LE, Marshall S, McGarry S, Rossi L, Bessette B, Baron C, Apte S, Banfield JF, Warren LA. O 2 partitioning of sulfur oxidizing bacteria drives acidity and thiosulfate distributions in mining waters. Nat Commun 2023; 14:2006. [PMID: 37037821 PMCID: PMC10086054 DOI: 10.1038/s41467-023-37426-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 03/14/2023] [Indexed: 04/12/2023] Open
Abstract
The acidification of water in mining areas is a global environmental issue primarily catalyzed by sulfur-oxidizing bacteria (SOB). Little is known about microbial sulfur cycling in circumneutral pH mine tailing impoundment waters. Here we investigate biological sulfur oxidation over four years in a mine tailings impoundment water cap, integrating aqueous sulfur geochemistry, genome-resolved metagenomics and metatranscriptomics. The microbial community is consistently dominated by neutrophilic, chemolithoautotrophic SOB (relative abundances of ~76% in 2015, ~55% in 2016/2017 and ~60% in 2018). Results reveal two SOB strategies alternately dominate across the four years, influencing acid generation and sulfur speciation. Under oxic conditions, novel Halothiobacillus drive lower pH conditions (as low as 4.3) and lower [S2O32-] via the complete Sox pathway coupled to O2. Under anoxic conditions, Thiobacillus spp. dominate in activity, via the incomplete Sox and rDSR pathways coupled to NO3-, resulting in higher [S2O32-] and no net significant acidity generation. This study provides genomic evidence explaining acidity generation and thiosulfate accumulation patterns in a circumneutral mine tailing impoundment and has significant environmental applications in preventing the discharge of sulfur compounds that can impact downstream environments. These insights illuminate opportunities for in situ biotreatment of reduced sulfur compounds and prediction of acidification events using gene-based monitoring and in situ RNA detection.
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Affiliation(s)
- Kelly J Whaley-Martin
- University of Toronto, Toronto, ON, Canada
- Environmental Resources management (ERM), Toronto, ON, Canada
| | - Lin-Xing Chen
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
| | | | | | - Rose Kantor
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
| | | | - Stephanie Marshall
- Environmental Resources management (ERM), Toronto, ON, Canada
- McMaster University, Hamilton, ON, Canada
| | - Sam McGarry
- Glencore, Sudbury Integrated Nickel Operations, Sudbury, ON, Canada
| | | | | | | | - Simon Apte
- CSIRO Land and Water, Clayton, NSW, Australia
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA.
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Nosek D, Mikołajczyk T, Cydzik-Kwiatkowska A. Anode Modification with Fe 2O 3 Affects the Anode Microbiome and Improves Energy Generation in Microbial Fuel Cells Powered by Wastewater. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:2580. [PMID: 36767954 PMCID: PMC9916399 DOI: 10.3390/ijerph20032580] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/24/2023] [Accepted: 01/28/2023] [Indexed: 06/18/2023]
Abstract
This study investigated how anode electrode modification with iron affects the microbiome and electricity generation of microbial fuel cells (MFCs) fed with municipal wastewater. Doses of 0.0 (control), 0.05, 0.1, 0.2, and 0.4 g Fe2O3 per the total anode electrode area were tested. Fe2O3 doses from 0.05 to 0.2 g improved electricity generation; with a dose of 0.10 g Fe2O3, the cell power was highest (1.39 mW/m2), and the internal resistance was lowest (184.9 Ω). Although acetate was the main source of organics in the municipal wastewater, propionic and valeric acids predominated in the outflows from all MFCs. In addition, Fe-modification stimulated the growth of the extracellular polymer producers Zoogloea sp. and Acidovorax sp., which favored biofilm formation. Electrogenic Geobacter sp. had the highest percent abundance in the anode of the control MFC, which generated the least electricity. However, with 0.05 and 0.10 g Fe2O3 doses, Pseudomonas sp., Oscillochloris sp., and Rhizobium sp. predominated in the anode microbiomes, and with 0.2 and 0.4 g doses, the electrogens Dechloromonas sp. and Desulfobacter sp. predominated. This is the first study to holistically examine how different amounts of Fe on the anode affect electricity generation, the microbiome, and metabolic products in the outflow of MFCs fed with synthetic municipal wastewater.
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Affiliation(s)
- Dawid Nosek
- Department of Environmental Biotechnology, University of Warmia and Mazury in Olsztyn, Słoneczna 45 G, 10-709 Olsztyn, Poland
| | - Tomasz Mikołajczyk
- Department of Chemistry, University of Warmia and Mazury in Olsztyn, plac Łódzki 4, 10-721 Olsztyn, Poland
| | - Agnieszka Cydzik-Kwiatkowska
- Department of Environmental Biotechnology, University of Warmia and Mazury in Olsztyn, Słoneczna 45 G, 10-709 Olsztyn, Poland
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Interesting Halophilic Sulphur-Oxidising Bacteria with Bioleaching Potential: Implications for Pollutant Mobilisation from Mine Waste. Microorganisms 2023; 11:microorganisms11010222. [PMID: 36677514 PMCID: PMC9866277 DOI: 10.3390/microorganisms11010222] [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: 11/17/2022] [Revised: 01/05/2023] [Accepted: 01/11/2023] [Indexed: 01/19/2023] Open
Abstract
For many years, research on the microbial-dissolution of metals from ores or waste materials mainly focussed on the study of acidophilic organisms. However, most acidophilic bioleaching microorganisms have limited tolerance to high chloride concentrations, thereby requiring fresh water for bioleaching operations. There is a growing interest in the use of seawater for leaching purposes, especially in regions with less access to fresh water. Consequently, there is a need to find halophilic organisms with bioleaching potentials. This study investigated the bioleaching potentials of four moderately halophilic sulphur-oxidising bacteria: Thiomicrospira cyclica, Thiohalobacter thiocyanaticus, Thioclava electrotropha and Thioclava pacifica. Results revealed T. electrotropha and T. pacifica as the most promising for bioleaching. Pure cultures of the two Thioclava strains liberated about 30% Co, and between 8-17% Cu, Pb, Zn, K, Cd, and Mn from a mine waste rock sample from the Neves Corvo mine, Portugal. Microwave roasting of the waste rock at 400 and 500 °C improved the bioleaching efficiency of T. electrotropha for Pb (13.7 to 45.7%), Ag (5.3 to 36%) and In (0 to 27.4%). Mineralogical analysis of the bioleached residues using SEM/MLA-GXMAP showed no major difference in the mineral compositions before or after bioleaching by the Thioclava spp. Generally, the bioleaching rates of the Thioclava spp. are quite low compared to that of the conventional acidophilic bioleaching bacteria. Nevertheless, their ability to liberate potential pollutants (metal(loid)s) into solution from mine waste raises environmental concerns. This is due to their relevance in the biogeochemistry of mine waste dumps, as similar neutrophile halophilic sulphur-oxidising organisms (e.g., Halothiobacillus spp.) have been isolated from mine wastes. On the other hand, the use of competent halophilic microorganisms could be the future of bioleaching due to their high tolerance to Cl- ions and their potential to catalyse mineral dissolution in seawater media, instead of fresh water.
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10
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Virpiranta H, Leiviskä T, Taskila S, Tanskanen J. Bioregeneration of sulfate-laden anion exchange resin. WATER RESEARCH 2022; 224:119110. [PMID: 36126630 DOI: 10.1016/j.watres.2022.119110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 09/09/2022] [Accepted: 09/12/2022] [Indexed: 06/15/2023]
Abstract
Ion exchange technology removes ionic compounds from waters effectively but treatment of the spent regenerant is expensive. The bioregeneration of sulfate-laden strong base anion exchange resin was successfully tested using both pure and mixed sulfate-reducing bacterial cultures. The resin was first used for removal of sulfate from neutral (pH 6.7 ± 0.5) synthetic sodium sulfate solutions, after which the spent resin was regenerated by incubating with a viable sulfate-reducing bacterial culture in batch and column modes. In the batch bioregeneration tests, the achieved bioregeneration was 36-95% of the original capacity of the fresh resin (112 mg SO42-/g) and it increased with regeneration time (1-14 days). The capacity achieved in the column tests during 24 hours of bioregeneration was 107 mg SO42-/g after the first regeneration cycle. During the bioregeneration, sulfate was mainly reduced by the sulfate-reducing bacteria (approx. 60%), but part of it was only detached from the resins (approx. 30%). The resin-attached sulfate was most likely replaced with ions present in the liquid sulfate-reducing bacterial culture (e.g., HCO3-, HS-, and Cl-). During the subsequent exhaustion cycles with the bioregenerated resin, the pH of the treated sodium sulfate solution increased from the original 6.7 ± 0.5 to around 9. The study showed that biological sulfate reduction could be used for sulfate removal in combination with ion exchange, and that the exhausted ion exchange resins could be regenerated using a liquid sulfate-reducing bacterial culture without producing any brine.
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Affiliation(s)
- Hanna Virpiranta
- University of Oulu, Chemical Process Engineering, PO Box 4300, 90014 Oulu, Finland.
| | - Tiina Leiviskä
- University of Oulu, Chemical Process Engineering, PO Box 4300, 90014 Oulu, Finland
| | - Sanna Taskila
- University of Oulu, Chemical Process Engineering, PO Box 4300, 90014 Oulu, Finland
| | - Juha Tanskanen
- University of Oulu, Chemical Process Engineering, PO Box 4300, 90014 Oulu, Finland
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11
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Santini TC, Gramenz L, Southam G, Zammit C. Microbial Community Structure Is Most Strongly Associated With Geographical Distance and pH in Salt Lake Sediments. Front Microbiol 2022; 13:920056. [PMID: 35756015 PMCID: PMC9221066 DOI: 10.3389/fmicb.2022.920056] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 05/09/2022] [Indexed: 11/16/2022] Open
Abstract
Salt lakes are globally significant microbial habitats, hosting substantial novel microbial diversity and functional capacity. Extremes of salinity and pH both pose major challenges for survival of microbial life in terrestrial and aquatic environments, and are frequently cited as primary influences on microbial diversity across a wide variety of environments. However, few studies have attempted to identify spatial and geochemical contributions to microbial community composition, functional capacity, and environmental tolerances in salt lakes, limiting exploration of novel halophilic and halotolerant microbial species and their potential biotechnological applications. Here, we collected sediment samples from 16 salt lakes at pH values that ranged from pH 4 to 9, distributed across 48,000 km2 of the Archaean Yilgarn Craton in southwestern Australia to identify associations between environmental factors and microbial community composition, and used a high throughput culturing approach to identify the limits of salt and pH tolerance during iron and sulfur oxidation in these microbial communities. Geographical distance between lakes was the primary contributor to variation in microbial community composition, with pH identified as the most important geochemical contributor to variation in microbial community composition. Microbial community composition split into two clear groups by pH: Bacillota dominated microbial communities in acidic saline lakes, whereas Euryarchaeota dominated microbial communities in alkaline saline lakes. Iron oxidation was observed at salinities up to 160 g L-1 NaCl at pH values as low as pH 1.5, and sulfur oxidation was observed at salinities up to 160 g L-1 NaCl between pH values 2-10, more than doubling previously observed tolerances to NaCl salinity amongst cultivable iron and sulfur oxidizers at these extreme pH values. OTU level diversity in the salt lake microbial communities emerged as the major indicator of iron- and sulfur-oxidizing capacity and environmental tolerances to extremes of pH and salinity. Overall, when bioprospecting for novel microbial functional capacity and environmental tolerances, our study supports sampling from remote, previously unexplored, and maximally distant locations, and prioritizing for OTU level diversity rather than present geochemical conditions.
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Affiliation(s)
- Talitha C. Santini
- UWA School of Agriculture and Environment, The University of Western Australia, Crawley, WA, Australia
| | - Lucy Gramenz
- School of Earth and Environmental Sciences, The University of Queensland, St Lucia, QLD, Australia
| | - Gordon Southam
- School of Earth and Environmental Sciences, The University of Queensland, St Lucia, QLD, Australia
| | - Carla Zammit
- School of Earth and Environmental Sciences, The University of Queensland, St Lucia, QLD, Australia
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12
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Gupta S, Plugge CM, Klok JBM, Muyzer G. Comparative analysis of microbial communities from different full-scale haloalkaline biodesulfurization systems. Appl Microbiol Biotechnol 2022; 106:1759-1776. [PMID: 35147744 PMCID: PMC8882115 DOI: 10.1007/s00253-022-11771-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 12/17/2021] [Accepted: 01/06/2022] [Indexed: 11/28/2022]
Abstract
Abstract In biodesulfurization (BD) at haloalkaline and dO2-limited conditions, sulfide-oxidizing bacteria (SOB) effectively convert sulfide into elemental sulfur that can be used in agriculture as a fertilizer and fungicide. Here we show which bacteria are present in this biotechnological process. 16S rRNA gene amplicon sequencing of biomass from ten reactors sampled in 2018 indicated the presence of 444 bacterial Amplicon Sequence Variants (ASVs). A core microbiome represented by 30 ASVs was found in all ten reactors, with Thioalkalivibrio sulfidiphilus as the most dominant species. The majority of these ASVs are phylogenetically related to bacteria previously identified in haloalkaline BD processes and in natural haloalkaline ecosystems. The source and composition of the feed gas had a great impact on the microbial community composition followed by alkalinity, sulfate, and thiosulfate concentrations. The halophilic SOB of the genus Guyparkeria (formerly known as Halothiobacillus) and heterotrophic SOB of the genus Halomonas were identified as potential indicator organisms of sulfate and thiosulfate accumulation in the BD process. Key points • Biodesulfurization (BD) reactors share a core microbiome • The source and composition of the feed gas affects the microbial composition in the BD reactors • Guyparkeria and Halomonas indicate high concentrations of sulfate and thiosulfate in the BD process Supplementary Information The online version contains supplementary material available at 10.1007/s00253-022-11771-y.
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Affiliation(s)
- Suyash Gupta
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Leeuwarden, The Netherlands.,Microbial Systems Ecology, Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Caroline M Plugge
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Leeuwarden, The Netherlands.,Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Johannes B M Klok
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Leeuwarden, The Netherlands.,Paqell B.V, Utrecht, The Netherlands
| | - Gerard Muyzer
- Microbial Systems Ecology, Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands.
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13
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Dev S, Galey M, Chun CL, Novotny C, Ghosh T, Aggarwal S. Enrichment of psychrophilic and acidophilic sulfate-reducing bacterial consortia - a solution toward acid mine drainage treatment in cold regions. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2021; 23:2007-2020. [PMID: 34821889 DOI: 10.1039/d1em00256b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Failure of sulfate-reducing bacteria (SRB)-mediated treatment of acid mine drainage (AMD) in cold regions due to inhibition of bacteria by acidic pH and low temperature can be overcome by enriching psychrophilic and acidophilic microbial consortia from local metal-rich sediments. In this study, we enriched microbial consortia from Arctic mine sediments at varying pH (3-7) and temperatures (15-37 °C) under anaerobic conditions with repeated sub-culturing in three successive stages, and analyzed the microbial community using 16S rRNA gene sequencing. The enriched SRB genera resulted in high sulfate reduction (85-88%), and significant metal removal (49-99.9%) during the initial stages (stage 1 and 2). Subsequently, sub-culturing the inoculum at pH 3-4.5 resulted in lower sulfate reduction (9-34%) due to the inhibition of SRB by accumulated acetic acid (0.3-9 mM). The microbial metabolic interactions for successful sulfate and metal removal involved initial glycerol co-fermentation to acetic acid at acidic pH (by Desulfosporosinus, Desulfotomaculum, Desulfurospora, and fermentative bacteria including Cellulomonas and Anaerovorax), followed by acetic acid oxidation to CO2 and H2 (by Desulfitobacterium) at neutral pH, and subsequent H2 utilization (by Desulfosporosinus). The results, including the structural and functional properties of enriched microbial consortia, can inform the development of effective biological treatment strategies for AMD in cold regions.
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Affiliation(s)
- Subhabrata Dev
- Water and Environmental Research Center, University of Alaska Fairbanks, 1760 Tanana Loop, Fairbanks, AK 99775, USA.
- Mineral Industry Research Laboratory, University of Alaska Fairbanks, Fairbanks, AK 99775, USA
| | - Miranda Galey
- Natural Resources Research Institute, University of Minnesota Duluth, Duluth, MN 55812, USA
| | - Chan Lan Chun
- Natural Resources Research Institute, University of Minnesota Duluth, Duluth, MN 55812, USA
- Department of Civil Engineering, University of Minnesota Duluth, Duluth, MN 55812, USA
| | - Chad Novotny
- Teck Resources Limited, Vancouver, BC V6C 0B3, Canada
| | - Tathagata Ghosh
- Mineral Industry Research Laboratory, University of Alaska Fairbanks, Fairbanks, AK 99775, USA
| | - Srijan Aggarwal
- Water and Environmental Research Center, University of Alaska Fairbanks, 1760 Tanana Loop, Fairbanks, AK 99775, USA.
- Department of Civil, Geological and Environmental Engineering, University of Alaska Fairbanks, Fairbanks, Alaska, 99775, USA
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14
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Mohapatra M, Yadav R, Rajput V, Dharne MS, Rastogi G. Metagenomic analysis reveals genetic insights on biogeochemical cycling, xenobiotic degradation, and stress resistance in mudflat microbiome. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 292:112738. [PMID: 34020306 DOI: 10.1016/j.jenvman.2021.112738] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 04/05/2021] [Accepted: 04/29/2021] [Indexed: 05/22/2023]
Abstract
Mudflats are highly productive coastal ecosystems that are dominated by halophytic vegetation. In this study, the mudflat sediment microbiome was investigated from Nalabana Island, located in a brackish water coastal wetland of India; Chilika, based on the MinION shotgun metagenomic analysis. Bacterial, archaeal, and fungal communities were mostly composed of Proteobacteria (38.3%), Actinobacteria (20.7%), Euryarchaeota (76.1%), Candidatus Bathyarchaeota (6.8%), Ascomycota (47.2%), and Basidiomycota (22.0%). Bacterial and archaeal community composition differed significantly between vegetated mudflat and un-vegetated bulk sediments. Carbon, nitrogen, sulfur metabolisms, oxidative phosphorylation, and xenobiotic biodegradation were the most common microbial functionalities in the mudflat metagenomes. Furthermore, genes involved in oxidative stresses, osmotolerance, secondary metabolite synthesis, and extracellular polymeric substance synthesis revealed adaptive mechanisms of the microbiome in mudflat habitat. Mudflat metagenome also revealed genes involved in the plant growth and development, suggesting that microbial communities could aid halophytic vegetation by providing tolerance to the abiotic stresses in a harsh mudflat environment. Canonical correspondence analysis and co-occurrence network revealed that both biotic (vegetation and microbial interactions) and abiotic factors played important role in shaping the mudflat microbiome composition. Among abiotic factors, pH accounted for the highest variance (20.10%) followed by available phosphorus (19.73%), total organic carbon (9.94%), salinity (8.28%), sediment texture (sand) (6.37%) and available nitrogen (5.53%) in the mudflat microbial communities. Overall, this first metagenomic study provided a comprehensive insight on the community structure, potential ecological interactions, and genetic potential of the mudflat microbiome in context to the cycling of organic matter, xenobiotic biodegradation, stress resistance, and in providing the ecological fitness to halophytes. These ecosystem services of the mudflat microbiome must be considered in the conservation and management plan of coastal wetlands. This study also advanced our understanding of fungal diversity which is understudied from the coastal lagoon ecosystems.
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Affiliation(s)
- Madhusmita Mohapatra
- Wetland Research and Training Centre, Chilika Development Authority, Balugaon, 752030, Odisha, India; School of Biotechnology, KIIT University, Bhubaneswar, Odisha, 751024, India
| | - Rakeshkumar Yadav
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences, CSIR-National Chemical Laboratory (NCL), Pune, 411008, India; Academic of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Vinay Rajput
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences, CSIR-National Chemical Laboratory (NCL), Pune, 411008, India
| | - Mahesh S Dharne
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences, CSIR-National Chemical Laboratory (NCL), Pune, 411008, India; Academic of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Gurdeep Rastogi
- Wetland Research and Training Centre, Chilika Development Authority, Balugaon, 752030, Odisha, India.
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15
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Sheik CS, Badalamenti JP, Telling J, Hsu D, Alexander SC, Bond DR, Gralnick JA, Lollar BS, Toner BM. Novel Microbial Groups Drive Productivity in an Archean Iron Formation. Front Microbiol 2021; 12:627595. [PMID: 33859627 PMCID: PMC8042283 DOI: 10.3389/fmicb.2021.627595] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 03/01/2021] [Indexed: 12/23/2022] Open
Abstract
Deep subsurface environments are decoupled from Earth's surface processes yet diverse, active, and abundant microbial communities thrive in these isolated environments. Microbes inhabiting the deep biosphere face unique challenges such as electron donor/acceptor limitations, pore space/fracture network limitations, and isolation from other microbes within the formation. Of the few systems that have been characterized, it is apparent that nutrient limitations likely facilitate diverse microbe-microbe interactions (i.e., syntrophic, symbiotic, or parasitic) and that these interactions drive biogeochemical cycling of major elements. Here we describe microbial communities living in low temperature, chemically reduced brines at the Soudan Underground Mine State Park, United States. The Soudan Iron mine intersects a massive hematite formation at the southern extent of the Canadian Shield. Fractured rock aquifer brines continuously flow from exploratory boreholes drilled circa 1960 and are enriched in deuterium compared to the global meteoric values, indicating brines have had little contact with surface derived waters, and continually degas low molecular weight hydrocarbons C1-C4. Microbial enrichments suggest that once brines exit the boreholes, oxidation of the hydrocarbons occur. Amplicon sequencing show these borehole communities are low in diversity and dominated by Firmicute and Proteobacteria phyla. From the metagenome assemblies, we recovered approximately thirty genomes with estimated completion over 50%. Analysis of genome taxonomy generally followed the amplicon data, and highlights that several of the genomes represent novel families and genera. Metabolic reconstruction shows two carbon-fixation pathways were dominant, the Wood-Ljungdahl (acetogenesis) and Calvin-Benson-Bassham (via RuBisCo), indicating that inorganic carbon likely enters into the microbial foodweb with differing carbon fractionation potentials. Interestingly, methanogenesis is likely driven by Methanolobus and suggests cycling of methylated compounds and not H2/CO2 or acetate. Furthermore, the abundance of sulfate in brines suggests cryptic sulfur cycling may occur, as we detect possible sulfate reducing and thiosulfate oxidizing microorganisms. Finally, a majority of the microorganisms identified contain genes that would allow them to participate in several element cycles, highlighting that in these deep isolated systems metabolic flexibility may be an important life history trait.
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Affiliation(s)
- Cody S. Sheik
- Department of Biology and the Large Lakes Observatory, University of Minnesota Duluth, Duluth, MN, United States
| | - Jonathan P. Badalamenti
- University of Minnesota Genomics Center, University of Minnesota Twin Cities, Minneapolis, MN, United States
- Biotechnology Institute, University of Minnesota Twin Cities, Saint Paul, MN, United States
| | - Jon Telling
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - David Hsu
- Biotechnology Institute, University of Minnesota Twin Cities, Saint Paul, MN, United States
- Plant and Microbial Biology, University of Minnesota Twin Cities, Saint Paul, MN, United States
| | - Scott C. Alexander
- Department of Earth and Environmental Sciences, University of Minnesota Twin Cities, Minneapolis, MN, United States
| | - Daniel R. Bond
- Biotechnology Institute, University of Minnesota Twin Cities, Saint Paul, MN, United States
- Plant and Microbial Biology, University of Minnesota Twin Cities, Saint Paul, MN, United States
| | - Jeffrey A. Gralnick
- Biotechnology Institute, University of Minnesota Twin Cities, Saint Paul, MN, United States
- Plant and Microbial Biology, University of Minnesota Twin Cities, Saint Paul, MN, United States
| | | | - Brandy M. Toner
- Department of Earth and Environmental Sciences, University of Minnesota Twin Cities, Minneapolis, MN, United States
- Department of Soil, Water, and Climate, University of Minnesota Twin Cities, Saint Paul, MN, United States
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16
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Identification and Metabolism of Naturally Prevailing Microorganisms in Zinc and Copper Mineral Processing. MINERALS 2021. [DOI: 10.3390/min11020156] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
It has only recently been discovered that naturally prevailing microorganisms have a notable role in flotation in addition to chemical process parameters and overall water quality. This study’s aim was to assess the prevailing microbial communities in relation to process chemistry in a zinc and copper mineral flotation plant. Due to the limitations of cultivation-based microbial methods that detect only a fraction of the total microbial diversity, DNA-based methods were utilised. However, it was discovered that the DNA extraction methods need to be improved for these environments with high mineral particle content. Microbial communities and metabolism were studied with quantitative PCR and amplicon sequencing of bacterial, archaeal and fungal marker genes and shotgun sequencing. Bacteria dominated the microbial communities, but in addition, both archaea and fungi were present. The predominant bacterial metabolism included versatile sulfur compound oxidation. Putative Thiovirga sp. dominated in the zinc plant and the water circuit samples, whereas Thiobacillus spp. dominated the copper plant. Halothiobacillus spp. were also an apparent part of the community in all samples. Nitrogen metabolism was more related to assimilatory than dissimilatory nitrate and nitrite oxidation/reduction reactions. Abundance of heavy metal resistance genes emphasized the adaptation and competitive edge of the core microbiome in these extreme conditions compared to microorganisms freshly entering the process.
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17
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Chen LX, Méheust R, Crits-Christoph A, McMahon KD, Nelson TC, Slater GF, Warren LA, Banfield JF. Large freshwater phages with the potential to augment aerobic methane oxidation. Nat Microbiol 2020; 5:1504-1515. [PMID: 32839536 PMCID: PMC7674155 DOI: 10.1038/s41564-020-0779-9] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 07/21/2020] [Indexed: 12/31/2022]
Abstract
There is growing evidence that phages with unusually large genomes are common across various microbiomes, but little is known about their genetic inventories or potential ecosystem impacts. In the present study, we reconstructed large phage genomes from freshwater lakes known to contain bacteria that oxidize methane. Of manually curated genomes, 22 (18 are complete), ranging from 159 kilobase (kb) to 527 kb in length, were found to encode the pmoC gene, an enzymatically critical subunit of the particulate methane monooxygenase, the predominant methane oxidation catalyst in nature. The phage-associated PmoC sequences show high similarity to (>90%), and affiliate phylogenetically with, those of coexisting bacterial methanotrophs, including members of Methyloparacoccus, Methylocystis and Methylobacter spp. In addition, pmoC-phage abundance patterns correlate with those of the coexisting bacterial methanotrophs, supporting host-phage relationships. Future work is needed to determine whether phage-associated PmoC has similar functions to additional copies of PmoC encoded in bacterial genomes, thus contributing to growth on methane. Transcriptomics data from Lake Rotsee (Switzerland) showed that some phage-associated pmoC genes were highly expressed in situ and, of interest, that the most rapidly growing methanotroph was infected by three pmoC-phages. Thus, augmentation of bacterial methane oxidation by pmoC-phages during infection could modulate the efflux of this potent greenhouse gas into the environment.
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Affiliation(s)
- Lin-Xing Chen
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA, USA
| | - Raphaël Méheust
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA, USA
| | | | - Katherine D McMahon
- Departments of Civil and Environmental Engineering, and Bacteriology, University of Wisconsin, Madison, WI, USA
| | | | - Gregory F Slater
- School of Geography and Earth Science, McMaster University, Hamilton, Ontario, Canada
| | - Lesley A Warren
- Department of Civil and Mineral Engineering, University of Toronto, Toronto, Ontario, Canada.,School of Geography and Earth Science, McMaster University, Hamilton, Ontario, Canada
| | - Jillian F Banfield
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA, USA. .,Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA. .,Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA. .,Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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18
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Chen LX, Zhao Y, McMahon KD, Mori JF, Jessen GL, Nelson TC, Warren LA, Banfield JF. Wide Distribution of Phage That Infect Freshwater SAR11 Bacteria. mSystems 2019. [PMID: 31641047 DOI: 10.1101/672428v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023] Open
Abstract
Fonsibacter (LD12 subclade) is among the most abundant bacterioplankton in freshwater ecosystems. These bacteria belong to the order Pelagibacterales (SAR11) and are related to Pelagibacter (marine SAR11), which dominates many marine habitats. Although a few Pelagibacter phage (Pelagiphage) have been described, no phage that infect Fonsibacter have been reported. In this study, we describe two groups of Podoviridae phage that infect Fonsibacter A complete Fonsibacter genome containing a prophage was reconstructed from metagenomic data. A circularized and complete genome related to the prophage, referred to as uv-Fonsiphage-EPL (lysogenic strategy), shows high similarity to marine Pelagiphage HTVC025P. Additionally, we reconstructed three complete genomes and one draft genome of phage related to marine Pelagiphage HTVC010P and predicted a lytic strategy. The similarity in codon usage and cooccurrence patterns of HTVC010P-related phage and Fonsibacter suggested that these phage infect Fonsibacter Similar phage were detected in Lake Mendota, Wisconsin, where Fonsibacter is also present. A search of related phage revealed the worldwide distribution of some genotypes in freshwater ecosystems, suggesting their substantial role in shaping indigenous microbial assemblages and influence on biogeochemical cycling. However, the uv-Fonsiphage-EPL and one group of HTVC010P-related phage have a more limited distribution in freshwater ecosystems. Overall, the findings provide insights into the genomic features of phage that infect Fonsibacter and expand understanding of the ecology and evolution of these important bacteria.IMPORTANCE Fonsibacter represents a significant microbial group of freshwater ecosystems. Although the genomic and metabolic features of these bacteria have been well studied, no phage infecting them has been reported. In this study, we reconstructed complete genomes of Fonsibacter and infecting phage and revealed their close relatedness to the phage infecting marine SAR11 members. Also, we illustrated that phage that infect Fonsibacter are widely distributed in freshwater habitats. In summary, the results contribute new insights into the ecology and evolution of Fonsibacter and phage.
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Affiliation(s)
- Lin-Xing Chen
- Department of Earth and Planetary Sciences, University of California, Berkeley, California, USA
| | - Yanlin Zhao
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Katherine D McMahon
- Department of Civil and Environmental Engineering, University of Wisconsin, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin, USA
| | - Jiro F Mori
- Department of Civil and Mineral Engineering, University of Toronto, Toronto, Canada
| | - Gerdhard L Jessen
- Department of Civil and Mineral Engineering, University of Toronto, Toronto, Canada
| | | | - Lesley A Warren
- Department of Civil and Mineral Engineering, University of Toronto, Toronto, Canada
- School of Geography and Earth Science, McMaster University, Hamilton, Canada
| | - Jillian F Banfield
- Department of Earth and Planetary Sciences, University of California, Berkeley, California, USA
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
- Innovative Genomics Institute at UC Berkeley, Berkeley, California, USA
- The University of Melbourne, Melbourne, Australia
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19
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Abstract
Fonsibacter represents a significant microbial group of freshwater ecosystems. Although the genomic and metabolic features of these bacteria have been well studied, no phage infecting them has been reported. In this study, we reconstructed complete genomes of Fonsibacter and infecting phage and revealed their close relatedness to the phage infecting marine SAR11 members. Also, we illustrated that phage that infect Fonsibacter are widely distributed in freshwater habitats. In summary, the results contribute new insights into the ecology and evolution of Fonsibacter and phage. Fonsibacter (LD12 subclade) is among the most abundant bacterioplankton in freshwater ecosystems. These bacteria belong to the order Pelagibacterales (SAR11) and are related to Pelagibacter (marine SAR11), which dominates many marine habitats. Although a few Pelagibacter phage (Pelagiphage) have been described, no phage that infect Fonsibacter have been reported. In this study, we describe two groups of Podoviridae phage that infect Fonsibacter. A complete Fonsibacter genome containing a prophage was reconstructed from metagenomic data. A circularized and complete genome related to the prophage, referred to as uv-Fonsiphage-EPL (lysogenic strategy), shows high similarity to marine Pelagiphage HTVC025P. Additionally, we reconstructed three complete genomes and one draft genome of phage related to marine Pelagiphage HTVC010P and predicted a lytic strategy. The similarity in codon usage and cooccurrence patterns of HTVC010P-related phage and Fonsibacter suggested that these phage infect Fonsibacter. Similar phage were detected in Lake Mendota, Wisconsin, where Fonsibacter is also present. A search of related phage revealed the worldwide distribution of some genotypes in freshwater ecosystems, suggesting their substantial role in shaping indigenous microbial assemblages and influence on biogeochemical cycling. However, the uv-Fonsiphage-EPL and one group of HTVC010P-related phage have a more limited distribution in freshwater ecosystems. Overall, the findings provide insights into the genomic features of phage that infect Fonsibacter and expand understanding of the ecology and evolution of these important bacteria. IMPORTANCEFonsibacter represents a significant microbial group of freshwater ecosystems. Although the genomic and metabolic features of these bacteria have been well studied, no phage infecting them has been reported. In this study, we reconstructed complete genomes of Fonsibacter and infecting phage and revealed their close relatedness to the phage infecting marine SAR11 members. Also, we illustrated that phage that infect Fonsibacter are widely distributed in freshwater habitats. In summary, the results contribute new insights into the ecology and evolution of Fonsibacter and phage.
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20
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Hur M, Park SJ. Identification of Microbial Profiles in Heavy-Metal-Contaminated Soil from Full-Length 16S rRNA Reads Sequenced by a PacBio System. Microorganisms 2019; 7:microorganisms7090357. [PMID: 31527468 PMCID: PMC6780547 DOI: 10.3390/microorganisms7090357] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 09/10/2019] [Accepted: 09/13/2019] [Indexed: 11/16/2022] Open
Abstract
Heavy metal pollution is a serious environmental problem as it adversely affects crop production and human activity. In addition, the microbial community structure and composition are altered in heavy-metal-contaminated soils. In this study, using full-length 16S rRNA gene sequences obtained by a PacBio RS II system, we determined the microbial diversity and community structure in heavy-metal-contaminated soil. Furthermore, we investigated the microbial distribution, inferred their putative functional traits, and analyzed the environmental effects on the microbial compositions. The soil samples selected in this study were heavily and continuously contaminated with various heavy metals due to closed mines. We found that certain microorganisms (e.g., sulfur or iron oxidizers) play an important role in the biogeochemical cycle. Using phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analysis, we predicted Kyoto Encyclopedia of Genes and Genomes (KEGG) functional categories from abundances of microbial communities and revealed a high proportion belonging to transport, energy metabolism, and xenobiotic degradation in the studied sites. In addition, through full-length analysis, Conexibacter-like sequences, commonly identified by environmental metagenomics among the rare biosphere, were detected. In addition to microbial composition, we confirmed that environmental factors, including heavy metals, affect the microbial communities. Unexpectedly, among these environmental parameters, electrical conductivity (EC) might have more importance than other factors in a community description analysis.
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Affiliation(s)
- Moonsuk Hur
- Microorganism Resources Division, National Institute of Biological Resources, 42 Hwangyeong-ro, Incheon 22689, Korea.
| | - Soo-Je Park
- Department of Biology, Jeju National University, 102 Jejudaehak-ro, Jeju 63243, Korea.
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