1
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Crow J, Geng H, Schultz D. Short-term evolution of antibiotic responses in highly dynamic environments favors loss of regulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.29.569327. [PMID: 38076825 PMCID: PMC10705423 DOI: 10.1101/2023.11.29.569327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
Abstract
Microbes inhabit natural environments that are remarkably dynamic, with sudden environmental shifts that require immediate action by the cell. To cope with changing environments, microbes are equipped with regulated response mechanisms that are only activated when needed. However, when exposed to extreme environments such as clinical antibiotic treatments, complete loss of regulation is frequently observed. Although recent studies suggest that the initial evolution of microbes in new environments tends to favor mutations in regulatory pathways, it is not clear how this evolution is affected by how quickly conditions change (i.e. dynamics), or which mechanisms are commonly used to implement new regulation. Here, we perform experimental evolution on continuous cultures of E. coli carrying the tetracycline resistance tet operon to identify specific types of mutations that adapt drug responses to different dynamical regimens of drug administration. When cultures are evolved under gradually increasing tetracycline concentrations, we observe no mutations in the tet operon, but a predominance of fine-tuning mutations increasing the affinity of alternative efflux pump AcrB to tetracycline. When cultures are instead periodically exposed to large drug doses, all populations developed transposon insertions in repressor TetR, resulting in loss of regulation of efflux pump TetA. We use a mathematical model of the dynamics of antibiotic responses to show that sudden exposure to large drug concentrations can overwhelm regulated responses, which cannot induce resistance fast enough, resulting in fitness advantage for constitutive expression of resistance. These results help explain the loss of regulation of antibiotic resistance by opportunistic pathogens evolving in clinical environments. Our experiment supports the notion that initial evolution in new ecological niches proceeds largely through regulatory mutations and suggests that transposon insertions are a main mechanism driving this process.
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Affiliation(s)
- John Crow
- Department of Microbiology & Immunology, Dartmouth – Geisel School of Medicine, Hanover, NH, USA
| | - Hao Geng
- Department of Microbiology & Immunology, Dartmouth – Geisel School of Medicine, Hanover, NH, USA
| | - Daniel Schultz
- Department of Microbiology & Immunology, Dartmouth – Geisel School of Medicine, Hanover, NH, USA
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2
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Cutugno L, Mc Cafferty J, Pané-Farré J, O'Byrne C, Boyd A. The Vibrio vulnificus stressosome is dispensable in nutrient-rich media. Access Microbiol 2023; 5:acmi000523.v4. [PMID: 37601438 PMCID: PMC10436020 DOI: 10.1099/acmi.0.000523.v4] [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: 11/18/2022] [Accepted: 05/27/2023] [Indexed: 08/22/2023] Open
Abstract
The stressosome is a protein complex that senses environmental stresses and mediates the stress response in several Gram-positive bacteria through the activation of the alternative sigma factor SigB. The stressosome locus is found in 44 % of Gram-negative Vibrio vulnificus isolates. However, V. vulnificus does not possess SigB. Nonetheless, in nutrient-limited media, the stressosome modulates gene transcription and bacterial behaviour. In this work, the expression of the stressosome genes was proven during stationary phase in nutrient-rich media and co-transcription as one operonic unit of the stressosome locus and its putative downstream regulatory locus was demonstrated. The construction of a stressosome mutant lacking the genes encoding the four proteins constituting the stressosome complex (VvRsbR, VvRsbS, VvRsbT, VvRsbX) allowed us to examine the role of this complex in vivo. Extensive phenotypic characterization of the ΔRSTX mutant in nutrient-rich media showed that the stressosome does not contribute to growth of V. vulnificus . Moreover, the stressosome did not modulate the tolerance or survival response of V. vulnificus to the range of stresses tested, which included ethanol, hyperosmolarity, hypoxia, high temperature, acidity and oxidative stress. Furthermore, the stressosome was dispensable for motility and exoenzyme production of V. vulnificus in nutrient-rich media. Therefore, in conclusion, although stressosome gene transcription occurs in nutrient-rich media, the stressosome neither has an essential role in stress responses of V. vulnificus nor does it seem to modulate these activities in these conditions. We hypothesise that the stressosome is expressed in nutrient-rich conditions as a sensor complex, but that activation of the complex does not occur in this environment.
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Affiliation(s)
- Laura Cutugno
- School of Natural Sciences, University of Galway, Galway, Ireland
| | | | - Jan Pané-Farré
- Centre for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Conor O'Byrne
- School of Biological and Chemical Sciences, University of Galway, Galway, Ireland
| | - Aoife Boyd
- School of Natural Sciences, University of Galway, Galway, Ireland
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3
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Li Y, Ling J, Xue J, Huang J, Zhou X, Wang F, Hou W, Zhao J, Xu Y. Acute stress of the typical disinfectant glutaraldehyde-didecyldimethylammonium bromide (GD) on sludge microecology in livestock wastewater treatment plants: Effect and its mechanisms. WATER RESEARCH 2022; 227:119342. [PMID: 36399842 DOI: 10.1016/j.watres.2022.119342] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 11/01/2022] [Accepted: 11/07/2022] [Indexed: 06/16/2023]
Abstract
Glutaraldehyde and didecyldimethylammonium bromide (GD) is a disinfectant widely used to prevent African swine fever (ASF) in livestock farms. However, the effect of residual GD on the activated sludge microbial ecology of receiving wastewater treatment plants (WWTPs) remains largely unknown. In this study, seven simulated systems were established to research the effects of GD on WWTPs and reveal the underlying mechanisms of microecological responses to GD at different concentrations. Both the nitrogen and carbon removal rates decreased with increasing GD concentrations, and nitrogen metabolism was inhibited more obviously, but the inhibition weakened with increasing stress duration. Microorganisms activated their SoxRS systems to promote ATP synthesis and electron transfer to support the hydrolysis and efflux of GD by producing a small number of ROS when exposed to GD at less than 1 mg/L. The overproduction of ROS led to a decrease of antioxidant and nitrogen removal enzyme activities, and upregulation of the porin gene increased the risk of GD entering the intracellular space upon exposure to GD at concentrations higher than 1 mg/L. Some denitrifiers survived via resistance and their basic capabilities of sugar metabolism and nitrogen assimilation. Notably, low concentrations of disinfectants could promote vertical and horizontal transfer of multiple resistance genes, especially aminoglycosides, among microorganisms, which might increase not only the adaptation capability of denitrifiers but also the risk to ecological systems. Therefore, the risks of disinfectants targeting ASF on ecology and health as well as the effects of disinfectant residuals from the COVID-19 epidemic should receive more attention.
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Affiliation(s)
- Yuxin Li
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou, 510006, China
| | - Jiayin Ling
- School of Environmental and Chemical Engineering, Zhaoqing University, Zhaoqing, 526061, China
| | - Jinghao Xue
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou, 510006, China
| | - Junwei Huang
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou, 510006, China
| | - Xiao Zhou
- Analysis and Test Center, Guangdong University of Technology, Guangzhou, 510006, China
| | - Fei Wang
- Analysis and Test Center, Guangdong University of Technology, Guangzhou, 510006, China
| | - Waner Hou
- Analysis and Test Center, Guangdong University of Technology, Guangzhou, 510006, China
| | - Jianbin Zhao
- Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou, 510006, China
| | - Yanbin Xu
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou, 510006, China; Analysis and Test Center, Guangdong University of Technology, Guangzhou, 510006, China.
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4
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Lenart-Boroń A, Boroń P, Kulik K, Prajsnar J, Żelazny M, Chmiel MJ. Anthropogenic pollution gradient along a mountain river affects bacterial community composition and genera with potential pathogenic species. Sci Rep 2022; 12:18140. [PMID: 36307524 PMCID: PMC9614195 DOI: 10.1038/s41598-022-22642-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 10/18/2022] [Indexed: 12/30/2022] Open
Abstract
Mountain regions in Poland are among the most frequently visited tourist destinations, causing a significant anthropogenic pressure put on the local rivers. In this study, based on numbers of 9 microorganisms, content of 17 antibiotics and 17 physicochemical parameters, we determined a pollution gradient in six sites along Białka, a typical mountain river in southern Poland. The E.coli/Staphylococcus ratio varied evidently between polluted and non-polluted sites, indicating that the possible utility of this parameter in assessing the anthropogenic impact on river ecosystems is worth further investigation. Then, using next generation sequencing, we assessed the changes in bacterial community structure and diversity as a response to the pollution gradient. Proteobacteria and Bacteroidetes were the most abundant phyla in the majority of samples. Actinobacteria were the most abundant in the most pristine (groundwater) sample, while Firmicutes and Verrucomicrobia were more prevalent in polluted sites. Bacterial diversity at various levels increased with water pollution. Eleven bacterial genera potentially containing pathogenic species were detected in the examined samples, among which Acinetobacter, Rhodococcus, and Mycobacterium were the most frequent. At the species level, Acinetobacter johnsonii was most prevalent potential pathogen, detected in all surface water samples, including the pristine ones. Two bacterial taxa-genus Flectobacillus and order Clostridiales showed very distinct variation in the relative abundance between the polluted and non-polluted sites, indicating their possible potential as biomarkers of anthropogenic impact on mountain river waters.
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Affiliation(s)
- Anna Lenart-Boroń
- grid.410701.30000 0001 2150 7124Department of Microbiology and Biomonitoring, Faculty of Agriculture and Economics, University of Agriculture in Kraków, Adam Mickiewicz Ave. 24/28, 30-059 Kraków, Poland
| | - Piotr Boroń
- grid.410701.30000 0001 2150 7124Department of Forest Ecosystems Protection, Faculty of Forestry, University of Agriculture in Kraków, 29 Listopada Ave. 46, 31-425 Kraków, Poland
| | - Klaudia Kulik
- grid.410701.30000 0001 2150 7124Department of Microbiology and Biomonitoring, Faculty of Agriculture and Economics, University of Agriculture in Kraków, Adam Mickiewicz Ave. 24/28, 30-059 Kraków, Poland
| | - Justyna Prajsnar
- grid.413454.30000 0001 1958 0162Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek Str. 8, 30-239 Kraków, Poland
| | - Mirosław Żelazny
- grid.5522.00000 0001 2162 9631Department of Hydrology, Institute of Geography and Spatial Management, Jagiellonian University in Kraków, Gronostajowa Str. 7, 30-387 Kraków, Poland
| | - Maria J. Chmiel
- grid.410701.30000 0001 2150 7124Department of Microbiology and Biomonitoring, Faculty of Agriculture and Economics, University of Agriculture in Kraków, Adam Mickiewicz Ave. 24/28, 30-059 Kraków, Poland
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5
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Marais TS, Huddy RJ, Harrison STL. Elemental sulphur recovery from a sulphate-rich aqueous stream in a single hybrid linear flow channel reactor is mediated through microbial community dynamics and adaptation to reactor zones. FEMS Microbiol Ecol 2022; 98:6763417. [PMID: 36259757 DOI: 10.1093/femsec/fiac059] [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: 11/03/2021] [Revised: 04/20/2022] [Accepted: 10/03/2022] [Indexed: 01/21/2023] Open
Abstract
The coupled application of biological sulphate reduction (BSR) and partial sulphide oxidation to treat sulphate-rich wastewater is an effective strategy to mitigate pollution and recover elemental sulphur for repurposing. The recent development of the hybrid linear flow channel reactor (LFCR) achieves simultaneous BSR and partial sulphide oxidation with biosulphur recovery via a floating sulphur biofilm (FSB). Here, we explore the microbial community zoning and dynamics facilitating the process. A total of three continuous LFCRs were used to evaluate the effect of reactor zones, hydraulic residence time (HRT), carbon source, namely lactate and acetate, as well as reactor geometry and scale on process performance and microbial community dynamics. Community composition of sessile and planktonic microbial consortia were resolved at a 5- and 2-day HRT through 16S rRNA amplicon sequencing. Preferential attachment and prevalence of specific phylotypes within the sessile and planktonic communities revealed clear adaptation of key microorganisms to different microenvironments. Key microbial taxa affiliated with sulphate reduction and sulphide oxidation as well as those implicated in fermentation and syntrophic metabolism, fluctuated in response to changes in HRT and process performance. Through understanding the relationship between microbial community dynamics and process performance, this research will inform better process design and optimization of the hybrid LFCR.
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Affiliation(s)
- T S Marais
- Centre for Bioprocess Engineering Research, Department of Chemical Engineering, University of Cape Town, Private Bag X1, Rondebosch 7701, South Africa.,Future Water Institute, 1 Madiba Circle, University of Cape Town, 7700, South Africa
| | - R J Huddy
- Centre for Bioprocess Engineering Research, Department of Chemical Engineering, University of Cape Town, Private Bag X1, Rondebosch 7701, South Africa.,Future Water Institute, 1 Madiba Circle, University of Cape Town, 7700, South Africa
| | - S T L Harrison
- Centre for Bioprocess Engineering Research, Department of Chemical Engineering, University of Cape Town, Private Bag X1, Rondebosch 7701, South Africa.,Future Water Institute, 1 Madiba Circle, University of Cape Town, 7700, South Africa
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6
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Pan C, Feng Q, Li Y, Li Y, Liu L, Yu X, Ren S. Rare soil bacteria are more responsive in desertification restoration than abundant bacteria. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:33323-33334. [PMID: 35025047 DOI: 10.1007/s11356-021-16830-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 09/27/2021] [Indexed: 06/14/2023]
Abstract
Soil microbes play key roles in ecosystem functions, especially in the recovery of ecosystems from disturbance, and exploring community assembly under changing environments has long been a central theme in microbial ecology. The response of abundant and rare bacteria in desertified land to restoration is still unclear. Here, we investigated the effects of vegetation restoration on the assemblage patterns of abundant and rare bacteria in soil across the four sandy lands (Hulunbeir, Horqin, Otindag, and Mu Us) in northern China. Our results revealed that abundant bacteria maintained a relatively stable state under restoration, whereas rare taxa were more responsive, indicating the higher resilience of the rare community to change. Our network analysis also showed that restoration promoted destabilizing properties in rare, but not in abundant, bacterial co-occurrence networks in soil. Environmental selection played a key role in abundant and rare community assembly under restoration. Of the two, the rare subcommunity was mainly affected by environmental filtering. The variations in the abundant and rare communities at the sampling sites under restoration were controlled mainly by plant species richness, and stronger effects were observed in the rare taxa. Overall, these results provide new insight into the mechanisms controlling bacterial community assembly in response to vegetation restoration.
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Affiliation(s)
- Chengchen Pan
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, Gansu, China
- Qilian Mountains Eco-Environment Research Center, Lanzhou, 730000, Gansu, China
| | - Qi Feng
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, Gansu, China.
- Qilian Mountains Eco-Environment Research Center, Lanzhou, 730000, Gansu, China.
| | - Yulin Li
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, Gansu, China
| | - Yuqiang Li
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, Gansu, China
| | - Linde Liu
- College of Life Sciences, Ludong University, Yantai, 264025, Shandong, China.
| | - Xiaoya Yu
- School of Tourism and Resource Environment, Qiannan Normal University for Nationalities, Duyun, 558000, Guizhou, China
| | - Shilong Ren
- Environmental Research Institute, Shandong University, Qingdao, 266237, Shandong, China
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7
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Choi A, Lee TK, Cho H, Lee WC, Hyun JH. Shifts in benthic bacterial communities associated with farming stages and a microbiological proxy for assessing sulfidic sediment conditions at fish farms. MARINE POLLUTION BULLETIN 2022; 178:113603. [PMID: 35390629 DOI: 10.1016/j.marpolbul.2022.113603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 02/22/2022] [Accepted: 03/20/2022] [Indexed: 06/14/2023]
Abstract
To assess the aquaculture-induced sediment conditions associated with sulfur cycles, shifts in bacterial communities across farming stages were investigated. The sulfate reduction rate (SRR), and concentrations of acid volatile sulfide (AVS) and H2S were significantly higher at the mid- and post-farming stages than at the early stage, indicating that the aquaculture effects persist even after harvest. Incomplete organic carbon-oxidizing sulfate-reducing bacteria (IO-SRB) affiliated with Desulfobulbaceae, and gammaproteobacterial sulfur oxidizing bacteria (SOB) (Thiohalobacter, Thioprofundum, and Thiohalomonas) were dominant during the early stage, whereas fermenting bacteria (Bacteroidetes and Firmicutes) and complete oxidizing SRB (CO-SRB) belonging to Desulfobacteraceae, and epsilonproteobacterial SOB (Sulfurovum) dominated during the mid- and post-stages. The shift in SRB and SOB communities well reflected the anoxic and sulfidic conditions of farm sediment. Especially, the Sulfurovum-like SOB correlated highly and positively with H2S, AVS, and SRR, suggesting that they could be relevant microbiological proxies to assess sulfidic conditions in farm sediment.
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Affiliation(s)
- Ayeon Choi
- Department of Marine Science and Convergence Technology, Hanyang University, 55 Hanyangdaehak-ro, Sangnok-gu, Ansan, Gyeonggi-do 15588, South Korea; Marine Biotechnology Research Center, Korean Institute of Ocean Science & Technology (KIOST), 385 Haeyang-ro, Yeongdo-gu, Busan Metropolitan City, South Korea
| | - Tae Kwon Lee
- Department of Environmental Engineering, Yonsei University,1Yonseidae-gil, Wonju, Gangwon-do 26493, South Korea
| | - Hyeyoun Cho
- Department of Marine Science and Convergence Technology, Hanyang University, 55 Hanyangdaehak-ro, Sangnok-gu, Ansan, Gyeonggi-do 15588, South Korea
| | - Won-Chan Lee
- Marine Environment Research Division, National Institute of Fisheries Science (NIFS), Busan 46083, South Korea
| | - Jung-Ho Hyun
- Department of Marine Science and Convergence Technology, Hanyang University, 55 Hanyangdaehak-ro, Sangnok-gu, Ansan, Gyeonggi-do 15588, South Korea.
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8
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Bi S, Lai H, Guo D, Liu X, Wang G, Chen X, Liu S, Yi H, Su Y, Li G. Spatio-temporal variation of bacterioplankton community structure in the Pearl River: impacts of artificial fishery habitat and physicochemical factors. BMC Ecol Evol 2022; 22:10. [PMID: 35114951 PMCID: PMC8812236 DOI: 10.1186/s12862-022-01965-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 01/22/2022] [Indexed: 11/30/2022] Open
Abstract
Background Artificial fishery habitat has been widely used in fishery resource protection and water habitat restoration. Although the bacterioplankton plays an important ecological role in fisheries ecosystems, the effect of artificial fishery habitat on bacterioplankton is not clear. In this study, high-throughput sequencing based on the 16S rRNA gene was carried out to study the characteristics of bacterioplankton community structure in artificial fishery habitat and to determine the principal environmental factors that shaped the composition, structure and function of bacterioplankton communities in an unfed aquaculture system. Results The results indicated that the most dominant phyla were Proteobacteria (Alphaproteobacteria and Gammaproteobacteria), Actinobacteria, Cyanobacteria, and Bacteroidetes, which accounted for 28.61%, 28.37%, 19.79%, and 10.25% of the total abundance, respectively. The factors that cause the differences in bacterioplankton community were mainly manifested in three aspects, including the diversity of the community, the role of artificial fishery habitat, and the change of environmental factors. The alpha diversity analysis showed that the diversity and richness index of the bacterioplankton communities were the highest in summer, which indicated that the seasonal variation characteristics had a great influence on it. The CCA analysis identified that the dissolved oxygen, temperature, and ammonium salt were the dominant environmental factors in an unfed aquaculture system. The LEfSe analysis founded 37 indicator species in artificial structure areas (AS group), only 9 kinds existing in the control areas of the open-water group (CW group). Meanwhile, the KEGG function prediction analysis showed that the genes which were related to metabolism in group AS were significantly enhanced. Conclusions This study can provide reference value for the effect of artificial habitat on bacterioplankton community and provide fundamental information for the follow-up study of ecological benefits of artificial fishery habitat. It may be contributed to apply artificial fishery habitat in more rivers. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-022-01965-3.
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Affiliation(s)
- Sheng Bi
- State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.,School of Agriculture, Sun Yat-Sen University, Guangzhou, China.,Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, 510006, China
| | - Han Lai
- State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.,Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, 510006, China
| | - Dingli Guo
- State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.,Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, 510006, China
| | - Xuange Liu
- State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.,Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, 510006, China
| | - Gongpei Wang
- State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.,Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, 510006, China.,Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Xiaoli Chen
- State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.,Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, 510006, China
| | - Shuang Liu
- State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.,Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, 510006, China
| | - Huadong Yi
- State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.,Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, 510006, China
| | - Yuqin Su
- State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.,Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, 510006, China
| | - Guifeng Li
- State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China. .,Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, 510006, China. .,School of Life Sciences, Institute of Aquatic Economic Animals, Sun Yat-Sen University, No. 132, East Outer Ring Road, Guangzhou, 510006, China.
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9
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Ye Z, Li S, Hennigan JN, Lebeau J, Moreb EA, Wolf J, Lynch MD. Two-stage dynamic deregulation of metabolism improves process robustness & scalability in engineered E. coli. Metab Eng 2021; 68:106-118. [PMID: 34600151 DOI: 10.1016/j.ymben.2021.09.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 08/12/2021] [Accepted: 09/25/2021] [Indexed: 10/20/2022]
Abstract
We report that two-stage dynamic control improves bioprocess robustness as a result of the dynamic deregulation of central metabolism. Dynamic control is implemented during stationary phase using combinations of CRISPR interference and controlled proteolysis to reduce levels of central metabolic enzymes. Reducing the levels of key enzymes alters metabolite pools resulting in deregulation of the metabolic network. Deregulated networks are less sensitive to environmental conditions improving process robustness. Process robustness in turn leads to predictable scalability, minimizing the need for traditional process optimization. We validate process robustness and scalability of strains and bioprocesses synthesizing the important industrial chemicals alanine, citramalate and xylitol. Predictive high throughput approaches that translate to larger scales are critical for metabolic engineering programs to truly take advantage of the rapidly increasing throughput and decreasing costs of synthetic biology.
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Affiliation(s)
- Zhixia Ye
- Department of Biomedical Engineering, Duke University, Durham, NC, USA; DMC Biotechnologies, Inc., Durham, NC, USA
| | - Shuai Li
- Department of Chemistry, Duke University, Durham, NC, USA
| | | | - Juliana Lebeau
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Eirik A Moreb
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Jacob Wolf
- DMC Biotechnologies, Inc., Boulder, CO, USA
| | - Michael D Lynch
- Department of Biomedical Engineering, Duke University, Durham, NC, USA.
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10
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Ritson JP, Alderson DM, Robinson CH, Burkitt AE, Heinemeyer A, Stimson AG, Gallego-Sala A, Harris A, Quillet A, Malik AA, Cole B, Robroek BJM, Heppell CM, Rivett DW, Chandler DM, Elliott DR, Shuttleworth EL, Lilleskov E, Cox F, Clay GD, Diack I, Rowson J, Pratscher J, Lloyd JR, Walker JS, Belyea LR, Dumont MG, Longden M, Bell NGA, Artz RRE, Bardgett RD, Griffiths RI, Andersen R, Chadburn SE, Hutchinson SM, Page SE, Thom T, Burn W, Evans MG. Towards a microbial process-based understanding of the resilience of peatland ecosystem service provisioning - A research agenda. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 759:143467. [PMID: 33199011 DOI: 10.1016/j.scitotenv.2020.143467] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/12/2020] [Accepted: 10/24/2020] [Indexed: 06/11/2023]
Abstract
Peatlands are wetland ecosystems with great significance as natural habitats and as major global carbon stores. They have been subject to widespread exploitation and degradation with resulting losses in characteristic biota and ecosystem functions such as climate regulation. More recently, large-scale programmes have been established to restore peatland ecosystems and the various services they provide to society. Despite significant progress in peatland science and restoration practice, we lack a process-based understanding of how soil microbiota influence peatland functioning and mediate the resilience and recovery of ecosystem services, to perturbations associated with land use and climate change. We argue that there is a need to: in the short-term, characterise peatland microbial communities across a range of spatial and temporal scales and develop an improved understanding of the links between peatland habitat, ecological functions and microbial processes; in the medium term, define what a successfully restored 'target' peatland microbiome looks like for key carbon cycle related ecosystem services and develop microbial-based monitoring tools for assessing restoration needs; and in the longer term, to use this knowledge to influence restoration practices and assess progress on the trajectory towards 'intact' peatland status. Rapid advances in genetic characterisation of the structure and functions of microbial communities offer the potential for transformative progress in these areas, but the scale and speed of methodological and conceptual advances in studying ecosystem functions is a challenge for peatland scientists. Advances in this area require multidisciplinary collaborations between peatland scientists, data scientists and microbiologists and ultimately, collaboration with the modelling community. Developing a process-based understanding of the resilience and recovery of peatlands to perturbations, such as climate extremes, fires, and drainage, will be key to meeting climate targets and delivering ecosystem services cost effectively.
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Affiliation(s)
- Jonathan P Ritson
- School of Environment Education and Development, The University of Manchester, Oxford Road, Manchester M13 9PL, UK.
| | - Danielle M Alderson
- School of Environment Education and Development, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Clare H Robinson
- Department of Earth & Environmental Sciences, The University of Manchester, Williamson Building, Oxford Road, Manchester M13 9PL, UK
| | | | - Andreas Heinemeyer
- Stockholm Environment Institute, Department of Environment & Geography, York YO10 5NG, UK
| | - Andrew G Stimson
- North Pennines AONB Partnership, Weardale Business Centre, The Old Co-op building, 1 Martin Street, Stanhope, County Durham DL13 2UY, UK
| | - Angela Gallego-Sala
- Department of Geography, University of Exeter, Laver, North Park Road, Exeter EX4 4QE, UK
| | - Angela Harris
- Department of Geography, The University of Manchester, Manchester M13 9PL, UK
| | - Anne Quillet
- Department of Geography and Environmental Science, University of Reading, Whiteknights RG6 6AB, UK
| | - Ashish A Malik
- School of Biological Sciences, University of Aberdeen, Aberdeen AB24 3UU, UK
| | - Beth Cole
- School of Geography, Geology and the Environment, University of Leicester, LE1 7RH, UK
| | - Bjorn J M Robroek
- Dept. of Aquatic Ecology & Environmental Biology, Institute for Water and Wetlands Research, Radboud University, Nijmegen, the Netherlands
| | - Catherine M Heppell
- School of Geography, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Damian W Rivett
- Department of Natural Sciences, Manchester Metropolitan University, Manchester, UK
| | - Dave M Chandler
- Moors for the Future Partnership, The Moorland Centre, Fieldhead, Edale, Derbyshire S33 7ZA, UK
| | - David R Elliott
- Environmental Sustainability Research Centre, University of Derby, Derby DE22 1GB, UK
| | - Emma L Shuttleworth
- School of Environment Education and Development, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Erik Lilleskov
- USDA Forest Service, Northern Research Station, Houghton, MI 49931, USA
| | - Filipa Cox
- Department of Earth and Environmental Sciences, University of Manchester, M13 9PL, UK
| | - Gareth D Clay
- School of Environment Education and Development, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Iain Diack
- Natural England, Parkside Court, Hall Park Way, Telford, Shropshire TF3 4LR, UK
| | - James Rowson
- Department of Geography and Geology, Edge Hill University, St Helens Road, Ormskirk Lancs L39 4QP, UK
| | - Jennifer Pratscher
- School of Energy, Geoscience, Infrastructure and Society, The Lyell Centre, Heriot-Watt University, Edinburgh EH14 4AP, UK
| | - Jonathan R Lloyd
- Department of Earth & Environmental Sciences, The University of Manchester, Williamson Building, Oxford Road, Manchester M13 9PL, UK
| | | | - Lisa R Belyea
- School of Geography, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Marc G Dumont
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Mike Longden
- Lancashire Wildlife Trust, 499-511 Bury new road, Bolton Bl2 6DH, UK
| | - Nicholle G A Bell
- School of Chemistry, University of Edinburgh, King's Buildings, David Brewster Road, Edinburgh EH93FJ, UK
| | - Rebekka R E Artz
- Ecological Sciences, The James Hutton Institute, Craigiebuckler, Aberdeen AB15 8QH, UK
| | - Richard D Bardgett
- Department of Earth and Environmental Sciences, The University of Manchester, Manchester M13 9PT, UK
| | | | - Roxane Andersen
- Environmental Research Institute, University of the Highlands and Islands, Castle St., Thurso KW14 7JD, UK
| | - Sarah E Chadburn
- College of Engineering, Mathematics and Physical Sciences, University of Exeter, Stocker Road, Exeter EX4 4PY, UK
| | - Simon M Hutchinson
- School of Science, Engineering and Environment, University of Salford, Salford M5 4WT, UK
| | - Susan E Page
- School of Geography, Geology and the Environment, University of Leicester, LE1 7RH, UK
| | - Tim Thom
- Yorkshire Peat Partnership, Yorkshire Wildlife Trust, Unit 23, Skipton Auction Mart, Gargrave Road, Skipton, North Yorkshire BD23 1UD, UK
| | - William Burn
- Stockholm Environment Institute, Department of Environment & Geography, York YO10 5NG, UK
| | - Martin G Evans
- School of Environment Education and Development, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
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Zhang X, Qi L, Li W, Hu BX, Dai Z. Bacterial community variations with salinity in the saltwater-intruded estuarine aquifer. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 755:142423. [PMID: 33017763 DOI: 10.1016/j.scitotenv.2020.142423] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 08/31/2020] [Accepted: 09/14/2020] [Indexed: 06/11/2023]
Abstract
Bacterial community has been significantly enrolled in the biogeochemical cycling of the coastal subsurface ecosystem. The bacterial community variations with salinity have been extensively investigated in the surface environment, such as lake, soil, and estuary, but not in the subsurface environment. Here we explore the responses of bacterial populations to the salinity and other environmental factors (EFs) by considering both the abundant and rare sub-community in a coastal Holocene groundwater system. Our study results indicate that the bacterial diversity was independent of the salinity in both the abundance and rare sub-community. Besides diversity, no flourishing of abundant bacteria relative abundance is observed with increasing or decreasing salinity. Yet the rare taxa exhibit a bio-growth with salinity, which has a significant correlation (p < 0.001) with sulfate concentration. The responses of the abundant sub-community taxa to nutrients, temperature, pH, and dissolved oxygen are insensitive. However, the correlation between δ18O, δD and the entire community diversity is significant, which demonstrates the bacterial community is affected by the groundwater origin. Besides, not all the species in one class or order are necessarily shaped by the same factor. To quantify the impact of EFs on the community properties, analyses in different taxonomic levels is suggested. These findings imply that the spatial organization of microbial communities is complicated and influenced by multiple factors on a regional scale. The investigated results are useful for understanding biogeochemical processes in the coastal groundwater.
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Affiliation(s)
- Xiaoying Zhang
- College of Construction Engineering, Jilin University, Changchun 130026, China
| | - Linlin Qi
- College of Construction Engineering, Jilin University, Changchun 130026, China
| | - Wenming Li
- Xi'an Center of China Geological Survey, Xi'an 710054, China
| | - Bill X Hu
- Institute of Groundwater and Earth Sciences, Jinan University, Guangdong 510632, China.
| | - Zhenxue Dai
- College of Construction Engineering, Jilin University, Changchun 130026, China.
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12
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Carratalà A, Bachmann V, Julian TR, Kohn T. Adaptation of Human Enterovirus to Warm Environments Leads to Resistance against Chlorine Disinfection. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:11292-11300. [PMID: 32875801 DOI: 10.1021/acs.est.0c03199] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Sunlight, temperature, and microbial grazing are among the environmental factors promoting the inactivation of viral pathogens in surface waters. Globally, these factors vary across time and space. The persistence of viral pathogens, and ultimately their ecology and dispersion, hinges on their ability to withstand the environmental conditions encountered. To understand how virus populations evolve under changing environmental conditions, we experimentally adapted echovirus 11 (E11) to four climate regimes. Specifically, we incubated E11 in lake water at 10 and 30 °C and in the presence and absence of sunlight. Temperature was the main driver of adaptation, resulting in an increased thermotolerance of the 30 °C adapted populations, whereas the 10 °C adapted strains were rapidly inactivated at higher temperatures. This finding is consistent with a source-sink model in which strains emerging in warm climates can persist in temperate regions, but not vice versa. A microbial risk assessment revealed that the enhanced thermotolerance increases the length of time in which there is an elevated probability of illness associated with swimming in contaminated water. Notably, 30 °C-adapted viruses also exhibited an increased tolerance toward disinfection by free chlorine. Viruses adapting to warm environments may thus become harder to eliminate by common disinfection strategies.
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Affiliation(s)
- Anna Carratalà
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering (ENAC), École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Virginie Bachmann
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering (ENAC), École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Timothy R Julian
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf8600, Switzerland
- Swiss Tropical and Public Health Institute, Basel 4051, Switzerland
- University of Basel, Basel 4051, Switzerland
| | - Tamar Kohn
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering (ENAC), École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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13
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Kim S, Kim JH, Lim JH, Jeong JH, Heo JM, Kim IN. Distribution and Control of Bacterial Community Composition in Marian Cove Surface Waters, King George Island, Antarctica during the Summer of 2018. Microorganisms 2020; 8:microorganisms8081115. [PMID: 32722258 PMCID: PMC7464920 DOI: 10.3390/microorganisms8081115] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 07/14/2020] [Accepted: 07/21/2020] [Indexed: 11/16/2022] Open
Abstract
Marian Cove is experiencing some of the most rapid environmental changes in the Antarctic region; however, little is known about the response of bacterial communities to these changes. The main purpose of this study was to investigate the spatial variation of physical‒biogeochemical‒bacterial community features in the Marian Cove surface waters and the environmental parameters governing the spatial variation in the bacterial community composition during the summer of 2018. The Marian Cove surface waters are largely composed of two different characteristics of water masses: relatively low-temperature, -salinity, and -nutrient surface glacier water (named SGW) and relatively high-temperature, -salinity, and -nutrient surface Maxwell Bay water (named SMBW). The SGW bacterial communities were dominated by unclassified Cryomorphaceae, Sedimenticola, and Salibacter genera, while the SMBW bacterial communities were dominated by Sulfitobacter, Arcobacter, and Odoribacter genera. Spatial variations in bacterial community composition were mainly attributed to physical and biogeochemical characteristics, suggesting that the bacterial community composition of the Marian Cove surface waters is mainly determined by environmental characteristics. These findings provide a foundation to improve the understanding of bacterial community variations in response to a rapidly changing Marian Cove in the Antarctic.
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Affiliation(s)
- Soyeon Kim
- Department of Marine Science, Incheon National University, Incheon 22012, Korea; (S.K.); (J.-M.H.)
| | - Ju-Hyoung Kim
- Faculty of Marine Applied Biosciences, Kunsan National University, Gunsan 54150, Korea
- Correspondence: (J.-H.K.); (I.-N.K.)
| | - Jae-Hyun Lim
- Fisheries Resources and Environmental Research Division, East Sea Fisheries Research Institute, National Institute of Fisheries Science, Gangneung 25435, Korea;
| | - Jin-Hyun Jeong
- Korea National Ocean Science Museum, Uljin 36315, Korea;
| | - Jang-Mu Heo
- Department of Marine Science, Incheon National University, Incheon 22012, Korea; (S.K.); (J.-M.H.)
| | - Il-Nam Kim
- Department of Marine Science, Incheon National University, Incheon 22012, Korea; (S.K.); (J.-M.H.)
- Correspondence: (J.-H.K.); (I.-N.K.)
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14
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Bacterial community composition and potential pathogens along the Pinheiros River in the southeast of Brazil. Sci Rep 2020; 10:9331. [PMID: 32518363 PMCID: PMC7283273 DOI: 10.1038/s41598-020-66386-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 05/07/2020] [Indexed: 11/08/2022] Open
Abstract
The Pinheiros River in São Paulo, Brazil, crosses through the capital city and has its confluence with the River Tiete, which comprises several reservoirs along its course. Although Pinheiros River is considered one of the heaviest polluted rivers in Brazil, little is known about its bacterial composition, their metabolic functions or how these communities are affected by the physicochemical parameters of the river. In this study, we used the 16S rRNA gene Illumina MiSeq sequencing to profile the bacterial community from the water surface at 11 points along the course of the River. Taxonomical composition revealed an abundance of Proteobacteria phyla, followed by Firmicutes and Bacteroidetes, with a total of 233 classified bacterial families and 558 known bacterial genera. Among the 35 potentially pathogenic bacteria identified, Arcobacter was the most predominant genus. The disrupted physicochemical parameters detected in this study may possibly contribute to the composition and distribution of the bacterial community in the Pinheiros River. Predictive functional analysis suggests the River is abundant in motility genes, including bacterial chemotaxis and flagellar assembly. These results provide novel and detailed insights into the bacterial communities and putative function of the surface water in the Pinheiros River.
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15
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Huang L, Bai J, Wen X, Zhang G, Zhang C, Cui B, Liu X. Microbial resistance and resilience in response to environmental changes under the higher intensity of human activities than global average level. GLOBAL CHANGE BIOLOGY 2020; 26:2377-2389. [PMID: 31943531 DOI: 10.1111/gcb.14995] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 11/20/2019] [Accepted: 12/17/2019] [Indexed: 06/10/2023]
Abstract
With the increasing intensity of global human activities, the ecosystem function, which is supported by the microbial community, will be dramatically changed and impaired. To investigate microbial resistance and resilience of microbial communities to human activities, we chose two typical types of human disturbances, urbanization, and reclamation under the higher intensity of human activities than the global average level. We examined microbial traits, including the abundance, diversity, phylogeny, and co-occurrence interactions in soil microbial communities, together with the nitrification activities observed in the subtropical coastal ecosystem of the Pearl River Estuary and in soil microcosm experiments. Microbial communities were less resistant to the environmental changes caused by urbanization than to those caused by reclamation, which was significantly reflected in the nitrogen and/or carbon-related patterns. However, most of the microbial traits could be recovered almost to the original level without significant differences in the microcosm after 40 days of incubation. The co-occurrence interactions between nitrifiers and other microbial communities were dramatically changed and could not be completely recovered, but this change did not affect their nitrification activities for balancing the ammonium in the soil to the original level during the recovery stage, suggesting that the interactions between microbial communities might have fewer effects on their activities than previously thought. This study quantitatively demonstrated that microbial communities as a whole can recover to a status similar to the original state in a short time after the removal of stress at a large ecosystem scale even under the higher intensity of human activities than global average level in coastal ecosystems, which implied a strong recovery capacity of soil microbial community even after intense human disturbance.
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Affiliation(s)
- Laibin Huang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Junhong Bai
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Xiaojun Wen
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Guangliang Zhang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Chengdong Zhang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Baoshan Cui
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Xinhui Liu
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
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16
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Soil Microbiota of Dystric Cambisol in the High Tatra Mountains (Slovakia) after Windthrow. SUSTAINABILITY 2019. [DOI: 10.3390/su11236851] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
There has been much more damage to forests in the Slovak Republic in the second half of the 20th century than to other European countries. Forested mountain massifs have become a filter of industrial and transportation emissions from abroad, as well as from domestic origins. There are not only acidic deposits of sulphur and heavy metals present in forest soils, but other additional environmental problems, such as climate change, storms, fires, floods, droughts, are worsening the situation. Therefore, forest terrestrial ecosystems are becoming more vulnerable due to changes in natural and environmental conditions. In the High Tatra Mountains in Slovakia, which are protected as a national park, four internationally monitored localities were established after the windthrow disaster in 2004 and fire in 2005: REF, with intact forest; EXT, with extracted wood mass; NEX, with non-extracted wood mass; and FIR, the burnt locality. Soils from these localities were microbiologically analysed with special attention to fungi. Bacterial microbiota detected by high-throughput sequencing showed the prevalence of the genera Acidothermus, Mycobacterium, and Nocardia, and a very low presence of the genera Acidibacter, Burkholderia-Paraburkholderia, Optitus and the uncultured genus Desulfurellaceae H16 in the soil sample from the burnt locality when compared with the unburned sites. Additionally, soil mycocoenoses showed a low similarity between the locality with an intact forest ecosystem and the localities with extracted (REF–EXT) and non-extracted (REF–NEX) wood mass. There was no similarity with the burnt locality (FIR), where heat-resistant fungi dominated. It was shown that the windthrow disaster and subsequent extraction or non-extraction of wood mass did not affect the soil microbial communities or their development. On the other hand, the influence of fire was significant.
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17
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Tobias-Hünefeldt SP, Wing SR, Espinel-Velasco N, Baltar F, Morales SE. Depth and location influence prokaryotic and eukaryotic microbial community structure in New Zealand fjords. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 693:133507. [PMID: 31377366 DOI: 10.1016/j.scitotenv.2019.07.313] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 07/19/2019] [Accepted: 07/19/2019] [Indexed: 06/10/2023]
Abstract
Systems with strong horizontal and vertical gradients, such as fjords, are useful models for studying environmental forcing. Here we examine microbial (prokaryotic and eukaryotic) community changes associated with the surface low salinity layer (LSL) and underlying seawater in multiple fjords in Fiordland National Park (New Zealand). High rainfall (1200-8000 mm annually) and linked runoff from native forested catchments results in surface LSLs with high tannin concentrations within each fjord. These gradients are expected to drive changes in microbial communities. We used amplicon sequencing (16S and 18S) to assess the impact of these gradients on microbial communities and identified depth linked changes in diversity and community structure. With increasing depth, we observed significant increases in Proteobacteria (15%) and SAR (37%), decreases in Opisthokonta (35%), and transiently increased Bacteroidetes (3% increase from 0 to 40 m, decreasing by 8% at 200 m). Community structure differences were observed along a transect from the head to the mouth, specifically 25% mean relative abundance decreases in Opisthokonta and Bacteroidetes, and increases in SAR (25%) and Proteobacteria (>5%) at the surface, indicating changes based on distance from the ocean. This provides the first in-depth view into the ecological drivers of microbial communities within New Zealand fjords.
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Affiliation(s)
- Sven P Tobias-Hünefeldt
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Stephen R Wing
- Department of Marine Science, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | | | - Federico Baltar
- Department of Marine Science, University of Otago, PO Box 56, Dunedin 9054, New Zealand; Department of Limnology and Oceanography, Division of Bio-Oceanography, University of Vienna, Althanstrasse 14, A-1090 Vienna, Austria.
| | - Sergio E Morales
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand.
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18
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Shen M, Li Q, Ren M, Lin Y, Wang J, Chen L, Li T, Zhao J. Trophic Status Is Associated With Community Structure and Metabolic Potential of Planktonic Microbiota in Plateau Lakes. Front Microbiol 2019; 10:2560. [PMID: 31787952 PMCID: PMC6853845 DOI: 10.3389/fmicb.2019.02560] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 10/23/2019] [Indexed: 12/22/2022] Open
Abstract
Microbes in various aquatic ecosystems play a key role in global energy fluxes and biogeochemical processes. However, the detailed patterns on the functional structure and the metabolic potential of microbial communities in freshwater lakes with different trophic status remain to be understood. We employed a metagenomics workflow to analyze the correlations between trophic status and planktonic microbiota in freshwater lakes on Yun-Gui Plateau, China. Our results revealed that microbial communities in the eutrophic and mesotrophic-oligotrophic lake ecosystems harbor distinct community structure and metabolic potential. Cyanobacteria were dominant in the eutrophic ecosystems, mainly driving the processes of aerobic respiration, fermentation, nitrogen assimilation, nitrogen mineralization, assimilatory sulfate reduction and sulfur mineralization in this ecosystem group. Actinobacteria, Proteobacteria (Alpha-, Beta-, and Gammaproteobacteria), Verrucomicrobia and Planctomycetes, occurred more often in the mesotrophic-oligotrophic ecosystems than those in the eutrophic ecosystems, and these taxa potentially mediate the above metabolic processes. In these two groups of ecosystems, a difference in the abundance of functional genes involved in carbohydrate metabolism, energy metabolism, glycan biosynthesis and metabolism, and metabolism of cofactors and vitamins significantly contribute to the distinct functional structure of microbiota from surface water. Furthermore, the microbe-mediated metabolic potentials for carbon, nitrogen and sulfur transformation showed differences in the two ecosystem groups. Compared with the mesotrophic-oligotrophic ecosystems, planktonic microbial communities in the eutrophic ecosystems showed higher potential for aerobic carbon fixation, fermentation, methanogenesis, anammox, denitrification, and sulfur mineralization, but they showed lower potential for aerobic respiration, CO oxidation, nitrogen fixation, and assimilatory sulfate reduction. This study offers insights into the relationships of trophic status to planktonic microbial community structure and its metabolic potential, and identifies the main taxa responsible for the biogeochemical cycles of carbon, nitrogen and sulfur in freshwater lake environments.
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Affiliation(s)
- Mengyuan Shen
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Qi Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Minglei Ren
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Yan Lin
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Juanping Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Li Chen
- Yunnan Key Laboratory of Plateau Geographical Processes and Environment Change, School of Tourism and Geography, Yunnan Normal University, Kunming, China
| | - Tao Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Jindong Zhao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Protein and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing, China
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19
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Amado AM, Roland F. Editorial: Microbial Role in the Carbon Cycle in Tropical Inland Aquatic Ecosystems. Front Microbiol 2017; 8:20. [PMID: 28154556 PMCID: PMC5243796 DOI: 10.3389/fmicb.2017.00020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 01/04/2017] [Indexed: 11/13/2022] Open
Affiliation(s)
- André M Amado
- Limnology Laboratory, Department of Oceanography and Limnology, Universidade Federal do Rio Grande do NorteRio Grande do Norte, Brazil; Aquatic Ecology Laboratory, Department of Biology, Universidade Federal de Juiz de ForaMinas Gerais, Brazil
| | - Fábio Roland
- Aquatic Ecology Laboratory, Department of Biology, Universidade Federal de Juiz de Fora Minas Gerais, Brazil
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20
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Singh JS, Koushal S, Kumar A, Vimal SR, Gupta VK. Book Review: Microbial Inoculants in Sustainable Agricultural Productivity- Vol. II: Functional Application. Front Microbiol 2016. [PMCID: PMC5179502 DOI: 10.3389/fmicb.2016.02105] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Jay Shankar Singh
- Department of Environmental Microbiology, Babasaheb Bhimrao Ambedkar (Central) UniversityLucknow, India
- *Correspondence: Jay Shankar Singh
| | - Sumit Koushal
- Department of Environmental Microbiology, Babasaheb Bhimrao Ambedkar (Central) UniversityLucknow, India
| | - Arun Kumar
- Department of Environmental Microbiology, Babasaheb Bhimrao Ambedkar (Central) UniversityLucknow, India
| | - Shobhit R. Vimal
- Department of Environmental Microbiology, Babasaheb Bhimrao Ambedkar (Central) UniversityLucknow, India
| | - Vijai K. Gupta
- Molecular Glyco-biotechnology Group, Discipline of Biochemistry, School of Natural Sciences, National University of Ireland Galway (NUI)Galway, Ireland
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Pajares S, Bohannan BJM, Souza V. Editorial: The Role of Microbial Communities in Tropical Ecosystems. Front Microbiol 2016; 7:1805. [PMID: 27891123 PMCID: PMC5104756 DOI: 10.3389/fmicb.2016.01805] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 10/27/2016] [Indexed: 11/29/2022] Open
Affiliation(s)
- Silvia Pajares
- Unidad Académica de Ecología y Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México Mexico City, Mexico
| | - Brendan J M Bohannan
- Department of Biology, Institute of Ecology and Evolution, University of Oregon Eugene, OR, USA
| | - Valeria Souza
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México Mexico City, Mexico
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