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Huang H, Yu J, Chen L, Zhang L, Li T, Ye D, Zhang X, Wang Y, Zheng Z, Liu T, Yu H. The effect of different amendments on Cd availability and bacterial community after three-year consecutive application in Cd-contaminated paddy soils. ENVIRONMENTAL RESEARCH 2024; 259:119459. [PMID: 38942257 DOI: 10.1016/j.envres.2024.119459] [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: 12/02/2023] [Revised: 05/20/2024] [Accepted: 06/18/2024] [Indexed: 06/30/2024]
Abstract
In situ immobilization is a widely used measure for passivating Cd-contaminated soils. Amendments need to be continuously applied to achieve stable remediation effects. However, few studies have evaluated the impact of consecutive application of amendments on soil health and the microecological environment. A field experiment was conducted in a Cd-contaminated paddy (available Cd concentration 0.40 mg kg-1) on the Chengdu Plain to investigate the changes in soil Cd availability and response characteristics of soil bacterial communities after consecutive application of rice straw biochar (SW), fly ash (FM) and marble powder (YH) amendments from 2018 to 2020. Compared with control treatment without amendments (CK), soil pH increased by 0.6, 0.5 and 1.5 under SW, FM and YH amendments, respectively, and the soil available Cd concentration decreased by 10.71%, 21.42% and 25.00%, respectively. The Cd concentration in rice grain was less than 0.2 mg kg-1 under YH amendment, which was within the Chinese Contaminant Limit in Food of National Food Safety Standards (GB2762-2022) in the second and third years. The three amendments had different effects on the transformation of Cd fractions in soil, which may be relevant to the specific bacterial communities shaped under different treatments. The proportion of Fe-Mn oxide-bound fraction Cd (OX-Cd) increased by 11% under YH treatment, which may be due to the promotion of Fe(III) and Cd binding by some enriched iron-oxidizing bacteria, such as Lysobacter, uncultured_Pelobacter sp. and Sulfurifusis. Candidatus_Tenderia and Sideroxydans were enriched under SW and FM amendments, respectively, and were likely beneficial for reducing Cd availability in soil through Cd immobilization. These results revealed the significance of the bacterial community in soil Cd immobilization after consecutive application of amendments and highlighted the potential of applying YH amendment to ensure the safe production of rice in Cd-contaminated soil.
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Affiliation(s)
- Huagang Huang
- College of Resources, Sichuan Agricultural University, 211 Huimin Road, Chengdu, Sichuan 611130, China.
| | - Jieyi Yu
- College of Resources, Sichuan Agricultural University, 211 Huimin Road, Chengdu, Sichuan 611130, China.
| | - Lan Chen
- College of Resources, Sichuan Agricultural University, 211 Huimin Road, Chengdu, Sichuan 611130, China.
| | - Lu Zhang
- College of Resources, Sichuan Agricultural University, 211 Huimin Road, Chengdu, Sichuan 611130, China.
| | - Tingxuan Li
- College of Resources, Sichuan Agricultural University, 211 Huimin Road, Chengdu, Sichuan 611130, China.
| | - Daihua Ye
- College of Resources, Sichuan Agricultural University, 211 Huimin Road, Chengdu, Sichuan 611130, China.
| | - Xizhou Zhang
- College of Resources, Sichuan Agricultural University, 211 Huimin Road, Chengdu, Sichuan 611130, China.
| | - Yongdong Wang
- College of Resources, Sichuan Agricultural University, 211 Huimin Road, Chengdu, Sichuan 611130, China.
| | - Zicheng Zheng
- College of Resources, Sichuan Agricultural University, 211 Huimin Road, Chengdu, Sichuan 611130, China.
| | - Tao Liu
- College of Resources, Sichuan Agricultural University, 211 Huimin Road, Chengdu, Sichuan 611130, China.
| | - Haiying Yu
- College of Resources, Sichuan Agricultural University, 211 Huimin Road, Chengdu, Sichuan 611130, China.
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Brooks CN, Field EK. Microbial community response to hydrocarbon exposure in iron oxide mats: an environmental study. Front Microbiol 2024; 15:1388973. [PMID: 38800754 PMCID: PMC11116660 DOI: 10.3389/fmicb.2024.1388973] [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: 02/20/2024] [Accepted: 04/16/2024] [Indexed: 05/29/2024] Open
Abstract
Hydrocarbon pollution is a widespread issue in both groundwater and surface-water systems; however, research on remediation at the interface of these two systems is limited. This interface is the oxic-anoxic boundary, where hydrocarbon pollutant from contaminated groundwaters flows into surface waters and iron mats are formed by microaerophilic iron-oxidizing bacteria. Iron mats are highly chemically adsorptive and host a diverse community of microbes. To elucidate the effect of hydrocarbon exposure on iron mat geochemistry and microbial community structure and function, we sampled iron mats both upstream and downstream from a leaking underground storage tank. Hydrocarbon-exposed iron mats had significantly higher concentrations of oxidized iron and significantly lower dissolved organic carbon and total dissolved phosphate than unexposed iron mats. A strong negative correlation between dissolved phosphate and benzene was observed in the hydrocarbon-exposed iron mats and water samples. There were positive correlations between iron and other hydrocarbons with benzene in the hydrocarbon-exposed iron mats, which was unique from water samples. The hydrocarbon-exposed iron mats represented two types, flocculent and seep, which had significantly different concentrations of iron, hydrocarbons, and phosphate, indicating that iron mat is also an important context in studies of freshwater mats. Using constrained ordination, we found the best predictors for community structure to be dissolved oxygen, pH, and benzene. Alpha diversity and evenness were significantly lower in hydrocarbon-exposed iron mats than unexposed mats. Using 16S rDNA amplicon sequences, we found evidence of three putative nitrate-reducing iron-oxidizing taxa in microaerophile-dominated iron mats (Azospira, Paracoccus, and Thermomonas). 16S rDNA amplicons also indicated the presence of taxa that are associated with hydrocarbon degradation. Benzene remediation-associated genes were found using metagenomic analysis both in exposed and unexposed iron mats. Furthermore, the results indicated that season (summer vs. spring) exacerbates the negative effect of hydrocarbon exposure on community diversity and evenness and led to the increased abundance of numerous OTUs. This study represents the first of its kind to attempt to understand how contaminant exposure, specifically hydrocarbons, influences the geochemistry and microbial community of freshwater iron mats and further develops our understanding of hydrocarbon remediation at the land-water interface.
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Affiliation(s)
- Chequita N. Brooks
- Department of Biology, East Carolina University, Greenville, NC, United States
- Louisiana Universities Marine Consortium, Chauvin, LA, United States
| | - Erin K. Field
- Department of Biology, East Carolina University, Greenville, NC, United States
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3
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Hoagland B, Rasmussen KL, Singha K, Spear JR, Navarre-Sitchler A. Metal-oxide precipitation influences microbiome structure in hyporheic zones receiving acid rock drainage. Appl Environ Microbiol 2024; 90:e0198723. [PMID: 38391193 PMCID: PMC10952486 DOI: 10.1128/aem.01987-23] [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: 11/03/2023] [Accepted: 01/14/2024] [Indexed: 02/24/2024] Open
Abstract
Streams impacted by historic mining activity are characterized by acidic pH, unique microbial communities, and abundant metal-oxide precipitation, all of which can influence groundwater-surface water exchange. We investigate how metal-oxide precipitates and hyporheic mixing mediate the composition of microbial communities in two streams receiving acid-rock and mine drainage near Silverton, Colorado, USA. A large, neutral pH hyporheic zone facilitated the precipitation of metal particles/colloids in hyporheic porewaters. A small, low pH hyporheic zone, limited by the presence of a low-permeability, iron-oxyhydroxide layer known as ferricrete, led to the formation of steep geochemical gradients and high dissolved-metal concentrations. To determine how these two hyporheic systems influence microbiome composition, we installed well clusters and deployed in situ microcosms in each stream to sample porewaters and sediments for 16S rRNA gene sequencing. Results indicated that distinct hydrogeochemical conditions were present above and below the ferricrete in the low pH system. A positive feedback loop may be present in the low pH stream where microbially mediated precipitation of iron-oxides contributes to additional clogging of hyporheic pore spaces, separating abundant, iron-oxidizing bacteria (Gallionella spp.) above the ferricrete from rare, low-abundance bacteria below the ferricrete. Metal precipitates and colloids that formed in the neutral pH hyporheic zone were associated with a more diverse phylogenetic community of nonmotile, nutrient-cycling bacteria that may be transported through hyporheic pore spaces. In summary, biogeochemical conditions influence, and are influenced by, hyporheic mixing, which mediates the distribution of micro-organisms and, thus, the cycling of metals in streams receiving acid-rock and mine drainage. IMPORTANCE In streams receiving acid-rock and mine drainage, the abundant precipitation of iron minerals can alter how groundwater and surface water mix along streams (in what is known as the "hyporheic zone") and may shape the distribution of microbial communities. The findings presented here suggest that neutral pH streams with large, well-mixed hyporheic zones may harbor and transport diverse microorganisms attached to particles/colloids through hyporheic pore spaces. In acidic streams where metal oxides clog pore spaces and limit hyporheic exchange, iron-oxidizing bacteria may dominate and phylogenetic diversity becomes low. The abundance of iron-oxidizing bacteria in acid mine drainage streams has the potential to contribute to additional clogging of hyporheic pore spaces and the accumulation of toxic metals in the hyporheic zone. This research highlights the dynamic interplay between hydrology, geochemistry, and microbiology at the groundwater-surface water interface of acid mine drainage streams.
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Affiliation(s)
- Beth Hoagland
- Department of Geology and Geological Engineering, Hydrologic Science and Engineering Program, Colorado School of Mines, Golden, Colorado, USA
- S.S. Papadopulos & Associates, Inc., Rockville, Maryland, USA
| | - Kalen L. Rasmussen
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, Colorado, USA
| | - Kamini Singha
- Department of Geology and Geological Engineering, Hydrologic Science and Engineering Program, Colorado School of Mines, Golden, Colorado, USA
| | - John R. Spear
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, Colorado, USA
| | - Alexis Navarre-Sitchler
- Department of Geology and Geological Engineering, Hydrologic Science and Engineering Program, Colorado School of Mines, Golden, Colorado, USA
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Hoover RL, Keffer JL, Polson SW, Chan CS. Gallionellaceae pangenomic analysis reveals insight into phylogeny, metabolic flexibility, and iron oxidation mechanisms. mSystems 2023; 8:e0003823. [PMID: 37882557 PMCID: PMC10734462 DOI: 10.1128/msystems.00038-23] [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: 01/25/2023] [Accepted: 09/20/2023] [Indexed: 10/27/2023] Open
Abstract
IMPORTANCE Neutrophilic iron-oxidizing bacteria (FeOB) produce copious iron (oxyhydr)oxides that can profoundly influence biogeochemical cycles, notably the fate of carbon and many metals. To fully understand environmental microbial iron oxidation, we need a thorough accounting of iron oxidation mechanisms. In this study, we show the Gallionellaceae FeOB genomes encode both characterized iron oxidases as well as uncharacterized multiheme cytochromes (MHCs). MHCs are predicted to transfer electrons from extracellular substrates and likely confer metabolic capabilities that help Gallionellaceae occupy a range of different iron- and mineral-rich niches. Gallionellaceae appear to specialize in iron oxidation, so it would be advantageous for them to have multiple mechanisms to oxidize various forms of iron, given the many iron minerals on Earth, as well as the physiological and kinetic challenges faced by FeOB. The multiple iron/mineral oxidation mechanisms may help drive the widespread ecological success of Gallionellaceae.
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Affiliation(s)
- Rene L. Hoover
- Microbiology Graduate Program, University of Delaware, Newark, Delaware, USA
- Department of Earth Sciences, University of Delaware, Newark, Delaware, USA
| | - Jessica L. Keffer
- Department of Earth Sciences, University of Delaware, Newark, Delaware, USA
| | - Shawn W. Polson
- Department of Computer and Information Sciences, University of Delaware, Newark, Delaware, USA
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware, USA
| | - Clara S. Chan
- Microbiology Graduate Program, University of Delaware, Newark, Delaware, USA
- Department of Earth Sciences, University of Delaware, Newark, Delaware, USA
- School of Marine Science and Policy, University of Delaware, Newark, Delaware, USA
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5
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Ju Y, Baik MH, Lee SY, Lee KK, Kaown D, Shin D, Ryu JH. Identifying the origin and fate of dissolved U in the Boeun aquifer based on microbial signatures and C, O, Fe, S, and U isotopes. JOURNAL OF HAZARDOUS MATERIALS 2023; 459:132051. [PMID: 37467612 DOI: 10.1016/j.jhazmat.2023.132051] [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: 04/18/2023] [Revised: 06/12/2023] [Accepted: 07/10/2023] [Indexed: 07/21/2023]
Abstract
The uranium inventory in the Boeun aquifer is situated near an artificial reservoir (40-70 m apart) intended to supply water to nearby cities. However, toxic radionuclides can enter the reservoir. To determine the U mobility in the system, we analyzed groundwater and fracture-filling materials (FFMs) for environmental tracers, including microbial signatures, redox-sensitive elements and isotopes. In the site, U mass flux ranged from only 9.59 × 10-7 µg/L/y to 1.70 × 10-4 µg/L/y. The δ18O-H2O and 14C signatures showed that groundwater originated mainly from upland recharges and was not influenced by oxic surface water. We observed U accumulations (∼157 mg/kg) in shallow FFMs and Fe enrichments (∼226798 mg/kg) and anomalies in the 230Th/238U activity ratio (AR), 230Th/234U AR, δ56Fe and δ57Fe isotopes, suggesting that low U mobility in shallow depths is associated with a Fe-rich environment. At shallow depths, anaerobic Fe-oxidizers, Gallionella was prevalent in the groundwater, while Acidovorax was abundant near the U ore deposit depth. The Fe-rich environment at shallow depths was formed by sulfide dissolution, as demonstrated by δ34S-SO4 and δ18O-SO4 distribution. Overall, the Fe-rich aquifer including abundant sulfide minerals immobilizes dissolved U through biotic and abiotic processes, without significant leaching into nearby reservoirs.
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Affiliation(s)
- YeoJin Ju
- Disposal Safety Evaluation Research Division, Korea Atomic Energy Research Institute, Daejeon 34057, Republic of Korea
| | - Min Hoon Baik
- Disposal Safety Evaluation Research Division, Korea Atomic Energy Research Institute, Daejeon 34057, Republic of Korea
| | - Seung Yeop Lee
- Disposal Safety Evaluation Research Division, Korea Atomic Energy Research Institute, Daejeon 34057, Republic of Korea
| | - Kang-Kun Lee
- School of Earth and Environmental Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Dugin Kaown
- School of Earth and Environmental Sciences, Seoul National University, Seoul 08826, Republic of Korea.
| | - Dongbok Shin
- Department of Geoenvironmental Sciences, Kongju National University, Kongju 32588, Republic of Korea
| | - Ji-Hun Ryu
- Disposal Safety Evaluation Research Division, Korea Atomic Energy Research Institute, Daejeon 34057, Republic of Korea.
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6
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Sriaporn C, Campbell KA, Van Kranendonk MJ, Handley KM. Bacterial and archaeal community distributions and cosmopolitanism across physicochemically diverse hot springs. ISME COMMUNICATIONS 2023; 3:80. [PMID: 37596308 PMCID: PMC10439147 DOI: 10.1038/s43705-023-00291-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 08/01/2023] [Accepted: 08/04/2023] [Indexed: 08/20/2023]
Abstract
Terrestrial hot springs harbor diverse microbial communities whose compositions are shaped by the wide-ranging physico-chemistries of individual springs. The effect of enormous physico-chemical differences on bacterial and archaeal distributions and population structures is little understood. We therefore analysed the prevalence and relative abundance of bacteria and archaea in the sediments (n = 76) of hot spring features, in the Taupō Volcanic Zone (New Zealand), spanning large differences in major anion water chemistry, pH (2.0-7.5), and temperature (17.5-92.9 °C). Community composition, based on 16S rRNA amplicon sequence variants (ASVs) was strongly influenced by both temperature and pH. However, certain lineages characterized diverse hot springs. At the domain level, bacteria and archaea shared broadly equivalent community abundances across physico-chemically diverse springs, despite slightly lower bacteria-to-archaea ratios and microbial 16S rRNA gene concentrations at higher temperatures. Communities were almost exclusively dominated by Proteobacteria, Euryarchaeota or Crenarchaeota. Eight archaeal and bacterial ASVs from Thermoplasmatales, Desulfurellaceae, Mesoaciditogaceae and Acidithiobacillaceae were unusually prevalent (present in 57.9-84.2% of samples) and abundant (1.7-12.0% sample relative abundance), and together comprised 44% of overall community abundance. Metagenomic analyses generated multiple populations associated with dominant ASVs, and showed characteristic traits of each lineage for sulfur, nitrogen and hydrogen metabolism. Differences in metabolic gene composition and genome-specific metabolism delineated populations from relatives. Genome coverage calculations showed that populations associated with each lineage were distributed across a physicochemically broad range of hot springs. Results imply that certain bacterial and archaeal lineages harbor different population structures and metabolic potentials for colonizing diverse hot spring environments.
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Affiliation(s)
- Chanenath Sriaporn
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Kathleen A Campbell
- School of Environment & Te Ao Mārama - Centre for Fundamental Inquiry, The University of Auckland, Auckland, New Zealand
| | - Martin J Van Kranendonk
- Australian Centre for Astrobiology, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Kim M Handley
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand.
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7
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Ma Y, Rui D, Dong H, Zhang X, Ye L. Large-scale comparative analysis reveals different bacterial community structures in full- and lab-scale wastewater treatment bioreactors. WATER RESEARCH 2023; 242:120222. [PMID: 37331228 DOI: 10.1016/j.watres.2023.120222] [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: 03/13/2023] [Revised: 05/16/2023] [Accepted: 06/12/2023] [Indexed: 06/20/2023]
Abstract
The activated sludge process is widely used for biological wastewater treatment due to its low cost and high efficiency. Although numerous lab-scale bioreactor experiments have been conducted to investigate the microorganism performance and mechanisms in activated sludge, understanding the bacterial community differences between full- and lab-scale bioreactors has remained elusive. In this study, we investigated the bacterial communities in 966 activated sludge samples obtained from various bioreactors, including both full- and lab-scale ones, from 95 previous studies. Our findings reveal significant differences in the bacterial communities between full- and lab-scale bioreactors, with thousands of bacterial genera exclusive to each scale. We also identified 12 genera that are frequently abundant in full-scale bioreactors but rarely observed in lab-scale reactors. By using a machine-learning method, organic matter and temperature were determined as the primary factors affecting microbial communities in full- and lab-scale bioreactors. Additionally, transient bacterial species from other environments may also contribute to the observed bacterial community differences. Furthermore, the bacterial community differences between full- and lab-scale bioreactors were verified by comparing the results of lab-scale bioreactor experiments to full-scale bioreactor sampling. Overall, this study sheds light on the bacteria overlooked in lab-scale studies and deepens our understanding of the differences in bacterial communities between full- and lab-scale bioreactors.
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Affiliation(s)
- Yanyan Ma
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing, Jiangsu, China
| | - Dongni Rui
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing, Jiangsu, China
| | - Haonan Dong
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing, Jiangsu, China
| | - Xuxiang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing, Jiangsu, China
| | - Lin Ye
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing, Jiangsu, China.
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8
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Groult B, St-Jean V, Lazar CS. Linking Groundwater to Surface Discharge Ecosystems: Archaeal, Bacterial, and Eukaryotic Community Diversity and Structure in Quebec (Canada). Microorganisms 2023; 11:1674. [PMID: 37512847 PMCID: PMC10384904 DOI: 10.3390/microorganisms11071674] [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: 05/18/2023] [Revised: 06/22/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
Aquifer systems are composed of water flowing from surface recharge areas, to the subsurface and back to the surface in discharge regions. Groundwater habitats harbor a large microbial biomass and diversity, potentially contributing to surface aquatic ecosystems. Although this contribution has been widely studied in marine environments, very little is known about the connection between underground and surface microbial communities in freshwater settings. Therefore, in this study, we used amplicon sequencing to analyze the archaeal, bacterial, and eukaryotic community diversity and structure in groundwater and surface water samples, spanning the vast regions of the Laurentides and Lanaudières in the Quebec province (Canada). Our results show significant differences between subsurface and surface taxa; with more fungi, Amoebozoa, and chemolithoautotrophic prokaryotes involved in nitrogen-, sulfur-, and iron-cycling dominating the underground samples; while algae, ciliates, methanogens, and Actinobacteria dominate the surface discharge waters. Microbial source tracking suggested that only a small portion of the microbial communities in the groundwater contributed to the surface discharge communities. However, many taxa were shared between both habitats, with a large range of functional diversity, likely explaining their survival in both subsurface and surface water ecosystems.
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Affiliation(s)
- Benjamin Groult
- Department of Biological Sciences, University of Québec at Montréal (UQAM), C.P. 8888, Succ. Centre-Ville, Montréal, QC H3C 3P8, Canada
| | - Vicky St-Jean
- Department of Biological Sciences, University of Québec at Montréal (UQAM), C.P. 8888, Succ. Centre-Ville, Montréal, QC H3C 3P8, Canada
| | - Cassandre Sara Lazar
- Department of Biological Sciences, University of Québec at Montréal (UQAM), C.P. 8888, Succ. Centre-Ville, Montréal, QC H3C 3P8, Canada
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9
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Huang C, Guo Z, Peng C, Anaman R, Zhang P. Immobilization of Cd in the soil of mining areas by FeMn oxidizing bacteria. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 873:162306. [PMID: 36801403 DOI: 10.1016/j.scitotenv.2023.162306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 01/13/2023] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
Microorganisms are widely used in large-scale pollution remediation due to their rapid reproduction and low cost. In this study, bioremediation batch experiments and characterization methods were adopted to investigate the mechanism of FeMn oxidizing bacteria on the immobilization of Cd in mining soil. The results showed that the FeMn oxidizing bacteria successfully reduced 36.84 % of the extractable Cd in the soil. The exchangeable forms, carbonate-bound forms, and organic-bound forms of Cd in the soil decreased by 11.4 %, 8 %, and 7.4 %, respectively, due to the addition of FeMn oxidizing bacteria, while FeMn oxides-bound and residual forms of Cd increased by 19.3 % and 7.5 %, as compared to the control treatments. The bacteria promotes the formation of amorphous FeMn precipitates such as lepidocrocite and goethite, which have high adsorption capacity on soil Cd. The oxidation rates of Fe and Mn in the soil treated with the oxidizing bacteria reached 70.32 % and 63.15 %, respectively. Meanwhile, the FeMn oxidizing bacteria increased soil pH and decreased soil organic matter content, further decreasing the extractable Cd in the soil. The FeMn oxidizing bacteria have the potential to be used in large mining areas to assist in the immobilization of heavy metals.
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Affiliation(s)
- Chiyue Huang
- Institute of Environmental Engineering, School of Metallurgy and Environment, Central South University, Changsha 410083, China
| | - Zhaohui Guo
- Institute of Environmental Engineering, School of Metallurgy and Environment, Central South University, Changsha 410083, China
| | - Chi Peng
- Institute of Environmental Engineering, School of Metallurgy and Environment, Central South University, Changsha 410083, China.
| | - Richmond Anaman
- Institute of Environmental Engineering, School of Metallurgy and Environment, Central South University, Changsha 410083, China
| | - Pan Zhang
- Department of Environment Ecology, School of Hunan Agricultural University, Changsha 410128, China
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10
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Hoover RL, Keffer JL, Polson SW, Chan CS. Gallionellaceae pangenomic analysis reveals insight into phylogeny, metabolic flexibility, and iron oxidation mechanisms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.26.525709. [PMID: 36747706 PMCID: PMC9900912 DOI: 10.1101/2023.01.26.525709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The iron-oxidizing Gallionellaceae drive a wide variety of biogeochemical cycles through their metabolisms and biominerals. To better understand the environmental impacts of Gallionellaceae, we need to improve our knowledge of their diversity and metabolisms, especially any novel iron oxidation mechanisms. Here, we used a pangenomic analysis of 103 genomes to resolve Gallionellaceae phylogeny and explore the range of genomic potential. Using a concatenated ribosomal protein tree and key gene patterns, we determined Gallionellaceae has four genera, divided into two groups-iron-oxidizing bacteria (FeOB) Gallionella, Sideroxydans, and Ferriphaselus with known iron oxidases (Cyc2, MtoA) and nitrite-oxidizing bacteria (NOB) Candidatus Nitrotoga with nitrite oxidase (Nxr). The FeOB and NOB have similar electron transport chains, including genes for reverse electron transport and carbon fixation. Auxiliary energy metabolisms including S oxidation, denitrification, and organotrophy were scattered throughout the Gallionellaceae FeOB. Within FeOB, we found genes that may represent adaptations for iron oxidation, including a variety of extracellular electron uptake (EEU) mechanisms. FeOB genomes encoded more predicted c-type cytochromes overall, notably more multiheme c-type cytochromes (MHCs) with >10 CXXCH motifs. These include homologs of several predicted outer membrane porin-MHC complexes, including MtoAB and Uet. MHCs are known to efficiently conduct electrons across longer distances and function across a wide range of redox potentials that overlap with mineral redox potentials, which can help expand the range of usable iron substrates. Overall, the results of pangenome analyses suggest that the Gallionellaceae genera Gallionella, Sideroxydans, and Ferriphaselus are primarily iron oxidizers, capable of oxidizing dissolved Fe2+ as well as a range of solid iron or other mineral substrates.
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Affiliation(s)
- Rene L Hoover
- Microbiology Graduate Program, University of Delaware, Newark, Delaware, USA
- Department of Earth Sciences, University of Delaware, Newark, Delaware, USA
| | - Jessica L Keffer
- Department of Earth Sciences, University of Delaware, Newark, Delaware, USA
| | - Shawn W Polson
- Department of Computer and Information Sciences, University of Delaware, Newark, Delaware, USA
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware, USA
| | - Clara S Chan
- Microbiology Graduate Program, University of Delaware, Newark, Delaware, USA
- Department of Earth Sciences, University of Delaware, Newark, Delaware, USA
- School of Marine Science and Policy, University of Delaware, Newark, Delaware, USA
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11
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Cooper RE, Finck J, Chan C, Küsel K. Mixotrophy broadens the ecological niche range of the iron oxidizer Sideroxydans sp. CL21 isolated from an iron-rich peatland. FEMS Microbiol Ecol 2023; 99:6979798. [PMID: 36623865 PMCID: PMC9925335 DOI: 10.1093/femsec/fiac156] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 11/17/2022] [Accepted: 01/06/2023] [Indexed: 01/11/2023] Open
Abstract
Sideroxydans sp. CL21 is a microaerobic, acid-tolerant Fe(II)-oxidizer, isolated from the Schlöppnerbrunnen fen. Since the genome size of Sideroxydans sp. CL21 is 21% larger than that of the neutrophilic Sideroxydans lithotrophicus ES-1, we hypothesized that strain CL21 contains additional metabolic traits to thrive in the fen. The common genomic content of both strains contains homologs of the putative Fe(II) oxidation genes, mtoAB and cyc2. A large part of the accessory genome in strain CL21 contains genes linked to utilization of alternative electron donors, including NiFe uptake hydrogenases, and genes encoding lactate uptake and utilization proteins, motility and biofilm formation, transposable elements, and pH homeostasis mechanisms. Next, we incubated the strain in different combinations of electron donors and characterized the fen microbial communities. Sideroxydans spp. comprised 3.33% and 3.94% of the total relative abundance in the peatland soil and peatland water, respectively. Incubation results indicate Sideroxydans sp. CL21 uses H2 and thiosulfate, while lactate only enhances growth when combined with Fe, H2, or thiosulfate. Rates of H2 utilization were highest in combination with other substrates. Thus, Sideroxydans sp. CL21 is a mixotroph, growing best by simultaneously using substrate combinations, which helps to thrive in dynamic and complex habitats.
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Affiliation(s)
- Rebecca E Cooper
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Jessica Finck
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Clara Chan
- School of Marine Science and Policy, University of Delaware, Newark, DE 19716, United States,Delaware Biotechnology Institute, University of Delaware, Newark, DE 19713, United States,Department of Earth Sciences, University of Delaware, Newark, DE 19716, United States
| | - Kirsten Küsel
- Corresponding author. Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Str. 159, 07743 Jena, Germany. Tel: +49 3641 949461; Fax: +49 3641 949462; E-mail:
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12
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Wan D, Cao Y, Shi Y, Li Q, Li Y, Zhang Z, Han X, Gao Y. Construction of heterotrophic-sulfur autotrophic integrated fluidized bed reactor for simultaneous and efficient removal of compound pollution of perchlorate and nitrate in water. CHEMOSPHERE 2022; 307:135944. [PMID: 35961446 DOI: 10.1016/j.chemosphere.2022.135944] [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] [Received: 05/05/2022] [Revised: 07/31/2022] [Accepted: 08/01/2022] [Indexed: 06/15/2023]
Abstract
A heterotrophic sulfur autotrophic integrated fluidized bed reactor was established for simultaneous and efficient removal of ClO4- and NO3- from water. The optimum operating conditions forecasted through the response surface method (RSM) were the hydraulic retention time (HRT) of 0.50 h, the influent acetate (CH3COO-) concentration of 55 mg/L and the reflux ratio of 14, contributing to ClO4- and NO3- removal of 98.99% and 99.96%, respectively, without secondary pollution caused by residual carbon (NPOC <3.89 mg/L). Meanwhile, the effluent pH fluctuated in a range of 6.70-8.02 and sulfur-containing by-products (i.e., SO42- and S2-) could be controlled by adjusting operation conditions throughout the experimental stage. The increase of the influent CH3COO- concentration reduced the load borne by autotrophic reduction process and further reduced SO42- production. Shortening HRT, increasing the influent CH3COO- concentration and decreasing the reflux ratio could all reduce alkalinity consumption. Shortening HRT and decreasing the reflux ratio could shorten contact time between sulfur and water and thus inhibit S0 disproportionation. High-throughput sequencing result showed that Proteobacteria and Chlorobi were the dominant bacteria. Sulfurovum, Sulfuricurvum and Ignavibacterium were the major heterotrophic denitrifying bacteria (DB)/perchlorate reducing bacteria (PRB), Ferritrophicum and Geothrix were DB, and Chlorobaculum was S0 disproportionation bacteria.
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Affiliation(s)
- Dongjin Wan
- College of Environmental Engineering, Henan University of Technology, Zhengzhou, Henan, 450001, China; Henan International Joint Laboratory of Environmental Pollution, Remediation and Grain Quality Security, Zhengzhou, Henan, 450001, China; Institute for Carbon Neutrality, Henan University of Technology, Zhengzhou, Henan, 450001, China.
| | - Yang Cao
- College of Environmental Engineering, Henan University of Technology, Zhengzhou, Henan, 450001, China
| | - Yahui Shi
- College of Environmental Engineering, Henan University of Technology, Zhengzhou, Henan, 450001, China; Henan International Joint Laboratory of Environmental Pollution, Remediation and Grain Quality Security, Zhengzhou, Henan, 450001, China; Institute for Carbon Neutrality, Henan University of Technology, Zhengzhou, Henan, 450001, China.
| | - Qi Li
- College of Environmental Engineering, Henan University of Technology, Zhengzhou, Henan, 450001, China
| | - Ying Li
- College of Environmental Engineering, Henan University of Technology, Zhengzhou, Henan, 450001, China; Henan International Joint Laboratory of Environmental Pollution, Remediation and Grain Quality Security, Zhengzhou, Henan, 450001, China; Institute for Carbon Neutrality, Henan University of Technology, Zhengzhou, Henan, 450001, China
| | - Zhixiang Zhang
- College of Environmental Engineering, Henan University of Technology, Zhengzhou, Henan, 450001, China
| | - Xinze Han
- College of Environmental Engineering, Henan University of Technology, Zhengzhou, Henan, 450001, China
| | - Yafei Gao
- College of Environmental Engineering, Henan University of Technology, Zhengzhou, Henan, 450001, China
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13
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Liu K, Schiff SL, Wu L, Molot LA, Venkiteswaran JJ, Paterson MJ, Elgood RJ, Tsuji JM, Neufeld JD. Large Fractionation in Iron Isotopes Implicates Metabolic Pathways for Iron Cycling in Boreal Shield Lakes. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:14840-14851. [PMID: 36162065 DOI: 10.1021/acs.est.2c04247] [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: 06/16/2023]
Abstract
Stable Fe isotopes have only recently been measured in freshwater systems, mainly in meromictic lakes. Here we report the δ56Fe of dissolved, particulate, and sediment Fe in two small dimictic boreal shield headwater lakes: manipulated eutrophic Lake 227, with annual cyanobacterial blooms, and unmanipulated oligotrophic Lake 442. Within the lakes, the range in δ56Fe is large (ca. -0.9 to +1.8‰), spanning more than half the entire range of natural Earth surface samples. Two layers in the water column with distinctive δ56Fe of dissolved (dis) and particulate (spm) Fe were observed, despite differences in trophic states. In the epilimnia of both lakes, a large Δ56Fedis-spm fractionation of 0.4-1‰ between dissolved and particulate Fe was only observed during cyanobacterial blooms in Lake 227, possibly regulated by selective biological uptake of isotopically light Fe by cyanobacteria. In the anoxic layers in both lakes, upward flux from sediments dominates the dissolved Fe pool with an apparent Δ56Fedis-spm fractionation of -2.2 to -0.6‰. Large Δ56Fedis-spm and previously published metagenome sequence data suggest active Fe cycling processes in anoxic layers, such as microaerophilic Fe(II) oxidation or photoferrotrophy, could regulate biogeochemical cycling. Large fractionation of stable Fe isotopes in these lakes provides a potential tool to probe Fe cycling and the acquisition of Fe by cyanobacteria, with relevance for understanding biogeochemical cycling of Earth's early ferruginous oceans.
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Affiliation(s)
- Kai Liu
- Department of Earth and Environmental Sciences, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
- Water Institute, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Sherry L Schiff
- Department of Earth and Environmental Sciences, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
- Water Institute, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Lingling Wu
- Department of Earth and Environmental Sciences, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
- Water Institute, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Lewis A Molot
- Faculty of Environmental and Urban Change, York University, Toronto, Ontario M3J 1P3, Canada
| | - Jason J Venkiteswaran
- Department of Geography and Environmental Studies, Wilfrid Laurier University, Waterloo, Ontario N2L 3C5, Canada
| | | | - Richard J Elgood
- Department of Earth and Environmental Sciences, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
- Water Institute, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Jackson M Tsuji
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
| | - Josh D Neufeld
- Water Institute, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
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14
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Indigenous microbial populations of abandoned mining sites and their role in natural attenuation. Arch Microbiol 2022; 204:251. [PMID: 35411412 DOI: 10.1007/s00203-022-02861-6] [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: 07/23/2021] [Revised: 03/17/2022] [Accepted: 03/20/2022] [Indexed: 11/02/2022]
Abstract
Environmental contamination by toxic effluents discharged by anthropogenic activities including the mining industries has increased extensively in the recent past. Microbial communities and their biofilms inhabiting these extreme habitats have developed different adaptive strategies in metabolizing and transforming the persistent pollutants. They also play a crucial role in natural attenuation of these abandoned mining sites and act as a major driver of many biogeochemical processes, which helps in ecological rehabilitation and is a viable approach for restoration of wide stretches of land. In this review, the types of mine wastes including the overburden and mine drainage and the types of microbial communities thriving in such environments were probed in detail. The types of biofilms formed along with their possible role in metal bioremediation were also reviewed. This review also provides an overview of the shift in microbial communities in natural reclamation process and also provides an insight into the restoration of the enzyme activities of the soils which may help in further revegetation of abundant mining areas in a sustainable manner. Moreover, the role of indigenous microbiota in bioremediation of heavy metals and their plant growth-promoting activity weres discussed to assess their role in phytoremedial processes.
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15
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Johnson A, Högfors-Rönnholm E, Engblom S, Österholm P, Åström M, Dopson M. Dredging and deposition of metal sulfide rich river sediments results in rapid conversion to acid sulfate soil materials. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 813:151864. [PMID: 34822903 DOI: 10.1016/j.scitotenv.2021.151864] [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: 10/03/2021] [Revised: 11/14/2021] [Accepted: 11/17/2021] [Indexed: 06/13/2023]
Abstract
Sediments along the Baltic Sea coast can contain considerable amounts of metal sulfides that if dredged and the spoils deposited such that they are exposed to air, can release high concentrations of acid and toxic metals into recipient water bodies. Two river estuaries in western Finland were dredged from 2013 to 2018 and the dredge spoils were deposited on land previously covered with agricultural limestone to buffer the pH and mitigate acid and metal release. In this study, the geochemistry and 16S rRNA gene amplicon based bacterial communities were investigated over time to explore whether the application of lime prevented a conversion of the dredge spoils into acid producing and metal releasing soil. The pH of the dredge spoils decreased with time indicating metal sulfide oxidation and resulted in elevated sulfate concentrations along with a concomitant release of metals. However, calculations indicated only approximately 5% of the added lime had been dissolved. The bacterial communities decreased in diversity with the lowering of the pH as taxa most similar to extremely acidophilic sulfur, and in some cases iron, oxidizing Acidithiobacillus species became the dominant characterized genus in the deposited dredge spoils as the oxidation front moved deeper. In addition, other taxa characterized as involved in oxidation of iron or sulfur were identified including Gallionella, Sulfuricurvum, and Sulfurimonas. These data suggest there was a rapid conversion of the dredge spoils to severely acidic soil similar to actual acid sulfate soil and that the lime placed on the land prior to deposition of the spoils, and later ploughed into the dry dredge spoils, was insufficient to halt this process. Hence, future dredging and deposition of dredge spoils containing metal sulfides should not only take into account the amount of lime used for buffering but also its grain size and mixing into the soil.
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Affiliation(s)
- Anders Johnson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, SE-39231 Kalmar, Sweden.
| | - Eva Högfors-Rönnholm
- Research and Development, Novia University of Applied Sciences, FI-65200 Vaasa, Finland.
| | - Sten Engblom
- Research and Development, Novia University of Applied Sciences, FI-65200 Vaasa, Finland.
| | - Peter Österholm
- Department of Geology and Mineralogy, Åbo Akademi University, FI-20500 Turku, Finland.
| | - Mats Åström
- Biology and Environmental Sciences, Linnaeus University, SE-39231 Kalmar, Sweden.
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, SE-39231 Kalmar, Sweden.
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16
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Zhou N, Keffer JL, Polson SW, Chan CS. Unraveling Fe(II)-Oxidizing Mechanisms in a Facultative Fe(II) Oxidizer, Sideroxydans lithotrophicus Strain ES-1, via Culturing, Transcriptomics, and Reverse Transcription-Quantitative PCR. Appl Environ Microbiol 2022; 88:e0159521. [PMID: 34788064 PMCID: PMC8788666 DOI: 10.1128/aem.01595-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 11/11/2021] [Indexed: 11/20/2022] Open
Abstract
Sideroxydans lithotrophicus ES-1 grows autotrophically either by Fe(II) oxidation or by thiosulfate oxidation, in contrast to most other isolates of neutrophilic Fe(II)-oxidizing bacteria (FeOB). This provides a unique opportunity to explore the physiology of a facultative FeOB and constrain the genes specific to Fe(II) oxidation. We compared the growth of S. lithotrophicus ES-1 on Fe(II), thiosulfate, and both substrates together. While initial growth rates were similar, thiosulfate-grown cultures had higher yield with or without Fe(II) present, which may give ES-1 an advantage over obligate FeOB. To investigate the Fe(II) and S oxidation pathways, we conducted transcriptomics experiments, validated with reverse transcription-quantitative PCR (RT-qPCR). We explored the long-term gene expression response at different growth phases (over days to a week) and expression changes during a short-term switch from thiosulfate to Fe(II) (90 min). The dsr and sox sulfur oxidation genes were upregulated in thiosulfate cultures. The Fe(II) oxidase gene cyc2 was among the top expressed genes during both Fe(II) and thiosulfate oxidation, and addition of Fe(II) to thiosulfate-grown cells caused an increase in cyc2 expression. These results support the role of Cyc2 as the Fe(II) oxidase and suggest that ES-1 maintains readiness to oxidize Fe(II), even in the absence of Fe(II). We used gene expression profiles to further constrain the ES-1 Fe(II) oxidation pathway. Notably, among the most highly upregulated genes during Fe(II) oxidation were genes for alternative complex III, reverse electron transport, and carbon fixation. This implies a direct connection between Fe(II) oxidation and carbon fixation, suggesting that CO2 is an important electron sink for Fe(II) oxidation. IMPORTANCE Neutrophilic FeOB are increasingly observed in various environments, but knowledge of their ecophysiology and Fe(II) oxidation mechanisms is still relatively limited. Sideroxydans isolates are widely observed in aquifers, wetlands, and sediments, and genome analysis suggests metabolic flexibility contributes to their success. The type strain ES-1 is unusual among neutrophilic FeOB isolates, as it can grow on either Fe(II) or a non-Fe(II) substrate, thiosulfate. Almost all our knowledge of neutrophilic Fe(II) oxidation pathways comes from genome analyses, with some work on metatranscriptomes. This study used culture-based experiments to test the genes specific to Fe(II) oxidation in a facultative FeOB and refine our model of the Fe(II) oxidation pathway. We gained insight into how facultative FeOB like ES-1 connect Fe, S, and C biogeochemical cycling in the environment and suggest a multigene indicator would improve understanding of Fe(II) oxidation activity in environments with facultative FeOB.
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Affiliation(s)
- Nanqing Zhou
- School of Marine Science and Policy, University of Delaware, Newark, Delaware, USA
| | - Jessica L. Keffer
- Department of Earth Sciences, University of Delaware, Newark, Delaware, USA
| | - Shawn W. Polson
- Department of Computer and Information Sciences, University of Delaware, Newark, Delaware, USA
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware, USA
| | - Clara S. Chan
- School of Marine Science and Policy, University of Delaware, Newark, Delaware, USA
- Department of Earth Sciences, University of Delaware, Newark, Delaware, USA
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17
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Draft Genome Sequence of Bordetella sp. Strain FB-8, Isolated from a Former Uranium Mining Area in Germany. Microbiol Resour Announc 2021; 10:10/14/e01035-19. [PMID: 33833027 PMCID: PMC8032469 DOI: 10.1128/mra.01035-19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Here, we present the draft genome sequence of Bordetella sp. strain FB-8, a mixotrophic iron-oxidizing bacterium isolated from creek sediment in the former uranium-mining district of Ronneburg, Germany. To date, iron oxidation has not been reported in Bordetella species, indicating that FB-8 may be an environmentally important Bordetella sp. Here, we present the draft genome sequence of Bordetella sp. strain FB-8, a mixotrophic iron-oxidizing bacterium isolated from creek sediment in the former uranium-mining district of Ronneburg, Germany. To date, iron oxidation has not been reported in Bordetella species, indicating that FB-8 may be an environmentally important Bordetella sp.
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18
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Qin S, Zhang X, He S, Huang J. Improvement of nitrogen removal with iron scraps in floating treatment wetlands. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:17878-17890. [PMID: 33398766 DOI: 10.1007/s11356-020-12177-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 12/21/2020] [Indexed: 06/12/2023]
Abstract
Floating treatment wetland (FTW) in restoration of low C/N ratio wastewater was deemed to a frequently used method. However, the nitrate removal performance in floating beds was limited due to insufficient organic carbon sources. Iron scraps as a potential electron donor was beneficial to the NO3--N reduction. To research the removal performance and mechanism of denitrification in FTW with iron scraps, FTW with Iris pseudacorus was built, and iron scraps were added as an electron donor to improve nitrogen removal efficiency. The batch experimental results demonstrated that the proper mass ratio of iron scraps to NO3--N was 500:1. With iron scraps, the NO3--N removal efficiency of FTW and control system increased significantly to 98.04% and 44.42% respectively in 2 weeks, while there was no obvious influence on the removal of NH4+-N. After adding iron scraps, the proportion of bacteria in the systems related to iron cycle and the relative abundance of nitrifying and denitrifying bacteria have increased obviously. By calculating the nitrogen balance, nitrogen reduction via plant uptake accounted for 8.79%, and the microbial denitrification was the main nitrogen removal pathway in FTW.
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Affiliation(s)
- Si Qin
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Dong Chuan Road 800, Shanghai, 200240, People's Republic of China
| | - Xiaoyi Zhang
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Dong Chuan Road 800, Shanghai, 200240, People's Republic of China
| | - Shengbing He
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Dong Chuan Road 800, Shanghai, 200240, People's Republic of China.
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, People's Republic of China.
- Shanghai Engineering Research Center of Landscape Water Environment, Shanghai, 200031, People's Republic of China.
| | - Jungchen Huang
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Dong Chuan Road 800, Shanghai, 200240, People's Republic of China
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19
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Prokhorova A, Kainuma M, Hiyane R, Boerner S, Goryanin I. Concurrent treatment of raw and aerated swine wastewater using an electrotrophic denitrification system. BIORESOURCE TECHNOLOGY 2021; 322:124508. [PMID: 33341711 DOI: 10.1016/j.biortech.2020.124508] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/28/2020] [Accepted: 12/02/2020] [Indexed: 06/12/2023]
Abstract
Enhanced nitrate removal in the cathode chamber of bioelectrochemical systems (BES) using aerated swine wastewater under high nitrate levels and low organic carbon was investigated in this study, focusing on the relationship between nitrogen and bacterial communities involved in denitrification pathways. BESs with the anion exchange membrane (AEM) under cathodic applied potentials of -0.6 V vs. AgCl/AgCl reference electrode showed a removal rate of 99 ± 2 mg L-1 d-1. Moreover, organic compounds from the untreated full-strength wastewater were simultaneously eliminated in the anode chamber with a removal rate of 0.46 g COD L-1 d-1 with achieved efficiency of 61.4 ± 0.5% from an initial concentration of around 5 g of COD L-1, measured over the course of 7 days. The highest microbial diversity was detected in BESs under potentials of -0.6 V, which include autotrophic denitrifiers such as Syderoxidans, Gallionela and Thiobacillus.
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Affiliation(s)
- Anna Prokhorova
- Biological Systems Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.
| | - Mami Kainuma
- Biological Systems Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Rie Hiyane
- Biological Systems Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Susan Boerner
- Biological Systems Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Igor Goryanin
- Biological Systems Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan; School of Informatics, University of Edinburgh, Edinburgh, UK
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20
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Huang Y, Xu D, Huang LY, Lou YT, Muhadesi JB, Qian HC, Zhou EZ, Wang BJ, Li XT, Jiang Z, Liu SJ, Zhang DW, Jiang CY. Responses of soil microbiome to steel corrosion. NPJ Biofilms Microbiomes 2021; 7:6. [PMID: 33479252 PMCID: PMC7820017 DOI: 10.1038/s41522-020-00175-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 11/24/2020] [Indexed: 11/09/2022] Open
Abstract
The process of microbiologically influenced corrosion (MIC) in soils has received widespread attention. Herein, long-term outdoor soil burial experiments were conducted to elucidate the community composition and functional interaction of soil microorganisms associated with metal corrosion. The results indicated that iron-oxidizing (e.g., Gallionella), nitrifying (e.g., Nitrospira), and denitrifying (e.g., Hydrogenophaga) microorganisms were significantly enriched in response to metal corrosion and were positively correlated with the metal mass loss. Corrosion process may promote the preferential growth of the abundant microbes. The functional annotation revealed that the metabolic processes of nitrogen cycling and electron transfer pathways were strengthened, and also that the corrosion of metals in soil was closely associated with the biogeochemical cycling of iron and nitrogen elements and extracellular electron transfer. Niche disturbance of microbial communities induced by the buried metals facilitated the synergetic effect of the major MIC participants. The co-occurrence network analysis suggested possible niche correlations among corrosion related bioindicators.
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Affiliation(s)
- Ye Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dake Xu
- Shenyang National Laboratory for Material Sciences, Northeastern University, Shenyang, 110819, China
| | - Lu-Yao Huang
- Beijing Advanced Innovation Center for Materials Genome Engineering, National Materials Corrosion and Protection Data Center, Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing, 100083, China
| | - Yun-Tian Lou
- Beijing Advanced Innovation Center for Materials Genome Engineering, National Materials Corrosion and Protection Data Center, Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing, 100083, China
| | - Jiang-Baota Muhadesi
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hong-Chang Qian
- Beijing Advanced Innovation Center for Materials Genome Engineering, National Materials Corrosion and Protection Data Center, Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing, 100083, China
| | - En-Ze Zhou
- Shenyang National Laboratory for Material Sciences, Northeastern University, Shenyang, 110819, China
| | - Bao-Jun Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiu-Tong Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhen Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Da-Wei Zhang
- Beijing Advanced Innovation Center for Materials Genome Engineering, National Materials Corrosion and Protection Data Center, Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing, 100083, China.
| | - Cheng-Ying Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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21
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Akob DM, Hallenbeck M, Beulig F, Fabisch M, Küsel K, Keffer JL, Woyke T, Shapiro N, Lapidus A, Klenk HP, Chan CS. Mixotrophic Iron-Oxidizing Thiomonas Isolates from an Acid Mine Drainage-Affected Creek. Appl Environ Microbiol 2020; 86:e01424-20. [PMID: 33008825 PMCID: PMC7688216 DOI: 10.1128/aem.01424-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 09/30/2020] [Indexed: 12/27/2022] Open
Abstract
Natural attenuation of heavy metals occurs via coupled microbial iron cycling and metal precipitation in creeks impacted by acid mine drainage (AMD). Here, we describe the isolation, characterization, and genomic sequencing of two iron-oxidizing bacteria (FeOB) species: Thiomonas ferrovorans FB-6 and Thiomonas metallidurans FB-Cd, isolated from slightly acidic (pH 6.3), Fe-rich, AMD-impacted creek sediments. These strains precipitated amorphous iron oxides, lepidocrocite, goethite, and magnetite or maghemite and grew at a pH optimum of 5.5. While Thiomonas spp. are known as mixotrophic sulfur oxidizers and As oxidizers, the FB strains oxidized Fe, which suggests they can efficiently remove Fe and other metals via coprecipitation. Previous evidence for Thiomonas sp. Fe oxidation is largely ambiguous, possibly because of difficulty demonstrating Fe oxidation in heterotrophic/mixotrophic organisms. Therefore, we also conducted a genomic analysis to identify genetic mechanisms of Fe oxidation, other metal transformations, and additional adaptations, comparing the two FB strain genomes with 12 other Thiomonas genomes. The FB strains fall within a relatively novel group of Thiomonas strains that includes another strain (b6) with solid evidence of Fe oxidation. Most Thiomonas isolates, including the FB strains, have the putative iron oxidation gene cyc2, but only the two FB strains possess the putative Fe oxidase genes mtoAB The two FB strain genomes contain the highest numbers of strain-specific gene clusters, greatly increasing the known Thiomonas genetic potential. Our results revealed that the FB strains are two distinct novel species of Thiomonas with the genetic potential for bioremediation of AMD via iron oxidation.IMPORTANCE As AMD moves through the environment, it impacts aquatic ecosystems, but at the same time, these ecosystems can naturally attenuate contaminated waters via acid neutralization and catalyzing metal precipitation. This is the case in the former Ronneburg uranium-mining district, where AMD impacts creek sediments. We isolated and characterized two iron-oxidizing Thiomonas species that are mildly acidophilic to neutrophilic and that have two genetic pathways for iron oxidation. These Thiomonas species are well positioned to naturally attenuate AMD as it discharges across the landscape.
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Affiliation(s)
| | - Michelle Hallenbeck
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA
- Delaware Biotechnology Institute, Newark, Delaware, USA
| | - Felix Beulig
- Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany
| | - Maria Fabisch
- Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany
| | - Kirsten Küsel
- Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany
| | - Jessica L Keffer
- Department of Earth Sciences, University of Delaware, Newark, Delaware, USA
- Delaware Biotechnology Institute, Newark, Delaware, USA
| | - Tanja Woyke
- Joint Genome Institute, U.S. Department of Energy, Berkeley, California, USA
| | - Nicole Shapiro
- Joint Genome Institute, U.S. Department of Energy, Berkeley, California, USA
| | - Alla Lapidus
- Joint Genome Institute, U.S. Department of Energy, Berkeley, California, USA
- Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Clara S Chan
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA
- Department of Earth Sciences, University of Delaware, Newark, Delaware, USA
- Delaware Biotechnology Institute, Newark, Delaware, USA
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22
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Cooper RE, Wegner CE, Kügler S, Poulin RX, Ueberschaar N, Wurlitzer JD, Stettin D, Wichard T, Pohnert G, Küsel K. Iron is not everything: unexpected complex metabolic responses between iron-cycling microorganisms. THE ISME JOURNAL 2020; 14:2675-2690. [PMID: 32690937 PMCID: PMC7784907 DOI: 10.1038/s41396-020-0718-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 06/30/2020] [Accepted: 07/08/2020] [Indexed: 02/02/2023]
Abstract
Coexistence of microaerophilic Fe(II)-oxidizers and anaerobic Fe(III)-reducers in environments with fluctuating redox conditions is a prime example of mutualism, in which both partners benefit from the sustained Fe-pool. Consequently, the Fe-cycling machineries (i.e., metal-reducing or -oxidizing pathways) should be most affected during co-cultivation. However, contrasting growth requirements impeded systematic elucidation of their interactions. To disentangle underlying interaction mechanisms, we established a suboxic co-culture system of Sideroxydans sp. CL21 and Shewanella oneidensis. We showed that addition of the partner's cell-free supernatant enhanced both growth and Fe(II)-oxidizing or Fe(III)-reducing activity of each partner. Metabolites of the exometabolome of Sideroxydans sp. CL21 are generally upregulated if stimulated with the partner´s spent medium, while S. oneidensis exhibits a mixed metabolic response in accordance with a balanced response to the partner. Surprisingly, RNA-seq analysis revealed genes involved in Fe-cycling were not differentially expressed during co-cultivation. Instead, the most differentially upregulated genes included those encoding for biopolymer production, lipoprotein transport, putrescine biosynthesis, and amino acid degradation suggesting a regulated inter-species biofilm formation. Furthermore, the upregulation of hydrogenases in Sideroxydans sp. CL21 points to competition for H2 as electron donor. Our findings reveal that a complex metabolic and transcriptomic response, but not accelerated formation of Fe-end products, drive interactions of Fe-cycling microorganisms.
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Affiliation(s)
- Rebecca E Cooper
- Institute of Biodiversity, Aquatic Geomicrobiology, Friedrich Schiller University Jena, Dornburger Strasse 159, 07743, Jena, Germany
| | - Carl-Eric Wegner
- Institute of Biodiversity, Aquatic Geomicrobiology, Friedrich Schiller University Jena, Dornburger Strasse 159, 07743, Jena, Germany
| | - Stefan Kügler
- Institute of Biodiversity, Aquatic Geomicrobiology, Friedrich Schiller University Jena, Dornburger Strasse 159, 07743, Jena, Germany
- Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, 07743, Jena, Germany
| | - Remington X Poulin
- Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, 07743, Jena, Germany
| | - Nico Ueberschaar
- Mass Spectrometry Platform, Faculty of Chemistry and Earth Sciences, Friedrich Schiller University Jena, Humboldstr. 8, 07743, Jena, Germany
| | - Jens D Wurlitzer
- Institute of Biodiversity, Aquatic Geomicrobiology, Friedrich Schiller University Jena, Dornburger Strasse 159, 07743, Jena, Germany
| | - Daniel Stettin
- Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, 07743, Jena, Germany
| | - Thomas Wichard
- Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, 07743, Jena, Germany
| | - Georg Pohnert
- Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, 07743, Jena, Germany
| | - Kirsten Küsel
- Institute of Biodiversity, Aquatic Geomicrobiology, Friedrich Schiller University Jena, Dornburger Strasse 159, 07743, Jena, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany.
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23
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Cabrol L, Thalasso F, Gandois L, Sepulveda-Jauregui A, Martinez-Cruz K, Teisserenc R, Tananaev N, Tveit A, Svenning MM, Barret M. Anaerobic oxidation of methane and associated microbiome in anoxic water of Northwestern Siberian lakes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 736:139588. [PMID: 32497884 DOI: 10.1016/j.scitotenv.2020.139588] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 05/07/2020] [Accepted: 05/19/2020] [Indexed: 05/16/2023]
Abstract
Arctic lakes emit methane (CH4) to the atmosphere. The magnitude of this flux could increase with permafrost thaw but might also be mitigated by microbial CH4 oxidation. Methane oxidation in oxic water has been extensively studied, while the contribution of anaerobic oxidation of methane (AOM) to CH4 mitigation is not fully understood. We have investigated four Northern Siberian stratified lakes in an area of discontinuous permafrost nearby Igarka, Russia. Analyses of CH4 concentrations in the water column demonstrated that 60 to 100% of upward diffusing CH4 was oxidized in the anoxic layers of the four lakes. A combination of pmoA and mcrA gene qPCR and 16S rRNA gene metabarcoding showed that the same taxa, all within Methylomonadaceae and including the predominant genus Methylobacter as well as Crenothrix, could be the major methane-oxidizing bacteria (MOB) in the anoxic water of the four lakes. Correlation between Methylomonadaceae and OTUs within Methylotenera, Geothrix and Geobacter genera indicated that AOM might occur in an interaction between MOB, denitrifiers and iron-cycling partners. We conclude that MOB within Methylomonadaceae could have a crucial impact on CH4 cycling in these Siberian Arctic lakes by mitigating the majority of produced CH4 before it leaves the anoxic zone. This finding emphasizes the importance of AOM by Methylomonadaceae and extends our knowledge about CH4 cycle in lakes, a crucial component of the global CH4 cycle.
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Affiliation(s)
- Léa Cabrol
- Aix-Marseille University, Univ Toulon, CNRS, IRD, M.I.O. UM 110, Mediterranean Institute of Oceanography, Marseille, France; Institute of Ecology and Biodiversity IEB, Faculty of Sciences, Universidad de Chile, Santiago, Chile; Escuela de Ingeniería Bioquímica, Pontificia Universidad de Valparaiso, Av Brasil 2085, Valparaiso, Chile
| | - Frédéric Thalasso
- Biotechnology and Bioengineering Department, Center for Research and Advanced Studies (Cinvestav), Mexico City, Mexico
| | - Laure Gandois
- Laboratory of Functional Ecology and Environment, Université de Toulouse, CNRS, Toulouse, France
| | - Armando Sepulveda-Jauregui
- ENBEELAB, University of Magallanes, Punta Arenas, Chile; Center for Climate and Resilience Research (CR)2, Santiago, Chile
| | | | - Roman Teisserenc
- Laboratory of Functional Ecology and Environment, Université de Toulouse, CNRS, Toulouse, France
| | | | - Alexander Tveit
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Mette M Svenning
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Maialen Barret
- Laboratory of Functional Ecology and Environment, Université de Toulouse, CNRS, Toulouse, France.
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24
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Hou D, Zhang P, Wei D, Zhang J, Yan B, Cao L, Zhou Y, Luo L. Simultaneous removal of iron and manganese from acid mine drainage by acclimated bacteria. JOURNAL OF HAZARDOUS MATERIALS 2020; 396:122631. [PMID: 32339872 DOI: 10.1016/j.jhazmat.2020.122631] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/31/2020] [Accepted: 03/31/2020] [Indexed: 05/28/2023]
Abstract
A bacterial consortium for efficient decontamination of high-concentration Fe-Mn acid mine drainage (AMD) was successfully isolated. The removal efficiencies of Fe and Mn were effective, reaching 99.8 % and 98.6 %, respectively. High-throughput sequencing of the 16S rRNA genes demonstrated that the microbial community had changed substantially during the treatment. The Fe-Mn oxidizing bacteria Flavobacterium, Brevundimonas, Stenotrophomonas and Thermomonas became dominant genera, suggesting that they might play vital roles in Fe and Mn removal. Moreover, the pH of culture increased obviously after incubation, which was benefit for depositing Fe and Mn from AMD. The specific surface area of the biogenic Fe-Mn oxides was 108-121 m2/g, and the surface contained reactive oxygen functional groups (-OH and -COOH), which also improved Fe and Mn removal efficiency. Thus, this study provides an alternative method to treat AMD containing high concentrations of Fe and Mn.
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Affiliation(s)
- Dongmei Hou
- College of Resources and Environment, Hunan Agricultural University, Changsha, 410128, PR China
| | - Pan Zhang
- College of Resources and Environment, Hunan Agricultural University, Changsha, 410128, PR China
| | - Dongning Wei
- College of Resources and Environment, Hunan Agricultural University, Changsha, 410128, PR China
| | - Jiachao Zhang
- College of Resources and Environment, Hunan Agricultural University, Changsha, 410128, PR China
| | - Binghua Yan
- College of Resources and Environment, Hunan Agricultural University, Changsha, 410128, PR China
| | - Linying Cao
- College of Resources and Environment, Hunan Agricultural University, Changsha, 410128, PR China
| | - Yaoyu Zhou
- College of Resources and Environment, Hunan Agricultural University, Changsha, 410128, PR China.
| | - Lin Luo
- College of Resources and Environment, Hunan Agricultural University, Changsha, 410128, PR China.
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25
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Vigliaturo R, Marengo A, Bittarello E, Pérez-Rodríguez I, Dražić G, Gieré R. Micro- and nano-scale mineralogical characterization of Fe(II)-oxidizing bacterial stalks. GEOBIOLOGY 2020; 18:606-618. [PMID: 32459887 PMCID: PMC7442631 DOI: 10.1111/gbi.12398] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/26/2020] [Accepted: 03/27/2020] [Indexed: 06/11/2023]
Abstract
Neutrophilic, microaerobic Fe(II)-oxidizing bacteria (FeOB) from marine and freshwater environments are known to generate twisted ribbon-like organo-mineral stalks. These structures, which are extracellularly precipitated, are susceptible to chemical influences in the environment once synthesized. In this paper, we characterize the minerals associated with freshwater FeOB stalks in order to evaluate key organo-mineral mechanisms involved in biomineral formation. Micro-Raman spectroscopy and Field Emission Scanning Electron Microscopy revealed that FeOB isolated from drinking water wells in Sweden produced stalks with ferrihydrite, lepidocrocite and goethite as main mineral components. Based on our observations made by micro-Raman Spectroscopy, field emission scanning electron microscopy and scanning transmission electron microscope combined with electron energy-loss spectroscopy, we propose a model that describes the crystal-growth mechanism, the Fe-oxidation state, and the mineralogical state of the stalks, as well as the biogenic contribution to these features. Our study suggests that the main crystal-growth mechanism in stalks includes nanoparticle aggregation and dissolution/re-precipitation reactions, which are dominant near the organic exopolymeric material produced by the microorganism and in the peripheral region of the stalk, respectively.
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Affiliation(s)
- Ruggero Vigliaturo
- Department of Earth and Environmental Science, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Erica Bittarello
- Department of Earth Science, University of Torino, Torino, Italy
| | - Ileana Pérez-Rodríguez
- Department of Earth and Environmental Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Goran Dražić
- Department for Materials Chemistry, National Institute of Chemistry, Ljubljana, Slovenia
| | - Reto Gieré
- Department of Earth and Environmental Science, University of Pennsylvania, Philadelphia, PA, USA
- Center of Excellence in Environmental Toxicology, University of Pennsylvania, Philadelphia, PA, USA
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26
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Sharma S, Lee M, Reinmann CS, Pumneo J, Cutright TJ, Senko JM. Impact of acid mine drainage chemistry and microbiology on the development of efficient Fe removal activities. CHEMOSPHERE 2020; 249:126117. [PMID: 32088465 DOI: 10.1016/j.chemosphere.2020.126117] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 02/02/2020] [Accepted: 02/03/2020] [Indexed: 06/10/2023]
Abstract
Coal mine derived acid mine drainage (AMD) is formed when oxygenated water infiltrates mine voids and oxidizes FeS phases, generating acidic fluid rich in heavy metals, polluting thousands of miles of streams. Existing remediation options are cost-prohibitive and difficult to sustain. In some cases, AMD flows over previously pristine soil in thin sheets over terrestrial surface, enhancing AMD aeration and Fe(II) oxidizing activities, leading to oxidative Fe(II) precipitation from AMD, without any human intervention. Since robust Fe(II) biooxidation occurs in the mixture of intruding AMD and pristine soil, understanding the effects of chemically variant AMD can be exploited for effective Fe(II) removal. We hypothesized that chemistry and microbiology of AMD intruding pristine soil on surface would influence the development of Fe(II) oxidizing capabilities. Therefore, to investigate the response of pristine soil to the addition of AMD varying in chemical and microbial characteristics, we mixed soil with a near-neutral and moderately acidic AMD, in separate incubations. Incubations with near-neutral AMD developed microbial Fe(II) oxidation activities after 10 days. However, Fe(II) oxidation in moderately acidic AMD incubations was mostly abiotic. 16S rRNA gene sequences and metabolic functional prediction (Tax4Fun) analysis of near-neutral AMD and soil mixture indicated development of taxonomically different communities capable of activities similar to microorganisms in a mine void. In conclusion, results indicate that AMD chemistry and microbiology affects development of Fe(II) biooxidation. Therefore, understanding of the effect of AMD chemistry on the development of FeOB activities in soil can be exploited to design site-specific and sustainable solutions.
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Affiliation(s)
- Shagun Sharma
- Department of Biology, The University of Akron, Akron, OH, USA; Integrated Bioscience Program, The University of Akron, Akron, OH, USA.
| | - Matthew Lee
- Department of Geosciences, The University of Akron, Akron, OH, USA
| | - Casey S Reinmann
- Department of Geosciences, The University of Akron, Akron, OH, USA
| | - Jenna Pumneo
- Department of Biology, The University of Akron, Akron, OH, USA
| | - Teresa J Cutright
- Department of Civil Engineering, The University of Akron, Akron, OH, USA
| | - John M Senko
- Department of Biology, The University of Akron, Akron, OH, USA; Integrated Bioscience Program, The University of Akron, Akron, OH, USA; Department of Geosciences, The University of Akron, Akron, OH, USA
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27
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Hädrich A, Taillefert M, Akob DM, Cooper RE, Litzba U, Wagner FE, Nietzsche S, Ciobota V, Rösch P, Popp J, Küsel K. Microbial Fe(II) oxidation by Sideroxydans lithotrophicus ES-1 in the presence of Schlöppnerbrunnen fen-derived humic acids. FEMS Microbiol Ecol 2020; 95:5381554. [PMID: 30874727 DOI: 10.1093/femsec/fiz034] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 03/14/2019] [Indexed: 11/14/2022] Open
Abstract
Controlled laboratory experiments were combined with field measurements to better understand the interactions between dissolved organic matter (DOM) and reduced iron in organic-rich peatlands. Addition of peat-derived humic acid extract (HA) to Sideroxydans lithotrophicus ES-1 liquid cultures led to higher cell numbers and up to 1.4 times higher Fe(II) oxidation rates compared to chemical controls. This effect was positively correlated with increasing HA concentrations. Similar Fe(III) (oxyhydr)oxide mineralogies were formed both abiotically and biotically irrespective of HA amendment, but minerals formed in the presence of ES-1 and HA were smaller. ES-1 growth with HA promoted aggregation of Fe(III) products in agarose-stabilized gradient tubes as shown by voltammetric profiling. In situ voltammetry in an acidic, iron-rich peatland revealed a gap between oxygen penetration and iron reduction that may reflect active Fe(II)-oxidizing microorganisms. The highest abundance of Fe(II) oxidizers Sideroxydans (4.9 × 107 gene copies gww-1) and Gallionella (1.5 × 107 gene copies gww-1) in the upper peat layer coincided with small-sized minerals resembling nanoparticulate ferrihydrite or goethite. Our results suggest that microbially mediated Fe(II) oxidation dominates in the presence of DOM leading to the formation of nano-sized biogenic Fe(III) (oxyhydr)oxides that might be readily bioavailable and likely important to iron and carbon cycling.
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Affiliation(s)
- Anke Hädrich
- Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Strasse 159, D-07743 Jena, Germany
| | - Martial Taillefert
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA 30332-0340, USA
| | - Denise M Akob
- Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Strasse 159, D-07743 Jena, Germany.,Water Resource Mission Area, U.S. Geological Survey, 12201 Sunrise Valley Dr., MS 430, Reston, VA 20192, USA
| | - Rebecca E Cooper
- Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Strasse 159, D-07743 Jena, Germany
| | - Ulrike Litzba
- Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Strasse 159, D-07743 Jena, Germany
| | - Friedrich E Wagner
- Department of Physics, Technical University Munich, James Frank Strasse, D-85748 Garching, Germany
| | - Sandor Nietzsche
- Centre of Electron Microscopy, University Hospital Jena, Friedrich Schiller University Jena, Ziegelmühlenweg 1, D-07743 Jena, Germany
| | - Valerian Ciobota
- Institute of Physical Chemistry, Friedrich Schiller University Jena, Helmholtzweg 4, D-07743 Jena, Germany.,Rigaku Analytical Devices, Inc., 30 Upton Drive, Wilmington, MA 01887, USA
| | - Petra Rösch
- Institute of Physical Chemistry, Friedrich Schiller University Jena, Helmholtzweg 4, D-07743 Jena, Germany
| | - Jürgen Popp
- Institute of Photonic Technology, Friedrich Schiller University Jena, Albert-Einstein-Straße 9, D-07745 Jena, Germany
| | - Kirsten Küsel
- Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Strasse 159, D-07743 Jena, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, D-04103 Leipzig, Germany
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28
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Shen X, Xu M, Li M, Zhao Y, Shao X. Response of sediment bacterial communities to the drainage of wastewater from aquaculture ponds in different seasons. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 717:137180. [PMID: 32065893 DOI: 10.1016/j.scitotenv.2020.137180] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 02/05/2020] [Accepted: 02/06/2020] [Indexed: 06/10/2023]
Abstract
Bacterial communities play an important role in diffuse sediment pollution in aquaculture farms. Previous studies have revealed the short-term influence of wastewater drainage on the bacterial communities but the seasonal response of the sediment bacterial communities to wastewater drainage from aquaculture farms remains unclear. This study used the 16S rRNA approach to explore the profiles of bacterial communities over four seasons in a typical crab aquaculture farm that included a pond and an outlet ditch. Nineteen sediment samples and an equal number of water samples were collected and analysed during spring, summer, autumn, and winter during 2018-19. Our results showed that Proteobacteria, Chloroflexi, and Bacteroides were the predominant phyla in aquaculture pond sediment with the relative abundance of 28.95%, 17.32%, and 15.31%, respectively. The relative abundance of Proteobacteria and Bacteroides was higher in autumn and winter, and the relative abundance of Chloroflexi was highest in spring. The Shannon diversity index value ranged from 6.17 to 9.30 and showed significant positive correlation (P < 0.01) with the concentrations of TN, NH4+-N, and TP in the water. The variation in the bacterial community and relative abundance in outlet ditch sediment were consistent with those in the pond sediment. Our results show that determinisation of the bacterial community composition in the outlet ditch sediment provides a novel tool to monitor watersheds sensitive to the influence of aquacultures.
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Affiliation(s)
- Xiaoxiao Shen
- College of Agricultural Engineering, HoHai University, Nanjing 210098, PR China
| | - Ming Xu
- College of Agricultural Engineering, HoHai University, Nanjing 210098, PR China
| | - Ming Li
- College of Agricultural Engineering, HoHai University, Nanjing 210098, PR China
| | - Yongjun Zhao
- College of Biological Chemical Science and Engineering, Jiaxing University, Jiaxing 314001, PR China.
| | - Xiaohou Shao
- College of Agricultural Engineering, HoHai University, Nanjing 210098, PR China.
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29
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In situ metabolic activities of uncultivated Ferrovum sp. CARN8 evidenced by metatranscriptomic analysis. Res Microbiol 2020; 171:37-43. [DOI: 10.1016/j.resmic.2019.09.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 09/26/2019] [Accepted: 09/26/2019] [Indexed: 11/23/2022]
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30
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Fei X, Sun S, He S, Huang J, Zhou W. Application of a novel two-stage biofiltration system for simulated brackish aquaculture wastewater treatment. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:636-646. [PMID: 31808093 DOI: 10.1007/s11356-019-06969-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 11/04/2019] [Indexed: 06/10/2023]
Abstract
Biofiltration is one kind of common technology used for treating micro-polluted brackish aquaculture wastewater. Based on the characteristics of actual water quality, a novel two-stage biofiltration system was set up to reduce potential nutrient pollution brought by the frequent exchange of water in brackish pond aquaculture. Zeolite was selected as filtration media for the first stage and pyrite mixed with a small amount of sulfur for the second stage. Apart from the adsorption of nutrients exerted by these natural minerals, biofilm played a leading role in nutrient removal. The surface and internal pore of zeolite-sheltered nitrifiers and sulfur-containing compounds enhanced autotrophic denitrification. It was found that ammonia adsorption capacity of zeolite was reduced by nearly 58% when salinity was increased to 1.5%, while phosphate adsorption capacity of pyrite was hardly influenced and systematic hydraulic retention time (HRT) of 24 h was proven appropriate, 9.6 h and 14.4 h for the two stages, respectively. Meanwhile, removal efficiency of 96.5% for NH4+-N and 92.1% for total inorganic nitrogen (TIN) was achieved under this condition. The analysis of microbial community of biofilm indicated that dominant genera responsible for nitritation and nitration on the surface of zeolite were Nitrosomonas and Nitrospira, respectively. Dominant genera responsible for autotrophic denitrification on the surface of pyrite and sulfur were both Thiobacillus. In addition, Ferritrophicum, related to the iron-oxidizing bacterium, also coexisted due to biological oxidation of pyrite. Long-term operation verified applicability and stability of this two-stage biofiltration system for brackish aquaculture wastewater purification.
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Affiliation(s)
- Xiang Fei
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Dong Chuan Road 800, Shanghai, 200240, People's Republic of China
| | - Shanshan Sun
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Dong Chuan Road 800, Shanghai, 200240, People's Republic of China
| | - Shengbing He
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Dong Chuan Road 800, Shanghai, 200240, People's Republic of China.
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, People's Republic of China.
| | - Jungchen Huang
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Dong Chuan Road 800, Shanghai, 200240, People's Republic of China
| | - Weili Zhou
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Dong Chuan Road 800, Shanghai, 200240, People's Republic of China
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Kaestli M, O’Donnell M, Rose A, Webb JR, Mayo M, Currie BJ, Gibb K. Opportunistic pathogens and large microbial diversity detected in source-to-distribution drinking water of three remote communities in Northern Australia. PLoS Negl Trop Dis 2019; 13:e0007672. [PMID: 31487283 PMCID: PMC6728021 DOI: 10.1371/journal.pntd.0007672] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 07/29/2019] [Indexed: 12/11/2022] Open
Abstract
In the wet-dry tropics of Northern Australia, drinking water in remote communities is mostly sourced from bores accessing groundwater. Many aquifers contain naturally high levels of iron and some are shallow with surface water intrusion in the wet season. Therefore, environmental bacteria such as iron-cycling bacteria promoting biofilm formation in pipes or opportunistic pathogens can occur in these waters. An opportunistic pathogen endemic to northern Australia and Southeast Asia and emerging worldwide is Burkholderia pseudomallei. It causes the frequently fatal disease melioidosis in humans and animals. As we know very little about the microbial composition of drinking water in remote communities, this study aimed to provide a first snapshot of the microbiota and occurrence of opportunistic pathogens in bulk water and biofilms from the source and through the distribution system of three remote water supplies with varying iron levels. Using 16s-rRNA gene sequencing, we found that the geochemistry of the groundwater had a substantial impact on the untreated microbiota. Different iron-cycling bacteria reflected differences in redox status and nutrients. We cultured and sequenced B. pseudomallei from bores with elevated iron and from a multi-species biofilm which also contained iron-oxidizing Gallionella, nitrifying Nitrospira and amoebae. Gallionella are increasingly used in iron-removal filters in water supplies and more research is needed to examine these interactions. Similar to other opportunistic pathogens, B. pseudomallei occurred in water with low organic carbon levels and with low heterotrophic microbial growth. No B. pseudomallei were detected in treated water; however, abundant DNA of another opportunistic pathogen group, non-tuberculous mycobacteria was recovered from treated parts of one supply. Results from this study will inform future studies to ultimately improve management guidelines for water supplies in the wet-dry tropics.
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Affiliation(s)
- Mirjam Kaestli
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory, Australia
- Global and Tropical Health, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | | | - Alea Rose
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Jessica R. Webb
- Global and Tropical Health, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Mark Mayo
- Global and Tropical Health, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Bart J. Currie
- Global and Tropical Health, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Karen Gibb
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory, Australia
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Kadnikov VV, Gruzdev EV, Ivasenko DA, Beletsky AV, Mardanov AV, Danilova EV, Karnachuk OV, Ravin NV. Selection of a Microbial Community in the Course of Formation of Acid Mine Drainage. Microbiology (Reading) 2019. [DOI: 10.1134/s0026261719030056] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Bacterial and Archaeal Assemblages from Two Size Fractions in Submarine Groundwater Near an Industrial Zone. WATER 2019. [DOI: 10.3390/w11061261] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Nutrients and organic pollutants transported by submarine groundwater discharge (SGD) play a significant role in controlling water quality, and can lead to the concerned deleterious effects on marine ecosystems. Subterranean estuaries are complicated habitats of diverse microbial communities that mediate different biogeochemical processes. However, there is less information on how microorganisms mediate biogeochemical cycles in the submarine groundwater system. In this study, we investigated the changes in bacterial and archaeal assemblages from two size fractions (0.2–0.45 μm and >0.45 μm) in the submarine groundwater of Qinzhou Bay, China. Phylogenetic analysis showed that Bathyarchaeota was dominant in archaeal communities in the >0.45 μm size fraction, but was seldom in the 0.2–0.45 μm fraction. The co-occurrence of sequences belonging to Bathyarchaeota and Methanosaeta was found in the >0.45 μm size fraction. Since a gene encoding acetate kinase of Bathyarchaeota is involved in acetate production, and acetate is also a necessary growth factor for Methanosaeta, the acetate produced by Bathyarchaeota can provide food or energy sources for Methanosaeta in this very >0.45 μm size fraction. The most abundant bacterial sequences in the >0.45 μm size fraction was closely related to biomineral iron-oxidizing Gallionella spp., whereas the dominant bacterial sequences in the 0.2–0.45 μm fraction were affiliated with Limnohabitans spp., which can utilize dissolved organic matter as an important source of growth substrates. Notably, approximately 10% of the bacterial sequences in both of the two size fractions belonged to Novosphingobium spp., which plays an important role in the degradation of pollutants, especially aromatic compounds. Furthermore, the predictive functional profiling also revealed that the pathways involved in the degradation of aromatic compounds by both bacteria and archaea were identified. The presence of nutrients or pollutants in our study site provides different substrates for the growth of the specific microbial groups; in turn, these microbes may help to deplete pollutants to the ocean through submarine groundwater. We suggest that these specific microbial groups could be potential candidates for effective in situ bioremediation of groundwater ecosystems.
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Kügler S, Cooper RE, Wegner CE, Mohr JF, Wichard T, Küsel K. Iron-organic matter complexes accelerate microbial iron cycling in an iron-rich fen. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 646:972-988. [PMID: 30235650 DOI: 10.1016/j.scitotenv.2018.07.258] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 07/09/2018] [Accepted: 07/18/2018] [Indexed: 06/08/2023]
Abstract
The accessibility of iron (Fe) species for microbial processes is dependent on solubility and redox state, which are influenced by complexation with dissolved organic matter (DOM) and water-extractable organic matter (WEOM). We evaluated the complexation of these pools of organic matter to soluble Fe(II) and Fe(III) in the slightly acidic Schlöppnerbrunnen fen and subsequent effects on Fe(II) oxidation and Fe(III) reduction. We found the majority of soluble Fe(II) and Fe(III) is complexed to DOM. High-resolution mass spectrometry identified potential complexing partners in peat-derived water extracts (PWE), including compound classes known to function as ligands or electron shuttles, like tannins and sulfur-containing compounds. Furthermore, we observed clear differences in the stability of Fe(II)- and Fe(III)-DOM, with more labile complexes dominating the upper, oxic layers (0-10 cm) and more stable complexes in lower, anoxic layers (15-30 cm). Metal isotope-coded profiling identified a single potential chemical formula (C42H57O13N9Fe2) associated with a stable Fe-DOM complex. Fe(III) reduction and Fe(II) oxidation incubations with Geobacter sulfurreducens PCA and Shewanella oneidensis MR-1 or Sideroxydans CL-21, respectively, were used to determine the influence of Fe-DOM complexes on Fe cycling rates. The addition of PWE led to a 2.3-fold increase in Fe(III) reduction rates and 0.5-fold increase in Fe(II) oxidation rates, indicating Fe-DOM complexes greatly influence microbial Fe cycling by potentially serving as electron shuttles. Molecular analyses revealed Fe(III)-reducing and Fe(II)-oxidizing bacteria co-exist across all depths, in approximately equal proportions (representing 0.1-1.0% of the total microbial community), despite observed changes in redox potential. The activity of Fe(III)-reducing bacteria might explain the presence of the detected Fe(II) stabilized via complexation with DOM even under oxic conditions in upper peat layers. Therefore, these Fe(II)-DOM complexes can be recycled by microaerophilic Fe(II)-oxidizers. Taken together, these results suggest Fe-DOM complexation in the fen accelerates microbial-mediated redox processes across the entire redox continuum.
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Affiliation(s)
- Stefan Kügler
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Jena 07743, Germany; Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Jena 07743, Germany
| | - Rebecca E Cooper
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Jena 07743, Germany
| | - Carl-Eric Wegner
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Jena 07743, Germany
| | - Jan Frieder Mohr
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Jena 07743, Germany
| | - Thomas Wichard
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Jena 07743, Germany
| | - Kirsten Küsel
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Jena 07743, Germany; The German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig 04103, Germany.
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Ullrich SR, Poehlein A, Levicán G, Mühling M, Schlömann M. Iron targeted transcriptome study draws attention to novel redox protein candidates involved in ferrous iron oxidation in “Ferrovum” sp. JA12. Res Microbiol 2018; 169:618-627. [DOI: 10.1016/j.resmic.2018.05.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 05/17/2018] [Accepted: 05/25/2018] [Indexed: 11/28/2022]
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Kisková J, Perháčová Z, Vlčko L, Sedláková J, Kvasnová S, Pristaš P. The Bacterial Population of Neutral Mine Drainage Water of Elizabeth's Shaft (Slovinky, Slovakia). Curr Microbiol 2018; 75:988-996. [PMID: 29532150 PMCID: PMC7160218 DOI: 10.1007/s00284-018-1472-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 03/05/2018] [Indexed: 11/25/2022]
Abstract
Although neutral mine drainage is the less frequent subject of the interest than acid mine drainage, it can have adverse environmental effects caused mainly by precipitation of dissolved Fe. The aim of the study was to characterize the composition of bacterial population in environment with high concentration of iron and sulfur compounds represented by neutral mine drainage water of Elizabeth's shaft, Slovinky (Slovakia). Direct microscopic observations, cultivation methods, and 454 pyrosequencing of the 16S rRNA gene amplicons were used to examine the bacterial population. Microscopic observations identified iron-oxidizing Proteobacteria of the genera Gallionella and Leptothrix which occurrence was not changed during the years 2008-2014. Using 454 pyrosequencing, there were identified members of 204 bacterial genera that belonged to 25 phyla. Proteobacteria (69.55%), followed by Chloroflexi (10.31%) and Actinobacteria (4.24%) dominated the bacterial community. Genera Azotobacter (24.52%) and Pseudomonas (14.15%), followed by iron-oxidizing Proteobacteria Dechloromonas (11%) and Methyloversatilis (8.53%) were most abundant within bacterial community. Typical sulfur bacteria were detected with lower frequency, e.g., Desulfobacteraceae (0.25%), Desulfovibrionaceae (0.16%), or Desulfobulbaceae (0.11%). Our data indicate that the composition of bacterial community of the Elizabeth's shaft drainage water reflects observed neutral pH, high level of iron and sulfur ions in this aquatic habitat.
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Affiliation(s)
- Jana Kisková
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, 041 54, Košice, Slovakia.
| | - Zuzana Perháčová
- Department of Biology and General Ecology, Faculty of Ecology and Environmental Sciences, Technical University in Zvolen, 960 53, Zvolen, Slovakia
| | - Ladislav Vlčko
- Department of Biology and General Ecology, Faculty of Ecology and Environmental Sciences, Technical University in Zvolen, 960 53, Zvolen, Slovakia
| | - Jana Sedláková
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, 041 54, Košice, Slovakia
| | - Simona Kvasnová
- Department of Biology and Ecology, Faculty of Natural Science, Matej Bel University, 974 01, Banská Bystrica, Slovakia
| | - Peter Pristaš
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, 041 54, Košice, Slovakia
- Institute of Animal Physiology, Centre of Biosciences of Slovak Academy of Sciences, 041 01, Košice, Slovakia
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Aguinaga OE, McMahon A, White KN, Dean AP, Pittman JK. Microbial Community Shifts in Response to Acid Mine Drainage Pollution Within a Natural Wetland Ecosystem. Front Microbiol 2018; 9:1445. [PMID: 30013541 PMCID: PMC6036317 DOI: 10.3389/fmicb.2018.01445] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 06/11/2018] [Indexed: 01/03/2023] Open
Abstract
Natural wetlands are known to play an important role in pollutant remediation, such as remediating acid mine drainage (AMD) from abandoned mine sites. However, many aspects of the microbiological mechanisms underlying AMD remediation within wetlands are poorly understood, including the role and composition of associated microbial communities. We have utilized an AMD-polluted river-wetland system to perform rRNA sequence analysis of microbial communities that play a role in biogeochemical activities that are linked to water quality improvement. Next-generation sequencing of bacterial 16S rRNA gene amplicons from river and wetland sediment samples identified variation in bacterial community structure and diversity on the basis of dissolved and particulate metal concentrations, sediment metal concentrations and other water chemistry parameters (pH and conductivity), and wetland plant presence. Metabolic reconstruction analysis allowed prediction of relative abundance of microbial metabolic pathways and revealed differences between samples that cluster on the basis of the severity of AMD pollution. Global metabolic activity was predicted to be significantly higher in unpolluted and wetland sediments in contrast to polluted river sediments, indicating a metabolic stress response to AMD pollution. This is one of the first studies to explore microbial community structure dynamics within a natural wetland exposed to AMD and our findings indicate that wetland ecosystems play critical roles in maintaining diversity and metabolic structure of sediment microbial communities subject to high levels of acidity and metal pollution. Moreover, these microbial communities are predicted to be important for the remediation action of the wetland.
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Affiliation(s)
- Oscar E. Aguinaga
- School of Earth and Environmental Sciences, Faculty of Science and Engineering, University of Manchester, Manchester, United Kingdom
| | - Anna McMahon
- School of Earth and Environmental Sciences, Faculty of Science and Engineering, University of Manchester, Manchester, United Kingdom
| | - Keith N. White
- School of Earth and Environmental Sciences, Faculty of Science and Engineering, University of Manchester, Manchester, United Kingdom
| | - Andrew P. Dean
- School of Science and the Environment, Faculty of Science and Engineering, Manchester Metropolitan University, Manchester, United Kingdom
| | - Jon K. Pittman
- School of Earth and Environmental Sciences, Faculty of Science and Engineering, University of Manchester, Manchester, United Kingdom
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Högfors-Rönnholm E, Christel S, Dalhem K, Lillhonga T, Engblom S, Österholm P, Dopson M. Chemical and microbiological evaluation of novel chemical treatment methods for acid sulfate soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 625:39-49. [PMID: 29287211 DOI: 10.1016/j.scitotenv.2017.12.287] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 12/21/2017] [Accepted: 12/23/2017] [Indexed: 06/07/2023]
Abstract
Naturally occurring sulfide rich deposits are common along the northern Baltic Sea coast that when exposed to air, release large amounts of acid and metals into receiving water bodies. This causes severe environmental implications for agriculture, forestry, and building of infrastructure. In this study, we investigated the efficiency of ultrafine-grained calcium carbonate and peat (both separately and in combination) to mitigate acid and metal release. The experiments were carried out aerobically that mimicked summer conditions when the groundwater level is low and acid sulfate soils are exposed to oxygen, and anaerobically that is similar to autumn to spring conditions. The ultrafine-grained calcium carbonate dissipated well in the soil and its effect alone and when mixed with peat raised the pH and reduced pyrite dissolution while peat alone was similar to the controls and did not halt metal and acid release. High throughput 16S rRNA gene sequencing identified populations most similar to characterized acidophiles in the control and peat treated incubations while the acidophilic like populations were altered in the calcium carbonate alone and calcium carbonate plus peat treated acid sulfate soils. Coupled with the geochemistry data, it was suggested that the acidophiles were inactivated by the high pH in the presence of calcium carbonate but catalyzed pyrite dissolution in the controls and peat incubations. In conclusion, the anaerobic conditions during winter would likely be sufficient to mitigate acid production and metal release from acid sulfate soils and in the summer, treatment with calcium carbonate was the best mitigation method.
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Affiliation(s)
- Eva Högfors-Rönnholm
- Research and Development, Novia University of Applied Sciences, FI-65200 Vaasa, Finland; Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, SE-39231 Kalmar, Sweden.
| | - Stephan Christel
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, SE-39231 Kalmar, Sweden.
| | - Krister Dalhem
- Department of Geology and Mineralogy, Åbo Akademi University, FI-20500 Turku, Finland.
| | - Tom Lillhonga
- Research and Development, Novia University of Applied Sciences, FI-65200 Vaasa, Finland.
| | - Sten Engblom
- Research and Development, Novia University of Applied Sciences, FI-65200 Vaasa, Finland.
| | - Peter Österholm
- Department of Geology and Mineralogy, Åbo Akademi University, FI-20500 Turku, Finland.
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, SE-39231 Kalmar, Sweden.
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Novel Microbial Assemblages Dominate Weathered Sulfide-Bearing Rock from Copper-Nickel Deposits in the Duluth Complex, Minnesota, USA. Appl Environ Microbiol 2017; 83:AEM.00909-17. [PMID: 28600313 DOI: 10.1128/aem.00909-17] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 06/02/2017] [Indexed: 11/20/2022] Open
Abstract
The Duluth Complex in northeastern Minnesota hosts economically significant deposits of copper, nickel, and platinum group elements (PGEs). The primary sulfide mineralogy of these deposits includes the minerals pyrrhotite, chalcopyrite, pentlandite, and cubanite, and weathering experiments show that most sulfide-bearing rock from the Duluth Complex generates moderately acidic leachate (pH 4 to 6). Microorganisms are important catalysts for metal sulfide oxidation and could influence the quality of water from mines in the Duluth Complex. Nevertheless, compared with that of extremely acidic environments, much less is known about the microbial ecology of moderately acidic sulfide-bearing mine waste, and so existing information may have little relevance to those microorganisms catalyzing oxidation reactions in the Duluth Complex. Here, we characterized the microbial communities in decade-long weathering experiments (kinetic tests) conducted on crushed rock and tailings from the Duluth Complex. Analyses of 16S rRNA genes and transcripts showed that differences among microbial communities correspond to pH, rock type, and experimental treatment. Moreover, microbial communities from the weathered Duluth Complex rock were dominated by taxa that are not typically associated with acidic mine waste. The most abundant operational taxonomic units (OTUs) were from the genera Meiothermus and Sulfuriferula, as well as from diverse clades of uncultivated Chloroflexi, Acidobacteria, and Betaproteobacteria Specific taxa, including putative sulfur-oxidizing Sulfuriferula spp., appeared to be primarily associated with Duluth Complex rock, but not pyrite-bearing rocks subjected to the same experimental treatment. We discuss the implications of these results for the microbial ecology of moderately acidic mine waste with low sulfide content, as well as for kinetic testing of mine waste.IMPORTANCE Economic sulfide mineral deposits in the Duluth Complex may represent the largest undeveloped source of copper and nickel on Earth. Microorganisms are important catalysts for sulfide mineral oxidation, and research on extreme acidophiles has improved our ability to manage and remediate mine wastes. We found that the microbial assemblages associated with weathered rock from the Duluth Complex are dominated by organisms not widely associated with mine waste or mining-impacted environments, and we describe geochemical and experimental influences on community composition. This report will be a useful foundation for understanding the microbial biogeochemistry of moderately acidic mine waste from these and similar deposits.
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Abstract
Widespread antibiotic resistance among bacterial pathogens is providing the impetus to explore novel sources of antimicrobial agents. Recently, the potent antibacterial activity of certain clay minerals has stimulated scientific interest in these materials. One such example is Kisameet glacial clay (KC), an antibacterial clay from a deposit on the central coast of British Columbia, Canada. However, our understanding of the active principles of these complex natural substances is incomplete. Like soils, clays may possess complex mixtures of bacterial taxa, including the Actinobacteria, a clade known to be rich in antibiotic-producing organisms. Here, we present the first characterization of both the microbial and geochemical characteristics of a glacial clay deposit. KC harbors surprising bacterial species richness, with at least three distinct community types. We show that the deposit has clines of inorganic elements that can be leached by pH, which may be drivers of community structure. We also note the prevalence of Gallionellaceae in samples recovered near the surface, as well as taxa that include medically or economically important bacteria such as Actinomycetes and Paenibacillus. These results provide insight into the microbial taxa that may be the source of KC antibacterial activity and suggest that natural clays may be rich sources of microbial and molecular diversity. Identifying and characterizing the resident microbial populations (bacteria, viruses, protozoa, and fungi) is key to understanding the ecology, chemistry, and homeostasis of virtually all sites on Earth. The Kisameet Bay deposit in British Columbia, Canada, holds a novel glacial clay with a history of medicinal use by local indigenous people. We previously showed that it has potent activity against a variety of antibiotic-resistant bacteria, suggesting it could complement our dwindling arsenal of antibiotics. Here, we have characterized the microbiome of this deposit to gain insight into what might make the clay antibacterial. Our analyses suggest that the deposit contains a surprising diversity of bacteria, which live in at least three distinct environments. In addition, the clay harbors bacteria that may have interesting potential as biocontrol/bioremediation agents or producers of novel bioactive compounds.
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Sulfur Isotope Fractionation as an Indicator of Biogeochemical Processes in an AMD Passive Bioremediation System. MINERALS 2017. [DOI: 10.3390/min7030041] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Jin L, Lee CS, Ahn CY, Lee HG, Lee S, Shin HH, Lim D, Oh HM. Abundant iron and sulfur oxidizers in the stratified sediment of a eutrophic freshwater reservoir with annual cyanobacterial blooms. Sci Rep 2017; 7:43814. [PMID: 28266642 PMCID: PMC5339789 DOI: 10.1038/srep43814] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 02/01/2017] [Indexed: 11/16/2022] Open
Abstract
The microbial community in eutrophic freshwater sediment was investigated from a 67-cm-deep sediment core collected from the Daechung Reservoir in South Korea, where cyanobacterial blooms have occurred annually for the past 30 years. The majority of core sediments were characterized by dark-grayish, fine-grained mud with abundant gas-escaped and thinly laminated layers. Intervals of summer and winter seasons were represented by periodic peaks of geochemical profiles of parameters such as grain size and relative carbon mass ratios to various nutrients such as nitrogen, sulfur, and phosphorus. In bacteria, Proteobacteria (66.6%) was the most prevalent phylum, followed by Chloroflexi (8.9%), Bacteroidetes (5.1%), and Spirochaetes (2.6%). Archaea were also abundant, representing approximately half of the total prokaryotes in the sediments. Notably, three Bacteria (Sulfuricurvum, Sideroxydans, and Gallionella) and one Archaea (Thermoplasmata) accounted for 43.4% and 38.4% of the total bacteria and archaea, respectively, implying that iron and sulfur oxidizing microorganisms dominate in this eutrophic freshwater sediment. These results indicate that 1) eutrophic freshwater lakes in monsoon climates undergo a stratified sedimentary process with seasonal and annual variations in geochemical and microbial profiles, and 2) the microbial oxidative metabolism of iron and sulfur is notably active in sediments from a eutrophic lake.
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Affiliation(s)
- Long Jin
- College of Biology and the Environment, Co-Innovation Centre for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210-037, China
| | - Chang Soo Lee
- Culture Collection Team, Freshwater Bioresources Culture Research Division, Nakdonggang National Institute of Biological Resources, Sangju 37242, Republic of Korea
| | - Chi-Yong Ahn
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Hyung-Gwan Lee
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Sanghyup Lee
- Centre for Water Resource Cycle Research, Korea Institute of Science & Technology (KIST), Seoul 02792, Republic of Korea
| | - Hyeon Ho Shin
- South Sea Research Institute, Korea Institute of Ocean Science & Technology (KIOST), Geoje 53201, Republic of Korea
| | - Dhongil Lim
- South Sea Research Institute, Korea Institute of Ocean Science & Technology (KIOST), Geoje 53201, Republic of Korea
| | - Hee-Mock Oh
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
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Wan D, Liu Y, Wang Y, Wang H, Xiao S. Simultaneous bio-autotrophic reduction of perchlorate and nitrate in a sulfur packed bed reactor: Kinetics and bacterial community structure. WATER RESEARCH 2017; 108:280-292. [PMID: 27838020 DOI: 10.1016/j.watres.2016.11.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 10/28/2016] [Accepted: 11/01/2016] [Indexed: 06/06/2023]
Abstract
This study investigated the simultaneous removal of perchlorate and nitrate from aqueous solution in an up-flow sulfur autotrophic reduction reactor. A nitrate and perchlorate containing pollution solution was treated with a remarkable removal efficiency greater than 97%. The concentration of nitrate was 22.03 ± 1.07 mg-N/L coexisting with perchlorate either 21.87 ± 1.03 mg/L or 471.7 ± 50.3 μg/L, in this case the reactor could be operated at a hydraulic retention time (HRT) ranging from 12.00 h to 0.75 h. Half-order kinetics model fit the experimental data well; this indicates that diffusion in the biofilm was the limiting step. Perchlorate reduction required a longer reaction time than the coexisting nitrate, regardless of the perchlorate concentration. Sulfur (S) disproportionation was inhibited when nitrate was not completely removed; whereas it was accelerated when perchlorate decreased to low concentrations. This process therefore generated excessive sulfate and consumed much more alkalinity. High-throughput sequencing method was used to analyze bacterial community spatial distribution in the reactor under different operational conditions. The reduction of the two contaminants was accompanied by a decrease in biodiversity. The results indicated that Sulfuricella, Sulfuritalea Thiobacillus, and Sulfurimonas are effective DB (denitrification bacteria)/PRB (perchlorate reduction bacteria). The Chlorobaculum genus was the dominant bacteria associated with S disproportionation.
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Affiliation(s)
- Dongjin Wan
- School of Chemistry and Chemical Engineering, Henan University of Technology, Zhengzhou, Henan, 450001, China.
| | - Yongde Liu
- School of Chemistry and Chemical Engineering, Henan University of Technology, Zhengzhou, Henan, 450001, China
| | - Yiyi Wang
- School of Chemistry and Chemical Engineering, Henan University of Technology, Zhengzhou, Henan, 450001, China
| | - Hongjie Wang
- College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Shuhu Xiao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China.
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Arce-Rodríguez A, Puente-Sánchez F, Avendaño R, Libby E, Rojas L, Cambronero JC, Pieper DH, Timmis KN, Chavarría M. Pristine but metal-rich Río Sucio (Dirty River) is dominated by Gallionella and other iron-sulfur oxidizing microbes. Extremophiles 2016; 21:235-243. [PMID: 27933457 DOI: 10.1007/s00792-016-0898-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 11/07/2016] [Indexed: 11/24/2022]
Abstract
Whether the extreme conditions of acidity and heavy metal pollution of streams and rivers originating in pyritic formations are caused primarily by mining activities or by natural activities of metal-oxidizing microbes living within the geological formations is a subject of considerable controversy. Most microbiological studies of such waters have so far focused on acid mine drainage sites, which are heavily human-impacted environments, so it has been problematic to eliminate the human factor in the question of the origin of the key metal compounds. We have studied the physico-chemistry and microbiology of the Río Sucio in the Braulio Carrillo National Park of Costa Rica, 22 km from its volcanic rock origin. Neither the remote origin, nor the length of the river to the sampling site, have experienced human activity and are thus pristine. The river water had a characteristic brownish-yellow color due to high iron-dominated minerals, was slightly acidic, and rich in chemolithoautotrophic iron- and sulfur-oxidizing bacteria, dominated by Gallionella spp. Río Sucio is thus a natural acid-rock drainage system whose metal-containing components are derived primarily from microbial activities.
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Affiliation(s)
- Alejandro Arce-Rodríguez
- Institute of Microbiology, Technical University of Braunschweig, 38106, Brunswick, Germany
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, 38124, Brunswick, Germany
| | - Fernando Puente-Sánchez
- Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC), Carretera de Ajalvir Km 4, Torrejón de Ardoz, 28850, Madrid, Spain
| | - Roberto Avendaño
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José, 1174-1200, Costa Rica
| | - Eduardo Libby
- Escuela de Química & Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, Sede Central, San Pedro de Montes de Oca, San José, 11501-2060, Costa Rica
| | - Leonardo Rojas
- Escuela de Química & Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, Sede Central, San Pedro de Montes de Oca, San José, 11501-2060, Costa Rica
| | - Juan Carlos Cambronero
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, 11501-2060, Costa Rica
- Centro de Investigación en Biología Celular y Molecular (CIBCM), Universidad de Costa Rica, San José, 11501-2060, Costa Rica
| | - Dietmar H Pieper
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, 38124, Brunswick, Germany
| | - Kenneth N Timmis
- Institute of Microbiology, Technical University of Braunschweig, 38106, Brunswick, Germany
| | - Max Chavarría
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José, 1174-1200, Costa Rica.
- Escuela de Química & Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, Sede Central, San Pedro de Montes de Oca, San José, 11501-2060, Costa Rica.
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, 11501-2060, Costa Rica.
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Kadnikov VV, Ivasenko DA, Beletsky AV, Mardanov AV, Danilova EV, Pimenov NV, Karnachuk OV, Ravin NV. Effect of metal concentration on the microbial community in acid mine drainage of a polysulfide ore deposit. Microbiology (Reading) 2016. [DOI: 10.1134/s0026261716060126] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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47
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A thermophilic-like ene-reductase originating from an acidophilic iron oxidizer. Appl Microbiol Biotechnol 2016; 101:609-619. [DOI: 10.1007/s00253-016-7782-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 07/21/2016] [Accepted: 08/03/2016] [Indexed: 01/25/2023]
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48
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Kadnikov VV, Ivasenko DA, Beletskii AV, Mardanov AV, Danilova EV, Pimenov NV, Karnachuk OV, Ravin NV. A novel uncultured bacterium of the family Gallionellaceae: Description and genome reconstruction based on metagenomic analysis of microbial community in acid mine drainage. Microbiology (Reading) 2016. [DOI: 10.1134/s002626171604010x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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49
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Ullrich SR, González C, Poehlein A, Tischler JS, Daniel R, Schlömann M, Holmes DS, Mühling M. Gene Loss and Horizontal Gene Transfer Contributed to the Genome Evolution of the Extreme Acidophile "Ferrovum". Front Microbiol 2016; 7:797. [PMID: 27303384 PMCID: PMC4886054 DOI: 10.3389/fmicb.2016.00797] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 05/11/2016] [Indexed: 01/07/2023] Open
Abstract
Acid mine drainage (AMD), associated with active and abandoned mining sites, is a habitat for acidophilic microorganisms that gain energy from the oxidation of reduced sulfur compounds and ferrous iron and that thrive at pH below 4. Members of the recently proposed genus “Ferrovum” are the first acidophilic iron oxidizers to be described within the Betaproteobacteria. Although they have been detected as typical community members in AMD habitats worldwide, knowledge of their phylogenetic and metabolic diversity is scarce. Genomics approaches appear to be most promising in addressing this lacuna since isolation and cultivation of “Ferrovum” has proven to be extremely difficult and has so far only been successful for the designated type strain “Ferrovum myxofaciens” P3G. In this study, the genomes of two novel strains of “Ferrovum” (PN-J185 and Z-31) derived from water samples of a mine water treatment plant were sequenced. These genomes were compared with those of “Ferrovum” sp. JA12 that also originated from the mine water treatment plant, and of the type strain (P3G). Phylogenomic scrutiny suggests that the four strains represent three “Ferrovum” species that cluster in two groups (1 and 2). Comprehensive analysis of their predicted metabolic pathways revealed that these groups harbor characteristic metabolic profiles, notably with respect to motility, chemotaxis, nitrogen metabolism, biofilm formation and their potential strategies to cope with the acidic environment. For example, while the “F. myxofaciens” strains (group 1) appear to be motile and diazotrophic, the non-motile group 2 strains have the predicted potential to use a greater variety of fixed nitrogen sources. Furthermore, analysis of their genome synteny provides first insights into their genome evolution, suggesting that horizontal gene transfer and genome reduction in the group 2 strains by loss of genes encoding complete metabolic pathways or physiological features contributed to the observed diversification.
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Affiliation(s)
- Sophie R Ullrich
- Institute of Biological Sciences, TU Bergakademie Freiberg Freiberg, Germany
| | - Carolina González
- Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida and Depto. de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andres BelloSantiago, Chile; Bio-Computing and Applied Genetics Division, Fraunhofer Chile Research Foundation, Center for Systems BiotechnologySantiago, Chile
| | - Anja Poehlein
- Göttingen Genomics Laboratory, Georg-August Universität Göttingen Göttingen, Germany
| | - Judith S Tischler
- Institute of Biological Sciences, TU Bergakademie Freiberg Freiberg, Germany
| | - Rolf Daniel
- Göttingen Genomics Laboratory, Georg-August Universität Göttingen Göttingen, Germany
| | - Michael Schlömann
- Institute of Biological Sciences, TU Bergakademie Freiberg Freiberg, Germany
| | - David S Holmes
- Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida and Depto. de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andres Bello Santiago, Chile
| | - Martin Mühling
- Institute of Biological Sciences, TU Bergakademie Freiberg Freiberg, Germany
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50
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Chen LX, Huang LN, Méndez-García C, Kuang JL, Hua ZS, Liu J, Shu WS. Microbial communities, processes and functions in acid mine drainage ecosystems. Curr Opin Biotechnol 2016; 38:150-8. [DOI: 10.1016/j.copbio.2016.01.013] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 01/27/2016] [Accepted: 01/28/2016] [Indexed: 10/22/2022]
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