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Hidalgo-Ulloa A, van der Graaf CM, Sánchez-Andrea I, Weijma J, Buisman CJN. Biological S 0 reduction at neutral and acidic conditions: Performance and microbial community shifts in a H 2/CO 2-fed bioreactor. WATER RESEARCH 2024; 263:122156. [PMID: 39121561 DOI: 10.1016/j.watres.2024.122156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 07/18/2024] [Accepted: 07/25/2024] [Indexed: 08/12/2024]
Abstract
Sulfidogenesis is a promising technology for the selective recovery of chalcophile bulk metals (e.g. Cu, Zn, and Co) from metal-contaminated waters such as acid mine drainage (AMD) and metallurgy waste streams. The use of elemental sulfur (S0) instead of sulfate (SO42-) as electron acceptor reduces electron donor requirements four-fold, lowering process costs, and expanding the range of operating conditions to a more acidic pH. We previously reported autotrophic S0 reduction using an industrial mesophilic granular sludge as inoculum under thermoacidophilic conditions. Here, we examined the effect of pH on the S0 reduction performance of the same inoculum, in a gas-lift reactor run at 30°C under neutral (pH 6.9) and acidic (pH 3.8) conditions, continuously fed with mineral media and H2 and CO2. Steady-state volumetric sulfide production rates (VSPR) dropped 2.5-fold upon transition to acidic pH, from 1.79 ± 0.18 g S2-·L-1·d-1 to 0.71 ± 0.07 g S2-·L-1·d-1. Microbial community composition was analyzed using 16S rRNA gene amplicon sequencing. At neutral pH (6.9), the high relative abundance of the S0-reducing genus Sulfurospirillum, previously known only for heterotrophic members, combined with the presence of Acetobacterium and detection of acetate, suggests an important role for heterotrophic S0 reduction facilitated by acetogenesis. Conversely, at acidic pH (3.9), S0 reduction appeared autotrophic, as indicated by the high relative abundance of Desulfurella.
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Affiliation(s)
- Adrian Hidalgo-Ulloa
- Department of Environmental Technology, Wageningen University & Research, the Netherlands
| | | | | | - Jan Weijma
- Department of Environmental Technology, Wageningen University & Research, the Netherlands
| | - Cees J N Buisman
- Department of Environmental Technology, Wageningen University & Research, the Netherlands.
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2
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Ma L, Banda JF, Wang Y, Yang Q, Zhao L, Hao C, Dong H. Metagenomic insight into the acidophilic functional communities driving elemental geochemical cycles in an acid mine drainage lake. JOURNAL OF HAZARDOUS MATERIALS 2024; 466:133070. [PMID: 38278071 DOI: 10.1016/j.jhazmat.2023.133070] [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: 09/06/2023] [Revised: 11/06/2023] [Accepted: 11/21/2023] [Indexed: 01/28/2024]
Abstract
Acidophiles play a key role in the generation, evolution and attenuation of acid mine drainage (AMD), which is characterized by strong acidity (pH<3.5) and high metal concentrations. In this study, the seasonal changes of acidophilic communities and their roles in elemental cycling in an AMD lake (pH∼3.0) in China were analyzed through metagenomics. The results showed eukaryotic algae thrived in the lake, and Coccomyxa was dominant in January (38.1%) and May (33.9%), while Chlorella in July (9.5%). The extensive growth of Chlamydomonas in December (22.7%) resulted in an ultrahigh chlorophyll a concentration (587 μg/L), providing abundant organic carbon for the ecosystem. In addition, the iron-oxidizing and nitrogen-fixing bacterium Ferrovum contributed to carbon fixation. Ammonia oxidation likely occurred in the acidic lake, as was revealed by archaea Ca. Nitrosotalea. To gain a competitive advantage in the nutrient-poor environment, some acidophiles exhibited facultative characteristics, e.g. the most abundant bacterium Acidiphilium utilized both organic and inorganic carbon, and obtained energy from organic matter, inorganic sulfur, and sunlight simultaneously. It was suggested that sunlight, rather than chemical energy of reduced iron-sulfur was the major driver of elemental cycling in the AMD lake. The results are beneficial to the development of bioremediation strategies for AMD.
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Affiliation(s)
- Linqiang Ma
- Center for Geomicrobiology and Biogeochemistry Research, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China; School of Water Resources and Environment, China University of Geosciences, Beijing 100083, China
| | - Joseph Frazer Banda
- Center for Geomicrobiology and Biogeochemistry Research, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China; School of Water Resources and Environment, China University of Geosciences, Beijing 100083, China
| | - Yikai Wang
- Center for Geomicrobiology and Biogeochemistry Research, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China; School of Water Resources and Environment, China University of Geosciences, Beijing 100083, China
| | - Qingwei Yang
- Center for Geomicrobiology and Biogeochemistry Research, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China; School of Water Resources and Environment, China University of Geosciences, Beijing 100083, China
| | - Linting Zhao
- Center for Geomicrobiology and Biogeochemistry Research, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China; School of Water Resources and Environment, China University of Geosciences, Beijing 100083, China
| | - Chunbo Hao
- Center for Geomicrobiology and Biogeochemistry Research, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China; School of Water Resources and Environment, China University of Geosciences, Beijing 100083, China.
| | - Hailiang Dong
- Center for Geomicrobiology and Biogeochemistry Research, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China
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Cuevas M, Francisco I, Díaz-González F, Diaz M, Quatrini R, Beamud G, Pedrozo F, Temporetti P. Nutrient structure dynamics and microbial communities at the water-sediment interface in an extremely acidic lake in northern Patagonia. Front Microbiol 2024; 15:1335978. [PMID: 38410393 PMCID: PMC10895001 DOI: 10.3389/fmicb.2024.1335978] [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: 11/09/2023] [Accepted: 01/23/2024] [Indexed: 02/28/2024] Open
Abstract
Lake Caviahue (37° 50 'S and 71° 06' W; Patagonia, Argentina) is an extreme case of a glacial, naturally acidic, aquatic environment (pH ~ 3). Knowledge of the bacterial communities in the water column of this lake, is incipient, with a basal quantification of the bacterioplankton abundance distribution in the North and South Basins of Lake Caviahue, and the described the presence of sulfur and iron oxidizing bacteria in the lake sediments. The role that bacterioplankton plays in nutrient utilization and recycling in this environment, especially in the phosphorus cycle, has not been studied. In this work, we explore this aspect in further depth by assessing the diversity of pelagic, littoral and sediment bacteria, using state of the art molecular methods and identifying the differences and commonalties in the composition of the cognate communities. Also, we investigate the interactions between the sediments of Lake Caviahue and the microbial communities present in both sediments, pore water and the water column, to comprehend the ecological relationships driving nutrient structure and fluxes, with a special focus on carbon, nitrogen, and phosphorus. Two major environmental patterns were observed: (a) one distinguishing the surface water samples due to temperature, Fe2+, and electrical conductivity, and (b) another distinguishing winter and summer samples due to the high pH and increasing concentrations of N-NH4+, DOC and SO42-, from autumn and spring samples with high soluble reactive phosphorus (SRP) and iron concentrations. The largest bacterial abundance was found in autumn, alongside higher levels of dissolved phosphorus, iron forms, and increased conductivity. The highest values of bacterial biomass were found in the bottom strata of the lake, which is also where the greatest diversity in microbial communities was found. The experiments using continuous flow column microcosms showed that microbial growth over time, in both the test and control columns, was accompanied by a decrease in the concentration of dissolved nutrients (SRP and N-NH4+), providing proof that sediment microorganisms are active and contribute significantly to nutrient utilization/mobilization.
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Affiliation(s)
- Mayra Cuevas
- Instituto de Investigaciones en Biodiversidad y Medioambiente (INIBIOMA), Centro Regional Universitario Bariloche-UNComahue, CCT-Patagonia Norte, CONICET, San Carlos de Bariloche, Argentina
| | - Issotta Francisco
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
- Department of Molecular Genetics and Microbiology, School of Biological Sciences, P. Universidad Católica de Chile, Santiago, Chile
| | - Fernando Díaz-González
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - Mónica Diaz
- Instituto de Investigaciones en Biodiversidad y Medioambiente (INIBIOMA), Centro Regional Universitario Bariloche-UNComahue, CCT-Patagonia Norte, CONICET, San Carlos de Bariloche, Argentina
| | - Raquel Quatrini
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - Guadalupe Beamud
- Instituto de Investigaciones en Biodiversidad y Medioambiente (INIBIOMA), Centro Regional Universitario Bariloche-UNComahue, CCT-Patagonia Norte, CONICET, San Carlos de Bariloche, Argentina
| | - Fernando Pedrozo
- Instituto de Investigaciones en Biodiversidad y Medioambiente (INIBIOMA), Centro Regional Universitario Bariloche-UNComahue, CCT-Patagonia Norte, CONICET, San Carlos de Bariloche, Argentina
| | - Pedro Temporetti
- Instituto de Investigaciones en Biodiversidad y Medioambiente (INIBIOMA), Centro Regional Universitario Bariloche-UNComahue, CCT-Patagonia Norte, CONICET, San Carlos de Bariloche, Argentina
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Chan CS, Dykes GE, Hoover RL, Limmer MA, Seyfferth AL. Gallionellaceae in rice root plaque: metabolic roles in iron oxidation, nutrient cycling, and plant interactions. Appl Environ Microbiol 2023; 89:e0057023. [PMID: 38009924 PMCID: PMC10734482 DOI: 10.1128/aem.00570-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 09/18/2023] [Indexed: 11/29/2023] Open
Abstract
IMPORTANCE In waterlogged soils, iron plaque forms a reactive barrier between the root and soil, collecting phosphate and metals such as arsenic and cadmium. It is well established that iron-reducing bacteria solubilize iron, releasing these associated elements. In contrast, microbial roles in plaque formation have not been clear. Here, we show that there is a substantial population of iron oxidizers in plaque, and furthermore, that these organisms (Sideroxydans and Gallionella) are distinguished by genes for plant colonization and nutrient fixation. Our results suggest that iron-oxidizing and iron-reducing bacteria form and remodel iron plaque, making it a dynamic system that represents both a temporary sink for elements (P, As, Cd, C, etc.) as well as a source. In contrast to abiotic iron oxidation, microbial iron oxidation results in coupled Fe-C-N cycling, as well as microbe-microbe and microbe-plant ecological interactions that need to be considered in soil biogeochemistry, ecosystem dynamics, and crop management.
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Affiliation(s)
- Clara S. Chan
- Department of Earth Sciences, University of Delaware, Newark, Delaware, USA
- School of Marine Science and Policy, University of Delaware, Newark, Delaware, USA
- Microbiology Graduate Program, University of Delaware, Newark, Delaware, USA
- Delaware Biotechnology Institute, Newark, Delaware, USA
| | - Gretchen E. Dykes
- Microbiology Graduate Program, University of Delaware, Newark, Delaware, USA
- Delaware Biotechnology Institute, Newark, Delaware, USA
- Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware, USA
| | - Rene L. Hoover
- Department of Earth Sciences, University of Delaware, Newark, Delaware, USA
- Microbiology Graduate Program, University of Delaware, Newark, Delaware, USA
- Delaware Biotechnology Institute, Newark, Delaware, USA
| | - Matt A. Limmer
- Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware, USA
| | - Angelia L. Seyfferth
- Department of Earth Sciences, University of Delaware, Newark, Delaware, USA
- Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware, USA
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Wang M, Wang X, Zhou S, Chen Z, Chen M, Feng S, Li J, Shu W, Cao B. Strong succession in prokaryotic association networks and community assembly mechanisms in an acid mine drainage-impacted riverine ecosystem. WATER RESEARCH 2023; 243:120343. [PMID: 37482007 DOI: 10.1016/j.watres.2023.120343] [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: 06/02/2023] [Revised: 07/10/2023] [Accepted: 07/11/2023] [Indexed: 07/25/2023]
Abstract
Acid mine drainage (AMD) serves as an ideal model system for investigating microbial ecology, interaction, and assembly mechanism in natural environments. While previous studies have explored the structure and function of microbial communities in AMD, the succession patterns of microbial association networks and underlying assembly mechanisms during natural attenuation processes remain elusive. Here, we investigated prokaryotic microbial diversity and community assembly along an AMD-impacted river, from the extremely acidic, heavily polluted headwaters to the nearly neutral downstream sites. Microbial diversity was increased along the river, and microbial community composition shifted from acidophile-dominated to freshwater taxa-dominated communities. The complexity and relative modularity of the microbial networks were also increased, indicating greater network stability during succession. Deterministic processes, including abiotic selection of pH and high contents of sulfur and iron, governed community assembly in the headwaters. Although the stochasticity ratio was increased downstream, manganese content, microbial negative cohesion, and relative modularity played important roles in shaping microbial community structure. Overall, this study provides valuable insights into the ecological processes that govern microbial community succession in AMD-impacted riverine ecosystems. These findings have important implications for in-situ remediation of AMD contamination.
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Affiliation(s)
- Mengmeng Wang
- Institute of Ecological Science and Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Xiaonan Wang
- Institute of Ecological Science and Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Sining Zhou
- Institute of Ecological Science and Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Zifeng Chen
- Institute of Ecological Science and Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Mengyun Chen
- Institute of Ecological Science and Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Shiwei Feng
- Institute of Ecological Science and Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Jintian Li
- Institute of Ecological Science and Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Wensheng Shu
- Institute of Ecological Science and Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Baichuan Cao
- Institute of Ecological Science and Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, China.
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Nagarajan V, Tsai HC, Chen JS, Hussain B, Fan CW, Asif A, Hsu BM. The Evaluation of Bacterial Abundance and Functional Potentials in the Three Major Watersheds, Located in the Hot Spring Zone of the Tatun Volcano Group Basin, Taiwan. Microorganisms 2022; 10:500. [PMID: 35336075 PMCID: PMC8949176 DOI: 10.3390/microorganisms10030500] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 12/10/2022] Open
Abstract
The Tatun Volcanic Group (TVG), located in northern Taiwan, is characterized by acidic hot springs where the outflow of the hot springs may affect the properties of the associated lotic water bodies. We investigated the bacterial diversity and functional profiles of the Peihuang (PHC), HuangGang (HGC), and Nanhuang Creeks (NHC) located in the TVG basin using 16S rRNA gene sequencing coupled with statistical analyses. Water samples were collected from various streams of the creeks for two months of the year. The NHC showed the highest diversity, richness, and a unique number of phyla, which was followed by the HGC. A reduced number of phyla and a lower diversity was noticed in the PHC. The NHC was found to be abundant in the genera Armatimonas, Prosthecobacter, Pirellula, and Bdellovibrio, whereas the HGC was rich in Thiomonas, Acidiphilium, Prevotella, Acidocella, Acidithiobacillus, and Metallibacterium. The PHC was abundant in Thiomonsa, Legionella, Acidocella, and Sulfuriferula. The samples did not show any strong seasonal variations with the bacterial diversity and abundance; however, the relative abundance of each sampling site varied within the sampling months. The iron transport protein- and the sulfur metabolism-related pathways were predicted to be the key functions in all the creeks, whereas the heavy metal-related functions, such as the cobalt/nickel transport protein and the cobalt-zinc-cadmium efflux system were found to be abundant in the HGC and PHC, respectively. The abundance of Bdellovibrio in the NHC, Diplorickettsia in the HGC, and Legionella in the PHC samples indicated a higher anthropogenic impact over the creek water quality. This study provides the data to understand the distinct bacterial community structure, as well as the functional potentials of the three major watersheds, and helps the knowledge of the impact of the physicochemical properties of the TVG hot springs upon the watersheds.
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Affiliation(s)
- Viji Nagarajan
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi 621, Taiwan; (V.N.); (B.H.); (C.-W.F.); (A.A.)
| | - Hsin-Chi Tsai
- Department of Psychiatry, School of Medicine, Tzu Chi University, Hualien 970, Taiwan;
- Department of Psychiatry, Tzu-Chi General Hospital, Hualien 970, Taiwan
| | - Jung-Sheng Chen
- Department of Medical Research, E-Da Hospital, Kaohsiung 824, Taiwan;
| | - Bashir Hussain
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi 621, Taiwan; (V.N.); (B.H.); (C.-W.F.); (A.A.)
- Department of Biomedical Sciences, National Chung Cheng University, Chiayi 621, Taiwan
| | - Cheng-Wei Fan
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi 621, Taiwan; (V.N.); (B.H.); (C.-W.F.); (A.A.)
| | - Aslia Asif
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi 621, Taiwan; (V.N.); (B.H.); (C.-W.F.); (A.A.)
- Doctoral Program in Science, Technology, Environment and Mathematics (STEM), National Chung Cheng University, Chiayi 621, Taiwan
| | - Bing-Mu Hsu
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi 621, Taiwan; (V.N.); (B.H.); (C.-W.F.); (A.A.)
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Abstract
Iron (Fe) oxidation is one of Earth’s major biogeochemical processes, key to weathering, soil formation, water quality, and corrosion. However, our understanding of microbial contribution is limited by incomplete knowledge of microbial iron oxidation mechanisms, particularly in neutrophilic iron oxidizers. The genomes of many diverse iron oxidizers encode a homolog to an outer membrane cytochrome (Cyc2) shown to oxidize iron in two acidophiles. Phylogenetic analyses show Cyc2 sequences from neutrophiles cluster together, suggesting a common function, though this function has not been verified in these organisms. Therefore, we investigated the iron oxidase function of heterologously expressed Cyc2 from a neutrophilic iron oxidizer Mariprofundus ferrooxydans PV-1. Cyc2PV-1 is capable of oxidizing iron, and its redox potential is 208 ± 20 mV, consistent with the ability to accept electrons from Fe2+ at neutral pH. These results support the hypothesis that Cyc2 functions as an iron oxidase in neutrophilic iron-oxidizing organisms. The results of sequence analysis and modeling reveal that the entire Cyc2 family shares a unique fused cytochrome-porin structure, with a defining consensus motif in the cytochrome region. On the basis of results from structural analyses, we predict that the monoheme cytochrome Cyc2 specifically oxidizes dissolved Fe2+, in contrast to multiheme iron oxidases, which may oxidize solid Fe(II). With our results, there is now functional validation for diverse representatives of Cyc2 sequences. We present a comprehensive Cyc2 phylogenetic tree and offer a roadmap for identifying cyc2/Cyc2 homologs and interpreting their function. The occurrence of cyc2 in many genomes beyond known iron oxidizers presents the possibility that microbial iron oxidation may be a widespread metabolism.
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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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