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Lancaster E, Winston R, Martin J, Lee J. Urban stormwater green infrastructure: Evaluating the public health service role of bioretention using microbial source tracking and bacterial community analyses. WATER RESEARCH 2024; 259:121818. [PMID: 38815337 DOI: 10.1016/j.watres.2024.121818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 04/30/2024] [Accepted: 05/20/2024] [Indexed: 06/01/2024]
Abstract
Bioretention cells (BRCs) control stormwater flow on-site during precipitation, reducing runoff and improving water quality through chemical, physical, and biological processes. While BRCs are effective in these aspects, they provide habitats for wildlife and may face microbial hazards from fecal shedding, posing a potential threat to human health and the nearby environment. However, limited knowledge exists regarding the ability to control microbial hazards (e.g., beyond using typical indicator bacteria) through stormwater biofiltration. Therefore, the purpose of this study is to characterize changes in the bacterial community of urban stormwater undergoing bioretention treatment, with the goal of assessing the public health implications of these green infrastructure solutions. Samples from BRC inflow and outflow in Columbus, Ohio, were collected post-heavy storms from October 2021 to March 2022. Conventional culture-based E. coli monitoring and microbial source tracking (MST) were conducted to identify major fecal contamination extent and its sources (i.e., human, canine, avian, and ruminant). Droplet digital polymerase chain reaction (ddPCR) was utilized to quantify the level of host-associated fecal contamination in addition to three antibiotic resistant genes (ARGs): tetracycline resistance gene (tetQ), sulfonamide resistance gene (sul1), and Klebsiella pneumoniae carbapenemase resistance gene (blaKPC). Subsequently, 16S rRNA gene sequencing was conducted to characterize bacterial community differences between stormwater BRC inflow and outflow. Untreated urban stormwater reflects anthropogenic contamination, suggesting it as a potential source of contamination to waterbodies and urban environments. When comparing inlet and outlet BRC samples, urban stormwater treated via biofiltration did not increase microbial hazards, and changes in bacterial taxa and alpha diversity were negligible. Beta diversity results reveal a significant shift in bacterial community structure, while simultaneously enhancing the water quality (i.e., reduction of metals, total suspended solids, total nitrogen) of urban stormwater. Significant correlations were found between the bacterial community diversity of urban stormwater with fecal contamination (e.g. dog) and ARG (sul1), rainfall intensity, and water quality (hardness, total phosphorous). The study concludes that bioretention technology can sustainably maintain urban microbial water quality without posing additional public health risks, making it a viable green infrastructure solution for heavy rainfall events exacerbated by climate change.
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Affiliation(s)
- Emma Lancaster
- Division of Environmental Health Sciences, College of Public Health, The Ohio State University, Columbus, OH, USA; Environmental Sciences Graduate Program, The Ohio State University, Columbus, OH, USA
| | - Ryan Winston
- Environmental Sciences Graduate Program, The Ohio State University, Columbus, OH, USA; Department of Food, Agricultural, and Biological Engineering, The Ohio State University, Columbus, OH, USA; Department of Civil, Environmental, and Geodetic Engineering, The Ohio State University, Columbus, OH, USA
| | - Jay Martin
- Department of Food, Agricultural, and Biological Engineering, The Ohio State University, Columbus, OH, USA; Sustainability Institute, The Ohio State University, Columbus, OH, USA
| | - Jiyoung Lee
- Division of Environmental Health Sciences, College of Public Health, The Ohio State University, Columbus, OH, USA; Environmental Sciences Graduate Program, The Ohio State University, Columbus, OH, USA; Department of Food Science & Technology, The Ohio State University, Columbus, OH, USA; Infectious Diseases Institute, The Ohio State University, Columbus, OH, USA.
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Fang C, Yang Y, Zhang S, He Y, Pan S, Zhou L, Wang J, Yang H. Unveiling the impact of microplastics with distinct polymer types and concentrations on tidal sediment microbiome and nitrogen cycling. JOURNAL OF HAZARDOUS MATERIALS 2024; 472:134387. [PMID: 38723479 DOI: 10.1016/j.jhazmat.2024.134387] [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: 12/28/2023] [Revised: 04/17/2024] [Accepted: 04/21/2024] [Indexed: 05/30/2024]
Abstract
Microplastics (MPs) are distributed widely in the ocean surface waters and sediments. Increasing MPs contamination in intertidal zone profoundly impacts microbial ecosystem services and biogeochemical process. Little is known about the response of tidal sediment microbiome to MPs. We conducted a 30-day laboratory microcosm study using five polymers (PE, PBS, PC, PLA and PET) at three concentrations (1 %, 2 % and 5 %, w/w). High throughput sequencing of 16 S rRNA, qPCR and enzyme activity test were applied to demonstrate the response of microbial community and nitrogen cycling functional genes to MPs. MPs reduced the microbial alpha diversity and the microbial dissimilarity while the effects of PLA-MPs were concentration dependent. LEfSe analysis indicated that the Proteobacteria predominated for all MP treatments. Mantel's test, RDA and correlation analysis implied that pH may be the key environmental factor for causing microbial alterations. MPs enhanced nitrogen fixation in tidal sediment. PLA levels of 1 % but not 5 % produced the most significant effects in nitrogen cycling functional microbiota and genes. PLS-PM revealed that impacts of MPs on tidal sediment microbial communities and nitrogen cycling were dominated by indirect effects. Our study deepened understanding and filled the knowledge gap of MP contaminants affecting tidal sediment microbial nitrogen cycling.
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Affiliation(s)
- Chang Fang
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China; Zhongshan Innovation Center of South China Agricultural University, Zhongshan 528400, China
| | - Yuting Yang
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China; Zhongshan Innovation Center of South China Agricultural University, Zhongshan 528400, China
| | - Shuping Zhang
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China; Zhongshan Innovation Center of South China Agricultural University, Zhongshan 528400, China
| | - Yinglin He
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China; Zhongshan Innovation Center of South China Agricultural University, Zhongshan 528400, China
| | - Sentao Pan
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China; Zhongshan Innovation Center of South China Agricultural University, Zhongshan 528400, China
| | - Lei Zhou
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Jun Wang
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Huirong Yang
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China; Zhongshan Innovation Center of South China Agricultural University, Zhongshan 528400, China.
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Kachi K, Sato T, Nagasawa M, Cann I, Atomi H. The Lreu_1276 protein from Limosilactobacillus reuteri represents a third family of dihydroneopterin triphosphate pyrophosphohydrolases in bacteria. Appl Environ Microbiol 2024:e0081424. [PMID: 38888337 DOI: 10.1128/aem.00814-24] [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: 04/25/2024] [Accepted: 05/14/2024] [Indexed: 06/20/2024] Open
Abstract
Tetrahydrofolate is a cofactor involved in C1 metabolism including biosynthesis pathways for adenine and serine. In the classical tetrahydrofolate biosynthesis pathway, the steps removing three phosphate groups from the precursor 7,8-dihydroneopterin triphosphate (DHNTP) remain unclear in many bacteria. DHNTP pyrophosphohydrolase hydrolyzes pyrophosphate from DHNTP and produces 7,8-dihydroneopterin monophosphate. Although two structurally distinct DHNTP pyrophosphohydrolases have been identified in the intestinal bacteria Lactococcus lactis and Escherichia coli, the distribution of their homologs is limited. Here, we aimed to identify a third DHNTP pyrophosphohydrolase gene in the intestinal lactic acid bacterium Limosilactobacillus reuteri. In a gene operon including genes involved in dihydrofolate biosynthesis, we focused on the lreu_1276 gene, annotated as Ham1 family protein or XTP/dITP diphosphohydrolase, as a candidate encoding DHNTP pyrophosphohydrolase. The Lreu_1276 recombinant protein was prepared using E. coli and purified. Biochemical analyses of the reaction product revealed that the Lreu_1276 protein displays significant pyrophosphohydrolase activity toward DHNTP. The optimal reaction temperature and pH were 35°C and around 7, respectively. Substrate specificity was relatively strict among 17 tested compounds. Although previously characterized DHNTP pyrophosphohydrolases prefer Mg2+, the Lreu_1276 protein exhibited maximum activity in the presence of Mn2+, with a specific activity of 28.2 ± 2.0 µmol min-1 mg-1 in the presence of 1 mM Mn2+. The three DHNTP pyrophosphohydrolases do not share structural similarity to one another, and the distribution of their homologs does not overlap, implying that the Lreu_1276 protein represents a third structurally novel DHNTP pyrophosphohydrolase in bacteria. IMPORTANCE The identification of a structurally novel DHNTP pyrophosphohydrolase in L. reuteri provides valuable information in understanding tetrahydrofolate biosynthesis in bacteria that possess lreu_1276 homologs. Interestingly, however, even with the identification of a third family of DHNTP pyrophosphohydrolases, there are still a number of bacteria that do not harbor homologs for any of the three genes while possessing other genes involved in the biosynthesis of the pterin ring structure. This suggests the presence of an unrecognized DHNTP pyrophosphohydrolase gene in bacteria. As humans do not harbor DHNTP pyrophosphohydrolase, the high structural diversity of enzymes responsible for a reaction in tetrahydrofolate biosynthesis may provide an advantage in designing inhibitors targeting a specific group of bacteria in the intestinal microbiota.
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Affiliation(s)
- Kaede Kachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Takaaki Sato
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
- Integrated Research Center for Carbon Negative Science, Kyoto University, Kyoto, Japan
| | - Maina Nagasawa
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Isaac Cann
- Department of Animal Science, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Haruyuki Atomi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
- Integrated Research Center for Carbon Negative Science, Kyoto University, Kyoto, Japan
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Lienhart PH, Rohra V, Clement C, Toppen LC, DeCola AC, Rizzo DM, Scarborough MJ. Landfill intermediate cover soil microbiomes and their potential for mitigating greenhouse gas emissions revealed through metagenomics. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 925:171697. [PMID: 38492594 DOI: 10.1016/j.scitotenv.2024.171697] [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: 12/06/2023] [Revised: 03/09/2024] [Accepted: 03/11/2024] [Indexed: 03/18/2024]
Abstract
Landfills are a major source of anthropogenic methane emissions and have been found to produce nitrous oxide, an even more potent greenhouse gas than methane. Intermediate cover soil (ICS) plays a key role in reducing methane emissions but may also result in nitrous oxide production. To assess the potential for microbial methane oxidation and nitrous oxide production, long sequencing reads were generated from ICS microbiome DNA and reads were functionally annotated for 24 samples across ICS at a large landfill in New York. Further, incubation experiments were performed to assess methane consumption and nitrous oxide production with varying amounts of ammonia supplemented. Methane was readily consumed by microbes in the composite ICS and all incubations with methane produced small amounts of nitrous oxide even when ammonia was not supplemented. Incubations without methane produced significantly less nitrous oxide than those incubated with methane. In incubations with methane added, the observed specific rate of methane consumption was 0.776 +/- 0.055 μg CH4 g dry weight (DW) soil-1 h-1 and the specific rate of nitrous oxide production was 3.64 × 10-5 +/- 1.30 × 10-5 μg N2O g DW soil-1 h-1. The methanotrophs Methylobacter and an unclassified genus within the family Methlyococcaceae were present in the original ICS samples and the incubation samples, and their abundance increased during incubations with methane. Genes encoding particulate methane monooxygenase/ ammonia monooxygenase (pMMO) were much more abundant than genes encoding soluble methane monooxygenase (sMMO) across the landfill ICS. Genes encoding proteins that convert hydroxylamine to nitrous oxide were not highly abundant in the ICS or incubation metagenomes. In total, these results suggest that although ammonia oxidation via methanotrophs may result in low levels of nitrous oxide production, ICS microbial communities have the potential to greatly reduce the overall global warming potential of landfill emissions.
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Affiliation(s)
- Peyton H Lienhart
- Department of Civil and Environmental Engineering, University of Vermont, Burlington, VT, United States
| | - Venus Rohra
- Department of Civil and Environmental Engineering, University of Vermont, Burlington, VT, United States
| | - Courtney Clement
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Lucinda C Toppen
- Department of Civil and Environmental Engineering, University of Vermont, Burlington, VT, United States.
| | - Amy C DeCola
- Department of Civil and Environmental Engineering, University of Vermont, Burlington, VT, United States
| | - Donna M Rizzo
- Department of Civil and Environmental Engineering, University of Vermont, Burlington, VT, United States; Gund Institute for Environment, University of Vermont, Burlington, VT, United States.
| | - Matthew J Scarborough
- Department of Civil and Environmental Engineering, University of Vermont, Burlington, VT, United States; Gund Institute for Environment, University of Vermont, Burlington, VT, United States.
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Pei H, Wang L, Xia X, Dong C, Tan B, Zhang Y, Lin Z, Ding J. Sulfamethoxazole stress endangers the gut health of sea cucumber (Apostichopus japonicus) and affects host metabolism. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 273:116099. [PMID: 38422788 DOI: 10.1016/j.ecoenv.2024.116099] [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: 12/06/2023] [Revised: 02/03/2024] [Accepted: 02/08/2024] [Indexed: 03/02/2024]
Abstract
Sulfamethoxazole (SMZ) is a frequently detected antibiotic in the environment, and there is a growing concern about its potential toxic effects on aquatic organisms. sea cucumber (Apostichopus japonicas) is a benthic invertebrate whose gut acts as a primary immune defense and serves critical protective barrier. In this study, growth performance, histology, gut microbiota, and metabolomics analyses were performed to investigate the toxic response in the intestine of sea cucumber effects caused by SMZ stress for 56 d by evaluating with different concentrations of SMZ (0, 1.2×10-3, and 1.2 mg/L). The weight gain rate of sea cucumbers under SMZ stress showed significant decrease, indicating that the growth of sea cucumbers was hindered. Analysis of the intestinal morphological features indicated that SMZ stimulation resulted in atrophy of the sea cucumber gut. In the 1.2×10-3 mg/L concentration, the thickness of muscle and mucosal layers was reduced by 12.40% and 21.39%, while in the 1.2 mg/L concentration, the reductions were 35.08% and 26.98%. The abundance and diversity of sea cucumber intestinal bacteria decreased significantly (P < 0.05) under the influence of SMZ. Notably, the intestinal bacteria of sea cucumber became homogenized with the increase in SMZ concentration, and the relative abundance of Ralstonia reached 81.64% under the stress of 1.2 mg/L concentration. The SMZ stress significantly impacted host metabolism and disrupted balance, particularly in L-threonine, L-tyrosine, neuronic acid, piperine, and docosapentaenoic acid. SMZ leads to dysregulation of metabolites, resulting in growth inhibition and potential inflammatory responses that could adversely affect the normal activities of aquatic organisms. Further metabolic pathway enrichment analyses demonstrated that impaired biosynthesis of unsaturated fatty acids and aminoacyl-tRNA biosynthesis metabolic pathway were major reasons for SMZ stress-induced intestinal bacteria dysbiosis. This research aims to provide some theoretical evidence for the ecological hazard assessment of antibiotics in water.
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Affiliation(s)
- Honglin Pei
- Key Laboratory of Mariculture & Stock Enhancement in North China Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian 116023, China
| | - Luo Wang
- Key Laboratory of Mariculture & Stock Enhancement in North China Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian 116023, China.
| | - Xinglong Xia
- Key Laboratory of Mariculture & Stock Enhancement in North China Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian 116023, China
| | - Changkun Dong
- Key Laboratory of Mariculture & Stock Enhancement in North China Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian 116023, China
| | - Bamei Tan
- Key Laboratory of Mariculture & Stock Enhancement in North China Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian 116023, China
| | - Yanmin Zhang
- Key Laboratory of Mariculture & Stock Enhancement in North China Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian 116023, China
| | - Zhiping Lin
- Key Laboratory of Mariculture & Stock Enhancement in North China Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian 116023, China
| | - Jun Ding
- Key Laboratory of Mariculture & Stock Enhancement in North China Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian 116023, China
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Zhao H, Ma J, Tang Y, Ma X, Li J, Li H, Liu Z. Genome-wide DNA N6-methyladenosine in Aeromonas veronii and Helicobacter pylori. BMC Genomics 2024; 25:161. [PMID: 38331763 PMCID: PMC10854192 DOI: 10.1186/s12864-024-10074-y] [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: 09/12/2023] [Accepted: 02/01/2024] [Indexed: 02/10/2024] Open
Abstract
BACKGROUND DNA N6-methyladenosine (6mA), as an important epigenetic modification, widely exists in bacterial genomes and participates in the regulation of toxicity, antibiotic resistance, and antioxidant. With the continuous development of sequencing technology, more 6mA sites have been identified in bacterial genomes, but few studies have focused on the distribution characteristics of 6mA at the whole-genome level and its association with gene expression and function. RESULTS This study conducted an in-depth analysis of the 6mA in the genomes of two pathogenic bacteria, Aeromonas veronii and Helicobacter pylori. The results showed that the 6mA was widely distributed in both strains. In A. veronii, 6mA sites were enriched at 3' end of protein-coding genes, exhibiting a certain inhibitory effect on gene expression. Genes with low 6mA density were associated with cell motility. While in H. pylori, 6mA sites were enriched at 5' end of protein-coding genes, potentially enhancing gene expression. Genes with low 6mA density were closely related to defense mechanism. CONCLUSIONS This study elucidated the distribution characteristics of 6mA in A. veronii and H. pylori, highlighting the effects of 6mA on gene expression and function. These findings provide valuable insights into the epigenetic regulation and functional characteristics of A. veronii and H. pylori.
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Affiliation(s)
- Honghao Zhao
- School of Life and Health Sciences, Hainan University, Haikou, China
| | - Jiayue Ma
- School of Life and Health Sciences, Hainan University, Haikou, China
| | - Yanqiong Tang
- School of Life and Health Sciences, Hainan University, Haikou, China
| | - Xiang Ma
- School of Life and Health Sciences, Hainan University, Haikou, China
| | - Juanjuan Li
- School of Life and Health Sciences, Hainan University, Haikou, China
| | - Hong Li
- School of Life and Health Sciences, Hainan University, Haikou, China.
| | - Zhu Liu
- School of Life and Health Sciences, Hainan University, Haikou, China.
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Liu L, Xin Y, Guang SB, Lin GF, Liu CX, Zeng LQ, He SQ, Zheng YM, Chen GY, Zhao QB. Planktonic microbial community and biological metabolism in a subtropical drinking water river-reservoir system. ENVIRONMENTAL RESEARCH 2023; 237:116999. [PMID: 37634690 DOI: 10.1016/j.envres.2023.116999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/22/2023] [Accepted: 08/25/2023] [Indexed: 08/29/2023]
Abstract
To understand the dynamics of planktonic microbial community and its metabolism processes in subtropical drinking water river-reservoir system with lower man-made pollution loading, this study selected Dongzhen river-reservoir system in Mulan Creek as object to investigate spatial-temporal characteristics of community profile and functional genes involved in biological metabolism, and to analyze the influence of environmental factors. The results indicated that Proteobacteria and Actinobacteria were the most diverse phyla with proportion ranges of 9%-80% in target system, and carbohydrate metabolism (5.76-7.12 × 10-2), amino acid metabolism (5.78-7.21 × 10-2) and energy metabolism (4.07-5.17 × 10-2) were found to be the dominant pathways of biological metabolism. Although there were variations in biological properties both spatially and temporally, seasonal variation had a greater influence on microbial community and biological metabolism, than locational differences. Regarding the role of environmental factors, this study revealed that microbial diversity could be affected by multiple abiotic factors, with total organic carbon, total phosphorus and temperature being more influential (absolute value of standardized regression weights >2.13). Stochastic processes dominated the microbial community assembly (R2 of neutral community model = 0.645), while niche-based processes differences represented by nutrients, temperature and pH level played secondary roles (R > 0.388, P < 0.01). Notably, the synergistic influences among the environmental factors accounted for the higher percentages of community variation (maximum proportion up to 17.6%). Additionally, pH level, temperature, and concentrations of dissolved oxygen, carbon and nitrogen were found to be the significant factors affecting carbon metabolism pathways (P < 0.05), yet only total organic carbon significantly affected on nitrogen transformation (P < 0.05). In summary, the microbial profile in reservoir is not completely dominated by that in feeding river, and planktonic microbial community and its metabolism in subtropical drinking water river-reservoir system are shaped by multiple abiotic and biotic factors with underlying interactions.
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Affiliation(s)
- Lin Liu
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Yu Xin
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shan-Bin Guang
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China; College of Environment and Safety Engineering, Fuzhou University, Fuzhou, 350108, China
| | - Guo-Fu Lin
- Putian River Management Center, Putian, 351100, China
| | - Chao-Xiang Liu
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China; College of Environment and Safety Engineering, Fuzhou University, Fuzhou, 350108, China.
| | - Li-Qin Zeng
- Dongzhen Reservoir Administration, Putian, 351100, China
| | - Shao-Qin He
- Dongzhen Reservoir Administration, Putian, 351100, China
| | - Yu-Ming Zheng
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| | - Guan-Yu Chen
- Dongzhen Reservoir Administration, Putian, 351100, China
| | - Quan-Bao Zhao
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
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Shittu AR, Iwaloye OF, Ojewole AE, Rabiu AG, Amechi MO, Herve OF. The effects of per- and polyfluoroalkyl substances on environmental and human microorganisms and their potential for bioremediation. Arh Hig Rada Toksikol 2023; 74:167-178. [PMID: 37791672 PMCID: PMC10549896 DOI: 10.2478/aiht-2023-74-3708] [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] [Received: 01/01/2023] [Revised: 01/01/2023] [Accepted: 08/01/2023] [Indexed: 10/05/2023] Open
Abstract
Utilised in a variety of consumer products, per- and polyfluoroalkyl substances (PFAS) are major environmental contaminants that accumulate in living organisms due to their highly hydrophobic, lipophobic, heat-resistant, and non-biodegradable properties. This review summarizes their effects on microbial populations in soils, aquatic and biogeochemical systems, and the human microbiome. Specific microbes are insensitive to and even thrive with PFAS contamination, such as Escherichia coli and the Proteobacteria in soil and aquatic environments, while some bacterial species, such as Actinobacteria and Chloroflexi, are sensitive and drop in population. Some bacterial species, in turn, have shown success in PFAS bioremediation, such as Acidimicrobium sp. and Pseudomonas parafulva.
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Affiliation(s)
- Adenike R. Shittu
- Bowling Green State University College of Arts and Sciences, Department of Biological Sciences, Bowling Green, OH, USA
| | - Opeoluwa F. Iwaloye
- Bowling Green State University College of Arts and Sciences, Department of Biological Sciences, Bowling Green, OH, USA
| | - Akinloye E. Ojewole
- Southern Illinois University, Department of Environmental Sciences, Edwardsville, IL, USA
| | - Akeem G. Rabiu
- University of Ibadan, Department of Microbiology, Ibadan, Nigeria
| | - Miracle O. Amechi
- University of Louisville, Department of Chemistry, Louisville, KY, USA
| | - Ouambo F. Herve
- Chantal Biya International Reference Centre, Laboratory of Vaccinology, Yaounde, Cameroon
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Ren Q, Zhang Y, Duan J, Li W, Dong X, Pei Y, Zhang R, Zhu Q. Distribution of corrosive microbial communities in rust layers of steel immersed in seawater. Can J Microbiol 2023; 69:309-320. [PMID: 37156011 DOI: 10.1139/cjm-2023-0015] [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: 05/10/2023]
Abstract
In this paper, high-throughput sequencing technology was adopted to visualize the microbial communities on the surfaces of two types of carbon steel immersed in Sea Area Ⅰ. The results showed that different microbial communities were formed on different carbon steel surfaces, in which the genus with the highest abundance on the surface of Q235 was Escherichia-Shigella, while anaerobic Desulfovibrio on the surface of 921a was the most abundant, and the dominant genus varied with the depth of the rust layer. In addition, the distribution of sulfate-reducing bacteria (SRB) on the surface of Q235 submerged in Sea Area Ⅱ was compared with the sulfate-reducing bacteria's distribution in Sea Area Ⅰ, using the environmental factors correlation analysis. The results showed that the concentrations of Ca2+, Na+, K+, Mg2+, and Al3+ were positively correlated with the distribution of SRB, while the concentrations of Cu2+, Zn2+, SO4 2-, Cl-, NO3 -, and organic carbon were negatively correlated with it. Furthermore, there was a highly significant correlation between each geochemical factor and Desulfotomaculum (p < 0.01).
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Affiliation(s)
- Qijing Ren
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
- Open Studio for Marine Corrosion and Protection, National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Yimeng Zhang
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Open Studio for Marine Corrosion and Protection, National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Jizhou Duan
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Open Studio for Marine Corrosion and Protection, National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Wangqiang Li
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
- Open Studio for Marine Corrosion and Protection, National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Xucheng Dong
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
- Open Studio for Marine Corrosion and Protection, National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Yingying Pei
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
- Open Studio for Marine Corrosion and Protection, National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Ruiyong Zhang
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Open Studio for Marine Corrosion and Protection, National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Qingjun Zhu
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Open Studio for Marine Corrosion and Protection, National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
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10
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Xing Y, Bian C, Xue H, Song Y, Men W, Hou W, Yang Y, Cai Q, Xu L. The effect of plant compartment and geographical location on shaping microbiome of Pulsatilla chinensis. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12641-x. [PMID: 37436481 DOI: 10.1007/s00253-023-12641-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 05/09/2023] [Accepted: 06/15/2023] [Indexed: 07/13/2023]
Abstract
The plant-associated microbiome has an effect on plant growth. Pulsatilla chinensis (Bge.) Regel is an important Chinese medicinal plant. Currently, there is little understanding of the P. chinensis-associated microbiome and its diversity and composition. Here, the core microbiome associated with the root, leaf, and rhizospheric soil compartments of P. chinensis from five geographical locations was analyzed by the metagenomics approach. The alpha and beta diversity analysis showed that the microbiome associated with P. chinensis was shaped by the compartment, especially in the bacterial community. The geographical location had little influence on microbial community diversity associated with root and leaf. Hierarchical clustering distinguished the microbial communities of rhizospheric soil based on their geographical location and among the soil properties, pH was showed the more stronger effect on the diversity of rhizospheric soil microbial communities. Proteobacteria was the most dominant bacterial phylum in the root, leaf, and rhizospheric soil. Ascomycota and Basidiomycota were the most dominant fungal phyla in different compartments. Rhizobacter, Anoxybacillus, and IMCC26256 were the most important marker bacterial species for root, leaf, and rhizospheric soil screened by random forest, respectively. The fungal marker species for root, leaf, and rhizospheric soil were not only different across the compartments but also the geographical locations. Functional analysis showed that P. chinensis-associated microbiome had the similar function which had no obvious relationship with geographical location and compartment. The associated microbiome indicated in this study can be used for identifying microorganisms related to the quality and growth of P. chinensis. KEY POINTS: • Microbiome associated with P. chinensis was shaped by the compartment • Microbiome composition and abundance associated with rhizospheric soil were affected by the geographical location • Compared with fungi, bacterial associated with P. chinensis composition and diversity were more stable in different geographical locations and compartments.
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Affiliation(s)
- Yanping Xing
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, 116600, China
| | - Che Bian
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, 116600, China
| | - Hefei Xue
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, 116600, China
| | - Yueyue Song
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, 116600, China
| | - Wenxiao Men
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, 116600, China
| | - Wenjuan Hou
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, 116600, China
| | - Yanyun Yang
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, 116600, China
| | - Qian Cai
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, 116600, China.
| | - Liang Xu
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, 116600, China.
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11
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Tang Y, Zhang H, Yan J, Luo N, Fu X, Wu X, Wu J, Liu C, Zhang D. Assessing the efficacy of bleaching powder in disinfecting marine water: Insights from the rapid recovery of microbiomes. WATER RESEARCH 2023; 241:120136. [PMID: 37295228 DOI: 10.1016/j.watres.2023.120136] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/20/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023]
Abstract
Single-bleaching powder disinfection is a highly prevalent practice to disinfect source water for marine aquaculture to prevent diseases. However, due to the decay of active chlorine and the presence of disinfectant resistance bacteria (DRB), the effects of bleaching powder on prokaryotic community compositions (PCCs) and function in marine water remain unknown. In the present study, the source water in a canvas pond was treated with the normal dose of bleaching powder, and the impact on PCCs and functional profiles was investigated using 16S rRNA gene amplicon sequencing. The bleaching powder strongly altered the PCCs within 0.5 h, but they began to recover at 16 h, eventually achieving 76% similarity with the initial time at 72 h. This extremely rapid recovery was primarily driven by the decay of Bacillus and the regrowth of Pseudoalteromonas, both of which are DRB. Abundant community not only help PCCs recover but also provide larger functional redundancy than rare community. During the recovery of PCCs, stochastic processes drove the community assembly. After 72 h, five out of seven identified disinfectant resistance genes related to efflux pump systems were highly enriched, primarily in Staphylococcus and Bacillus. However, 15 out of the 16 identified antibiotic resistance genes (ARGs) remained unchanged compared to the initial time, indicating that bleaching powder does not contribute to ARGs removal. Overall, the findings demonstrate that single-bleaching powder disinfection cannot successfully meet the objective of disease prevention in marine aquaculture water due to the extremely rapid recovery of PCCs. Hence, secondary disinfection or novel disinfection strategies should be explored for source water disinfection.
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Affiliation(s)
- Yawen Tang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Huajun Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, China; Marine Economic Research Center, Donghai Academy, Ningbo University, Ningbo 315211, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo 315211, China.
| | - Jiaojiao Yan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Nan Luo
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Xuezhi Fu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Xiaoyu Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Jialin Wu
- Ningbo Haiwei Ecological Technology Co., Ltd., Ningbo 315141, China
| | - Changjun Liu
- Xiangshan Fisheries Technical Extension Center, Ningbo 315700, China
| | - Demin Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo 315211, China.
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12
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Humphries NH, Thornton SF, Chen X, Bray AW, Stewart DI. Response of soil bacterial populations to application of biosolids under short-term flooding. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023:10.1007/s11356-023-27424-0. [PMID: 37184786 DOI: 10.1007/s11356-023-27424-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 05/01/2023] [Indexed: 05/16/2023]
Abstract
Biosolids are applied to agricultural land as a soil conditioner and source of crop nutrients. However, there is concern that bacteria from biosolids may become established in soils, particularly if that soil becomes water-logged. This study examined the microbial community of arable soils cultivated with barley under different applications of biosolids (0, 24t/ha, 48t/ha) in laboratory mesocosms which simulated a 10-day flood. Nutrients (P and N) and organic matter in the soil increased with application rate, but plant growth was not affected by biosolid application. The biosolids contained 10× more genetic material than the soil, with much lower bacterial diversity, yet application did not significantly change the taxonomy of the soil microbiome, with minor changes related to increased nutrients and SOM. Anaerobic conditions developed rapidly during flooding, causing shifts in the native soil microbiome. Some bacterial taxa that were highly abundant in biosolids had slightly increased relative abundance in amended soils during the flood. After flooding, soil bacterial populations returned to their pre-flood profiles, implying that the native microbial community is resilient to transient changes. The short-term changes in the microbiome of biosolid-amended soils during flooding do not appear to increase the environmental risk posed by biosolid application.
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Affiliation(s)
- Nicholas H Humphries
- School of Civil Engineering, University of Leeds, Leeds, LS2 9JT, UK.
- Currently Anglo American plc, 17 Charterhouse St, London, EC1N 6RA, UK.
| | - Steven F Thornton
- Department of Civil and Structural Engineering, University of Sheffield, S1 3JD, Sheffield, UK
| | - Xiaohui Chen
- School of Civil Engineering, University of Leeds, Leeds, LS2 9JT, UK
| | - Andrew W Bray
- School of Earth and Environment, University of Leeds, Leeds, LS2 9JT, UK
- Currently Calder Rivers Trust, Halifax, HX1 5ER, UK
| | - Douglas I Stewart
- School of Civil Engineering, University of Leeds, Leeds, LS2 9JT, UK
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13
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Das S, Najar IN, Sherpa MT, Kumar S, Sharma P, Mondal K, Tamang S, Thakur N. Baseline metagenome-assembled genome (MAG) data of Sikkim hot springs from Indian Himalayan geothermal belt (IHGB) showcasing its potential CAZymes, and sulfur-nitrogen metabolic activity. World J Microbiol Biotechnol 2023; 39:179. [PMID: 37133792 DOI: 10.1007/s11274-023-03631-2] [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: 08/25/2022] [Accepted: 04/26/2023] [Indexed: 05/04/2023]
Abstract
Here we present the construction and characterization of metagenome assembled genomes (MAGs) from two hot springs residing in the vicinity of Indian Himalayan Geothermal Belt (IHGB). A total of 78 and 7 taxonomic bins were obtained for Old Yume Samdong (OYS) and New Yume Samdong (NYS) hot springs respectively. After passing all the criteria only 21 and 4 MAGs were further studied based on the successful prediction of their 16 S rRNA. Various databases were used such as GTDB, Kaiju, EzTaxon, BLAST XY Plot and NCBI BLAST to get the taxonomic classification of various 16 S rRNA predicted MAGs. The bacterial genomes found were from both thermophilic and mesophilic bacteria among which Proteobacteria, Chloroflexi, Bacteroidetes and Firmicutes were the abundant phyla. However, in case of OYS, two genomes belonged to archaeal Methanobacterium and Methanocaldococcus. Functional characterization revealed the richness of CAZymes such as Glycosyl Transferase (GT) (56.7%), Glycoside Hydrolase (GH) (37.4%), Carbohydrate Esterase family (CE) (8.2%), and Polysaccharide Lyase (PL) (1.9%). There were negligible antibiotic resistance genes in the MAGs however, a significant heavy metal tolerance gene was found in the MAGs. Thus, it may be assumed that there is no coexistence of antibiotic and heavy metal resistance genes in these hot spring microbiomes. Since the selected hot springs possess good sulfur content thus, we also checked the presence of genes for sulfur and nitrogen metabolism. It was found that MAGs from both the hot springs possess significant number of genes related to sulfur and nitrogen metabolism.
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Affiliation(s)
- Sayak Das
- Department of Microbiology, School of Life Sciences, Sikkim University, 6th Mile, Samdur, Gangtok, Sikkim, 737102, India
- Department of Life Science and Bioinformatics, Hargobind Khurana School of Life Sciences, Assam University, Silchar, Assam, 788011, India
| | - Ishfaq Nabi Najar
- Department of Microbiology, School of Life Sciences, Sikkim University, 6th Mile, Samdur, Gangtok, Sikkim, 737102, India
| | - Mingma Thundu Sherpa
- Department of Microbiology, School of Life Sciences, Sikkim University, 6th Mile, Samdur, Gangtok, Sikkim, 737102, India
| | - Santosh Kumar
- Department of Microbiology, School of Life Sciences, Sikkim University, 6th Mile, Samdur, Gangtok, Sikkim, 737102, India
| | - Prayatna Sharma
- Department of Microbiology, School of Life Sciences, Sikkim University, 6th Mile, Samdur, Gangtok, Sikkim, 737102, India
| | - Krishnendu Mondal
- Department of Microbiology, Vidyasagar University, Midnapore, West Bengal, 721102, India
| | - Sonia Tamang
- Department of Microbiology, School of Life Sciences, Sikkim University, 6th Mile, Samdur, Gangtok, Sikkim, 737102, India
| | - Nagendra Thakur
- Department of Microbiology, School of Life Sciences, Sikkim University, 6th Mile, Samdur, Gangtok, Sikkim, 737102, India.
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14
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Chen LJ, Liu Y, Yang JW, Lin Y, Hsu C, Zhang KK, Liu JL, Li JH, Li XW, Yang JZ, Chen L, Zeng JH, Xie XL, Xu JT, Wang Q. Microbial community succession in the intestine of mice with deep partial-thickness burns. Front Microbiol 2023; 14:1140440. [PMID: 37180225 PMCID: PMC10167003 DOI: 10.3389/fmicb.2023.1140440] [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: 01/11/2023] [Accepted: 04/06/2023] [Indexed: 05/16/2023] Open
Abstract
Introduction Burn injury has been shown to lead to changes in the composition of the gut microbiome and cause other damage in patients. However, little is known about how the gut microbial community evolves in individuals who have recovered from burn injury. Methods In this study, we established a model of deep partial-thickness burn in mice and collected fecal samples at eight time points (pre-burn, 1, 3, 5, 7, 14, 21, and 28 days post-burn) for 16S rRNA amplification and high-throughput sequencing. Results The results of the sequencing were analyzed using measures of alpha diversity, and beta diversity and taxonomy. We observed that the richness of the gut microbiome declined from day 7 post-burn and that the principal component and microbial community structure varied over time. On day 28 after the burn, the microbiome composition largely returned to the pre-burn level, although day 5 was a turning point for change. Some probiotics, such as the Lachnospiraceae_NK4A136_group, decreased in composition after the burn but were restored in the later recovery period. In contrast, Proteobacteria showed an opposite trend, which is known to include potential pathogenic bacteria. Conclusion These findings demonstrate gut microbial dysbiosis after burn injury and provide new insights into the burn-related dysbiosis of the gut microbiome and strategies for improving the treatment of burn injury from the perspective of the microbiota.
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Affiliation(s)
- Li-Jian Chen
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Yi Liu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Jing-Wen Yang
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Yan Lin
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Clare Hsu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Kai-Kai Zhang
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Jia-Li Liu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Jia-Hao Li
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Xiu-Wen Li
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Jian-Zheng Yang
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Long Chen
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Jia-Hao Zeng
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Xiao-Li Xie
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Toxicology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Jing-Tao Xu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Qi Wang
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
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15
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Lu B, Qian J, Hu J, Huang Y, Wang P, Shen J, He Y, Tang S, Liu Y, Zhang Y. Plant rhizosphere defense system respond differently to emerging polyfluoroalkyl substances F-53B and PFOS stress. JOURNAL OF HAZARDOUS MATERIALS 2023; 443:130119. [PMID: 36265386 DOI: 10.1016/j.jhazmat.2022.130119] [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: 05/07/2022] [Revised: 09/30/2022] [Accepted: 10/01/2022] [Indexed: 06/16/2023]
Abstract
Chlorinated polyfluoroalkyl ether sulfonate (F-53B) and perfluorooctanesulfonate (PFOS) are used and emitted as fog inhibitors in the chromium plating industry, and they are widely detected worldwide. To study the effects of F-53B and PFOS on the rhizosphere defense system, they were added at two levels (0.1 and 50 mg L-1) to the soil where different plants (Lythrum salicaria and Phragmites communis) were grown. In bulk soils, high concentrations of F-53B/PFOS resulted in significant increases in soil pH, NH4+-N, and NO3--N (the effect of PFOS on NO3--N was not significant). Moreover, the extent of the effects of PFOS and F-53B on the physicochemical properties of bulk soils were different (e.g., PFOS caused an increase of NH4+-N by 8.94%-45.97% compared to 1.63%-25.20% for F-53B). Root exudates and PFASs together influenced the physicochemical properties of rhizosphere soils (e.g., TOC increased significantly in contaminated rhizosphere soils but did not change in non-bulk soils). Under the influence of F-53B/PFOS, the root exudates regulated by plants were changed and weakened the effect of F-53B/PFOS on microbial community of rhizosphere soil. The rhizosphere defense systems of different plants have both similarities and differences in response to different substances and concentrations.
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Affiliation(s)
- Bianhe Lu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, People's Republic of China; College of Environment, Hohai University, Nanjing 210098, People's Republic of China
| | - Jin Qian
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, People's Republic of China; College of Environment, Hohai University, Nanjing 210098, People's Republic of China.
| | - Jing Hu
- Geosystems Research Institute, Mississippi State University, MS 39759, USA
| | | | - Peifang Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, People's Republic of China; College of Environment, Hohai University, Nanjing 210098, People's Republic of China.
| | - Junwei Shen
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, People's Republic of China; College of Environment, Hohai University, Nanjing 210098, People's Republic of China
| | - Yuxuan He
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, People's Republic of China; College of Environment, Hohai University, Nanjing 210098, People's Republic of China
| | - Sijing Tang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, People's Republic of China; College of Environment, Hohai University, Nanjing 210098, People's Republic of China
| | - Yin Liu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, People's Republic of China; College of Environment, Hohai University, Nanjing 210098, People's Republic of China
| | - Yuhang Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, People's Republic of China; College of Environment, Hohai University, Nanjing 210098, People's Republic of China
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16
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Langrand J, Lounès-Hadj Sahraoui A, Duclercq J, Raveau R, Laruelle F, Bert V, Facon N, Tisserant B, Fontaine J. Coriander ( Coriandrum sativum) Cultivation Combined with Arbuscular Mycorrhizal Fungi Inoculation and Steel Slag Application Influences Trace Elements-Polluted Soil Bacterial Functioning. PLANTS (BASEL, SWITZERLAND) 2023; 12:618. [PMID: 36771702 PMCID: PMC9920375 DOI: 10.3390/plants12030618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/19/2023] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
The cultivation of aromatic plants for the extraction of essential oils has been presented as an innovative and economically viable alternative for the remediation of areas polluted with trace elements (TE). Therefore, this study focuses on the contribution of the cultivation of coriander and the use of arbuscular mycorrhizal fungi (AMF) in combination with mineral amendments (steel slag) on the bacterial function of the rhizosphere, an aspect that is currently poorly understood and studied. The introduction of soil amendments, such as steel slag or mycorrhizal inoculum, had no significant effect on coriander growth. However, steel slag changed the structure of the bacterial community in the rhizosphere without affecting microbial function. In fact, Actinobacteria were significantly less abundant under slag-amended conditions, while the relative proportion of Gemmatimonadota increased. On the other hand, the planting of coriander affects the bacterial community structure and significantly increased the bacterial functional richness of the amended soil. Overall, these results show that planting coriander most affected the structure and functioning of bacterial communities in the TE-polluted soils and reversed the effects of mineral amendments on rhizosphere bacterial communities and their activities. This study highlights the potential of coriander, especially in combination with steel slag, for phytomanagement of TE-polluted soils, by improving soil quality and health.
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Affiliation(s)
- Julien Langrand
- Unité de Chimie Environnementale et Interactions sur le Vivant (UCEIV-UR 4492), Université Littoral Côte d’Opale, SFR Condorcet FR CNRS 3417, CS 80699, 62228 Calais, France
| | - Anissa Lounès-Hadj Sahraoui
- Unité de Chimie Environnementale et Interactions sur le Vivant (UCEIV-UR 4492), Université Littoral Côte d’Opale, SFR Condorcet FR CNRS 3417, CS 80699, 62228 Calais, France
| | - Jérôme Duclercq
- Unité Écologie et Dynamique des Systèmes Anthropisés (EDYSAN UMR CNRS 7058 CNRS), Université de Picardie Jules Verne, UFR des Sciences, 80029 Amiens, France
| | - Robin Raveau
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), UMR Santé et Agroécologie du Vignoble (SAVE), Bordeaux Sciences Agro, ISVV, 33882 Villenave d’Ornon, France
| | - Frédéric Laruelle
- Unité de Chimie Environnementale et Interactions sur le Vivant (UCEIV-UR 4492), Université Littoral Côte d’Opale, SFR Condorcet FR CNRS 3417, CS 80699, 62228 Calais, France
| | - Valérie Bert
- Unité Technologies Propres et Economie Circulaire, INERIS, Parc Technologique Alata, BP2, 60550 Verneuil en Halatte, France
| | - Natacha Facon
- Unité de Chimie Environnementale et Interactions sur le Vivant (UCEIV-UR 4492), Université Littoral Côte d’Opale, SFR Condorcet FR CNRS 3417, CS 80699, 62228 Calais, France
| | - Benoît Tisserant
- Unité de Chimie Environnementale et Interactions sur le Vivant (UCEIV-UR 4492), Université Littoral Côte d’Opale, SFR Condorcet FR CNRS 3417, CS 80699, 62228 Calais, France
| | - Joël Fontaine
- Unité de Chimie Environnementale et Interactions sur le Vivant (UCEIV-UR 4492), Université Littoral Côte d’Opale, SFR Condorcet FR CNRS 3417, CS 80699, 62228 Calais, France
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17
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Swanson CS, Dhand R, Cao L, Ferris J, Elder CS, He Q. Microbiome-scale analysis of aerosol facemask contamination during nebulization therapy in hospital. J Hosp Infect 2023; 134:80-88. [PMID: 36690253 DOI: 10.1016/j.jhin.2023.01.008] [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] [Received: 10/10/2022] [Revised: 12/31/2022] [Accepted: 01/17/2023] [Indexed: 01/22/2023]
Abstract
BACKGROUND Microbial contamination of aerosol facemasks could be a source of nosocomial infections during nebulization therapy in hospital, prompting efforts to identify these contaminants. Identification of micro-organisms in medical devices has traditionally relied on culture-dependent methods, which are incapable of detecting the majority of these microbial contaminants. This challenge could be overcome with culture-independent sequencing-based techniques that are suited for the profiling of complex microbiomes. AIM To characterize the microbial contaminants in aerosol facemasks used for nebulization therapy, and identify factors influencing the composition of these microbial contaminants with the acquisition and analysis of comprehensive microbiome-scale profiles using culture-independent high-throughput sequencing. METHODS Used aerosol facemasks collected from hospitalized patients were analysed with culture-independent 16S rRNA gene-based amplicon sequencing to acquire microbiome-scale comprehensive profiles of the microbial contaminants. Microbiome-based analysis was performed to identify potential sources of microbial contamination in facemasks. FINDINGS Culture-independent high-throughput sequencing was demonstrated for the capacity to acquire microbiome-scale profiles of microbial contaminants on aerosol facemasks. Microbial source identification enabled by the microbiome-scale profiles linked microbial contamination on aerosol facemasks to the human skin and oral microbiota. Antibiotic treatment with levofloxacin was found to reduce contamination of the facemasks by oral microbiota. CONCLUSION Sequencing-based microbiome-scale analysis is capable of providing comprehensive characterization of microbial contamination in aerosol facemasks. Insight gained from microbiome-scale analysis facilitates the development of effective strategies for the prevention and mitigation of the risk of nosocomial infections arising from exposure to microbial contamination of aerosol facemasks, such as targeted elimination of potential sources of contamination.
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Affiliation(s)
- C S Swanson
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, TN, USA
| | - R Dhand
- Department of Medicine, The University of Tennessee Graduate School of Medicine, Knoxville, TN, USA
| | - L Cao
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, TN, USA
| | - J Ferris
- Department of Medicine, The University of Tennessee Graduate School of Medicine, Knoxville, TN, USA
| | - C S Elder
- Respiratory Therapy Department, The University of Tennessee Medical Center, Knoxville, TN, USA
| | - Q He
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, TN, USA; Institute for a Secure and Sustainable Environment, The University of Tennessee, Knoxville, TN, USA.
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Mills M, Lee S, Mollenkopf D, Wittum T, Sullivan SMP, Lee J. Comparison of environmental microbiomes in an antibiotic resistance-polluted urban river highlights periphyton and fish gut communities as reservoirs of concern. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 851:158042. [PMID: 35973543 DOI: 10.1016/j.scitotenv.2022.158042] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 06/15/2023]
Abstract
Natural waterways near urban areas are heavily impacted by anthropogenic activities, including their microbial communities. A contaminant of growing public health concern in rivers is antibiotic resistant genes (ARGs), which can spread between neighboring bacteria and increase the potential for transmission of AR bacteria to animals and humans. To identify the matrices of most concern for AR, we compared ARG burdens and microbial community structures between sample types from the Scioto River Watershed, Ohio, the United States, from 2017 to 2018. Five environmental matrices (water, sediment, periphyton, detritus, and fish gut) were collected from 26 river sites. Due to our focus on clinically relevant ARGs, three carbapenem resistance genes (blaKPC, blaNDM, and blaOXA-48) were quantified via DropletDigital™ PCR. At a subset of nine urbanized sites, we conducted16S rRNA gene sequencing and functional gene predictions. Carbapenem resistance genes were quantified from all matrices, with blaKPC being the most detected (88 % of samples), followed by blaNDM (64 %) and blaOXA-48 (23 %). Fish gut samples showed higher concentrations of blaKPC and blaNDM than any other matrix, indicating potential ARG bioaccumulation, and risk of broader dissemination through aquatic and nearshore food webs. Periphyton had higher concentrations of blaNDM than water, sediment, or detritus. Microbial community analysis identified differences by sample type in community diversity and structure. Sediment samples had the most diverse microbial communities, and detritus, the least. Spearman correlations did not reveal significant relationships between the concentrations of the monitored ARGs and microbial community diversity. However, several differentially abundant taxa and microbial functions were identified by sample type that is definitive of these matrices' roles in the river ecosystem and habitat type. In summary, the fish gut and periphyton are a concern as AR reservoirs due to their relatively high concentration of carbapenem resistance genes, diverse microbial communities, and natural functions that promote AR.
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Affiliation(s)
- Molly Mills
- Division of Environmental Health Sciences, College of Public Health, The Ohio State University, Columbus, OH, USA; Environmental Sciences Graduate Program, The Ohio State University, Columbus, OH, USA
| | - Seungjun Lee
- Department of Food Science and Nutrition, Pukyong National University, Busan, Republic of Korea
| | - Dixie Mollenkopf
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH, USA
| | - Thomas Wittum
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH, USA; Infectious Diseases Institute, The Ohio State University, Columbus, OH, USA
| | - S Mažeika Patricio Sullivan
- Schiermeier Olentangy River Wetland Research Park, School of Environment and Natural Resources, The Ohio State University, Columbus, OH 43210, USA
| | - Jiyoung Lee
- Division of Environmental Health Sciences, College of Public Health, The Ohio State University, Columbus, OH, USA; Environmental Sciences Graduate Program, The Ohio State University, Columbus, OH, USA; Infectious Diseases Institute, The Ohio State University, Columbus, OH, USA; Department of Food Science & Technology, The Ohio State University, Columbus, OH, USA.
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Mija A, Jules M B, Alexandre J P. Arsenate decreases production of methylmercury across increasing sulfate concentration amendments in freshwater lake sediments. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2022; 24:1508-1516. [PMID: 35671194 DOI: 10.1039/d1em00543j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Arsenic (As) and sulfate pollution are often found co-occurring as a result of smelting metal ores. Previous studies showed that sulfate reducing microbes (SRMs) can use As(V) as a terminal electron acceptor, while others reported that SRMs are the main mercury (Hg) methylators in freshwater systems. However, we have yet to fully explore how As(V) can affect methylmercury (MeHg) production. In this study, we examined whether additions of As(V) and sulfate in freshwater sediments collected near a major gold mine with a history of S and As emissions affect Hg methylation. First, we show that Hg methylation in lake sediments was primarily limited by carbon substrate availability rather than by that of sulfate as terminal electron acceptors. Then, under conditions where carbon is not limiting, sulfate addition to the system significantly increased Hg methylation rate constants. Finally, we show that MeHg production rates in sediments significantly decreased with increasing As(V) concentrations, regardless of the sulfate concentration amended to sediments. This work underscores the apparent antagonistic effects of As(V) on the one hand, and carbon and sulfate on the other hand on the kinetics of Hg methylation. Arsenic controls on Hg methylation are complex and a combination of direct impact on the methylators' fitness, the formation of As-bearing mineral phases affecting Hg bioavailability, or changes in the microbial community structures over increasing As concentrations should be the focus of additional investigations.
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Affiliation(s)
- Aždajić Mija
- Department of Biology, University of Ottawa, 30 Marie-Curie, Ottawa, Ontario K1N 6N5, Canada.
| | - Blais Jules M
- Department of Biology, University of Ottawa, 30 Marie-Curie, Ottawa, Ontario K1N 6N5, Canada.
| | - Poulain Alexandre J
- Department of Biology, University of Ottawa, 30 Marie-Curie, Ottawa, Ontario K1N 6N5, Canada.
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20
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Lan J, Wang S, Wang J, Qi X, Long Q, Huang M. The Shift of Soil Bacterial Community After Afforestation Influence Soil Organic Carbon and Aggregate Stability in Karst Region. Front Microbiol 2022; 13:901126. [PMID: 35832811 PMCID: PMC9271926 DOI: 10.3389/fmicb.2022.901126] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/08/2022] [Indexed: 11/13/2022] Open
Abstract
Soil microbes regulate the carbon cycle and affect the formation and stabilization of soil aggregates. However, the interactions between the soil microbial community and soil organic carbon (SOC) fractions, organic carbon (OC) content in aggregates, and soil aggregate stability after afforestation are remain poorly understood. In our study, we investigated SOC fractions in bulk soil, aggregate-associated OC content, soil aggregate stability, and soil bacterial community with high-throughput 16S rRNA sequencing at sites representing natural secondary forest (NF) and managed forest (MF), with cropland (CL) as reference in a degraded karst region of Southwest China. Our results showed that afforestation remarkably increased the SOC fraction and OC content in aggregates, the mean weight diameter (MWD), and the mean geometric diameter (GMD). The most dominant bacterial phyla detected were Acidobacteriota, Actinobacteriota, Proteobacteria, and Chloroflexi across all soils. Afforestation remarkably altered the relative abundances of most of the dominant soil bacteria at the phylum, class, and order levels. Interestingly, such changes in the abundance of soil bacteria taxa had significantly effects on SOC fraction, aggregate-associated OC content, MWD, and MGD. The abundance of dominant bacterial taxa such as Methylomirabilota, Latescibacterota, Methylomirabilia, MB-A2-108, norank_Latescibacterota; Dehalococcoidia, Rokubacteriales, Gaiellales, Microtrichales, norank_c__MB-A2-108, norank_c__norank_p__Latescibacterota, Rhizobiales, and S085 not only remarkably increased but also had significant positive effects on SOC fractions and aggregate-associated OC content after afforestation. Moreover, MWD and MGD were positively correlated with the relative abundance of Methylomirabilota, Methylomirabilia, Rokubacteriales, Latescibacterota, and Rhizobiales. Results indicated the importance of certain soil bacteria for regulating SOC storage and soil aggregate stability. We concluded that afforestation on cropland could alter the abundance of soil bacteria, and these changes modulate the stability of soil aggregates and SOC fractions.
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21
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Sharma V, Vashishtha A, Jos ALM, Khosla A, Basu N, Yadav R, Bhatt A, Gulani A, Singh P, Lakhera S, Verma M. Phylogenomics of the Phylum Proteobacteria: Resolving the Complex Relationships. Curr Microbiol 2022; 79:224. [PMID: 35704242 DOI: 10.1007/s00284-022-02910-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 05/20/2022] [Indexed: 11/28/2022]
Abstract
Proteobacteria is one of the largest and phenotypically most diverse divisions within the domain bacteria. Due to the economic importance, this phylum demands an urgent need for a clear and scientifically sound classification system to streamline their characterization. The goal of our study was to carefully reevaluate the current system of classification and suggest changes wherein necessary. Phylogenetic trees of 84 Proteobacteria were constructed using single gene-based phylogeny involving 16S rRNA genes and protein sequences of 85 conserved genes, whole genome-based phylogenetic tree using CVtree3.0, amino acid Identity matrix tree, and concatenated tree with aforementioned conserved genes. The results of our study confirm the polyphyletic relationship between Desulfurella acetivorans, a Deltaproteobacteria with Epsilonproteobacteria. The group Syntrophobacterales was found to be polyphyletic with respect to Desulfarculus baarsii and the group Thiotrichales was found to be splitting in different phylogenetic trees. Placement of phylogenetic groups belonging to Rhodocyclales, Oceonospirilalles, and Chromatiales is controversial and requires further study and revisions. Based on our analysis, we strongly support reclassification of Magnetococcales as a separate class Etaproteobacteria. From our results, we conclude that concatenated trees of conserved proteins are a more accurate method for phylogenetic analysis, as compared to other methods used.
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Affiliation(s)
- Vaibhav Sharma
- Sri Venkateswara College, University of Delhi, Benito Juarez Road, Dhaula Kuan, New Delhi, Delhi, 110021, India
| | - Amit Vashishtha
- Sri Venkateswara College, University of Delhi, Benito Juarez Road, Dhaula Kuan, New Delhi, Delhi, 110021, India
| | - Arsha Liz M Jos
- Sri Venkateswara College, University of Delhi, Benito Juarez Road, Dhaula Kuan, New Delhi, Delhi, 110021, India
| | - Akshita Khosla
- Sri Venkateswara College, University of Delhi, Benito Juarez Road, Dhaula Kuan, New Delhi, Delhi, 110021, India
| | - Nirmegh Basu
- Sri Venkateswara College, University of Delhi, Benito Juarez Road, Dhaula Kuan, New Delhi, Delhi, 110021, India
| | - Rishabh Yadav
- Sri Venkateswara College, University of Delhi, Benito Juarez Road, Dhaula Kuan, New Delhi, Delhi, 110021, India
| | - Amit Bhatt
- Sri Venkateswara College, University of Delhi, Benito Juarez Road, Dhaula Kuan, New Delhi, Delhi, 110021, India
| | - Akshanshi Gulani
- Sri Venkateswara College, University of Delhi, Benito Juarez Road, Dhaula Kuan, New Delhi, Delhi, 110021, India
| | - Pushpa Singh
- Swami Shraddhanand College, University of Delhi, Alipur, New Delhi, Delhi, 110036, India
| | - Sanidhya Lakhera
- Sri Venkateswara College, University of Delhi, Benito Juarez Road, Dhaula Kuan, New Delhi, Delhi, 110021, India
| | - Mansi Verma
- Sri Venkateswara College, University of Delhi, Benito Juarez Road, Dhaula Kuan, New Delhi, Delhi, 110021, India. .,Department of Zoology, Sri Venkateswara College, South Campus, University of Delhi, New Delhi, Delhi, 110021, India.
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22
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Abstract
Lagoons are fragile marine ecosystems that are considerably affected by anthropogenic pollutants. We performed a spatiotemporal characterization of the microbiome of two Moroccan lagoons, Marchica and Oualidia, both classified as Ramsar sites, the former on the Mediterranean coast and the latter on the Atlantic coast. We investigated their microbial diversity and abundance using 16S rRNA amplicon- and shotgun-based metagenomics approaches during the summers of 2014 and 2015. The bacterial microbiome was composed primarily of Proteobacteria (25–53%, 29–29%), Cyanobacteria (34–12%, 11–0.53%), Bacteroidetes (24–16%, 23–43%), Actinobacteria (7–11%, 13–7%), and Verrucomicrobia (4–1%, 15–14%) in Marchica and Oualidia in 2014 and 2015, respectively. Interestingly, 48 strains were newly reported in lagoon ecosystems, while eight unknown viruses were detected in Mediterranean Marchica only. Statistical analysis showed higher microbial diversity in the Atlantic lagoon than in the Mediterranean lagoon and a robust relationship between alpha diversity and geographic sampling locations. This first-ever metagenomics study on Moroccan aquatic ecosystems enriched the national catalog of marine microorganisms. They will be investigated as candidates for bioindication properties, biomonitoring potential, biotechnology valorization, biodiversity protection, and lagoon health assessment.
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23
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Swanson CS, Dhand R, Cao L, Ferris J, Elder CS, He Q. Microbiome Profiles of Nebulizers in Hospital Use. J Aerosol Med Pulm Drug Deliv 2022; 35:212-222. [PMID: 35230145 DOI: 10.1089/jamp.2021.0032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Background: Nebulizers are used to provide treatment to respiratory patients. Concerns over nosocomial infection risks from contaminated nebulizers raise the critical need to identify all microbial populations in nebulizers used by patients. However, conventional culture-dependent techniques are inadequate with the ability to identify specific microbial populations only. Therefore, the aims of this study were to acquire complete profiles of microbiomes in nebulizers used by in-patients with culture-independent high-throughput sequencing and identify sources of microbial contaminants for the development of effective practices to reduce microbial contamination in nebulizer devices. Methods: This study was conducted at the University of Tennessee Medical Center in Knoxville, TN. Nebulizers were collected between May 2018 and October 2018 from inpatients admitted to the floors for pneumonia or chronic obstructive pulmonary disease exacerbations. Nebulizers were sampled for 16S rRNA gene-based amplicon sequencing to profile nebulizer microbiomes and perform phylogenetic analysis. A Bayesian community-wide culture-independent microbial source tracking technique was used to quantify the contribution of human-associated microbiota as potential sources of nebulizer contamination. Results: Culture-independent sequencing detected diverse microbial populations in nebulizers, represented by 18 abundant genera. Stenotrophomonas was identified as the most abundant genus, accounting for 12.4% of the nebulizer microbiome, followed by Rhizobium, Staphylococcus, Streptococcus, and Ralstonia. Phylogenetic analysis revealed the presence of multiple phylotypes with close relationship to potential pathogens. Contributing up to 15% to nebulizer microbiomes, human-associated microbiota was not identified as the primary sources of nebulizer contamination. Conclusion: Culture-independent sequencing was demonstrated to be capable of acquiring comprehensive profiles of microbiomes in nebulizers used by in-patients. Phylogenetic analysis identified differences in pathogenicity between closely related phylotypes. Microbiome profile-enabled community-wide culture-independent microbial source tracking suggested greater importance of environmental sources than human sources as contributors to nebulizer microbiomes, providing important insight for the development of effective strategies for the monitoring and control of nebulizer devices to mitigate infection risks in the hospital.
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Affiliation(s)
- Clifford S Swanson
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, Tennessee, USA
| | - Rajiv Dhand
- Department of Medicine, The University of Tennessee Graduate School of Medicine, Knoxville, Tennessee, USA
| | - Liu Cao
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, Tennessee, USA
| | - Jennifer Ferris
- Department of Medicine, The University of Tennessee Graduate School of Medicine, Knoxville, Tennessee, USA
| | - C Scott Elder
- Department of Respiratory Therapy, The University of Tennessee Medical Center, Knoxville, Tennessee, USA
| | - Qiang He
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, Tennessee, USA.,Institute for a Secure and Sustainable Environment, The University of Tennessee, Knoxville, Tennessee, USA
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24
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Blandón LM, Marín MA, Quintero M, Jutinico-Shubach LM, Montoya-Giraldo M, Santos-Acevedo M, Gómez-León J. Diversity of cultivable bacteria from deep-sea sediments of the Colombian Caribbean and their potential in bioremediation. Antonie van Leeuwenhoek 2022; 115:421-431. [PMID: 35066712 DOI: 10.1007/s10482-021-01706-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 12/28/2021] [Indexed: 11/26/2022]
Abstract
The diversity of deep-sea cultivable bacteria was studied in seven sediment samples of the Colombian Caribbean. Three hundred and fifty two marine bacteria were isolated according to its distinct morphological character on the solid media, then DNA sequences of the 16S rRNA were amplified to identify the isolated strains. The identified bacterial were arranged in three phylogenetic groups, Firmicutes, Proteobacteria, and Actinobacteria, with 34 different OTUs defined at ≥ 97% of similarity and 70 OTUs at ≥ 98.65%, being the 51% Firmicutes, 34% Proteobacteria and 15% Actinobacteria. Bacillus and Fictibacillus were the dominant genera in Firmicutes, Halomonas and Pseudomonas in Proteobacteria and Streptomyces and Micromonospora in Actinobacteria. In addition, the strains were tested for biosurfactants and lipolytic enzymes production, with 120 biosurfactant producing strains (mainly Firmicutes) and, 56 lipolytic enzymes producing strains (Proteobacteria). This report contributes to the understanding of the diversity of the marine deep-sea cultivable bacteria from the Colombian Caribbean, and their potential application as bioremediation agents.
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Affiliation(s)
- Lina Marcela Blandón
- Marine Bioprospecting Line, Marine and Coastal Research Institute "José Benito Vives de Andréis"- INVEMAR, Calle 25 No. 2-55, Playa Salguero, Santa Marta D.T.C.H., Colombia
| | - Mario Alejandro Marín
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas - UNICAMP, Campinas, SP, 13083-970, Brazil
| | - Marynes Quintero
- Marine Bioprospecting Line, Marine and Coastal Research Institute "José Benito Vives de Andréis"- INVEMAR, Calle 25 No. 2-55, Playa Salguero, Santa Marta D.T.C.H., Colombia
| | - Laura Marcela Jutinico-Shubach
- Marine Bioprospecting Line, Marine and Coastal Research Institute "José Benito Vives de Andréis"- INVEMAR, Calle 25 No. 2-55, Playa Salguero, Santa Marta D.T.C.H., Colombia
| | - Manuela Montoya-Giraldo
- Marine Bioprospecting Line, Marine and Coastal Research Institute "José Benito Vives de Andréis"- INVEMAR, Calle 25 No. 2-55, Playa Salguero, Santa Marta D.T.C.H., Colombia
| | - Marisol Santos-Acevedo
- Marine Bioprospecting Line, Marine and Coastal Research Institute "José Benito Vives de Andréis"- INVEMAR, Calle 25 No. 2-55, Playa Salguero, Santa Marta D.T.C.H., Colombia
| | - Javier Gómez-León
- Marine Bioprospecting Line, Marine and Coastal Research Institute "José Benito Vives de Andréis"- INVEMAR, Calle 25 No. 2-55, Playa Salguero, Santa Marta D.T.C.H., Colombia.
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25
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Pilch HE, Steinberger AJ, Sockett DC, Aulik N, Suen G, Czuprynski CJ. Assessing the microbiota of recycled bedding sand on a Wisconsin dairy farm. J Anim Sci Biotechnol 2021; 12:114. [PMID: 34758888 PMCID: PMC8582206 DOI: 10.1186/s40104-021-00635-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 09/05/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Sand is often considered the preferred bedding material for dairy cows as it is thought to have lower bacterial counts than organic bedding materials and cows bedded on sand experience fewer cases of lameness and disease. Sand can also be efficiently recycled and reused, making it cost-effective. However, some studies have suggested that the residual organic material present in recycled sand can serve as a reservoir for commensal and pathogenic bacteria, although no studies have yet characterized the total bacterial community composition. Here we sought to characterize the bacterial community composition of a Wisconsin dairy farm bedding sand recycling system and its dynamics across several stages of the recycling process during both summer and winter using 16S rRNA gene amplicon sequencing. RESULTS Bacterial community compositions of the sand recycling system differed by both seasons and stage. Summer samples had higher richness and distinct community compositions, relative to winter samples. In both summer and winter samples, the diversity of recycled sand decreased with time drying in the recycling room. Compositionally, summer sand 14 d post-recycling was enriched in operational taxonomic units (OTUs) belonging to the genera Acinetobacter and Pseudomonas, relative to freshly washed sand and sand from cow pens. In contrast, no OTUs were found to be enriched in winter sand. The sand recycling system contained an overall core microbiota of 141 OTUs representing 68.45% ± 10.33% SD of the total bacterial relative abundance at each sampled stage. The 4 most abundant genera in this core microbiota included Acinetobacter, Psychrobacter, Corynebacterium, and Pseudomonas. Acinetobacter was present in greater abundance in summer samples, whereas Psychrobacter and Corynebacterium had higher relative abundances in winter samples. Pseudomonas had consistent relative abundances across both seasons. CONCLUSIONS These findings highlight the potential of recycled bedding sand as a bacterial reservoir that warrants further study.
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Affiliation(s)
- Hannah E. Pilch
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, 53706 USA
| | - Andrew J. Steinberger
- Department of Bacteriology, University of Wisconsin-Madison, Madison, 53706 USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, 53706 USA
| | - Donald C. Sockett
- Wisconsin Veterinary Diagnostic Laboratory, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, 53706 USA
| | - Nicole Aulik
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, 53706 USA
- Wisconsin Veterinary Diagnostic Laboratory, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, 53706 USA
| | - Garret Suen
- Department of Bacteriology, University of Wisconsin-Madison, Madison, 53706 USA
| | - Charles J. Czuprynski
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, 53706 USA
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26
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Burut-Archanai S, Ubertino D, Chumtong P, Mhuantong W, Powtongsook S, Piyapattanakorn S. Dynamics of Microbial Community During Nitrification Biofilter Acclimation with Low and High Ammonia. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2021; 23:671-681. [PMID: 34414527 DOI: 10.1007/s10126-021-10056-1] [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: 06/04/2021] [Accepted: 08/09/2021] [Indexed: 06/13/2023]
Abstract
The acclimation of a nitrifying biofilter is a crucial and time-consuming task for setting up a recirculating aquaculture system (RAS). Gaining a better understanding of the dynamics of the microbial community during the acclimation period in the system could be useful for the development of mature nitrifying biofilters. In this study, high-throughput DNA sequencing was applied to monitor the microbial communities on a biofilter during the acclimation period (7 weeks) in high (100 mg N/L) and low (5 mg N/L) total ammonia nitrogen (TAN) treatments. Both treatments were successful for developing a mature nitrifying biofilter, dominated by Proteobacteria, Bacteroidetes, and Nitrospirae. Complete nitrification was found after 7 days of biofilter acclimation as indicated by decreasing TAN concentration, increasing nitrate concentration, and high abundances of the nitrifying bacteria, Nitrosomonadaceae and Nitrospiraceae. The beta diversity analysis of microbial communities showed different clustering of the samples between high and low TAN treatment groups. A greater abundance of nitrifying bacteria was found in the high TAN treatments (27-51%) than in the low TAN treatment (15-29%). The bacterial diversity in biofilters acclimated at high TAN concentration (Shannon's index 5.40-6.15) were lower than those found at low TAN treatment levels (Shannon's index 6.40-7.01). The higher diversity in biofilters acclimated at low TAN concentrations, consisting of Planctomycetes and Archaea, might benefit the nutrient recycling in the system. Although nitrification activity was observed from the first week of the acclimation period, the acclimation period should be taken as at least 6 weeks for full development of nitrifying biofilm. Moreover, the reduction of potentially pathogenic Vibrio on biofilters was found at that period.
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Affiliation(s)
- Surachet Burut-Archanai
- Center of Excellence for Marine Biotechnology, Department of Marine Science, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
- Marine Biotechnology Research Team, Integrative Aquaculture Biotechnology Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Déborah Ubertino
- University of Clermont Auvergne, 49 bd Francois Mitterrand, 63000, Clermont-Ferrand, France
| | - Parichat Chumtong
- Center of Excellence for Marine Biotechnology, Department of Marine Science, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
- Marine Biotechnology Research Team, Integrative Aquaculture Biotechnology Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Wuttichai Mhuantong
- Enzyme Technology Research Team, Biorefinery and Bioproduct Technology Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, 12120, Khlong Luang, Pathum Thani, Thailand
| | - Sorawit Powtongsook
- Center of Excellence for Marine Biotechnology, Department of Marine Science, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
- Marine Biotechnology Research Team, Integrative Aquaculture Biotechnology Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Sanit Piyapattanakorn
- Center of Excellence for Marine Biotechnology, Department of Marine Science, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.
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27
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Granatto CF, Grosseli GM, Sakamoto IK, Fadini PS, Varesche MBA. Influence of metabolic cosubstrates on methanogenic potential and degradation of triclosan and propranolol in sanitary sewage. ENVIRONMENTAL RESEARCH 2021; 199:111220. [PMID: 33992637 DOI: 10.1016/j.envres.2021.111220] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/27/2021] [Accepted: 04/22/2021] [Indexed: 06/12/2023]
Abstract
Triclosan (TCS) and propranolol (PRO) are emerging micropollutants that are difficult to remove in wastewater treatment plants. In this study, methanogenic potential (P) of anaerobic sludge submitted to TCS (3.6 ± 0.1 to 15.5 ± 0.1 mg L-1) and PRO (6.1 ± 0.1 to 55.9 ± 1.2 mg L-1) in sanitary sewage, was investigated in batch reactors. The use of cosubstrates (200 mg L-1 of organic matter) ethanol, methanol:ethanol and fumarate was evaluated for micropollutant degradation. Without cosubstrates, P values for 5.0 ± 0.1 mgTCS L-1, 15.5 ± 0.1 mgTCS L-1 and 55.0 ± 1.3 mgPRO L-1 were 50.53%, 98.24% and 17.66% lower in relation to Control assay (855 ± 5 μmolCH4) with sanitary sewage, without micropollutants and cosubstrates, respectively. The use of fumarate, ethanol and methanol:ethanol favored greater methane production, with P values of 2144 ± 45 μmolCH4, 2960 ± 185 μmolCH4 and 2239 ± 171 μmolCH4 for 5.1 ± 0.1 mgTCS L-1, respectively; and of 10,827 ± 185 μmolCH4, 10,946 ± 108 μmolCH4 and 10,809 ± 210 μmolCH4 for 55.0 ± 1.3 mgPRO L-1, respectively. Greater degradation of TCS (77.1 ± 0.1% for 5.1 ± 0.1 mg L-1) and PRO (24.1 ± 0.1% for 55.9 ± 1.2 mg L-1) was obtained with ethanol. However, with 28.5 ± 0.5 mg PRO L-1, greater degradation (88.4 ± 0.9%) was obtained without cosubstrates. With TCS, via sequencing of rRNA 16S gene, for Bacteria Domain, greater abundance of phylum Chloroflexi and of the genera Longilinea, Arcobacter, Mesotoga and Sulfuricurvum were identified. With PRO, the genus VadinBC27 was the most abundant. Methanosaeta was dominant in TCS with ethanol, while in PRO without cosubstrates, Methanobacterium and Methanosaeta were the most abundant. The use of metabolic cosubstrates is a favorable strategy to obtain greater methanogenic potential and degradation of TCS and PRO.
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Affiliation(s)
- Caroline F Granatto
- Department of Hydraulics and Sanitation, São Carlos School of Engineering, University of São Paulo. Ave Trabalhador São-Carlense, no. 400, Zipcode, 13566-590, São Carlos, SP, Brazil.
| | - Guilherme M Grosseli
- Federal University of São Carlos, Washington Luiz Highway, Km 235, Zipcode 13565-905, São Carlos, SP, Brazil.
| | - Isabel K Sakamoto
- Department of Hydraulics and Sanitation, São Carlos School of Engineering, University of São Paulo. Ave Trabalhador São-Carlense, no. 400, Zipcode, 13566-590, São Carlos, SP, Brazil.
| | - Pedro S Fadini
- Federal University of São Carlos, Washington Luiz Highway, Km 235, Zipcode 13565-905, São Carlos, SP, Brazil.
| | - Maria Bernadete A Varesche
- Department of Hydraulics and Sanitation, São Carlos School of Engineering, University of São Paulo. Ave Trabalhador São-Carlense, no. 400, Zipcode, 13566-590, São Carlos, SP, Brazil.
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28
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Sheinman M, Arkhipova K, Arndt PF, Dutilh BE, Hermsen R, Massip F. Identical sequences found in distant genomes reveal frequent horizontal transfer across the bacterial domain. eLife 2021; 10:62719. [PMID: 34121661 PMCID: PMC8270642 DOI: 10.7554/elife.62719] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 06/13/2021] [Indexed: 12/19/2022] Open
Abstract
Horizontal gene transfer (HGT) is an essential force in microbial evolution. Despite detailed studies on a variety of systems, a global picture of HGT in the microbial world is still missing. Here, we exploit that HGT creates long identical DNA sequences in the genomes of distant species, which can be found efficiently using alignment-free methods. Our pairwise analysis of 93,481 bacterial genomes identified 138,273 HGT events. We developed a model to explain their statistical properties as well as estimate the transfer rate between pairs of taxa. This reveals that long-distance HGT is frequent: our results indicate that HGT between species from different phyla has occurred in at least 8% of the species. Finally, our results confirm that the function of sequences strongly impacts their transfer rate, which varies by more than three orders of magnitude between different functional categories. Overall, we provide a comprehensive view of HGT, illuminating a fundamental process driving bacterial evolution.
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Affiliation(s)
- Michael Sheinman
- Theoretical Biology and Bioinformatics, Biology Department, Utrecht University, Utrecht, Netherlands.,Division of Molecular Carcinogenesis, the Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Ksenia Arkhipova
- Theoretical Biology and Bioinformatics, Biology Department, Utrecht University, Utrecht, Netherlands
| | - Peter F Arndt
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Biology Department, Utrecht University, Utrecht, Netherlands
| | - Rutger Hermsen
- Theoretical Biology and Bioinformatics, Biology Department, Utrecht University, Utrecht, Netherlands
| | - Florian Massip
- Berlin Institute for Medical Systems Biology, Max Delbrück Center, Berlin, Germany.,Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Villleurbanne, France
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29
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Duan B, Ding P, Navarre WW, Liu J, Xia B. Xenogeneic Silencing and Bacterial Genome Evolution: Mechanisms for DNA Recognition Imply Multifaceted Roles of Xenogeneic Silencers. Mol Biol Evol 2021; 38:4135-4148. [PMID: 34003286 PMCID: PMC8476142 DOI: 10.1093/molbev/msab136] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 04/08/2021] [Indexed: 12/14/2022] Open
Abstract
Horizontal gene transfer (HGT) is a major driving force for bacterial evolution. To avoid the deleterious effects due to the unregulated expression of newly acquired foreign genes, bacteria have evolved specific proteins named xenogeneic silencers to recognize foreign DNA sequences and suppress their transcription. As there is considerable diversity in genomic base compositions among bacteria, how xenogeneic silencers distinguish self- from nonself DNA in different bacteria remains poorly understood. This review summarizes the progress in studying the DNA binding preferences and the underlying molecular mechanisms of known xenogeneic silencer families, represented by H-NS of Escherichia coli, Lsr2 of Mycobacterium, MvaT of Pseudomonas, and Rok of Bacillus. Comparative analyses of the published data indicate that the differences in DNA recognition mechanisms enable these xenogeneic silencers to have clear characteristics in DNA sequence preferences, which are further correlated with different host genomic features. These correlations provide insights into the mechanisms of how these xenogeneic silencers selectively target foreign DNA in different genomic backgrounds. Furthermore, it is revealed that the genomic AT contents of bacterial species with the same xenogeneic silencer family proteins are distributed in a limited range and are generally lower than those species without any known xenogeneic silencers in the same phylum/class/genus, indicating that xenogeneic silencers have multifaceted roles on bacterial genome evolution. In addition to regulating horizontal gene transfer, xenogeneic silencers also act as a selective force against the GC to AT mutational bias found in bacterial genomes and help the host genomic AT contents maintained at relatively low levels.
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Affiliation(s)
- Bo Duan
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, and School of Life Sciences, Peking University, Beijing, 100871, China
| | - Pengfei Ding
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, and School of Life Sciences, Peking University, Beijing, 100871, China
| | - William Wiley Navarre
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5G 1M1, Canada
| | - Jun Liu
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5G 1M1, Canada
| | - Bin Xia
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, and School of Life Sciences, Peking University, Beijing, 100871, China
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30
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Kaltenegger A, Humer E, Pacífico C, Zebeli Q. Feeding dairy cows bakery by-products enhanced nutrient digestibility, but affected fecal microbial composition and pH in a dose-dependent manner. J Dairy Sci 2021; 104:7781-7793. [PMID: 33865598 DOI: 10.3168/jds.2020-19998] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 03/07/2021] [Indexed: 11/19/2022]
Abstract
We reported recently that adding bakery by-products (BP) to the diets of dairy cows up to 30% improved performance and rumen pH, but caused major shifts in the nutrient profile and availability, likely modifying nutrient degradation patterns throughout the gastrointestinal tract. The aim of this study was to investigate the effects of the gradual replacement of cereals by BP on the apparent total-tract digestibility (ATTD), the fermentation patterns, and the microbial community in feces of dairy cows. Twenty-four mid-lactating Simmental cows (149 ± 22.3 days in milk, 756 ± 89.6 kg of initial body weight) were fed a total mixed ration ad libitum (fresh feed was offered twice per day) containing a 50:50 ratio of forage to concentrate (dry matter basis) throughout the experiment. The trial lasted 5 wk, whereby the first week was used for baseline measurements, in which all cows received the same diet, without BP. Cows were then randomly allocated into 3 groups differing in the BP content of diets (0% BP, 15% BP, and 30% BP on a DM basis) and fed for 4 wk. Fecal samples were taken for analysis of pH, volatile fatty acids (VFA), and 16S rRNA gene sequencing. The inclusion of BP resulted in an increase of ether extract and sugars, and a reduction of starch and neutral detergent fiber in the diet. Feeding BP linearly increased the ATTD of almost all nutrients resulting in up to 2 kg more digestible organic matter intake (DOMI). Increasing BP level up to 30% increased fecal total VFA concentration and decreased the pH. The proportion of butyrate in feces increased linearly, but the proportion of all other VFA was not affected by BP-feeding. The richness and diversity indices of the fecal microbiota linearly declined by the inclusion of BP. The cellulolytic phyla Fibrobacteres decreased, whereas amylolytic phyla, such as Proteobacteria, increased. Overall, results showed that feeding BP linearly increased ATTD and DOMI, but impaired fecal microbial diversity and pH. In the interest of the optimization of BP inclusion in the dairy cows' feeding, a dietary level between 15 to 30% of BP might be a better compromise than 30% in terms of an enhanced DOMI and performance with still lowered risk of hindgut dysbiosis, but this will require further investigations.
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Affiliation(s)
- A Kaltenegger
- Department for Farm Animals and Veterinary Public Health, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine, Veterinärplatz 1, 1210 Vienna, Austria
| | - E Humer
- Department for Farm Animals and Veterinary Public Health, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine, Veterinärplatz 1, 1210 Vienna, Austria
| | - C Pacífico
- Department for Farm Animals and Veterinary Public Health, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine, Veterinärplatz 1, 1210 Vienna, Austria
| | - Q Zebeli
- Department for Farm Animals and Veterinary Public Health, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine, Veterinärplatz 1, 1210 Vienna, Austria.
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31
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Deryusheva E, Machulin A, Matyunin M, Galzitskaya O. Sequence and evolutionary analysis of bacterial ribosomal S1 proteins. Proteins 2021; 89:1111-1124. [PMID: 33843105 DOI: 10.1002/prot.26084] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 03/17/2021] [Accepted: 04/07/2021] [Indexed: 12/21/2022]
Abstract
The multi-domain bacterial S1 protein is the largest and most functionally important ribosomal protein of the 30S subunit, which interacts with both mRNA and proteins. The family of ribosomal S1 proteins differs in the classical sense from a protein with tandem repeats and has a "bead-on-string" organization, where each repeat is folded into a globular domain. Based on our recent data, the study of evolutionary relationships for the bacterial phyla will provide evidence for one of the proposed theories of the evolutionary development of proteins with structural repeats: from multiple repeats of assembles to single repeats, or vice versa. In this comparative analysis of 1333 S1 sequences that were identified in 24 different phyla, we demonstrate how such phyla can form independently/dependently during evolution. To the best of our knowledge, this work is the first study of the evolutionary history of bacterial ribosomal S1 proteins. The collected and structured data can be useful to computer biologists as a resource for determining percent identity, amino acid composition and logo motifs, as well as dN/dS ratio in bacterial S1 protein. The obtained research data indicate that the evolutionary development of bacterial ribosomal S1 proteins evolved from multiple assemblies to single repeat. The presented data are integrated into the server, which can be accessed at http://oka.protres.ru:4200.
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Affiliation(s)
- Evgeniya Deryusheva
- Institute for Biological Instrumentation, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Russian Federation
| | - Andrey Machulin
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Russian Federation
| | - Maxim Matyunin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russian Federation
| | - Oxana Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russian Federation.,Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Russian Federation
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32
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Bacterial diversity changes in agricultural soils influenced by poultry litter fertilization. Braz J Microbiol 2021; 52:675-686. [PMID: 33590447 DOI: 10.1007/s42770-021-00437-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 02/02/2021] [Indexed: 01/28/2023] Open
Abstract
Poultry litter is widely applied as agricultural fertilizer and can affect the soil microbiome through nutrient overload and antibiotic contamination. In this study, we assessed changes in soil bacterial diversity using high-throughput sequencing approaches. Four samples in triplicate were studied: soils with short- and long-term fertilization by poultry litter (S1 = 10 months and S2 = 30 years, respectively), a soil inside a poultry shed (S3), and a forest soil used as control (S0). Samples S0, S1, and S2 revealed a relatively high richness, with confirmed operational taxonomic units (OTUs) in the three replicates of each sample ranging from 1243 to 1279, while richness in S3 was about three times lower (466). The most abundant phyla were Proteobacteria, Bacteroidetes, and Actinobacteria. Acidobacteria, Planctomycetes, and Verrucomicrobia were also abundant but highly diminished in S3, while Firmicutes was less abundant in S0. Changes in bacterial communities were very evident at the genera level. The genera Gaiella, Rhodoplanes, Solirubacter, and Sphingomonas were predominant in S0 but strongly decreased in the other soils. Pedobacter and Devosia were the most abundant in S1 and were diminished in S2, while Herbiconiux, Brevundimonas, Proteiniphilum, and Petrimonas were abundant in S2. The most abundant genera in S3 were Deinococcus, Truepera, Rhodanobacter, and Castellaniella. A predictive analysis of the metabolic functions with Tax4Fun2 software suggested the potential presence of enzymes associated with antibiotic resistance as well as with denitrification pathways, indicating that the S3 soil is a potential source of nitrous oxide, a powerful greenhouse gas.
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33
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Su W, Liu ML, Yang YH, Wang JS, Li SH, Lv H, Dao FY, Yang H, Lin H. PPD: A Manually Curated Database for Experimentally Verified Prokaryotic Promoters. J Mol Biol 2021; 433:166860. [PMID: 33539888 DOI: 10.1016/j.jmb.2021.166860] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 12/13/2020] [Accepted: 01/27/2021] [Indexed: 12/16/2022]
Abstract
As a key region, promoter plays a key role in transcription regulation. A eukaryotic promoter database called EPD has been constructed to store eukaryotic POL II promoters. Although there are some promoter databases for specific prokaryotic species or specific promoter type, such as RegulonDB for Escherichia coli K-12, DBTBS for Bacillus subtilis and Pro54DB for sigma 54 promoter, because of the diversity of prokaryotes and the development of sequencing technology, huge amounts of prokaryotic promoters are scattered in numerous published articles, which is inconvenient for researchers to explore the process of gene regulation in prokaryotes. In this study, we constructed a Prokaryotic Promoter Database (PPD), which records the experimentally validated promoters in prokaryotes, from published articles. Up to now, PPD has stored 129,148 promoters across 63 prokaryotic species manually extracted from published papers. We provided a friendly interface for users to browse, search, blast, visualize, submit and download data. The PPD will provide relatively comprehensive resources of prokaryotic promoter for the study of prokaryotic gene transcription. The PPD is freely available and easy accessed at http://lin-group.cn/database/ppd/.
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Affiliation(s)
- Wei Su
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Meng-Lu Liu
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Yu-He Yang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Jia-Shu Wang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Shi-Hao Li
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Hao Lv
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Fu-Ying Dao
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Hui Yang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Hao Lin
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China.
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34
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Gweon HS, Bowes MJ, Moorhouse HL, Oliver AE, Bailey MJ, Acreman MC, Read DS. Contrasting community assembly processes structure lotic bacteria metacommunities along the river continuum. Environ Microbiol 2021; 23:484-498. [PMID: 33258525 PMCID: PMC7898806 DOI: 10.1111/1462-2920.15337] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 11/03/2020] [Accepted: 11/24/2020] [Indexed: 01/26/2023]
Abstract
The heterogeneous nature of lotic habitats plays an important role in the complex ecological and evolutionary processes that structure the microbial communities within them. Due to such complexity, our understanding of lotic microbial ecology still lacks conceptual frameworks for the ecological processes that shape these communities. We explored how bacterial community composition and underlying ecological assembly processes differ between lotic habitats by examining community composition and inferring community assembly processes across four major habitat types (free-living, particle-associated, biofilm on benthic stones and rocks, and sediment). This was conducted at 12 river sites from headwater streams to the main river in the River Thames, UK. Our results indicate that there are distinct differences in the bacterial communities between four major habitat types, with contrasting ecological processes shaping their community assembly processes. While the mobile free-living and particle-associated communities were consistently less diverse than the fixed sediment and biofilm communities, the latter two communities displayed higher homogeneity across the sampling sites. This indicates that the relative influence of deterministic environmental filtering is elevated in sediment and biofilm communities compared with free-living and particle-associated communities, where stochastic processes play a larger role.
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Affiliation(s)
- Hyun S. Gweon
- UK Centre for Ecology & HydrologyWallingford, OxfordshireOX10 8BBUK
- School of Biological SciencesUniversity of ReadingReadingRG6 6EXUK
| | - Michael J. Bowes
- UK Centre for Ecology & HydrologyWallingford, OxfordshireOX10 8BBUK
| | - Heather L. Moorhouse
- UK Centre for Ecology & HydrologyWallingford, OxfordshireOX10 8BBUK
- Lancaster Environment CentreLancaster UniversityLibrary Avenue, LancasterLA1 4YQUK
| | - Anna E. Oliver
- UK Centre for Ecology & HydrologyWallingford, OxfordshireOX10 8BBUK
| | - Mark J. Bailey
- UK Centre for Ecology & HydrologyWallingford, OxfordshireOX10 8BBUK
| | | | - Daniel S. Read
- UK Centre for Ecology & HydrologyWallingford, OxfordshireOX10 8BBUK
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35
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Exploring the diversity of mechanosensitive channels in bacterial genomes. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2020; 50:25-36. [PMID: 33244613 DOI: 10.1007/s00249-020-01478-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 10/08/2020] [Accepted: 11/08/2020] [Indexed: 10/22/2022]
Abstract
Mechanosensitive ion channels are responsible for touch sensation and proprioception in higher level organisms such as humans and recovery after osmotic stress in bacteria. Bacterial mechanosensitive channels are homologous to either the mechanosensitive channel of large conductance (MscL) or the mechanosensitive channel of small conductance (MscS). In the E. coli genome there are seven unique mechanosensitive channels, a single MscL homologue, and six MscS homologues. The six MscS homologues are members of the diverse MscS superfamily of ion channels, and these channels show variation on both the N and C termini when compared to E. coli MscS. In bacterial strains with phenotypic analysis of the endogenous mechanosensors, the quantity of MscS superfamily members in the genome range from 2 to 6 and all of the strains contain a copy of MscL. Here, we show an in-depth analysis of over 150 diverse bacterial genomes, encompassing nine phyla, to determine the number of genomes that contain an MscL homologue and the average number of MscS superfamily members per genome. We determined that the average genome contains 4 ± 3 MscS homologues and 67% of bacterial genomes encode for a MscL homologue.
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36
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Mungan MD, Alanjary M, Blin K, Weber T, Medema MH, Ziemert N. ARTS 2.0: feature updates and expansion of the Antibiotic Resistant Target Seeker for comparative genome mining. Nucleic Acids Res 2020; 48:W546-W552. [PMID: 32427317 PMCID: PMC7319560 DOI: 10.1093/nar/gkaa374] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/19/2020] [Accepted: 04/29/2020] [Indexed: 01/21/2023] Open
Abstract
Multi-drug resistant pathogens have become a major threat to human health and new antibiotics are urgently needed. Most antibiotics are derived from secondary metabolites produced by bacteria. In order to avoid suicide, these bacteria usually encode resistance genes, in some cases within the biosynthetic gene cluster (BGC) of the respective antibiotic compound. Modern genome mining tools enable researchers to computationally detect and predict BGCs that encode the biosynthesis of secondary metabolites. The major challenge now is the prioritization of the most promising BGCs encoding antibiotics with novel modes of action. A recently developed target-directed genome mining approach allows researchers to predict the mode of action of the encoded compound of an uncharacterized BGC based on the presence of resistant target genes. In 2017, we introduced the ‘Antibiotic Resistant Target Seeker’ (ARTS). ARTS allows for specific and efficient genome mining for antibiotics with interesting and novel targets by rapidly linking housekeeping and known resistance genes to BGC proximity, duplication and horizontal gene transfer (HGT) events. Here, we present ARTS 2.0 available at http://arts.ziemertlab.com. ARTS 2.0 now includes options for automated target directed genome mining in all bacterial taxa as well as metagenomic data. Furthermore, it enables comparison of similar BGCs from different genomes and their putative resistance genes.
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Affiliation(s)
- Mehmet Direnç Mungan
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany.,German Centre for Infection Research (DZIF), Partner Site Tübingen, Germany
| | - Mohammad Alanjary
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB Wageningen, the Netherlands
| | - Kai Blin
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Bygning 220, 2800 Kgs. Lyngby, Denmark
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Bygning 220, 2800 Kgs. Lyngby, Denmark
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB Wageningen, the Netherlands
| | - Nadine Ziemert
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany.,German Centre for Infection Research (DZIF), Partner Site Tübingen, Germany
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37
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Granatto CF, Grosseli GM, Sakamoto IK, Fadini PS, Varesche MBA. Methanogenic potential of diclofenac and ibuprofen in sanitary sewage using metabolic cosubstrates. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 742:140530. [PMID: 32629260 DOI: 10.1016/j.scitotenv.2020.140530] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 06/23/2020] [Accepted: 06/24/2020] [Indexed: 06/11/2023]
Abstract
Diclofenac (DCF) and ibuprofen (IBU) are widely used anti-inflammatory drugs and are frequently detected in wastewater from Wastewater Treatment Plants and in aquatic environments. In this study, the methanogenic potential (P) of anaerobic sludge subjected to DCF (7.11 ± 0.02 to 44.41 ± 0.05 mg L-1) and IBU (6.11 ± 0.01 to 42.61 ± 0.05 mg L-1), in sanitary sewage, was investigated in batch reactors. Cosubstrates (200 mg L-1 of organic matter) in the form of ethanol, methanol:ethanol and fumarate were tested separately for the removal of drugs. In the DCF assays, P was 6943 ± 121 μmolCH4, 9379 ± 259 μmolCH4, 9897 ± 212 μmolCH4 and 11,530 ± 368 μmolCH4 for control, fumarate, methanol:ethanol and ethanol conditions, respectively. In the IBU assays, under the same conditions, P was 6145 ± 101 μmolCH4, 6947 ± 66 μmolCH4, 8141 ± 191 μmolCH4and 10,583 ± 512 μmolCH4, respectively. Without cosubstrates, drug removal was below 18% for 43.10 ± 0.01 mgDCF L-1 and 43.12 ± 0.03 mgIBU L-1, respectively. Higher P and removal of DCF (28.24 ± 1.10%) and IBU (18.72 ± 1.60%) with ethanol was observed for 43.20 ± 0.01 mgDCF L-1 and 43.42 ± 0.03 mgIBU L-1, respectively. This aspect was better evidenced with DCF due to its molecular structure, a condition that resulted in a higher diversity of bacterial populations. Through the 16S rRNA sequencing, bacteria genera capable of performing aromatic ring cleavage, β-oxidation and oxidation of ethanol and fatty acids were identified. Higher relative abundance (>0.6%) was observed for Smithella, Sulfuricurvum and Synthophus for the Bacteria Domain and Methanosaeta (>79%) for the Archaea Domain. The use of ethanol favored greater mineralization of organic matter and greater methane production, which can directly assist in the metabolic pathways of microorganisms.
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Affiliation(s)
- Caroline F Granatto
- Department of Hydraulics and Sanitation Engineering, São Carlos School of Engineering, University of São Paulo, Ave Trabalhador São-Carlense, No. 400, 13566-590 São Carlos, SP, Brazil..
| | - Guilherme M Grosseli
- Federal University of São Carlos, Washington Luiz Highway, Km 235, 13565-905 São Carlos, SP, Brazil
| | - Isabel K Sakamoto
- Department of Hydraulics and Sanitation Engineering, São Carlos School of Engineering, University of São Paulo, Ave Trabalhador São-Carlense, No. 400, 13566-590 São Carlos, SP, Brazil
| | - Pedro S Fadini
- Federal University of São Carlos, Washington Luiz Highway, Km 235, 13565-905 São Carlos, SP, Brazil
| | - Maria Bernadete A Varesche
- Department of Hydraulics and Sanitation Engineering, São Carlos School of Engineering, University of São Paulo, Ave Trabalhador São-Carlense, No. 400, 13566-590 São Carlos, SP, Brazil..
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38
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Ferro L, Hu YO, Gentili FG, Andersson AF, Funk C. DNA metabarcoding reveals microbial community dynamics in a microalgae-based municipal wastewater treatment open photobioreactor. ALGAL RES 2020. [DOI: 10.1016/j.algal.2020.102043] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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39
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Punyapwar S, Mutnuri S. Diversity and functional annotation of microorganisms in French vertical flow constructed wetland treating greywater. World J Microbiol Biotechnol 2020; 36:148. [PMID: 32909146 DOI: 10.1007/s11274-020-02923-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 09/03/2020] [Indexed: 11/29/2022]
Abstract
Constructed wetlands form a unique ecosystem having plants, soil, microbes in which microorganisms play a vital role in the transformation and degradation of pollutants from wastewater. In the present study, French type two-stage vertical flow constructed wetland (VFCW) was used for the treatment of single household greywater (GW). Pilot-scale VFCW having sand and gravel as the filter substrate was constructed with Canna indica plantation for treating GW. To understand the pollutant removal mechanism in VFCW, microbial diversity and functional annotation was carried out by metagenomics analysis of sequences obtained from illumina platform. Efficiency of VFCW was measured with respect to water quality parameters like COD, BOD5, Total Nitrogen, Nitrate, Nitrite, Ammoniacal-N, ortho-phosphate and TOC from inlet and outlet of system. The removal efficiency was 90%, 93%, 34%, 26%, 89%, 68%, 80%, and 80% for COD, BOD5, Total Nitrogen, Nitrate, Nitrite, Ammoniacal-N, ortho-phosphate and TOC respectively. Microbial diversity was much more diversified and unique in VFCW compared to GW. Metagenomes exhibited Proteobacteria and Bacteroidetes as major phyla in GW whereas Actinobacteria, Proteobacteria, Nitrospirae abundance in VFCW layers. Total of 809 and 695 genus were found in VFCW and GW respectively with minimum abundance of 10 hits. From functional annotation of sequences, VFCW microbes have the potential to transform various aromatic and xenobiotic compounds along with the removal of pollutants present in the form of Carbon, Nitrogen, and Phosphorus. These data reveal French type VFCW can efficiently treat GW and with its own unique, variable habitat VFCW harbours diverse community of microorganisms that transform and degrade the pollutants in GW.
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Affiliation(s)
- Swapnil Punyapwar
- Applied Environmental Biotechnology Laboratory, Birla Institute of Technology & Science Pilani, KK Birla Goa Campus, NH-17-B Bypass Road, Zuarinagar, Sancoale, Goa, 403726, India
| | - Srikanth Mutnuri
- Applied Environmental Biotechnology Laboratory, Birla Institute of Technology & Science Pilani, KK Birla Goa Campus, NH-17-B Bypass Road, Zuarinagar, Sancoale, Goa, 403726, India.
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40
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Royes J, Biou V, Dautin N, Tribet C, Miroux B. Inducible intracellular membranes: molecular aspects and emerging applications. Microb Cell Fact 2020; 19:176. [PMID: 32887610 PMCID: PMC7650269 DOI: 10.1186/s12934-020-01433-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 08/27/2020] [Indexed: 02/08/2023] Open
Abstract
Membrane remodeling and phospholipid biosynthesis are normally tightly regulated to maintain the shape and function of cells. Indeed, different physiological mechanisms ensure a precise coordination between de novo phospholipid biosynthesis and modulation of membrane morphology. Interestingly, the overproduction of certain membrane proteins hijack these regulation networks, leading to the formation of impressive intracellular membrane structures in both prokaryotic and eukaryotic cells. The proteins triggering an abnormal accumulation of membrane structures inside the cells (or membrane proliferation) share two major common features: (1) they promote the formation of highly curved membrane domains and (2) they lead to an enrichment in anionic, cone-shaped phospholipids (cardiolipin or phosphatidic acid) in the newly formed membranes. Taking into account the available examples of membrane proliferation upon protein overproduction, together with the latest biochemical, biophysical and structural data, we explore the relationship between protein synthesis and membrane biogenesis. We propose a mechanism for the formation of these non-physiological intracellular membranes that shares similarities with natural inner membrane structures found in α-proteobacteria, mitochondria and some viruses-infected cells, pointing towards a conserved feature through evolution. We hope that the information discussed in this review will give a better grasp of the biophysical mechanisms behind physiological and induced intracellular membrane proliferation, and inspire new applications, either for academia (high-yield membrane protein production and nanovesicle production) or industry (biofuel production and vaccine preparation).
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Affiliation(s)
- Jorge Royes
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Université de Paris, LBPC-PM, CNRS, UMR7099, 75005, Paris, France. .,Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild pour le Développement de la Recherche Scientifique, 75005, Paris, France. .,Département de Chimie, École Normale Supérieure, PASTEUR, PSL University, CNRS, Sorbonne Université, 24 Rue Lhomond, 75005, Paris, France.
| | - Valérie Biou
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Université de Paris, LBPC-PM, CNRS, UMR7099, 75005, Paris, France.,Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild pour le Développement de la Recherche Scientifique, 75005, Paris, France
| | - Nathalie Dautin
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Université de Paris, LBPC-PM, CNRS, UMR7099, 75005, Paris, France.,Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild pour le Développement de la Recherche Scientifique, 75005, Paris, France
| | - Christophe Tribet
- Département de Chimie, École Normale Supérieure, PASTEUR, PSL University, CNRS, Sorbonne Université, 24 Rue Lhomond, 75005, Paris, France
| | - Bruno Miroux
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Université de Paris, LBPC-PM, CNRS, UMR7099, 75005, Paris, France. .,Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild pour le Développement de la Recherche Scientifique, 75005, Paris, France.
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41
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Cui C, Lin H, Pu W, Guo C, Liu Y, Pei XQ, Wu ZL. Asymmetric Epoxidation and Sulfoxidation Catalyzed by a New Styrene Monooxygenase from Bradyrhizobium. Appl Biochem Biotechnol 2020; 193:65-78. [PMID: 32808246 DOI: 10.1007/s12010-020-03413-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 08/12/2020] [Indexed: 10/23/2022]
Abstract
Asymmetric epoxidation catalyzed with styrene monooxygenase (SMO) is a powerful enzymatic process producing enantiopure styrene epoxide derivatives. To establish a more diversified reservoir of SMOs, a new SMO from Bradyrhizobium sp. ORS 375, named BrSMO, was mined from the database and characterized. BrSMO was constituted of an epoxygenase component of 415 amino acid residues and an NADH-dependent flavin reductase component of 175 residues. BrSMO catalyzed the epoxidation of styrene and 7 more styrene derivatives, yielding the corresponding (S)-epoxides with excellent enantiomeric excesses (95- > 99% ee), with the highest activity achieved for styrene. BrSMO also catalyzed the asymmetric sulfoxidation of 7 sulfides, producing the corresponding (R)-sulfoxides (20-90% ee) with good yields.
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Affiliation(s)
- Can Cui
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hui Lin
- College of Life Sciences, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002, China.
| | - Wei Pu
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chao Guo
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Yan Liu
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Xiao-Qiong Pei
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Zhong-Liu Wu
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
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42
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Nurul AAN, Danish-Daniel AM, Okomoda VT, Asma NA. Microbiota composition of captive bluestreak cleaner wrasse Labroides dimidiatus (Valenciennes, 1839). Appl Microbiol Biotechnol 2020; 104:7391-7407. [PMID: 32676710 DOI: 10.1007/s00253-020-10781-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/02/2020] [Accepted: 07/07/2020] [Indexed: 01/09/2023]
Abstract
The Labroides dimidiatus is one of the most traded marine ornamental fishes worldwide, yet not much is known about the microflora associated with this fish. This study is designed to investigate the bacteria composition associated with captive L. dimidiatus and its surrounding aquarium water. The fish and carriage water were obtained from well-known ornamental fish suppliers in Terengganu Malaysia. Bacteria present on the skin and in the stomach and the aquarium water were enumerated using culture-independent approaches and next-generation sequencing (NGS) technology. A total of 3,238,564 valid reads and 828 total operational taxonomic units (OTUs) were obtained from the three metagenomic libraries using NGS analysis. Of all the 15 phyla identified in this study, Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria were the most prevalent in all samples. Also, 170 families belonging to 36 bacteria classes were identified. Although many of the bacteria families were common in the skin, gut, and aquarium water (39%), about 26% of the families were exclusive to the aquarium water alone. Therefore, any substantial change in the structure and abundance of microbiota (especially pathogenic bacteria) reported in this study may serve as an early sign for disease infection in the species under captivity. KEY POINTS: • Proteobacteria was the most dominant. • The microbiota was either shared or exclusively in samples.
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Affiliation(s)
- Ahmad Ashyikin Noor Nurul
- Faculty of Fisheries and Food Science, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia
| | | | - Victor Tosin Okomoda
- Institute of Tropical Aquaculture and Fisheries, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia.
- Department of Fisheries and Aquaculture, University of Agriculture Makurdi, PMB, 2373, Makurdi, Benue State, Nigeria.
| | - Nur Ariffin Asma
- Faculty of Fisheries and Food Science, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia.
- Institute of Tropical Aquaculture and Fisheries, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia.
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43
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Changes in soil organic carbon fractions and microbial community under rice straw return in Northeast China. Glob Ecol Conserv 2020. [DOI: 10.1016/j.gecco.2020.e00962] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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44
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Gebhardt JT, Thomson KA, Woodworth JC, Dritz SS, Tokach MD, DeRouchey JM, Goodband RD, Jones CK, Cochrane RA, Niederwerder MC, Fernando S, Abbas W, Burkey TE. Effect of dietary medium-chain fatty acids on nursery pig growth performance, fecal microbial composition, and mitigation properties against porcine epidemic diarrhea virus following storage. J Anim Sci 2020; 98:skz358. [PMID: 31758795 PMCID: PMC6978897 DOI: 10.1093/jas/skz358] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 11/21/2019] [Indexed: 12/15/2022] Open
Abstract
An experiment was conducted to evaluate the effect of dietary medium-chain fatty acid (MCFA) addition on nursery pig growth performance, fecal microbial composition, and mitigation of porcine epidemic diarrhea virus (PEDV) following storage. A total of 360 pigs (DNA 400 × 200, Columbus, NE; initially 6.7 ± 0.07 kg) were randomized to pens (5 pigs per pen) on the day of weaning (approximately 20 d of age), allowed a 6-d acclimation, blocked by BW, and randomized to dietary treatment (9 pens per treatment). All MCFA (Sigma-Aldrich, St. Louis, MO) were guaranteed ≥98% purity, including hexanoic (C6:0), octanoic (C8:0), and decanoic (C10:0) acids. Treatment diets were formulated in 2 phases (7 to 11 and 11 to 23 kg BW) and formulated to meet or exceed NRC requirement estimates. Treatments (n = 8) were a dose response including 0%, 0.25%, 0.5%, 1.0%, and 1.5% added MCFA blend (1:1:1 ratio C6:0, C8:0, and C10:0), as well as treatments with individual additions of 0.5% C6:0, C8:0, or C10:0. Fecal samples were collected from pigs fed control and 1.5% MCFA blend diets on days 0 and 14 and analyzed using 16s rDNA sequencing. Following feed manufacture, feed was stored in bags at barn temperature and humidity for 40 d before laboratory inoculation with PEDV. Subsamples of retained feed were inoculated with PEDV to achieve a titer of 104 TCID50/g and separate sample bottles were analyzed on 0 and 3 d post-inoculation (dpi). Overall, ADG and ADFI were increased (linear, P ≤ 0.010) and feed efficiency (G:F) improved (linear, P = 0.004) with increasing MCFA blend. Pigs fed 0.5% C8:0 had greater (P = 0.038) ADG compared with pigs fed the control diet, and G:F was improved (P ≤ 0.024) when pigs were fed 0.5% C6:0, 0.5% C8:0, or 0.5% C10:0 compared with control. An inclusion level × day interaction was observed (quadratic, P = 0.023), where PEDV Ct values increased (quadratic, P = 0.001) on 0 dpi with increasing levels of MCFA blend inclusion and also increased on 3 dpi (linear, P < 0.001). Fecal microbial diversity and composition were similar between control and 1.5% MCFA blend. In summary, the use of MCFA in nursery pig diets improves growth performance, provides residual mitigation activity against PEDV, and does not significantly alter fecal microbial composition.
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Affiliation(s)
- Jordan T Gebhardt
- Department of Animal Sciences and Industry, College of Agriculture, Kansas State University, Manhattan, KS
| | - Katelyn A Thomson
- Department of Animal Sciences and Industry, College of Agriculture, Kansas State University, Manhattan, KS
| | - Jason C Woodworth
- Department of Animal Sciences and Industry, College of Agriculture, Kansas State University, Manhattan, KS
| | - Steve S Dritz
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS
| | - Michael D Tokach
- Department of Animal Sciences and Industry, College of Agriculture, Kansas State University, Manhattan, KS
| | - Joel M DeRouchey
- Department of Animal Sciences and Industry, College of Agriculture, Kansas State University, Manhattan, KS
| | - Robert D Goodband
- Department of Animal Sciences and Industry, College of Agriculture, Kansas State University, Manhattan, KS
| | - Cassandra K Jones
- Department of Animal Sciences and Industry, College of Agriculture, Kansas State University, Manhattan, KS
| | - Roger A Cochrane
- Department of Animal Sciences and Industry, College of Agriculture, Kansas State University, Manhattan, KS
| | - Megan C Niederwerder
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS
| | - Samodha Fernando
- Department of Animal Science, College of Agricultural Sciences and Natural Resources, University of Nebraska, Lincoln, NE
| | - Waseem Abbas
- Department of Animal Science, College of Agricultural Sciences and Natural Resources, University of Nebraska, Lincoln, NE
| | - Thomas E Burkey
- Department of Animal Science, College of Agricultural Sciences and Natural Resources, University of Nebraska, Lincoln, NE
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45
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Influence of Sampling Site and other Environmental Factors on the Bacterial Community Composition of Domestic Washing Machines. Microorganisms 2019; 8:microorganisms8010030. [PMID: 31877898 PMCID: PMC7022543 DOI: 10.3390/microorganisms8010030] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 12/16/2019] [Accepted: 12/20/2019] [Indexed: 12/19/2022] Open
Abstract
Modern, mainly sustainability-driven trends, such as low-temperature washing or bleach-free liquid detergents, facilitate microbial survival of the laundry processes. Favourable growth conditions like humidity, warmth and sufficient nutrients also contribute to microbial colonization of washing machines. Such colonization might lead to negatively perceived staining, corrosion of washing machine parts and surfaces, as well as machine and laundry malodour. In this study, we characterized the bacterial community of 13 domestic washing machines at four different sampling sites (detergent drawer, door seal, sump and fibres collected from the washing solution) using 16S rRNA gene pyrosequencing and statistically analysed associations with environmental and user-dependent factors. Across 50 investigated samples, the bacterial community turned out to be significantly site-dependent with the highest alpha diversity found inside the detergent drawer, followed by sump, textile fibres isolated from the washing solution, and door seal. Surprisingly, out of all other investigated factors only the monthly number of wash cycles at temperatures ≥ 60 °C showed a significant influence on the community structure. A higher number of hot wash cycles per month increased microbial diversity, especially inside the detergent drawer. Potential reasons and the hygienic relevance of this finding need to be assessed in future studies.
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46
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Hira P, Singh P, Pinnaka AK, Korpole S, Lal R. Taxonomically Characterized and Validated Bacterial Species Based on 16S rRNA Gene Sequences from India During the Last Decade. Indian J Microbiol 2019; 60:54-61. [PMID: 32089574 DOI: 10.1007/s12088-019-00845-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 11/27/2019] [Indexed: 12/26/2022] Open
Abstract
Microbial taxonomy dealing with identification and characterization of prokaryotes like bacteria and archaea has always been a major area of research all over the world. Exploring diversity of microbes and description of novel species with different genes and secondary compounds is of utmost importance for better future and sustenance of life. India having an enormous range of ecosystems and diverse species inhabiting these niches is considered to be one of the richest biodiversity regions of the world. During the last decade, with newer methodologies and better technology, the prokaryotic taxonomy from India has extended our inventory of microbial communities in specific niches. However, there still exist some limitations in classifying the microbes from India as compared to that is done world-over. This review enlists the taxonomic description of novel taxa of prokaryotes from India in the past decade. A total of 378 new bacterial species have been classified from different habitats in India in the last ten years and no descriptions of archaeal species is documented till date.
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Affiliation(s)
- Princy Hira
- 1Department of Zoology, Maitreyi College (University of Delhi), Chanakyapuri, New Delhi 110021 India
| | - Priya Singh
- 2Department of Zoology, Acharya Narendra Dev College (University of Delhi), Govindpuri, Kalkaji, New Delhi, 110019 India
| | - Anil Kumar Pinnaka
- 3CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036 India
| | - Suresh Korpole
- 3CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036 India
| | - Rup Lal
- The Energy and Resource Institute, Darbari Seth Block, IHC Complex, Lodhi Road, New Delhi, 110003 India
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Misra P, Maji D, Awasthi A, Pandey SS, Yadav A, Pandey A, Saikia D, Babu CSV, Kalra A. Vulnerability of Soil Microbiome to Monocropping of Medicinal and Aromatic Plants and Its Restoration Through Intercropping and Organic Amendments. Front Microbiol 2019; 10:2604. [PMID: 31803153 PMCID: PMC6877478 DOI: 10.3389/fmicb.2019.02604] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 10/28/2019] [Indexed: 12/22/2022] Open
Abstract
Cultivation of medicinal and aromatic plants (MAPs) is persistently increasing due to excessive demands of naturals. Agricultural land and its microbial diversity are primarily adapted to conventional crops, and introduction of MAP and their continuous monocropping may disturb the ecological stability of soil microbiome. Here, the effect of cultivation of MAPs on soil microbial diversity was studied. The aim of the study is to examine the effects of cultivation of MAPs on the possible shift in soil microbial diversity and to restore such impacts by using organic amendments or intercropping. Terminal restriction fragments polymorphism (TRFLP) and next-generation sequencing (NGS) studies showed that of the various selected MAPs, maximal modulation in the soil microbial diversity patterns was noticed in fields of Mentha arvensis and Artemisia annua, and the traces of essential oil/phytochemicals were detected in bulk and rhizospheric soil. In both Artemisia- and Mentha-cultivated soil, the total operating taxonomic unit (OTU) declined in both bulk and rhizospheric soil in comparison to control (Zea mays), but the bacterial richness of Mentha soil was slightly higher than that of control. However, cultivation of Mentha improved the evenness of the microbial community. The inclusion of crops like Sesbania and Chlorophytum and the application of vermicompost (VC) enhanced the microbial richness and evenness, thereby restoring the soil microbial state shift and resulting in higher productivity in the continuously Mentha cropped field. Our study concludes that long-term cultivation of some MAPs may affect the richness but promote the evenness of microbial diversity. The state shift could be restored to some extent, and crop productivity could be enhanced by the inclusion of selected crops and organic manures in cropping systems.
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Affiliation(s)
- Pooja Misra
- Microbial Technology Department, Central Institute of Medicinal and Aromatic Plants, Council of Scientific and Industrial Research, Lucknow, India
- Academy of Scientific and Innovative Research, Central Institute of Medicinal and Aromatic Plants, Council of Scientific and Industrial Research, Lucknow, India
| | - Deepamala Maji
- Microbial Technology Department, Central Institute of Medicinal and Aromatic Plants, Council of Scientific and Industrial Research, Lucknow, India
| | - Ashutosh Awasthi
- Microbial Technology Department, Central Institute of Medicinal and Aromatic Plants, Council of Scientific and Industrial Research, Lucknow, India
| | - Shiv Shanker Pandey
- Microbial Technology Department, Central Institute of Medicinal and Aromatic Plants, Council of Scientific and Industrial Research, Lucknow, India
| | - Anju Yadav
- Analytical Chemistry Department, Central Institute of Medicinal and Aromatic Plants, Council of Scientific and Industrial Research, Lucknow, India
| | - Alok Pandey
- Microbial Technology Department, Central Institute of Medicinal and Aromatic Plants, Council of Scientific and Industrial Research, Lucknow, India
| | - Dharmendra Saikia
- Department of Molecular Bioprospection, Council of Scientific and Industrial Research, Lucknow, India
| | - C. S. Vivek Babu
- Academy of Scientific and Innovative Research, Central Institute of Medicinal and Aromatic Plants, Council of Scientific and Industrial Research, Lucknow, India
- Central Institute of Medicinal and Aromatic Plants, Research Centre, Council of Scientific and Industrial Research, Bengaluru, India
| | - Alok Kalra
- Microbial Technology Department, Central Institute of Medicinal and Aromatic Plants, Council of Scientific and Industrial Research, Lucknow, India
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Jayanetti DR, Braun DR, Barns KJ, Rajski SR, Bugni TS. Bulbiferates A and B: Antibacterial Acetamidohydroxybenzoates from a Marine Proteobacterium, Microbulbifer sp. JOURNAL OF NATURAL PRODUCTS 2019; 82:1930-1934. [PMID: 31181927 PMCID: PMC6660402 DOI: 10.1021/acs.jnatprod.9b00312] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Here we report the discovery of two new 3-acetamido-4-hydroxybenzoate esters, bulbiferates A (1) and B (2), isolated from Microbulbifer sp. cultivated from the marine tunicate Ecteinascidia turbinata. The structures of 1 and 2 were determined by analysis of 2D NMR and MS data. Additionally, three synthetic analogues (3-5), differing in ester sizes/lengths, were prepared for the purposes of evaluating potential structure-activity relationships; no clear correlations tying ester lengths to activity were evident. Bulbiferates A (1) and B (2) demonstrated antibacterial activity against both Escherichia coli (E. coli) and methicillin-sensitive Staphylococcus aureus (MSSA), whereas the synthetic analogues 3 and 4 displayed activity only against MSSA.
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Affiliation(s)
- Dinith R. Jayanetti
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, Madison, Wisconsin 53705, United States
| | - Doug R. Braun
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, Madison, Wisconsin 53705, United States
| | - Kenneth J. Barns
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, Madison, Wisconsin 53705, United States
| | - Scott Raymond Rajski
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, Madison, Wisconsin 53705, United States
| | - Tim S. Bugni
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, Madison, Wisconsin 53705, United States
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49
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Molecular Biology-Based Analysis of the Interactive Effect of Nickel and Xanthates on Soil Bacterial Community Diversity and Structure. SUSTAINABILITY 2019. [DOI: 10.3390/su11143888] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Metals and mineral flotation collector’s toxicity to the soil living system greatly compromise the sustainability of mining and ore processing. Their effects on the soil microbial community, the most active soil component, remain less understood and addressed particularly with regards to xanthates and their combination with metals. This study analyzed the interactive effects of Ni and xanthates, potassium ethyl xanthate and sodium isopropyl xanthate, on the soil bacterial community through an efficient molecular biology-based technique, the Miseq (Illumina). Both soil microbial community diversity and structure were more affected by xanthates than by Ni. The five most dominant phyla, representing 96.31% of the whole bacterial community, comprised Proteobacteria (54.16%), Firmicutes (17.51%), Actinobacteria (15.59%), Acidobacteria (4.87%), and Chloroflexi (4.16%). Different soil treatments exhibited greater difference in the species abundance/dominance than in the species numbers. Proteobacteria was the most dominant in the presence of xanthates, individually or in mixtures with nickel, while Firmicutes exhibited its highest proportion in the Ni/xanthate-treated samples. The most abundant and proportionally different bacterial species between different treatments were presented. The most abundant bacterial strains identified should be explored more for their potential application in biomining and for the prediction and biologically-based treatment and remediation of Ni and xanthate-contaminated systems.
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50
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Sirois SH, Buckley DH. Factors governing extracellular DNA degradation dynamics in soil. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:173-184. [PMID: 30507072 DOI: 10.1111/1758-2229.12725] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 10/15/2018] [Accepted: 11/23/2018] [Indexed: 05/19/2023]
Abstract
We examined the impacts of soil moisture, temperature, agricultural management and habitat type on the degradation dynamics of eDNA in soils. Synthetic eDNA was added to soil microcosms, and its disappearance over time was measured using both high-throughput sequencing and qPCR. The synthetic eDNA was degraded rapidly, but a small fraction remained detectable throughout the experiments (39-80 days). The eDNA degradation rate was positively correlated with moisture and temperature, but negatively correlated with soil organic carbon content. End-point stabilization of eDNA was highest at low moisture and temperature, but exhibited no relationship with soil organic carbon. Tilled soils had higher rates of degradation and less stabilization than no-till soils. Among different habitats we observed that forest soils had the slowest degradation rate, and meadow soils had the greatest stabilization of eDNA. While eDNA was detectable by qPCR in all treatments across all time-points, it became inconsistently detectable with high-throughput gene sequencing in less than 1 week. We conclude that eDNA degradation and stabilization dynamics vary with moisture, temperature and habitat characteristics, that small amounts of eDNA may persist in soils indefinitely, and that the ability of persistent eDNA to impact microbial community estimates depends on method sensitivity and experimental objectives.
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Affiliation(s)
- Sara Hope Sirois
- Cornell University, Section of Soil and Crop Sciences, Ithaca, NY, USA
| | - Daniel H Buckley
- Cornell University, Section of Soil and Crop Sciences, Ithaca, NY, USA
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