1
|
Huang Y, Xiao Z, Wu S, Zhang X, Wang J, Huangfu X. Biochemical transformation and bioremediation of thallium in the environment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 953:176028. [PMID: 39265674 DOI: 10.1016/j.scitotenv.2024.176028] [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: 06/19/2024] [Revised: 08/22/2024] [Accepted: 09/02/2024] [Indexed: 09/14/2024]
Abstract
Thallium (Tl) is a toxic element associated with minerals, and its redistribution is facilitated by both geological and anthropogenic activities. In the natural environment, the transformation and migration of Tl mediated by (micro)organisms have attracted increasing attention. This review presents an overview of the biochemical transformation of Tl and the bioremediation strategies for Tl contamination. In the environment, Tl exists in various forms and originates from diverse sources. The global distribution characteristics of Tl in various media are summarized here, while its speciation and toxicity mechanism to organisms are elucidated. Interactions between (micro)organisms and Tl are commonly observed in the environment. Microbial response mechanisms to typical Tl exposure are analyzed at both species and gene levels, and the possibility of microorganisms as bio-indicators for monitoring Tl contamination is also highlighted. The processes and mechanisms involved in the microbial and benthic mediated transformation of Tl, as well as its enrichment by plants, are discussed. Additionally, in situ bioremediation strategies for Tl contamination and bio-treatment techniques for Tl-containing wastewater are summarized. Finally, the existing knowledge gaps and future research challenges are emphasized, including Tl distribution characteristics in the atmosphere and ocean, the key molecular mechanisms underlying Tl transformation by organisms, the screening of potential Tl oxidizing microorganisms and hyperaccumulators, as well as the revelation of global biogeochemical cycling pathways of Tl.
Collapse
Affiliation(s)
- Yuheng Huang
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, Ministry of Education, College of Environment and Ecology, Chongqing University, Chongqing 400044, China
| | - Zhentao Xiao
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, Ministry of Education, College of Environment and Ecology, Chongqing University, Chongqing 400044, China
| | - Sisi Wu
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, Ministry of Education, College of Environment and Ecology, Chongqing University, Chongqing 400044, China
| | - Xiaoling Zhang
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, Ministry of Education, College of Environment and Ecology, Chongqing University, Chongqing 400044, China
| | - Jingrui Wang
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, Ministry of Education, College of Environment and Ecology, Chongqing University, Chongqing 400044, China
| | - Xiaoliu Huangfu
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, Ministry of Education, College of Environment and Ecology, Chongqing University, Chongqing 400044, China.
| |
Collapse
|
2
|
Guo XY, Zhang QM, Fu JC, Qiu LH. Terrirubrum flagellatum gen. nov., sp. nov. of Terrirubraceae fam. nov. and Lichenibacterium dinghuense sp. nov. from forest soil and proposal of Rhodoblastaceae fam. nov. Int J Syst Evol Microbiol 2024; 74. [PMID: 38652005 DOI: 10.1099/ijsem.0.006348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024] Open
Abstract
Two Gram-negative, aerobic, rod-shaped bacterial strains, 7MK25T and 6Y81T, were isolated from forest soil of Dinghushan Biosphere Reserve, Guangdong Province, PR China. Based on the results of 16S rRNA gene sequence analysis, strain 7MK25T showed the highest similarity (93.6 %) to Methyloferula stellata AR4T, followed by Bosea thiooxidans DSM 9653T (93.3 %). Strain 6Y81T had the highest similarity of 97.9 % to Lichenibacterium minor RmlP026T, followed by Lichenibacterium ramalinae RmlP001T (97.2 %). Phylogenomic analysis using the UBCG and PhyloPhlAn methods consistently showed that strain 7MK25T formed a sister clade to Boseaceae, while strain 6Y81T formed an independent clade within the genus Lichenibacterium, both in the order Hyphomicrobiales. The digital DNA-DNA hybridization and average nucleotide identity values between strains 7MK25T, 6Y81T and their close relatives were in the ranges of 19.1-29.9 % and 72.5-85.5 %, respectively. The major fatty acids of 7MK25T were summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c), C19 : 0 cyclo ω8c, C16 : 0 and C17 : 0 cyclo, while those of 6Y81T were summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c), C16 : 0 and C16 : 0 3-OH. Strains 7MK25T and 6Y81T took diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine as their dominant polar lipids, and Q-10 as their major respiratory quinone. On the basis of phenotypic and phylogenetic data, strain 7MK25T is proposed to represent a novel species of a novel genus with name Terrirubrum flagellatum gen. nov., sp. nov., within a novel family Terrirubraceae fam. nov., with 7MK25T (=KCTC 62738T=GDMCC 1.1452T) as its type strain. Strain 6Y81T represents a novel species in the genus Lichenibacterium, for which the name Lichenibacterium dinghuense sp. nov. (type strain 6Y81T=KACC 21 727T=GDMCC 1.2176T) is proposed. Rhodoblastaceae fam. nov. with Rhodoblastus as the type genus is also proposed to solve the non-monophylectic problem of the family Roseiarcaceae.
Collapse
Affiliation(s)
- Xiu-Yin Guo
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Qiu-Mei Zhang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Jia-Cheng Fu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Li-Hong Qiu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| |
Collapse
|
3
|
Bao Z, Wang C, Cao J, Zhang T, Guo Y, Sato Y, Nishizawa T, Ohta H. Tardiphaga alba sp. nov., a heavy-metal-tolerant bacterium isolated from garden soil. Int J Syst Evol Microbiol 2024; 74. [PMID: 38197779 DOI: 10.1099/ijsem.0.006238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2024] Open
Abstract
A previously undescribed, heavy-metal-tolerant, motile, Gram-negative bacterium, designated strain SK50-23T, was characterized using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SK50-23T was closely related to Tardiphaga robiniae LMG 26467T and the non-phototrophic 'Rhodopseudomonas boonkerdii' NS23T (98.1 and 97.3 % 16S rRNA gene sequence similarity, respectively). Strain SK50-23T possessed a circular genome of 5.86 Mb, with a DNA G+C content of 61.9 mol%. Digital DNA-DNA hybridization showed 20.8-21.6 % similarity between strain SK50-23T and related species. In addition, the whole-genome average nucleotide identity values between strain SK50-23T and related species ranged from 75.1 to 83.5 %. The major cellular fatty acid identified in strain SK50-23T was C18 : 1ω7c, and the main isoprenoid quinone present was ubiquinone Q-10. Strain SK50-23T could be assigned to the genus Tardiphaga with the species name Tardiphaga alba sp. nov. based on morphological, chemotaxonomic and genome-based taxonomic characteristics, and 16S rRNA gene-based phylogenetic characteristics. The type strain of the proposed novel species is SK50-23T (=NBRC 108825T=CGMCC No. 1.12037T).
Collapse
Affiliation(s)
- Zhihua Bao
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China
- Department of Bioresource Science, Ibaraki University College of Agriculture, Ami-machi, Ibaraki 300-0393, Japan
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Fuchu-shi, Tokyo 183-8509, Japan
| | - Chaojun Wang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China
| | - Jiahui Cao
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China
| | - Tingting Zhang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China
| | - Yong Guo
- Department of Bioresource Science, Ibaraki University College of Agriculture, Ami-machi, Ibaraki 300-0393, Japan
- Present address: Institute for Plant Protection, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki 305-8605, Japan
| | - Yoshinori Sato
- Department of Bioresource Science, Ibaraki University College of Agriculture, Ami-machi, Ibaraki 300-0393, Japan
- Present address: Center for Conservation Science and Restoration Techniques, National Research Institute for Cultural Properties, Tokyo, Taito-ku, Tokyo 110-8713, Japan
| | - Tomoyasu Nishizawa
- Department of Bioresource Science, Ibaraki University College of Agriculture, Ami-machi, Ibaraki 300-0393, Japan
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Fuchu-shi, Tokyo 183-8509, Japan
| | - Hiroyuki Ohta
- Department of Bioresource Science, Ibaraki University College of Agriculture, Ami-machi, Ibaraki 300-0393, Japan
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Fuchu-shi, Tokyo 183-8509, Japan
| |
Collapse
|
4
|
Deng QQ, Luo XQ, Li SH, Li JL, Wang PD, Yuan Y, Yang ZW, Li WJ. Alsobacter ponti sp. nov., a novel denitrification and sulfate reduction bacterium isolated from Pearl River sediment. Antonie Van Leeuwenhoek 2023; 116:987-994. [PMID: 37568066 DOI: 10.1007/s10482-023-01861-w] [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: 03/21/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023]
Abstract
A Gram-staining negative, aerobic, motile, and short rods strain, designated SYSU M60028T, was isolated from a Pearl River sediment sample in Guangzhou, Guangdong, China. The isolate could be able to grow at pH 6.0-8.0 (optimum, pH 7.0), 25-37 °C (optimum, 28 °C) and in the presence of 0-2% (w/v) NaCl (optimum, 0% NaCl). The cellular polar lipids of this strain were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, one unidentified aminolipid and three unidentified lipids. The respiratory quinone of SYSU M60028T was found to be Q-10. The major fatty acids (> 5% of total) were summed feature 8, C16:0, and C18:1 ω7c 11-methy1. The genomic DNA G + C content was 69.9%. Phylogenetic analyses based on 16S rRNA gene sequences and core genes indicated that strain SYSU M60028T belonged to the genus Alsobacter and had the highest sequences similarities to Alsobacter metallidurans SK200a-9T (96.87%) and Alsobacter soli SH9T (96.87%). Based on the phenotypic, genotypic, and phylogenetic data, strain SYSU M0028T should be considered to represent a novel species of the genus Alsobacter, for which the name Alsobacter ponti sp. nov. is proposed. The type strain is SYSU M60028T (= CGMCC 1.19341T = KCTC 92046T).
Collapse
Affiliation(s)
- Qi-Qi Deng
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Xiao-Qing Luo
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Shan-Hui Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Jia-Ling Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Pan-Deng Wang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Yang Yuan
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Zi-Wen Yang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China.
| |
Collapse
|
5
|
Deng Y, Borewicz K, van Loo J, Olabarrieta MZ, Kokou F, Sipkema D, Verdegem MCJ. In-Situ Biofloc Affects the Core Prokaryotes Community Composition in Gut and Enhances Growth of Nile Tilapia (Oreochromis niloticus). MICROBIAL ECOLOGY 2022; 84:879-892. [PMID: 34609532 PMCID: PMC9622544 DOI: 10.1007/s00248-021-01880-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 09/20/2021] [Indexed: 05/03/2023]
Abstract
Biofloc technology is commonly applied in intensive tilapia (Oreochromis niloticus) culture to maintain water quality, supply the fish with extra protein, and improve fish growth. However, the effect of dietary supplementation of processed biofloc on the gut prokaryotic (bacteria and archaea) community composition of tilapia is not well understood. In this study one recirculating aquaculture system was used to test how biofloc, including in-situ biofloc, dietary supplementation of ex-situ live or dead biofloc, influence fish gut prokaryotic community composition and growth performance in comparison to a biofloc-free control treatment. A core gut prokaryotic community was identified among all treatments by analyzing the temporal variations in gut prokaryotes. In-situ produced biofloc significantly increased the prokaryotic diversity in the gut by reducing the relative abundance of dominant Cetobacterium and increasing the relative abundance of potentially beneficial bacteria. The in-situ biofloc delivered a unique prokaryotic community in fish gut, while dietary supplementation of tilapias with 5% and 10% processed biofloc (live or dead) only changed the relative abundance of minor prokaryotic taxa outside the gut core microbiota. The modulatory effect of in-situ biofloc on tilapia gut microbiota was associated with the distinct microbial community in the biofloc water and undisturbed biofloc. The growth-promoting effect on tilapia was only detected in the in-situ biofloc treatment, while dietary supplementation of processed biofloc had no effect on fish growth performance as compared to the control treatment.
Collapse
Affiliation(s)
- Yale Deng
- Aquaculture and Fisheries Group, Wageningen University and Research, Wageningen, The Netherlands
| | - Klaudyna Borewicz
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
- Trouw Nutrition R&D, 3811 MH, Amersfoort, The Netherlands
| | - Joost van Loo
- Aquaculture and Fisheries Group, Wageningen University and Research, Wageningen, The Netherlands
| | | | - Fotini Kokou
- Aquaculture and Fisheries Group, Wageningen University and Research, Wageningen, The Netherlands
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Marc C J Verdegem
- Aquaculture and Fisheries Group, Wageningen University and Research, Wageningen, The Netherlands.
| |
Collapse
|
6
|
Characterization of Terrihabitans soli gen. nov., sp. nov., a Novel 0.2 μm-Filterable Soil Bacterium Belonging to a Widely Distributed Lineage of Hyphomicrobiales (Rhizobiales). DIVERSITY 2021. [DOI: 10.3390/d13090422] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We previously showed that novel filterable bacteria remain in “sterile” (<0.2 μm filtered) terrestrial environmental samples from Japan, China, and Arctic Norway. Here, we characterized the novel filterable strain IZ6T, a representative strain of a widely distributed lineage. Phylogenetic analysis showed that this strain was affiliated with the Rhizobiales (now proposed as Hyphomicrobiales) of Alphaproteobacteria, but distinct from any other type strains. Strain IZ6T shared the following chemotaxonomic features with the closest (but distantly) related type strain, Flaviflagellibacter deserti SYSU D60017T: ubiquinone-10 as the major quinone; phosphatidylethanolamine, phosphatidylcholine, and phosphatidylglycerol as major polar lipids; and slightly high G+C content of 62.2 mol%. However, the cellular fatty acid composition differed between them, and the unsaturated fatty acid (C18:1ω7c/C18:1ω6c) was predominantly found in our strain. Moreover, unlike methyrotrophs and nitrogen-fixers of the neighboring genera of Hyphomicrobiales (Rhizobiales), strain IZ6T cannot utilize a one-carbon compound (e.g., methanol) and fix atmospheric nitrogen gas. These findings were consistent with the genome-inferred physiological potential. Based on the phylogenetic, physiological, and chemotaxonomic traits, we propose that strain IZ6T represents a novel genus and species with the name Terrihabitans soli gen. nov., sp. nov. (=NBRC 106741T = NCIMB 15058T). The findings will provide deeper insight into the eco-physiology of filterable microorganisms.
Collapse
|
7
|
Pseudomonas pratensis sp. nov., Isolated from Grassland Soil from Inner Mongolia, China. Curr Microbiol 2021; 78:789-795. [PMID: 33389060 DOI: 10.1007/s00284-020-02296-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 11/11/2020] [Indexed: 10/22/2022]
Abstract
A novel bacterial strain, designated MHJ-10JT, was isolated from a soil sample obtained from a grassland in Inner Mongolia, China. MHJ-10JT strain could grow at 4-37 °C (optimum: 30 °C) and pH 4-9 (optimum: pH 6), as well as in the presence of 0-6% NaCl (optimum: 1%). Cells of strain MHJ-10JT are Gram-negative, rod-shaped, and motile. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain MHJ-10JT was most closely related to Pseudomonas lutea OK2T (98.5% 16S rRNA gene sequence similarity). The values of the average nucleotide identities (ANI) and digital DNA-DNA hybridization (dDDH) between strain MHJ-10JT and its related species were all below 80.5% and 24.4%, respectively, which are significantly lower than the thresholds of 95% for ANI and 70% for DDH for species delineation. The genomic G + C content of the MHJ-10JT strain is 64.8 mol%. Based on the phenotypic, genotypic, chemotaxonomic, and phylogenetic analyses, strain MHJ-10JT can be assigned to the genus Pseudomonas. In this study, we propose that strain MHJ-10JT be classified as a novel species belonging to the genus Pseudomonas with the species name Pseudomonas pratensis sp. nov. The type strain of the proposed novel species is MHJ-10JT (= KCTC 82206T = CGMCC 17322T).
Collapse
|
8
|
Hördt A, López MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, Gronow S, Kyrpides NC, Woyke T, Göker M. Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria. Front Microbiol 2020; 11:468. [PMID: 32373076 PMCID: PMC7179689 DOI: 10.3389/fmicb.2020.00468] [Citation(s) in RCA: 259] [Impact Index Per Article: 64.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 03/04/2020] [Indexed: 11/13/2022] Open
Abstract
The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.
Collapse
Affiliation(s)
- Anton Hördt
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Marina García López
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Jan P. Meier-Kolthoff
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Marcel Schleuning
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Lisa-Maria Weinhold
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czechia
| | - Brian J. Tindall
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Sabine Gronow
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, Berkeley, CA, United States
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Berkeley, CA, United States
| | - Markus Göker
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| |
Collapse
|
9
|
Rasool A, Nasim W, Xiao T, Ali W, Shafeeque M, Sultana SR, Fahad S, Munis MFH, Chaudhary HJ. Microbial diversity response in thallium polluted riverbank soils of the Lanmuchang. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 187:109854. [PMID: 31678700 DOI: 10.1016/j.ecoenv.2019.109854] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 10/19/2019] [Accepted: 10/21/2019] [Indexed: 06/10/2023]
Abstract
Thallium (Tl) is a toxic element, but little is known about microbial communities' response to TI mobilization and sequestration. Here, we characterize the microbial communities and their feedbacks to Tl-pollution in riverbank soils to understand the distribution of microbial metal tolerance. These soils have been affected by pollution sourced from a Tl-rich mineralized area in Lanmuchang, Guizhou, China. In all studied soil samples, Proteobacteria, Acidobacteria, and Actinobacteria were revealed relatively in higher abundance at the phylum level. The results indicated that a number of microbial communities including Gemmatimonadetes, and Actinobacteria were correlated with total Tl, suggesting potential roles of these microbes to Tl tolerance. The patterns of phylogenetic beta-diversity in studied samples showed a high diversity of the microbial community in soils with high Tl concentrations. Sequence analysis of microbial community indicated that most of the environmental parameters in soils were associated with the major phylogenetic groups such as Gemmobacteria, Bryobacteria, Proteobacteria, Actinobacteria, Firmicutes, and Rhodobacteria. Some species of microbes, Nocardioides (genus), Actinomycetales (Order), Ralstonia (phyla) and Sphingomonas (genus) might are tolerant of Tl. These results provide direction to the microbial communities in the presence of elevated Tl concentration in Lanmuchang and shed light on bioremediation of Tl polluted locations.
Collapse
Affiliation(s)
- Atta Rasool
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, 550081, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Department of Environmental Sciences, COMSATS University, Islamabad (CUI), Vehari, 61100, Pakistan
| | - Wajid Nasim
- Department of Environmental Sciences, COMSATS University, Islamabad (CUI), Vehari, 61100, Pakistan; CIHEAM-Institut Agronomique Méditerranéen de Montpellier (IAMM), 3191Route de Mende, Montpellier, France; CSIRO Sustainable Ecosystems, National Research Flagship, Towoomba, QLD, 4350, Australia; Department of Agronomy, University College of Agriculture and Environmental Sciences, The Islamia University of Bahawalpur (IUB), Bahawalpur, Pakistan
| | - Tangfu Xiao
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China.
| | - Waqar Ali
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, 550081, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Muhammad Shafeeque
- University of Chinese Academy of Sciences, Beijing, 100049, China; Key Lab of Ecosystem Network Observation and Modelling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, 100101, Beijing, China
| | - Syeda Refat Sultana
- Department of Environmental Sciences, COMSATS University, Islamabad (CUI), Vehari, 61100, Pakistan
| | - Shah Fahad
- Department of Agriculture, University of Swabi, Khyber Pakhtunkhwa (KPK), Pakistan
| | | | - Hassan Javed Chaudhary
- Department of Plant Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| |
Collapse
|
10
|
Liu J, Yin M, Zhang W, Tsang DCW, Wei X, Zhou Y, Xiao T, Wang J, Dong X, Sun Y, Chen Y, Li H, Hou L. Response of microbial communities and interactions to thallium in contaminated sediments near a pyrite mining area. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 248:916-928. [PMID: 30856507 DOI: 10.1016/j.envpol.2019.02.089] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 02/23/2019] [Accepted: 02/25/2019] [Indexed: 06/09/2023]
Abstract
Thallium (Tl) is a well-recognized hazardous heavy metal with very high toxicity. It is usually concentrated in sulfide minerals, such as pyrite (FeS2), sphalerite (ZnS), chalcopyrite (CuS) and galena (PbS). Here, this study was carried out to investigate the indigenous microbial communities via 16S rRNA gene sequence analysis in typical surface sediments with various levels of Tl pollution (1.8-16.1 mg/kg) due to acid mine drainage from an active Tl-containing pyrite mining site in South China. It was found with more than 50 phyla from the domain Bacteria and 1 phyla from the domain Archaea. Sequences assigned to the genera Ferroplasma, Leptospirillum, Ferrovum, Metallibacterium, Acidithiobacillus, and Sulfuriferula manifested high relative abundances in all sequencing libraries from the relatively high Tl contamination. Canonical correspondence analysis further uncovered that the overall microbial community in this area was dominantly structured by the geochemical fractionation of Tl and geochemical parameters such as pH and Eh. Spearman's rank correlation analysis indicated a strong positive correlation between acidophilic Fe-metabolizing species and Tltotal, Tloxi, and Tlres. The findings clarify potential roles of such phylotypes in the biogeochemical cycling of Tl, which may facilitate the development of in-situ bioremediation technology for Tl-contaminated sediments.
Collapse
Affiliation(s)
- Juan Liu
- Institute of Environmental Research at Greater Bay, Key Laboratory of Water Quality and Conservation in the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Meiling Yin
- Institute of Environmental Research at Greater Bay, Key Laboratory of Water Quality and Conservation in the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Weilong Zhang
- Institute of Environmental Research at Greater Bay, Key Laboratory of Water Quality and Conservation in the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Daniel C W Tsang
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Xudong Wei
- Institute of Environmental Research at Greater Bay, Key Laboratory of Water Quality and Conservation in the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Yuting Zhou
- Institute of Environmental Research at Greater Bay, Key Laboratory of Water Quality and Conservation in the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Tangfu Xiao
- Institute of Environmental Research at Greater Bay, Key Laboratory of Water Quality and Conservation in the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Jin Wang
- Institute of Environmental Research at Greater Bay, Key Laboratory of Water Quality and Conservation in the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China.
| | - Xinjiao Dong
- School of Life & Environmental Science, Wenzhou University, Wenzhou, 325027, China
| | - Yubing Sun
- MOE Key Laboratory of Resources and Environmental System Optimization, College of Environmental Science and Engineering, North China Electric Power University, Beijing, 102206, China
| | - Yongheng Chen
- Institute of Environmental Research at Greater Bay, Key Laboratory of Water Quality and Conservation in the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Hui Li
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, Department of Ecology, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Liping Hou
- School of Life Sciences, Guangzhou University, Guangzhou, 510655, China.
| |
Collapse
|
11
|
Sun L, Liu H, Chen W, Huang K, Lyu W, Gao X. Alsobacter soli sp. nov., a novel bacterium isolated from paddy soil, emended description of the genus Alsobacter and description of the family Alsobacteraceae fam. nov. Int J Syst Evol Microbiol 2018; 68:3902-3907. [DOI: 10.1099/ijsem.0.003088] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Lina Sun
- 1Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, PR China
- 2Shanghai Engineering Research Center of Low-carbon Agriculture (SERCLA), Shanghai, 201403, PR China
| | - Hongming Liu
- 3Institute of Molecular Biology and Biotechnology, Anhui Normal University, Wuhu, 241000, PR China
| | - Wei Chen
- 1Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, PR China
- 4Shanghai Key Laboratory of Horticultural Technology, Shanghai, 201403, PR China
| | - Kaihua Huang
- 1Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, PR China
- 5Environmental Protection Monitoring Station of Shanghai, Shanghai, 201403, PR China
| | - Weiguang Lyu
- 1Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, PR China
- 2Shanghai Engineering Research Center of Low-carbon Agriculture (SERCLA), Shanghai, 201403, PR China
- 6Shanghai Agricultural Environment and Farmland Conservation Experiment Station of Ministry of Agriculture, Shanghai, 201403, PR China
| | - Xinhua Gao
- 1Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, PR China
- 5Environmental Protection Monitoring Station of Shanghai, Shanghai, 201403, PR China
| |
Collapse
|
12
|
Osborne CD, Haritos VS. Horizontal gene transfer of three co-inherited methane monooxygenase systems gave rise to methanotrophy in the Proteobacteria. Mol Phylogenet Evol 2018; 129:171-181. [PMID: 30149053 DOI: 10.1016/j.ympev.2018.08.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 08/01/2018] [Accepted: 08/19/2018] [Indexed: 12/22/2022]
Abstract
The critical role that bacterial methanotrophs have in regulating the environmental concentrations of the potent greenhouse gas, methane, under aerobic conditions is dependent on monooxygenase enzymes which oxidise the substrate as both a carbon and energy source. Despite the importance of these organisms, the evolutionary origins of aerobic methane oxidation capability and its relationship to proteobacterial evolution is not well understood. Here we investigated the phylogenetic relationship of proteobacterial methanotrophs with related, non-methanotrophic bacteria using 16S rRNA and the evolution of two forms of methane monooxygenase: membrane bound (pMMO and pXMO) and cytoplasmic (sMMO). Through analysis we have concluded that extant proteobacterial methanotrophs evolved from up to five ancestral species, and that all three methane monooxygenase systems, pMMO, pXMO and sMMO, were likely present in the ancestral species (although pXMO and sMMO are not present in most of the present day methanotrophs). Here we propose that the three monooxygenase systems entered the ancestral species by horizontal gene transfer, with these likely to have pre-existing physiological and metabolic attributes that supported conversion to methanotrophy. Further, we suggest that prior to these enzyme systems developing methane oxidation capabilities, the membrane-bound and cytoplasmic monooxygenases were already both functionally and phylogenetically associated. These results not only suggest that sMMO and pXMO have a far greater role in methanotrophic evolution than previously understood but also implies that the co-inheritance of membrane bound and cytoplasmic monooxygenases have roles additional to that of supporting methanotrophy.
Collapse
Affiliation(s)
- Craig D Osborne
- Department of Chemical Engineering, Monash University, Wellington Road, Clayton 3800, Australia
| | - Victoria S Haritos
- Department of Chemical Engineering, Monash University, Wellington Road, Clayton 3800, Australia.
| |
Collapse
|
13
|
Sun J, Zou X, Xiao T, Jia Y, Ning Z, Sun M, Liu Y, Jiang T. Biosorption and bioaccumulation of thallium by thallium-tolerant fungal isolates. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:16742-16748. [PMID: 26087929 DOI: 10.1007/s11356-015-4859-y] [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: 04/02/2015] [Accepted: 06/08/2015] [Indexed: 06/04/2023]
Abstract
Little is known about the biosorption and bioaccumulation capacity of thallium (Tl) by microorganisms that occur in Tl-polluted soil. The present study focused on characterizing the biosorption and bioaccumulation of Tl by Tl-tolerant fungi isolated from Tl-polluted soils. Preliminary data showed a positive correlation between the biomass and the biosorbed Tl content. The Tl-tolerant strains were capable of bioaccumulating Tl, up to 7189 mg kg(-1) dry weight. The subcellular distribution of Tl showed obvious compartmentalization: cytoplasm ≫ cell wall > organelle. The majority of Tl (up to 79%) was found in the cytoplasm, suggesting that intracellular compartmentalization appeared to be responsible for detoxification. These findings further suggest the applicability of the fungal isolates for cleanup of Tl in Tl-polluted water and soil.
Collapse
Affiliation(s)
- Jialong Sun
- School of Resources and Environmental Engineering, Guizhou Institute of Technology, Guiyang, 550001, China
- Guizhou Institute of Environmental Science and Design, Guiyang, 550002, China
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, 550002, China
| | - Xiao Zou
- Institute of Fungal Resources, Guizhou University, Guiyang, 550081, China
| | - Tangfu Xiao
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, 550002, China.
| | - Yanlong Jia
- School of Resources and Environmental Engineering, Guizhou Institute of Technology, Guiyang, 550001, China
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, 550002, China
| | - Zengping Ning
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, 550002, China
| | - Min Sun
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, 550002, China
| | - Yizhang Liu
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, 550002, China
| | - Tao Jiang
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, 550002, China
| |
Collapse
|