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Hernández SR, Siqueira JF, Voigt DD, Soimu G, Brasil SC, Provenzano JC, Mdala I, Alves FRF, Rôças IN. Bacteriologic Conditions of the Apical Root Canal System of Teeth with and without Posttreatment Apical Periodontitis: A Correlative Multianalytical Approach. J Endod 2024; 50:154-163. [PMID: 37977217 DOI: 10.1016/j.joen.2023.11.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 11/09/2023] [Accepted: 11/09/2023] [Indexed: 11/19/2023]
Abstract
INTRODUCTION This study used a correlative multianalytical approach to investigate the bacteriologic conditions in the apical root canal system of treated teeth with or without apical periodontitis and their correlation with the technical quality of the previous root canal obturation and the presence and volume of apical periodontitis lesions. METHODS Root apexes were obtained from recently extracted root canal-treated teeth with (n = 23) and without (n = 22) apical periodontitis lesions as demonstrated by cone-beam computed tomographic examination. The root apexes were sectioned and subjected to micro-computed tomographic (micro-CT) scanning. The specimens were cryopulverized, and DNA extracted from the powder was used as a template in real-time polymerase chain reaction assays to quantify total bacteria and members of the Streptococcus genus and Actinobacteria phylum. The bacteriologic findings were compared between the 2 groups and also evaluated for associations with cone-beam computed tomographic and micro-computed tomographic data. RESULTS Bacteria were detected in all apical canal samples except 1. The mean counts of total bacteria, streptococci, and actinobacteria did not differ significantly between teeth with or without apical periodontitis (P > .05). Streptococcus levels were significantly lower by 80% in the apical canals of teeth with small lesions compared with those without lesions (P < .05). The limit of filling >2 mm short was significantly associated with more total bacterial counts compared with canals filled 0-2 mm short (P < .05). An adequate coronal restoration was significantly associated with lesser counts of Streptococcus (P < .05). CONCLUSIONS Comparable bacterial loads were observed in the apical canal system of treated teeth with and without apical periodontitis, suggesting that factors other than only the total bacterial levels may also influence the development and progression of apical periodontitis. Bacteria were found in the apical canal in virtually all cases with a high prevalence of streptococci and actinobacteria. Streptococci counts were significantly higher in the apical canal of teeth with inadequate restorations and teeth with no lesions. Underfilled canals showed higher bacterial counts.
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Affiliation(s)
- Sandra R Hernández
- Postgraduate Program in Dentistry, University of Grande Rio, Rio de Janeiro, Rio de Janeiro, Brazil; Department of Endodontics, Faculty of Dentistry, Francisco Marroquín University, Guatemala City, Guatemala
| | - José F Siqueira
- Postgraduate Program in Dentistry, University of Grande Rio, Rio de Janeiro, Rio de Janeiro, Brazil; Department of Dental Research, Faculty of Dentistry, Iguaçu University, Nova Iguaçu, Rio de Janeiro, Brazil
| | - Danielle D Voigt
- Postgraduate Program in Dentistry, University of Grande Rio, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Giuliana Soimu
- Postgraduate Program in Dentistry, University of Grande Rio, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Sabrina C Brasil
- Postgraduate Program in Dentistry, University of Grande Rio, Rio de Janeiro, Rio de Janeiro, Brazil
| | - José C Provenzano
- Postgraduate Program in Dentistry, University of Grande Rio, Rio de Janeiro, Rio de Janeiro, Brazil; Department of Dental Research, Faculty of Dentistry, Iguaçu University, Nova Iguaçu, Rio de Janeiro, Brazil
| | - Ibrahimu Mdala
- Department of General Practice, University of Oslo, Oslo, Norway
| | - Flávio R F Alves
- Postgraduate Program in Dentistry, University of Grande Rio, Rio de Janeiro, Rio de Janeiro, Brazil; Department of Dental Research, Faculty of Dentistry, Iguaçu University, Nova Iguaçu, Rio de Janeiro, Brazil.
| | - Isabela N Rôças
- Postgraduate Program in Dentistry, University of Grande Rio, Rio de Janeiro, Rio de Janeiro, Brazil; Department of Dental Research, Faculty of Dentistry, Iguaçu University, Nova Iguaçu, Rio de Janeiro, Brazil
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Pothula SK, Adams BJ. Community assembly in the wake of glacial retreat: A meta-analysis. GLOBAL CHANGE BIOLOGY 2022; 28:6973-6991. [PMID: 36087341 DOI: 10.1111/gcb.16427] [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: 01/07/2022] [Revised: 08/11/2022] [Accepted: 08/22/2022] [Indexed: 06/15/2023]
Abstract
Ecosystems shaped by retreating glaciers provide a unique opportunity to study the order and timing of biotic colonization, and how this influences the structure of successive ecological communities. In the last century glaciers across most of the cryosphere have receded at an unprecedented pace. Many studies have been published from different parts of the world testing hypotheses about how soil ecosystems are responding to rapid, contemporary deglaciation events. To better understand and draw general conclusions about how soil ecosystems respond to deglaciation, we conducted a global meta-analysis of 95 published articles focused on the succession of various organisms and soil physicochemical properties in glacier forefields along the chronosequence. Our global synthesis reveals that key soil properties and the abundance and richness of biota follow two conspicuous patterns: (1) some taxa demonstrate a persistent increase in abundance and richness over the entire chronosequence, (2) other taxa increase in abundance and richness during the first 50 years of succession, then gradually decline 50 years onward. The soil properties and soil organisms that are intimately tied to vegetation follow the first pattern, consistent with the idea that aboveground patterns of vegetation can drive patterns of belowground biodiversity. The second pattern may be due to an initial increase and subsequent decline in available nutrients and habitat suitability caused by increased biotic interactions, including resource competition among soil biota. A consensus view of the patterns of historical and contemporary soil ecosystem responses to deglaciation provides a better understanding of the processes that generate these patterns and informs predictions of ongoing and future responses to environmental changes.
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Affiliation(s)
| | - Byron J Adams
- Department of Biology, Brigham Young University, Provo, Utah, USA
- Evolutionary Ecology Laboratories, Brigham Young University, Provo, Utah, USA
- Life Science Museum, Brigham Young University, Provo, Utah, USA
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3
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Vimercati L, Bueno de Mesquita CP, Johnson BW, Mineart D, DeForce E, Vimercati Molano Y, Ducklow H, Schmidt SK. Dynamic trophic shifts in bacterial and eukaryotic communities during the first 30 years of microbial succession following retreat of an Antarctic glacier. FEMS Microbiol Ecol 2022; 98:6762214. [PMID: 36251461 DOI: 10.1093/femsec/fiac122] [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: 06/02/2022] [Revised: 09/30/2022] [Accepted: 10/10/2022] [Indexed: 01/21/2023] Open
Abstract
We examined microbial succession along a glacier forefront in the Antarctic Peninsula representing ∼30 years of deglaciation to contrast bacterial and eukaryotic successional dynamics and abiotic drivers of community assembly using sequencing and soil properties. Microbial communities changed most rapidly early along the chronosequence, and co-occurrence network analysis showed the most complex topology at the earliest stage. Initial microbial communities were dominated by microorganisms derived from the glacial environment, whereas later stages hosted a mixed community of taxa associated with soils. Eukaryotes became increasingly dominated by Cercozoa, particularly Vampyrellidae, indicating a previously unappreciated role for cercozoan predators during early stages of primary succession. Chlorophytes and Charophytes (rather than cyanobacteria) were the dominant primary producers and there was a spatio-temporal sequence in which major groups became abundant succeeding from simple ice Chlorophytes to Ochrophytes and Bryophytes. Time since deglaciation and pH were the main abiotic drivers structuring both bacterial and eukaryotic communities. Determinism was the dominant assembly mechanism for Bacteria, while the balance between stochastic/deterministic processes in eukaryotes varied along the distance from the glacier front. This study provides new insights into the unexpected dynamic changes and interactions across multiple trophic groups during primary succession in a rapidly changing polar ecosystem.
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Affiliation(s)
- Lara Vimercati
- Department of Ecology and Evolutionary Biology, University of Colorado at Boulder, UCB 334, 1900 Pleasant St, Boulder, CO 80309, United States
| | - Clifton P Bueno de Mesquita
- DOE Joint Genome Institute Lawrence Berkeley National Laboratory 1 Cyclotron Road, Berkeley, CA 94720, United States
| | - Ben W Johnson
- Department of Geological and Atmospheric Sciences 253 Science Hall 2237 Osborn Drive Ames, Iowa 50011-3212, United States
| | - Dana Mineart
- Department of Geological and Atmospheric Sciences 253 Science Hall 2237 Osborn Drive Ames, Iowa 50011-3212, United States
| | - Emelia DeForce
- Integrative Oceanography Division Scripps Institution of Oceanography 9500 Gilman Drive La Jolla, CA 92093 5, United States
| | - Ylenia Vimercati Molano
- Department of Ecology and Evolutionary Biology, University of Colorado at Boulder, UCB 334, 1900 Pleasant St, Boulder, CO 80309, United States
| | - Hugh Ducklow
- Lamont-Doherty Earth Observatory P.O. Box 1000 61 Route 9W Palisades, NY 10964-1000, United States
| | - Steven K Schmidt
- Department of Ecology and Evolutionary Biology, University of Colorado at Boulder, UCB 334, 1900 Pleasant St, Boulder, CO 80309, United States
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TNFAIP8 protein functions as a tumor suppressor in inflammation-associated colorectal tumorigenesis. Cell Death Dis 2022; 13:311. [PMID: 35387985 PMCID: PMC8986800 DOI: 10.1038/s41419-022-04769-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 03/16/2022] [Accepted: 03/25/2022] [Indexed: 12/21/2022]
Abstract
Tumor necrosis factor-α-induced protein 8 (TNFAIP8 or TIPE) is a member of the TNFAIP8 family. While TIPE was broadly considered to be pro-cancerous, its precise roles in carcinogenesis especially those of the intestinal tract are not clear. Here, we show that genetic deletion of TIPE in mice exacerbated chemical-induced colitis and colitis-associated colon cancer. Loss of TIPE exacerbated inflammatory responses and inflammation-associated dysbiosis, leading to the activation of NF-κB and STAT3, and it also accelerated dysplasia, DNA damage and proliferation of intestinal epithelial cells. We further show that colon microbiota were essential for increased tumor growth and progression in Tipe−/− mice. The tumor suppressive function of TIPE originated primarily from the non-hematopoietic compartment. Importantly, TIPE was downregulated in human colorectal cancers, and patients with low levels of Tipe mRNA were associated with reduced survival. These results indicate that TIPE serves as an important modulator of colitis and colitis-associated colon cancer.
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Du P, He H, Zhou L, Dong F, Liu X, Zheng Y. Different biodegradation potential and the impacted soil functions of epoxiconazole in two soils. JOURNAL OF HAZARDOUS MATERIALS 2022; 422:126787. [PMID: 34399219 DOI: 10.1016/j.jhazmat.2021.126787] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 06/13/2023]
Abstract
Epoxiconazole is an effective pesticide to control Fusarium head blight (FHB), and the application will increase. To investigate the ecotoxicity of epoxiconazole to soil microbiome, we carried out an indoor experiment in which soils from two main regions of wheat production in China (Nanjing and Anyang) were treated with epoxiconazole (0, 0.0625, 0.625, or 6.25 mg kg-1) and incubated for 90 days. Under epoxiconazole stress, for bacteria and fungi, the abundance was increased and the diversity and community were impacted. In Anyang soil, the half-life of epoxiconazole was short with more increased species (linear discriminant analysis effect size biomarkers) and more increased xenobiotics biodegradation pathways in epoxiconazole treatments. The increased species mostly due to high abundance in initial state and more positive connections of the species. Co-occurrences revealed that epoxiconazole tightened bacterial connection, and increased positive correlations in Anyang soil. The N transformation was influenced with increased nifH and amoA; and the contents of NH4+-N and NO3--N were also increased. The functions of C, S, and manganese metabolisms were also impacted by epoxiconazole. This work expands our understanding about epoxiconazole degradation and help us to properly assess the risk of epoxiconazole in soil.
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Affiliation(s)
- Pengqiang Du
- College of Plant Protection, Henan Agricultural University, No. 63, Agricultural Road, Zhengzhou 450002, China.
| | - Hairong He
- College of Pharmacy, Henan University of Chinese Medicine, No. 156, Jinshui East Road, Zhengzhou 450046, China
| | - Lin Zhou
- College of Plant Protection, Henan Agricultural University, No. 63, Agricultural Road, Zhengzhou 450002, China.
| | - Fengshou Dong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Beijing 100193, China
| | - Xingang Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Beijing 100193, China
| | - Yongquan Zheng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Beijing 100193, China.
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Du P, He H, Wu X, Xu J, Dong F, Liu X, Zheng Y. Mesosulfuron-methyl influenced biodegradability potential and N transformation of soil. JOURNAL OF HAZARDOUS MATERIALS 2021; 416:125770. [PMID: 33838509 DOI: 10.1016/j.jhazmat.2021.125770] [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: 11/27/2020] [Revised: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 06/12/2023]
Abstract
The wide application of mesosulfuron-methyl (MS) in soil may affect soil microbial community, yet the information is limited. In this work, two distinct soil types from Anyang (AY) and Nanjing (NJ) were spiked with MS (0, 0.006, 0.06, or 0.6 mg kg-1) and incubated for 90 days. MS decreased bacterial and fungal (except the last sampling) abundance and altered their diversity and community. Five biomarkers of bacterial species may help MS degradation and more increased xenobiotics biodegradation pathways were also observed in 0.6 mg kg-1 treatment in AY soil. A co-occurrence network revealed the biomarkers grouped in one module in all AY soils, suggesting these biomarkers act in concert to degrade MS. MS impacted soil N transformation with increasing N2-fixing bacteria in both soils and ammonia-oxidising bacteria (AOB) in NJ and decreasing ammonia-oxidizing archaea (AOA) in AY. The contents of NO3--N and NH4+-N were increased by MS. Structural equation models revealed that the abundance of bacteria and fungi was responsible for the NO3--N and NH4+-N contents. In conclusion, this work aids safety assessments and degradation-related research of MS in soil.
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Affiliation(s)
- Pengqiang Du
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Beijing 100193, China; College of Plant Protection, Henan Agricultural University, No. 63, Agricultural Road, Zhengzhou 450002, China
| | - Hairong He
- College of Pharmacy, Henan University of Chinese Medicine, No. 156, Jinshui East Road, Zhengzhou 450046, China
| | - Xiaohu Wu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Beijing 100193, China.
| | - Jun Xu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Beijing 100193, China
| | - Fengshou Dong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Beijing 100193, China
| | - Xingang Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Beijing 100193, China
| | - Yongquan Zheng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Beijing 100193, China.
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Liu Q, Li W, Liu D, Li L, Li J, Lv N, Liu F, Zhu B, Zhou Y, Xin Y, Dong X. Light stimulates anoxic and oligotrophic growth of glacial Flavobacterium strains that produce zeaxanthin. ISME JOURNAL 2021; 15:1844-1857. [PMID: 33452478 DOI: 10.1038/s41396-020-00891-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 12/15/2020] [Accepted: 12/17/2020] [Indexed: 01/17/2023]
Abstract
Bacteria that inhabit glaciers usually produce carotenoids. Here, we report that a group of zeaxanthin-producing glacial Flavobacterium exhibited light-promoted growth. Of the tested 47 strains, 45 showed increased growths but two died under illumination at 50 μmol photon m-2 s-1. Light stimulation occurred mainly in either anoxic or nutrient-poor cultures, while the same levels of light promotion were found for that grown at 14 and 7 °C. Pigment assays identified overrepresentative zeaxanthin but trace retinal in the light promoted 45 strains, while flexirubin was exclusively in the light-lethal two. Genomic analysis revealed the gene cluster for zeaxanthin synthesis in the 45 strains, in which 37 strains also harbored the proteorhodopsin gene prd. Transcriptomic analysis found that light-induced expressions of both the zeaxanthin synthesis and proteorhodopsin genes. Whereas, deletion of the prd gene in one strain did not diminish light promotion, inhibition of zeaxanthin synthesis did. In comparison, no light promotion was determined in a glacier Cryobacterium luteum that produced a non-zeaxanthin-type carotenoid. Therefore, light stimulation on the glacial Flavobacterium is mostly likely related to zeaxanthin, which could provide better photoprotection and sustain membrane integrity for the organisms living in cold environments.
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Affiliation(s)
- Qing Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing, 100101, China.,China General Microorganism Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Wei Li
- Computational Virology Group, Center for Bacteria and Viruses Resources and Bioinformation, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Di Liu
- Computational Virology Group, Center for Bacteria and Viruses Resources and Bioinformation, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lingyan Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Jie Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Na Lv
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Fei Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Baoli Zhu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yuguang Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing, 100101, China. .,China General Microorganism Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing, 100101, China.
| | - Yuhua Xin
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing, 100101, China. .,China General Microorganism Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing, 100101, China.
| | - Xiuzhu Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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Aguilar-Romero I, Romero E, Wittich RM, van Dillewijn P. Bacterial ecotoxicity and shifts in bacterial communities associated with the removal of ibuprofen, diclofenac and triclosan in biopurification systems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 741:140461. [PMID: 32886990 DOI: 10.1016/j.scitotenv.2020.140461] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 05/17/2020] [Accepted: 06/21/2020] [Indexed: 06/11/2023]
Abstract
The proliferation and possible adverse effects of emerging contaminants such as pharmaceutical and personal care products (PPCPs) in waters and the environment is a cause for increasing concern. We investigated the dissipation of three PPCPs: ibuprofen (IBP), diclofenac (DCF) and triclosan (TCS), separately and in mixtures, in the ppm range in biopurification system (BPS) microcosms, paying special attention to their effect on bacterial ecotoxicity, as well as bacterial community structure and composition. The results reveal that BPS microcosms efficiently dissipate IBP and DCF with 90% removed after 45 and 84 days of incubation, respectively. However, removal of TCS required a longer incubation period of 127 days for 90% removal. Furthermore, dissipation of the PPCPs was slower when a mixture of all three was applied to BPS microcosms. TCS had an initial negative effect on bacterial viability by a decrease of 34-43% as measured by live bacterial cell counts using LIVE/DEAD® microscopy; however, this effect was mitigated when the three PPCPs were present simultaneously. The bacterial communities in BPS microcosms were more affected by incubation time than by the PPCPs used. Nonetheless, the PPCPs differentially affected the composition and relative abundance of bacterial taxa. IBP and DCF initially increased bacterial diversity and richness, while exposure to TCS generally provoked an opposite effect without full recovery at the end of the incubation period. TCS, which negatively affected the relative abundance of Acidobacteria, Methylophilales, and Legionellales, had the largest impact on bacterial groups. Biomarker OTUs were identified in the BPS microcosms which were constrained to higher concentrations of the PPCPs and thus are likely to harbour degradation and/or detoxification mechanisms. This study reveals for the first time the effect of PPCPs on bacterial ecotoxicity and diversity in biopurification system microcosms and also facilitates the design of further applications of biomixtures to eliminate PPCPs.
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Affiliation(s)
- Inés Aguilar-Romero
- Department of Environmental Protection, Estación Experimental del Zaidín - Consejo Superior de Investigaciones Científicas (EEZ-CSIC), Calle Profesor Albareda 1, 18008 Granada, Spain
| | - Esperanza Romero
- Department of Environmental Protection, Estación Experimental del Zaidín - Consejo Superior de Investigaciones Científicas (EEZ-CSIC), Calle Profesor Albareda 1, 18008 Granada, Spain
| | - Regina-Michaela Wittich
- Department of Environmental Protection, Estación Experimental del Zaidín - Consejo Superior de Investigaciones Científicas (EEZ-CSIC), Calle Profesor Albareda 1, 18008 Granada, Spain
| | - Pieter van Dillewijn
- Department of Environmental Protection, Estación Experimental del Zaidín - Consejo Superior de Investigaciones Científicas (EEZ-CSIC), Calle Profesor Albareda 1, 18008 Granada, Spain..
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The Apical Root Canal System of Teeth with Posttreatment Apical Periodontitis: Correlating Microbiologic, Tomographic, and Histopathologic Findings. J Endod 2020; 46:1195-1203. [DOI: 10.1016/j.joen.2020.05.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/28/2020] [Accepted: 05/28/2020] [Indexed: 01/20/2023]
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10
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A global synthesis of biodiversity responses to glacier retreat. Nat Ecol Evol 2019; 3:1675-1685. [DOI: 10.1038/s41559-019-1042-8] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 10/15/2019] [Indexed: 11/08/2022]
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Khan A, Kong W, Muhammad S, Wang F, Zhang G, Kang S. Contrasting environmental factors drive bacterial and eukaryotic community successions in freshly deglaciated soils. FEMS Microbiol Lett 2019; 366:5628325. [PMID: 31738416 DOI: 10.1093/femsle/fnz229] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 11/15/2019] [Indexed: 11/14/2022] Open
Abstract
Glacier retreats expose deglaciated soils to microbial colonization and succession; however, the differences in drivers of bacterial and eukaryotic succession remain largely elusive. We explored soil bacterial and eukaryotic colonization and yearly community succession along a deglaciation chronosequence (10 years) on the Tibetan Plateau using qPCR, terminal restriction fragment length polymorphism (T-RFLP) and sequencing of clone libraries. The results exhibited that bacteria and eukaryotes rapidly colonized the soils in the first year of deglaciation, thereafter slowly increasing from 107 up to 1010 and 1011 gene copies g-1 soil, respectively. Bacterial and eukaryotic community changes were observed to group into distinct stages, including early (0-2 year old), transition (3-5 year old) and late stages (6-10 year old). Bacterial community succession was dominantly driven by soil factors (47.7%), among which soil moisture played a key role by explaining 26.9% of the variation. In contrast, eukaryotic community succession was dominantly driven by deglaciation age (22.2%). The dominant bacterial lineage was Cyanobacteria, which rapidly decreased from the early to the transition stage. Eukaryotes were dominated by glacier-originated Cercozoa in early stage soils, while green algae Chlorophyta substantially increased in late stage soils. Our findings revealed contrasting environmental factors driving bacterial and eukaryotic community successions.
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Affiliation(s)
- Ajmal Khan
- Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, No. 16 Lincui Road, Chaoyang District, Beijing 100101, China.,College of Resources and Environmnet, University of Chinese Academy of Sciences, No.19 (A) Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Weidong Kong
- Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, No. 16 Lincui Road, Chaoyang District, Beijing 100101, China.,College of Resources and Environmnet, University of Chinese Academy of Sciences, No.19 (A) Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Said Muhammad
- Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, No. 16 Lincui Road, Chaoyang District, Beijing 100101, China
| | - Fei Wang
- Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, No. 16 Lincui Road, Chaoyang District, Beijing 100101, China.,College of Resources and Environmnet, University of Chinese Academy of Sciences, No.19 (A) Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Guoshuai Zhang
- Key Laboratory of Tibetan Environmental Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, No. 16 Lincui Road, Chaoyang District, Beijing 100101, China
| | - Shichang Kang
- State Key Laboratory of Cryospheric Sciences, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Donggang West Road 320, Lanzhou 730000, China
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12
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Kong W, Liu J, Ji M, Yue L, Kang S, Morgan-Kiss RM. Autotrophic microbial community succession from glacier terminus to downstream waters on the Tibetan Plateau. FEMS Microbiol Ecol 2019; 95:5498296. [DOI: 10.1093/femsec/fiz074] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 05/23/2019] [Indexed: 11/13/2022] Open
Affiliation(s)
- Weidong Kong
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, P.R. China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100039, China
| | - Jinbo Liu
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, P.R. China
- Department of Microbiology, Miami University, Oxford, OH 45056, USA
| | - Mukan Ji
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Linyan Yue
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, P.R. China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100039, China
| | - Shichang Kang
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Southwest Medical University, Luzhou 646000, P.R. China
| | - Rachael M Morgan-Kiss
- State Key Laboratory of Cryospheric Sciences, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou 730000, P.R. China
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13
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Courty PE, Buée M, Tech JJT, Brulé D, Colin Y, Leveau JHJ, Uroz S. Impact of soil pedogenesis on the diversity and composition of fungal communities across the California soil chronosequence of Mendocino. MYCORRHIZA 2018; 28:343-356. [PMID: 29574496 DOI: 10.1007/s00572-018-0829-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 02/27/2018] [Indexed: 06/08/2023]
Abstract
Understanding how soil pedogenesis affects microbial communities and their in situ activities according to ecosystem functioning is a central issue in soil microbial ecology, as soils represent essential nutrient reservoirs and habitats for the biosphere. To address this question, soil chronosequences developed from a single, shared mineralogical parent material and having the same climate conditions are particularly useful, as they isolate the factor of time from other factors controlling the character of soils. In our study, we considered a natural succession of uplifted marine terraces in Mendocino, CA, ranging from highly fertile in the younger terrace (about 100,000 years old) to infertile in the older terraces (about 300,000 years old). Using ITS amplicon pyrosequencing, we analysed and compared the diversity and composition of the soil fungal communities across the first terraces (T1 to T3), with a specific focus in the forested terraces (T2 and T3) on soil samples collected below trees of the same species (Pinus muricata) and of the same age. While diversity and richness indices were highest in the grassland (youngest) terrace (T1), they were higher in the older forested terrace (T3) compared to the younger forested terrace (T2). Interestingly, the most abundant ectomycorrhizal (ECM) taxa that we found within these fungal communities showed high homology with ITS Sanger sequences obtained previously directly from ECM root tips from trees in the same study site, revealing a relative conservation of ECM diversity over time. Altogether, our results provide new information about the diversity and composition of the fungal communities as well as on the dominant ECM species in the soil chronosequence of Mendocino in relation to soil age and ecosystem development.
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Affiliation(s)
- P E Courty
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, 21000, Dijon, France
| | - M Buée
- INRA, UMR 1136 INRA, Université de Lorraine "Interactions Arbres Micro-organismes", Centre INRA de Nancy, 54280, Champenoux, France
| | - J J T Tech
- Department of Plant Pathology, University of California, One Shields Avenue, Davis, CA, 95616, USA
| | - D Brulé
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, 21000, Dijon, France
| | - Y Colin
- INRA, UMR 1136 INRA, Université de Lorraine "Interactions Arbres Micro-organismes", Centre INRA de Nancy, 54280, Champenoux, France
- INRA UR 1138 "Biogéochimie des Ecosystèmes Forestiers", Centre INRA de Nancy, 54280, Champenoux, France
| | - J H J Leveau
- Department of Plant Pathology, University of California, One Shields Avenue, Davis, CA, 95616, USA
| | - S Uroz
- INRA, UMR 1136 INRA, Université de Lorraine "Interactions Arbres Micro-organismes", Centre INRA de Nancy, 54280, Champenoux, France.
- INRA UR 1138 "Biogéochimie des Ecosystèmes Forestiers", Centre INRA de Nancy, 54280, Champenoux, France.
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14
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Wu X, Zhang G, Zhang W, Liu G, Chen T, Wang Y, Long H, Tai X, Zhang B, Li Z. Variations in culturable bacterial communities and biochemical properties in the foreland of the retreating Tianshan No. 1 glacier. Braz J Microbiol 2018; 49:443-451. [PMID: 29631894 PMCID: PMC6066779 DOI: 10.1016/j.bjm.2018.01.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 10/24/2016] [Indexed: 11/25/2022] Open
Abstract
As a glacier retreats, barren areas are exposed, and these barren areas are ideal sites to study microbial succession. In this study, we characterized the soil culturable bacterial communities and biochemical parameters of early successional soils from a receding glacier in the Tianshan Mountains. The total number of culturable bacteria ranged from 2.19 × 105 to 1.30 × 106 CFU g−1 dw and from 9.33 × 105 to 2.53 × 106 CFU g−1 dw at 4 °C and 25 °C, respectively. The number of culturable bacteria in the soil increased at 25 °C but decreased at 4 °C along the chronosequence. The total organic carbon, total nitrogen content, and enzymatic activity were relatively low in the glacier foreland. The number of culturable bacteria isolated at 25 °C was significantly positively correlated with the TOC and TN as well as the soil urease, protease, polyphenoloxidase, sucrase, catalase, and dehydrogenase activities. We obtained 358 isolates from the glacier foreland soils that clustered into 35 groups using amplified ribosomal DNA restriction analysis. These groups are affiliated with 20 genera that belong to six taxa, namely, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Actinobacteria, Bacteroides, and Deinococcus-Thermus, with a predominance of members of Actinobacteria and Proteobacteria in all of the samples. A redundancy analysis showed that the bacterial succession was divided into three periods, an early stage (10a), a middle stage (25–74a), and a late stage (100–130a), with the total number of culturable bacteria mainly being affected by the soil enzymatic activity, suggesting that the microbial succession correlated with the soil age along the foreland.
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Affiliation(s)
- Xiukun Wu
- Chinese Academy of Sciences, Northwest Institute of Eco-Environment and Resources, Key Laboratory of Desert and Desertification, Lanzhou, China; Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, Gansu Province, China
| | - Gaosen Zhang
- Chinese Academy of Sciences, Northwest Institute of Eco-Environment and Resources, Key Laboratory of Desert and Desertification, Lanzhou, China; Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, Gansu Province, China
| | - Wei Zhang
- Chinese Academy of Sciences, Northwest Institute of Eco-Environment and Resources, Key Laboratory of Desert and Desertification, Lanzhou, China; Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, Gansu Province, China
| | - Guangxiu Liu
- Chinese Academy of Sciences, Northwest Institute of Eco-Environment and Resources, Key Laboratory of Desert and Desertification, Lanzhou, China; Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, Gansu Province, China.
| | - Tuo Chen
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, Gansu Province, China; Chinese Academy of Sciences, Northwest Institute of Eco-Environment and Resources, State Key Laboratory of Cryospheric Sciences, Lanzhou, China
| | - Yun Wang
- Chinese Academy of Sciences, Northwest Institute of Eco-Environment and Resources, Key Laboratory of Desert and Desertification, Lanzhou, China; Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, Gansu Province, China
| | - Haozhi Long
- Chinese Academy of Sciences, Northwest Institute of Eco-Environment and Resources, Key Laboratory of Desert and Desertification, Lanzhou, China
| | - Xisheng Tai
- Chinese Academy of Sciences, Northwest Institute of Eco-Environment and Resources, Key Laboratory of Desert and Desertification, Lanzhou, China
| | - Baogui Zhang
- Chinese Academy of Sciences, Northwest Institute of Eco-Environment and Resources, Key Laboratory of Desert and Desertification, Lanzhou, China; Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, Gansu Province, China
| | - Zhongqin Li
- Chinese Academy of Sciences, Northwest Institute of Eco-Environment and Resources, State Key Laboratory of Cryospheric Sciences, Lanzhou, China
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15
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Takahama A, Rôças IN, Faustino ISP, Alves FRF, Azevedo RS, Gomes CC, Araújo-Filho WR, Siqueira JF. Association between bacteria occurring in the apical canal system and expression of bone-resorbing mediators and matrix metalloproteinases in apical periodontitis. Int Endod J 2018; 51:738-746. [DOI: 10.1111/iej.12895] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Accepted: 01/18/2018] [Indexed: 12/16/2022]
Affiliation(s)
- A. Takahama
- Department of Oral Medicine and Pediatric Dentistry; State University of Londrina; Londrina PR Brazil
| | - I. N. Rôças
- Department of Endodontics; Faculty of Dentistry; Estácio de Sá University; Rio de Janeiro RJ Brazil
| | - I. S. P. Faustino
- Department of Oral Pathology; Nova Friburgo Health Institute; Federal Fluminense University; Nova Friburgo RJ Brazil
| | - F. R. F. Alves
- Department of Endodontics; Faculty of Dentistry; Estácio de Sá University; Rio de Janeiro RJ Brazil
| | - R. S. Azevedo
- Department of Oral Pathology; Nova Friburgo Health Institute; Federal Fluminense University; Nova Friburgo RJ Brazil
| | - C. C. Gomes
- Department of Endodontics; Nova Friburgo Health Institute; Federal Fluminense University; Nova Friburgo RJ Brazil
| | - W. R. Araújo-Filho
- Department of Endodontics; Nova Friburgo Health Institute; Federal Fluminense University; Nova Friburgo RJ Brazil
| | - J. F. Siqueira
- Department of Endodontics; Faculty of Dentistry; Estácio de Sá University; Rio de Janeiro RJ Brazil
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Ju C, Xu J, Wu X, Dong F, Liu X, Tian C, Zheng Y. Effects of hexaconazole application on soil microbes community and nitrogen transformations in paddy soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 609:655-663. [PMID: 28763662 DOI: 10.1016/j.scitotenv.2017.07.146] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 07/16/2017] [Accepted: 07/16/2017] [Indexed: 06/07/2023]
Abstract
The ecological risks of widely used hexaconazole on soil microbes remain obscure. Thus, a 3-month-long experiment using two typical paddy soils in China (red soil and black soil) was conducted to assess the effects of hexaconazole (0.6 (T1) and 6 (T10) mgkg-1 soil) on the overall microbial biomass, respiratory activity, bacterial abundance and community structure, and nitrogen transformations. Soil was sampled after 7, 15, 30, 60, and 90days of incubation. The half-lives of the two doses of hexaconazole varied from 122 to 135d in the black soil and from 270 to 845d in the red soil. Both dosages of hexaconazole did not affect NH+4-N content, N2-fixing bacterial populations, total bacterial diversity, and community structure, but transitorily decreased the populations of total bacteria in both soil types. In the black soil, T10 negatively affected microbial biomass carbon (MBC) and soil basal respiration (RB), but transitorily increased NO-3-N concentration and ammonia-oxidizing bacteria populations, while T1 had almost no effect on most of the indicators. As for red soil, both concentrations of fungicide significantly, but transitorily, inhibited MBC and RB, while only T10 had a relatively long stimulatory effect on NO-3-N concentration and ammonia-oxidizing archaea populations. This study showed that over application of hexaconazole is indeed harmful to soil microorganisms and may reduce soil quality and increase the risk of nitrogen loss in paddy soils.
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Affiliation(s)
- Chao Ju
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jun Xu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Xiaohu Wu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Fengshou Dong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xingang Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Chunyan Tian
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yongquan Zheng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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17
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Basu S, Paul T, Yadav P, Debnath A, Sarkar K. Molecular Study of Indigenous Bacterial Community Composition on Exposure to Soil Arsenic Concentration Gradient. Pol J Microbiol 2017; 66:209-221. [PMID: 28735305 DOI: 10.5604/01.3001.0010.7838] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Community structure of bacteria present in arsenic contaminated agricultural soil was studied with qPCR (quantitative PCR) and DGGE (Denaturing Gradient Gel Electrophoresis) as an indicator of extreme stresses. Copy number of six common bacterial taxa (Acidobacteria, Actinobacteria, α-, β- and γ-Proteobacteria, Firmicutes) was calculated using group specific primers of 16S rDNA. It revealed that soil contaminated with low concentration of arsenic was dominated by both Actinobacteria and Proteobacteria but a shift towards Proteobacteria was observed with increasing arsenic concentration, and number of Actinobacteria eventually decreases. PCA (Principle Component Analysis) plot of bacterial community composition indicated a distinct resemblance among high arsenic content samples, while low arsenic content samples remained separated from others. Cluster analysis of soil parameters identifies three clusters, each of them was related to the arsenic content. Further, cluster analysis of 16S rDNA based DGGE fingerprint markedly distributed the soil bacterial populations into low (< 10 ppm) and high (> 10 ppm) arsenic content subgroups. Following analysis of diversity indices shows significant variation in bacterial community structure. MDS (Multi Dimensional Scaling) plot revealed distinction in the distribution of each sample denoting variation in bacterial diversity. Phylogenetic sequence analysis of fragments excised from DGGE gel revealed the presence of γ-Proteobacteria group across the study sites. Collectively, our experiments indicated that gradient of arsenic contamination affected the shape of the soil bacterial population by significant structural shift.
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Affiliation(s)
- Semanti Basu
- Department of Microbiology, University of Kalyani, Nadia, West Bengal, India
| | - Tanima Paul
- Department of Microbiology, University of Kalyani, Nadia, West Bengal, India
| | - Priya Yadav
- Department of Microbiology, University of Kalyani, Nadia, West Bengal, India
| | - Abhijit Debnath
- Department of Agricultural Chemistry and Soil Science, BCKV, Mohanpur, Nadia, West Bengal, India
| | - Keka Sarkar
- Department of Microbiology, University of Kalyani, Nadia, West Bengal, India
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18
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Soil Bacterial and Fungal Communities Show Distinct Recovery Patterns during Forest Ecosystem Restoration. Appl Environ Microbiol 2017; 83:AEM.00966-17. [PMID: 28476769 DOI: 10.1128/aem.00966-17] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 04/28/2017] [Indexed: 01/06/2023] Open
Abstract
Bacteria and fungi are important mediators of biogeochemical processes and play essential roles in the establishment of plant communities, which makes knowledge about their recovery after extreme disturbances valuable for understanding ecosystem development. However, broad ecological differences between bacterial and fungal organisms, such as growth rates, stress tolerance, and substrate utilization, suggest they could follow distinct trajectories and show contrasting dynamics during recovery. In this study, we analyzed both the intra-annual variability and decade-scale recovery of bacterial and fungal communities in a chronosequence of reclaimed mined soils using next-generation sequencing to quantify their abundance, richness, β-diversity, taxonomic composition, and cooccurrence network properties. Bacterial communities shifted gradually, with overlapping β-diversity patterns across chronosequence ages, while shifts in fungal communities were more distinct among different ages. In addition, the magnitude of intra-annual variability in bacterial β-diversity was comparable to the changes across decades of chronosequence age, while fungal communities changed minimally across months. Finally, the complexity of bacterial cooccurrence networks increased with chronosequence age, while fungal networks did not show clear age-related trends. We hypothesize that these contrasting dynamics of bacteria and fungi in the chronosequence result from (i) higher growth rates for bacteria, leading to higher intra-annual variability; (ii) higher tolerance to environmental changes for fungi; and (iii) stronger influence of vegetation on fungal communities.IMPORTANCE Both bacteria and fungi play essential roles in ecosystem functions, and information about their recovery after extreme disturbances is important for understanding whole-ecosystem development. Given their many differences in phenotype, phylogeny, and life history, a comparison of different bacterial and fungal recovery patterns improves the understanding of how different components of the soil microbiota respond to ecosystem recovery. In this study, we highlight key differences between soil bacteria and fungi during the restoration of reclaimed mine soils in the form of long-term diversity patterns, intra-annual variability, and potential interaction networks. Cooccurrence networks revealed increasingly complex bacterial community interactions during recovery, in contrast to much simpler and more isolated fungal network patterns. This study compares bacterial and fungal cooccurrence networks and reveals cooccurrences persisting through successional ages.
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19
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Ambrosini R, Musitelli F, Navarra F, Tagliaferri I, Gandolfi I, Bestetti G, Mayer C, Minora U, Azzoni RS, Diolaiuti G, Smiraglia C, Franzetti A. Diversity and Assembling Processes of Bacterial Communities in Cryoconite Holes of a Karakoram Glacier. MICROBIAL ECOLOGY 2017; 73:827-837. [PMID: 27999874 DOI: 10.1007/s00248-016-0914-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 12/09/2016] [Indexed: 06/06/2023]
Abstract
Cryoconite holes are small ponds that form on the surface of glaciers that contain a dark debris, the cryoconite, at the bottom and host active ecological communities. Differences in the structure of bacterial communities have been documented among Arctic and mountain glaciers, and among glaciers in different areas of the world. In this study, we investigated the structure of bacterial communities of cryoconite holes of Baltoro Glacier, a large (62 km in length and 524 km2 of surface) glacier of the Karakoram, by high-throughput sequencing of the V5-V6 hypervariable regions of the 16S rRNA gene. We found that Betaproteobacteria dominated bacterial communities, with large abundance of genera Polaromonas, probably thanks to its highly versatile metabolism, and Limnohabitans, which may have been favoured by the presence of supraglacial lakes in the area where cryoconite holes were sampled. Variation in bacterial communities among different sampling areas of the glacier could be explained by divergent selective processes driven by variation in environmental conditions, particularly pH, which was the only environmental variable that significantly affected the structure of bacterial communities. This variability may be due to both temporal and spatial patterns of variation in environmental conditions.
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Affiliation(s)
- Roberto Ambrosini
- Dept. of Earth and Environmental Sciences (DISAT), University of Milano-Bicocca, Piazza della Scienza 1, 20126, Milan, Italy
| | - Federica Musitelli
- Dept. of Earth and Environmental Sciences (DISAT), University of Milano-Bicocca, Piazza della Scienza 1, 20126, Milan, Italy
| | - Federico Navarra
- Dept. of Earth and Environmental Sciences (DISAT), University of Milano-Bicocca, Piazza della Scienza 1, 20126, Milan, Italy
| | - Ilario Tagliaferri
- Dept. of Earth and Environmental Sciences (DISAT), University of Milano-Bicocca, Piazza della Scienza 1, 20126, Milan, Italy
| | - Isabella Gandolfi
- Dept. of Earth and Environmental Sciences (DISAT), University of Milano-Bicocca, Piazza della Scienza 1, 20126, Milan, Italy
| | - Giuseppina Bestetti
- Dept. of Earth and Environmental Sciences (DISAT), University of Milano-Bicocca, Piazza della Scienza 1, 20126, Milan, Italy
| | - Christoph Mayer
- Bavarian Academy of Sciences and Humanities, Munich, Germany
| | - Umberto Minora
- "A. Desio" Dept. of Earth Sciences, Università degli Studi di Milano, Milan, Italy
| | | | | | - Claudio Smiraglia
- "A. Desio" Dept. of Earth Sciences, Università degli Studi di Milano, Milan, Italy
| | - Andrea Franzetti
- Dept. of Earth and Environmental Sciences (DISAT), University of Milano-Bicocca, Piazza della Scienza 1, 20126, Milan, Italy.
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20
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Microbial succession dynamics along glacier forefield chronosequences in Tierra del Fuego (Chile). Polar Biol 2017. [DOI: 10.1007/s00300-017-2110-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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21
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Mosimann C, Oberhänsli T, Ziegler D, Nassal D, Kandeler E, Boller T, Mäder P, Thonar C. Tracing of Two Pseudomonas Strains in the Root and Rhizoplane of Maize, as Related to Their Plant Growth-Promoting Effect in Contrasting Soils. Front Microbiol 2017; 7:2150. [PMID: 28119675 PMCID: PMC5222796 DOI: 10.3389/fmicb.2016.02150] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 12/20/2016] [Indexed: 11/18/2022] Open
Abstract
TaqMan-based quantitative PCR (qPCR) assays were developed to study the persistence of two well-characterized strains of plant growth-promoting rhizobacteria (PGPR), Pseudomonas fluorescens Pf153 and Pseudomonas sp. DSMZ 13134, in the root and rhizoplane of inoculated maize plants. This was performed in pot experiments with three contrasting field soils (Buus, Le Caron and DOK-M). Potential cross-reactivity of the qPCR assays was assessed with indigenous Pseudomonas and related bacterial species, which had been isolated from the rhizoplane of maize roots grown in the three soils and then characterized by Matrix-Assisted Laser Desorption Ionization (MALDI) Time-of-Flight (TOF) mass spectrometry (MS). Sensitivity of the qPCR expressed as detection limit of bacterial cells spiked into a rhizoplane matrix was 1.4 × 102 CFU and 1.3 × 104 CFU per gram root fresh weight for strain Pf153 and DSMZ 13134, respectively. Four weeks after planting and inoculation, both strains could readily be detected in root and rhizoplane, whereas only Pf153 could be detected after 8 weeks. The colonization rate of maize roots by strain Pf153 was significantly influenced by the soil type, with a higher colonization rate in the well fertile and organic soil of Buus. Inoculation with strain DSMZ 13134, which colonized roots and rhizoplane to the same degree, independently of the soil type, increased yield of maize, in terms of biomass accumulation, only in the acidic soil of Le Caron, whereas inoculation with strain Pf153 reduced yield in the soil Buus, despite of its high colonization rate and persistence. These results indicate that the colonization rate and persistence of inoculated Pseudomonas strains can be quantitatively assessed by the TaqMan-based qPCR technique, but that it cannot be taken for granted that inoculation with a well-colonizing and persistent Pseudomonas strain has a positive effect on yield of maize.
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Affiliation(s)
- Carla Mosimann
- Department of Environmental Sciences, Botany, Zürich-Basel Plant Science Center, University of BaselBasel, Switzerland; Research Institute of Organic Agriculture (FIBL)Frick, Switzerland
| | | | | | - Dinah Nassal
- Institute of Soil Science and Land Evaluation, University of Hohenheim Stuttgart, Germany
| | - Ellen Kandeler
- Institute of Soil Science and Land Evaluation, University of Hohenheim Stuttgart, Germany
| | - Thomas Boller
- Department of Environmental Sciences, Botany, Zürich-Basel Plant Science Center, University of Basel Basel, Switzerland
| | - Paul Mäder
- Research Institute of Organic Agriculture (FIBL) Frick, Switzerland
| | - Cécile Thonar
- Research Institute of Organic Agriculture (FIBL) Frick, Switzerland
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22
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Castillo Diaz JM, Delgado-Moreno L, Núñez R, Nogales R, Romero E. Enhancing pesticide degradation using indigenous microorganisms isolated under high pesticide load in bioremediation systems with vermicomposts. BIORESOURCE TECHNOLOGY 2016; 214:234-241. [PMID: 27136610 DOI: 10.1016/j.biortech.2016.04.105] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 04/18/2016] [Accepted: 04/21/2016] [Indexed: 06/05/2023]
Abstract
In biobed bioremediation systems (BBSs) with vermicomposts exposed to a high load of pesticides, 6 bacteria and 4 fungus strains were isolated, identified, and investigated to enhance the removal of pesticides. Three different mixtures of BBSs composed of vermicomposts made from greenhouse (GM), olive-mill (OM) and winery (WM) wastes were contaminated, inoculated, and incubated for one month (GMI, OMI and WMI). The inoculums maintenance was evaluated by DGGE and Q-PCR. Pesticides were monitored by HPLC-DAD. The highest bacterial and fungal abundance was observed in WMI and OMI respectively. In WMI, the consortia improved the removal of tebuconazole, metalaxyl, and oxyfluorfen by 1.6-, 3.8-, and 7.7-fold, respectively. The dissipation of oxyfluorfen was also accelerated in OMI, with less than 30% remaining after 30d. One metabolite for metalaxyl and 4 for oxyfluorfen were identified by GC-MS. The isolates could be suitable to improve the efficiency of bioremediation systems.
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Affiliation(s)
- Jean Manuel Castillo Diaz
- Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (EEZ-CSIC), Department of Environmental Protection, C/Profesor Albareda, 1, 18008 Granada, Spain
| | - Laura Delgado-Moreno
- Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (EEZ-CSIC), Department of Environmental Protection, C/Profesor Albareda, 1, 18008 Granada, Spain
| | - Rafael Núñez
- Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (EEZ-CSIC), Scientific Instrumentation Service, C/Profesor Albareda, 1, 18008 Granada, Spain
| | - Rogelio Nogales
- Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (EEZ-CSIC), Department of Environmental Protection, C/Profesor Albareda, 1, 18008 Granada, Spain
| | - Esperanza Romero
- Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (EEZ-CSIC), Department of Environmental Protection, C/Profesor Albareda, 1, 18008 Granada, Spain.
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23
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Liu J, Kong W, Zhang G, Khan A, Guo G, Zhu C, Wei X, Kang S, Morgan-Kiss RM. Diversity and succession of autotrophic microbial community in high-elevation soils along deglaciation chronosequence. FEMS Microbiol Ecol 2016; 92:fiw160. [PMID: 27465079 DOI: 10.1093/femsec/fiw160] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/24/2016] [Indexed: 11/12/2022] Open
Abstract
Global warming has resulted in substantial glacier retreats in high-elevation areas, exposing deglaciated soils to harsh environmental conditions. Autotrophic microbes are pioneering colonizers in the deglaciated soils and provide nutrients to the extreme ecosystem devoid of vegetation. However, autotrophic communities remain less studied in deglaciated soils. We explored the diversity and succession of the cbbL gene encoding the large subunit of form I RubisCO, a key CO2-fixing enzyme, using molecular methods in deglaciated soils along a 10-year deglaciation chronosequence on the Tibetan Plateau. Our results demonstrated that the abundance of all types of form I cbbL (IA/B, IC and ID) rapidly increased in young soils (0-2.5 years old) and kept stable in old soils. Soil total organic carbon (TOC) and total nitrogen (TN) gradually increased along the chronosequence and both demonstrated positive correlations with the abundance of bacteria and autotrophs, indicating that soil TOC and TN originated from autotrophs. Form IA/B autotrophs, affiliated with cyanobacteria, exhibited a substantially higher abundance than IC and ID. Cyanobacterial diversity and evenness increased in young soils (<6 years old) and then remained stable. Our findings suggest that cyabobacteria play an important role in accumulating TOC and TN in the deglaciated soils.
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Affiliation(s)
- Jinbo Liu
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Building 3, Courtyard 16, Lincui Road, Chaoyang District, Beijing 100101, China
| | - Weidong Kong
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Building 3, Courtyard 16, Lincui Road, Chaoyang District, Beijing 100101, China
| | - Guoshuai Zhang
- Key Laboratory of Tibetan Environmental Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Building 3, Courtyard 16, Lincui Road, Chaoyang District, Beijing 100101, China
| | - Ajmal Khan
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Building 3, Courtyard 16, Lincui Road, Chaoyang District, Beijing 100101, China
| | - Guangxia Guo
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Building 3, Courtyard 16, Lincui Road, Chaoyang District, Beijing 100101, China
| | - Chunmao Zhu
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Building 3, Courtyard 16, Lincui Road, Chaoyang District, Beijing 100101, China
| | - Xiaojie Wei
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Building 3, Courtyard 16, Lincui Road, Chaoyang District, Beijing 100101, China
| | - Shichang Kang
- State Key Laboratory of Cryospheric Sciences, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou 730000, China Center for Excellence in Tibetan Plateau Earth Sciences, CAS, Beijing 100101, China
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Brinkmeyer R. Diversity of bacteria in ships ballast water as revealed by next generation DNA sequencing. MARINE POLLUTION BULLETIN 2016; 107:277-285. [PMID: 27076378 DOI: 10.1016/j.marpolbul.2016.03.058] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 03/23/2016] [Accepted: 03/24/2016] [Indexed: 06/05/2023]
Abstract
The bacterial diversity in ballast water from five general cargo ships calling at the Port of Houston was determined with ion semiconductor DNA sequencing (Ion Torrent PGM) of PCR amplified 16S rRNA genes. Phylogenetic analysis revealed that the composition of bacteria in ballast water did not resemble that of typical marine habitats or even open ocean waters where BWEs occur. The predominant group of bacteria in ships conducting BWEs was the Roseobacter clade within the Alphaproteobacteria. In contrast, Gammaproteobacteria were predominant in the ship that did not conduct a BWE. All the ships contained human, fish, and terrestrial plant pathogens as well as bacteria indicative of fecal or activated sludge contamination. Most of the 60 pathogens had not been detected in ballast water previously. Among these were the human pathogens Corynebacterium diptheriae and several Legionella species and the fish pathogens Francisella piscicida and Piscirickettsia salmonis.
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Affiliation(s)
- Robin Brinkmeyer
- Department of Marine Sciences, Texas A&M University at Galveston, Galveston, TX 77551, USA.
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Li J, Liu F, Chen J. The Effects of Various Land Reclamation Scenarios on the Succession of Soil Bacteria, Archaea, and Fungi Over the Short and Long Term. Front Ecol Evol 2016. [DOI: 10.3389/fevo.2016.00032] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Mateos-Rivera A, Yde JC, Wilson B, Finster KW, Reigstad LJ, Øvreås L. The effect of temperature change on the microbial diversity and community structure along the chronosequence of the sub-arctic glacier forefield of Styggedalsbreen (Norway). FEMS Microbiol Ecol 2016; 92:fnw038. [DOI: 10.1093/femsec/fiw038] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/18/2016] [Indexed: 11/14/2022] Open
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Ju C, Xu J, Wu X, Dong F, Liu X, Zheng Y. Effects of myclobutanil on soil microbial biomass, respiration, and soil nitrogen transformations. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2016; 208:811-820. [PMID: 26590854 DOI: 10.1016/j.envpol.2015.11.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 10/30/2015] [Accepted: 11/01/2015] [Indexed: 06/05/2023]
Abstract
A 3-month-long experiment was conducted to ascertain the effects of different concentrations of myclobutanil (0.4 mg kg(-1) soil [T1]; 1.2 mg kg(-1) soil [T3]; and 4 mg kg(-1) soil [T10]) on soil microbial biomass, respiration, and soil nitrogen transformations using two typical agricultural soils (Henan fluvo-aquic soil and Shanxi cinnamon soil). Soil was sampled after 7, 15, 30, 60, and 90 days of incubation to determine myclobutanil concentration and microbial parameters: soil basal respiration (RB), microbial biomass carbon (MBC) and nitrogen (MBN), NO(-)3-N and NH(+)4-N concentrations, and gene abundance of total bacteria, N2-fixing bacteria, fungi, ammonia-oxidizing archaea (AOA), and ammonia-oxidizing bacteria (AOB). The half-lives of the different doses of myclobutanil varied from 20.3 to 69.3 d in the Henan soil and from 99 to 138.6 d in the Shanxi soil. In the Henan soil, the three treatments caused different degrees of short-term inhibition of RB and MBC, NH(+)4-N, and gene abundance of total bacteria, fungi, N2-fixing bacteria, AOA, and AOB, with the exception of a brief increase in NO(-)3-N content during the T10 treatment. The MBN (immobilized nitrogen) was not affected. In the Shanxi soil, MBC, the populations of total bacteria, fungi, and N2-fixing bacteria, and NH(+)4-N concentration were not significantly affected by myclobutanil. The RB and MBN were decreased transitorily in the T10 treatment. The NO(-)3-N concentrations and the abundance of both AOA and AOB were erratically stimulated by myclobutanil. Regardless of whether stimulation or suppression occurred, the effects of myclobutanil on the two soil types were short term. In summary, myclobutanil had no long-term negative effects on the soil microbial biomass, respiration, and soil nitrogen transformations in the two types of soil, even at 10-fold the recommended dosage.
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Affiliation(s)
- Chao Ju
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jun Xu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Xiaohu Wu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Fengshou Dong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xingang Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yongquan Zheng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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Liu Q, Zhou YG, Xin YH. High diversity and distinctive community structure of bacteria on glaciers in China revealed by 454 pyrosequencing. Syst Appl Microbiol 2015; 38:578-85. [DOI: 10.1016/j.syapm.2015.09.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Revised: 09/15/2015] [Accepted: 09/21/2015] [Indexed: 11/28/2022]
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Zhang Z, Zhao J, Yu C, Dong S, Zhang D, Yu R, Wang C, Liu Y. Evaluation of aerobic co-composting of penicillin fermentation fungi residue with pig manure on penicillin degradation, microbial population dynamics and composting maturity. BIORESOURCE TECHNOLOGY 2015; 198:403-409. [PMID: 26409851 DOI: 10.1016/j.biortech.2015.09.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 09/02/2015] [Accepted: 09/05/2015] [Indexed: 06/05/2023]
Abstract
Improper treatment of penicillin fermentation fungi residue (PFFR), one of the by-products of penicillin production process, may result in environmental pollution due to the high concentration of penicillin. Aerobic co-composting of PFFR with pig manure was determined to degrade penicillin in PFFR. Results showed that co-composting of PFFR with pig manure can significantly reduce the concentration of penicillin in PFFR, make the PFFR-compost safer as organic fertilizer for soil application. More than 99% of penicillin in PFFR were removed after 7-day composting. PFFR did not affect the composting process and even promote the activity of the microorganisms in the compost. Quantitative PCR (qPCR) indicated that the bacteria and actinomycetes number in the AC samples were 40-80% higher than that in the pig-manure compost (CK) samples in the same composting phases. This research indicated that the aerobic co-composting was a feasible PFFR treatment method.
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Affiliation(s)
- Zhenhua Zhang
- Nanjing Institute of Environmental Sciences, Ministry of Environmental Protection, Nanjing 210042, China
| | - Juan Zhao
- Department of Energy and Environment, Southeast University, Nanjing 210096, China
| | - Cigang Yu
- Nanjing Institute of Environmental Sciences, Ministry of Environmental Protection, Nanjing 210042, China
| | - Shanshan Dong
- Nanjing Institute of Environmental Sciences, Ministry of Environmental Protection, Nanjing 210042, China
| | - Dini Zhang
- Nanjing Institute of Environmental Sciences, Ministry of Environmental Protection, Nanjing 210042, China
| | - Ran Yu
- Department of Energy and Environment, Southeast University, Nanjing 210096, China
| | - Changyong Wang
- Nanjing Institute of Environmental Sciences, Ministry of Environmental Protection, Nanjing 210042, China
| | - Yan Liu
- Nanjing Institute of Environmental Sciences, Ministry of Environmental Protection, Nanjing 210042, China.
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Soil development and bacterial community shifts along the chronosequence of the Midtre Lovénbreen glacier foreland in Svalbard. ACTA ACUST UNITED AC 2015. [DOI: 10.5141/ecoenv.2015.049] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Lazzaro A, Hilfiker D, Zeyer J. Structures of Microbial Communities in Alpine Soils: Seasonal and Elevational Effects. Front Microbiol 2015; 6:1330. [PMID: 26635785 PMCID: PMC4660872 DOI: 10.3389/fmicb.2015.01330] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 11/12/2015] [Indexed: 11/13/2022] Open
Abstract
Microbial communities in alpine environments are exposed to several environmental factors related to elevation and local site conditions and to extreme seasonal variations. However, little is known on the combined impact of such factors on microbial community structure. We assessed the effects of seasonal variations on soil fungal and bacterial communities along an elevational gradient (from alpine meadows to a glacier forefield, 1930-2519 m a.s.l.) over 14 months. Samples were taken during all four seasons, even under the winter snowpack and at snowmelt. Microbial community structures and abundances were investigated using Terminal Restriction Fragment Length Polymorphism (T-RFLP) and quantitative PCR (qPCR) of the 16S and 18S rRNA genes. Illumina sequencing was performed to identify key bacterial groups in selected samples. We found that the soil properties varied significantly with the seasons and along the elevational gradient. For example, concentrations of soluble nutrients (e.g., [Formula: see text], [Formula: see text], [Formula: see text]) significantly increased in October but decreased drastically under the winter snowpack. At all times, the alpine meadows showed higher soluble nutrient concentrations than the glacier forefield. Microbial community structures at the different sites were strongly affected by seasonal variations. Under winter snowpack, bacterial communities were dominated by ubiquitous groups (i.e., beta-Proteobacteria, which made up to 25.7% of the total reads in the glacier forefield). In the snow-free seasons, other groups (i.e., Cyanobacteria) became more abundant (from 1% under winter snow in the glacier forefield samples to 8.1% in summer). In summary, elevation had a significant effect on soil properties, whereas season influenced soil properties as well as microbial community structure. Vegetation had a minor impact on microbial communities. At every elevation analyzed, bacterial, and fungal community structures exhibited a pronounced annual cycle.
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Affiliation(s)
- Anna Lazzaro
- Environmental Microbiology, Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich Zurich, Switzerland
| | - Daniela Hilfiker
- Environmental Microbiology, Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich Zurich, Switzerland
| | - Josef Zeyer
- Environmental Microbiology, Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich Zurich, Switzerland
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Hill R, Saetnan ER, Scullion J, Gwynn-Jones D, Ostle N, Edwards A. Temporal and spatial influences incur reconfiguration of Arctic heathland soil bacterial community structure. Environ Microbiol 2015; 18:1942-53. [DOI: 10.1111/1462-2920.13017] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 08/05/2015] [Accepted: 08/06/2015] [Indexed: 01/04/2023]
Affiliation(s)
- Richard Hill
- Institute of Biological, Rural and Environmental Sciences; Cledwyn Building; Aberystwyth University; Aberystwyth SY23 3FG UK
- Interdisciplinary Centre for Environmental Microbiology; Aberystwyth University; Aberystwyth UK
| | - Eli R. Saetnan
- Institute of Biological, Rural and Environmental Sciences; Cledwyn Building; Aberystwyth University; Aberystwyth SY23 3FG UK
| | - John Scullion
- Institute of Biological, Rural and Environmental Sciences; Cledwyn Building; Aberystwyth University; Aberystwyth SY23 3FG UK
| | - Dylan Gwynn-Jones
- Institute of Biological, Rural and Environmental Sciences; Cledwyn Building; Aberystwyth University; Aberystwyth SY23 3FG UK
| | - Nick Ostle
- Plant and Soil Ecology Laboratory; Lancaster Environmental Centre; Lancaster University; Lancaster LA1 4YQ UK
| | - Arwyn Edwards
- Institute of Biological, Rural and Environmental Sciences; Cledwyn Building; Aberystwyth University; Aberystwyth SY23 3FG UK
- Interdisciplinary Centre for Environmental Microbiology; Aberystwyth University; Aberystwyth UK
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Hofmann K, Illmer P. Temporal patterns of prokaryotic abundance, community structure and microbial activity in glacier foreland soils. Antonie Van Leeuwenhoek 2015; 108:793-9. [DOI: 10.1007/s10482-015-0534-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 07/11/2015] [Indexed: 11/29/2022]
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Antunes HS, Rôças IN, Alves FR, Siqueira JF. Total and Specific Bacterial Levels in the Apical Root Canal System of Teeth with Post-treatment Apical Periodontitis. J Endod 2015; 41:1037-42. [DOI: 10.1016/j.joen.2015.03.008] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 02/09/2015] [Accepted: 03/08/2015] [Indexed: 11/26/2022]
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Provenzano JC, Rôças IN, Tavares LFD, Neves BC, Siqueira JF. Short-chain Fatty Acids in Infected Root Canals of Teeth with Apical Periodontitis before and after Treatment. J Endod 2015; 41:831-5. [PMID: 25799538 DOI: 10.1016/j.joen.2015.02.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 12/01/2014] [Accepted: 02/04/2015] [Indexed: 10/23/2022]
Abstract
INTRODUCTION Short-chain fatty acids (SCFAs) are bacterial metabolic end products that may function as virulence factors. This study evaluated the occurrence of SCFAs in infected root canals before and after treatment. METHODS Samples were taken from root canals of teeth with apical periodontitis before (S1) and after (S2) chemomechanical preparation with either NaOCl or chlorhexidine as the irrigant and then after interappointment medication with calcium hydroxide (S3). High-performance liquid chromatography was used for detection of SCFAs. Selected bacterial taxa that are recognized producers of the target SCFAs were identified by real-time polymerase chain reaction. RESULTS Butyric acid was the most common fatty acid in S1, followed by propionic acid. Both molecules were also found in S2 and S3 from both NaOCl and chlorhexidine groups. Lactic acid was not present in detectable levels in S1, but it occurred in 1 postinstrumentation sample and in 9 samples taken after calcium hydroxide medication. Of the target taxa, Fusobacterium nucleatum was the most prevalent in S1 (76%), followed by members of the Actinobacteria phylum (71%), Streptococcus species (59%), and Parvimonas micra (53%). Gram-positive taxa, especially streptococci, were the most prevalent bacteria in S2 and S3. SCFA detection was matched with the respective potential producer species in most cases. CONCLUSIONS This first report of SCFAs in infected root canals suggests that these molecules may play a role in the pathogenesis of apical periodontitis. Significance of persistence of SCFAs after treatment and its effects on the long-term outcome await elucidation.
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Affiliation(s)
- José Claudio Provenzano
- Molecular Microbiology Laboratory, Department of Endodontics, Faculty of Dentistry, Estácio de Sá University, Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Isabela N Rôças
- Molecular Microbiology Laboratory, Department of Endodontics, Faculty of Dentistry, Estácio de Sá University, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Luís Fernando D Tavares
- Laboratory of Molecular Microbiology and Proteins, Department of Biochemistry, Chemistry Institute, Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Bianca Cruz Neves
- Laboratory of Molecular Microbiology and Proteins, Department of Biochemistry, Chemistry Institute, Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - José F Siqueira
- Molecular Microbiology Laboratory, Department of Endodontics, Faculty of Dentistry, Estácio de Sá University, Rio de Janeiro, Rio de Janeiro, Brazil
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Yarwood S, Wick A, Williams M, Daniels WL. Parent material and vegetation influence soil microbial community structure following 30-years of rock weathering and pedogenesis. MICROBIAL ECOLOGY 2015; 69:383-94. [PMID: 25370885 DOI: 10.1007/s00248-014-0523-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2013] [Accepted: 10/20/2014] [Indexed: 05/10/2023]
Abstract
The process of pedogenesis and the development of biological communities during primary succession begin on recently exposed mineral surfaces. Following 30 years of surface exposure of reclaimed surface mining sites (Appalachian Mountains, USA), it was hypothesized that microbial communities would differ between sandstone and siltstone parent materials and to a lesser extent between vegetation types. Microbial community composition was examined by targeting bacterial and archaeal (16S ribosomal RNA (rRNA)) and fungal (internal transcribed spacer (ITS)) genes and analyzed using Illumina sequencing. Microbial community composition significantly differed between parent materials and between plots established with tall fescue grass or pitch x loblolly pine vegetation types, suggesting that both factors are important in shaping community assembly during early pedogenesis. At the phylum level, Acidobacteria and Proteobacteria differed in relative abundance between sandstone and siltstone. The amount of the heavy fraction carbon (C) was significantly different between sandstone (2.0 mg g(-1)) and siltstone (5.2 mg g(-1)) and correlated with microbial community composition. Soil nitrogen (N) cycling was examined by determining gene copy numbers of ureC, archaeal amoA, and bacterial amoA. Gene quantities tended to be higher in siltstone compared to sandstone but did not differ by vegetation type. This was consistent with differences in extractable ammonium (NH4 (+)) concentrations between sandstone and siltstone (16.4 vs 8.5 μg NH4 (+)-N g(-1) soil), suggesting that nitrification rates may be higher in siltstone. Parent material and early vegetation are important determinants of early microbial community assembly and could be drivers for the trajectory of ecosystem development over longer time scales.
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Affiliation(s)
- Stephanie Yarwood
- Environmental Science and Technology Department, University of Maryland, 1109 HJ Patterson Hall, College Park, MD, 20742, USA,
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Primary succession of soil enzyme activity and heterotrophic microbial communities along the chronosequence of Tianshan Mountains No. 1 Glacier, China. Antonie van Leeuwenhoek 2014; 107:453-66. [PMID: 25472706 DOI: 10.1007/s10482-014-0343-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 11/27/2014] [Indexed: 10/24/2022]
Abstract
We investigated the primary successions of soil enzyme activity and heterotrophic microbial communities at the forefields of the Tianshan Mountains No. 1 Glacier by investigating soil microbial processes (microbial biomass and nitrogen mineralization), enzyme activity and community-level physiological profiling. Soils deglaciated between 1959 and 2008 (0, 5, 17, 31 and 44 years) were collected. Soils >1,500 years in age were used as a reference (alpine meadow soils). Soil enzyme activity and carbon-source utilization ability significantly increased with successional time. Amino-acid utilization rates were relatively higher in early, unvegetated soils (0 and 5 years), but carbohydrate utilization was higher in later stages (from 31 years to the reference soil). Discriminant analysis, including data on microbial processes and soil enzyme activities, revealed that newly exposed soils (0-5 years) and older soils (17-44 years) were well-separated from each other and obviously different from the reference soil. Correlation analysis revealed that soil organic carbon, was the primary factor influencing soil enzyme activity and heterotrophic microbial community succession. Redundancy analysis suggested that soil pH and available P were also affect microbial activity to a considerable degree. Our results indicated that glacier foreland soils have continued to develop over 44 years and soils were significantly affected by the geographic location of the glacier and the local topography. Soil enzyme activities and heterotrophic microbial communities were also significantly influenced by these variables.
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Ricucci D, Siqueira JF, Lopes WSP, Vieira AR, Rôças IN. Extraradicular infection as the cause of persistent symptoms: a case series. J Endod 2014; 41:265-73. [PMID: 25282379 DOI: 10.1016/j.joen.2014.08.020] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Revised: 08/21/2014] [Accepted: 08/26/2014] [Indexed: 11/20/2022]
Abstract
INTRODUCTION This article describes 3 cases that presented persistent symptoms after appropriate endodontic treatment. Histopathologic and histobacteriologic investigation were conducted for determination of the cause. METHODS Three cases are reported that presented with persistent symptoms after endodontic retreatment (cases 1 and 2) or treatment (case 3). Periapical surgery was indicated and performed in these cases. The biopsy specimens, consisting of root apices and the apical periodontitis lesions, were subjected to histopathologic and histobacteriologic analyses. RESULTS Case 1 was an apical cyst with necrotic debris, heavily colonized by ramifying bacteria, in the lumen. No bacteria were found in the apical root canal system. Case 2 was a granuloma displaying numerous bacterial aggregations through the inflammatory tissue. Infection was also present in the dentinal tubules at the apical root canal. Case 3 was a cyst with bacterial colonies floating in its lumen; bacterial biofilms were also seen on the external apical root surface, filling a large lateral canal and other apical ramifications, and between layers of cementum detached from the root surface. No bacteria were detected in the main root canal. CONCLUSIONS Different forms of extraradicular infection were associated with symptoms in these cases, leading to short-term endodontic failure only solved by periapical surgery.
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Affiliation(s)
| | - José F Siqueira
- Faculty of Dentistry, Department of Endodontics, Estácio de Sá University, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Weber S P Lopes
- Specialization Course, Brazilian Association of Dentistry, Juiz de Fora, Minas Gerais, Brazil
| | - Adalberto R Vieira
- Specialization Course, Brazilian Association of Dentistry, Juiz de Fora, Minas Gerais, Brazil
| | - Isabela N Rôças
- Faculty of Dentistry, Department of Endodontics, Estácio de Sá University, Rio de Janeiro, Rio de Janeiro, Brazil
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Edwards A, Mur LA, Girdwood SE, Anesio AM, Stibal M, Rassner SM, Hell K, Pachebat JA, Post B, Bussell JS, Cameron SJ, Griffith GW, Hodson AJ, Sattler B. Coupled cryoconite ecosystem structure-function relationships are revealed by comparing bacterial communities in alpine and Arctic glaciers. FEMS Microbiol Ecol 2014; 89:222-37. [DOI: 10.1111/1574-6941.12283] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 12/23/2013] [Accepted: 01/07/2014] [Indexed: 11/28/2022] Open
Affiliation(s)
- Arwyn Edwards
- Institute of Biological, Rural and Environmental Sciences; Aberystwyth University; Aberystwyth UK
| | - Luis A.J. Mur
- Institute of Biological, Rural and Environmental Sciences; Aberystwyth University; Aberystwyth UK
| | - Susan E. Girdwood
- Institute of Biological, Rural and Environmental Sciences; Aberystwyth University; Aberystwyth UK
| | - Alexandre M. Anesio
- Bristol Glaciology Centre; School of Geographical Sciences; University of Bristol; Bristol UK
| | - Marek Stibal
- Department of Geochemistry; Geological Survey of Denmark and Greenland; University of Copenhagen; Copenhagen Denmark
- Centre for Permafrost; University of Copenhagen; Copenhagen Denmark
| | - Sara M.E. Rassner
- Institute of Biological, Rural and Environmental Sciences; Aberystwyth University; Aberystwyth UK
| | - Katherina Hell
- Institute of Ecology and Austrian Institute of Polar Research; University of Innsbruck; Innsbruck Austria
| | - Justin A. Pachebat
- Institute of Biological, Rural and Environmental Sciences; Aberystwyth University; Aberystwyth UK
| | - Barbara Post
- Institute of Ecology and Austrian Institute of Polar Research; University of Innsbruck; Innsbruck Austria
| | - Jennifer S. Bussell
- Institute of Biological, Rural and Environmental Sciences; Aberystwyth University; Aberystwyth UK
| | - Simon J.S. Cameron
- Institute of Biological, Rural and Environmental Sciences; Aberystwyth University; Aberystwyth UK
| | - Gareth Wyn Griffith
- Institute of Biological, Rural and Environmental Sciences; Aberystwyth University; Aberystwyth UK
| | | | - Birgit Sattler
- Institute of Ecology and Austrian Institute of Polar Research; University of Innsbruck; Innsbruck Austria
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Castillo JM, Romero E, Nogales R. Dynamics of microbial communities related to biochemical parameters during vermicomposting and maturation of agroindustrial lignocellulose wastes. BIORESOURCE TECHNOLOGY 2013; 146:345-354. [PMID: 23948272 DOI: 10.1016/j.biortech.2013.07.093] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 07/15/2013] [Accepted: 07/20/2013] [Indexed: 06/02/2023]
Abstract
Scarce information is available on the changes in abundance of microbial taxa during vermicomposting. Quantitative PCR and DGGE analysis were used to monitor variations in the microbial structure, relative abundance of four bacterial classes and fungi over the vermicomposting and maturation period of wet olive cake (O) and vine shoots (W). Multivariate correlation analysis between microbial structure and abundance, earthworm biomass and enzyme activities revealed similar and divergent interactions in both processes. Although Eisenia fetida development was different, significant correlations were found with β-glucosidase activity and with bacterial and fungal structure. In the vermicomposting period of O and W, a decline was found in bacteria (94% and 77%), fungi (93% and 94%), and Gammaproteobacteria (56% and 71%) but an increase in Betaproteobacteria and Actinobacteria (62-79%). Alphaproteobacteria increased only in O (26%). Despite the different initial lignocellulose wastes, the mature vermicomposts were similar in microbial and biochemical properties.
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Affiliation(s)
- Jean Manuel Castillo
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Cientificas (EEZ-CSIC), C/Profesor Albareda 1, 18008 Granada, Spain.
| | - Esperanza Romero
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Cientificas (EEZ-CSIC), C/Profesor Albareda 1, 18008 Granada, Spain
| | - Rogelio Nogales
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Cientificas (EEZ-CSIC), C/Profesor Albareda 1, 18008 Granada, Spain
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41
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Franzetti A, Tatangelo V, Gandolfi I, Bertolini V, Bestetti G, Diolaiuti G, D'Agata C, Mihalcea C, Smiraglia C, Ambrosini R. Bacterial community structure on two alpine debris-covered glaciers and biogeography of Polaromonas phylotypes. ISME JOURNAL 2013; 7:1483-92. [PMID: 23535918 DOI: 10.1038/ismej.2013.48] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2012] [Revised: 12/25/2012] [Accepted: 02/13/2013] [Indexed: 11/09/2022]
Abstract
High-elevation cold environments are considered ideal places to test hypotheses about mechanisms of bacterial colonization and succession, and about bacterial biogeography. Debris-covered glaciers (glaciers whose ablation area is mainly covered by a continuous layer of rock debris fallen from the surrounding mountains) have never been investigated in this respect so far. We used the Illumina technology to analyse the V5 and V6 hypervariable regions of the bacterial 16S rRNA gene amplified from 38 samples collected in July and September 2009 at different distances from the terminus on two debris-covered glaciers (Miage and Belvedere--Italian Alps). Heterotrophic taxa-dominated communities and bacterial community structure changed according to ice ablation rate, organic carbon content of the debris and distance from the glacier terminus. Bacterial communities therefore change during downwards debris transport, and organic carbon of these recently exposed substrates is probably provided more by allochthonous deposition of organic matter than by primary production by autotrophic organisms. We also investigated whether phylotypes of the genus Polaromonas, which is ubiquitous in cold environments, do present a biogeographical distribution by analysing the sequences retrieved in this study together with others available in the literature. We found that the genetic distance among phylotypes increased with geographic distance; however, more focused analyses using discrete distance classes revealed that both sequences collected at sites <100 km and at sites 9400-13,500 km to each other were more similar than those collected at other distance classes. Evidences of biogeographic distribution of Polaromonas phylotypes were therefore contrasting.
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Affiliation(s)
- Andrea Franzetti
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milano, Italy
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42
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Enowashu E, Kandeler E, Schloter M, Rasche F, Engel M. Development of a primer system to study abundance and diversity of the gene coding for alanine aminopeptidase pepN gene in Gram-negative soil bacteria. J Microbiol Methods 2012; 91:14-21. [PMID: 22796679 DOI: 10.1016/j.mimet.2012.07.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Accepted: 07/03/2012] [Indexed: 11/27/2022]
Abstract
A new set of primers was developed allowing the specific detection of the pepN gene (coding for alanine aminopeptidase) from Gram-negative bacteria. The primers were designed in silico by sequence alignments based on available DNA sequence data. The PCR assay was validated using DNA from selected pure cultures. The analysis of gene libraries from extracted DNA from different soil samples revealed a high diversity of pepN related sequences mainly related to α-Proteobacteria. Most sequences obtained from clone libraries were closely related to already published sequences (<80% homology on amino acid level), which may be related to the conserved character of the amplified region of pepN. By linking the diversity data obtained by the clone library studies to potential enzymatic activities of alanine aminopeptidase, lowest diversity of pepN was found in those soil samples which displayed lowest activity levels, which confirms the importance of diversity for the ecosystem function mainly when transformation processes of complex molecules are studied.
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Affiliation(s)
- Esther Enowashu
- Institute of Soil Science and Land Evaluation, Soil Biology Section, University of Hohenheim, Emil-Wolf Straße 27, Stuttgart, D-70593, Germany.
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43
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Variations in soil culturable bacteria communities and biochemical characteristics in the Dongkemadi glacier forefield along a chronosequence. Folia Microbiol (Praha) 2012; 57:485-94. [PMID: 22614182 DOI: 10.1007/s12223-012-0159-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Accepted: 05/01/2012] [Indexed: 10/28/2022]
Abstract
The variations in the soil culturable bacterial communities and biochemical parameters of early successional soils from a receding glacier in the Tanggula Mountain were investigated. We examined low organic carbon (C) and nitrogen (N) contents and enzymatic activity, correlated with fewer bacterial groups and numbers in the glacier forefield soils. The soil pH values decreased, but the soil water content, organic C and total N significantly increased, along the chronosequence. The soil C/N ratio decreased in the early development soils and increased in the late development soils and it did not correlate with the soil age since deglaciation. The activities of soil urease, sucrase, protease, polyphenol oxidase, catalase, and dehydrogenase increased along the chronosequence. The numbers of culturable bacteria in the soils increased as cultured at 25°C while decreased at 4°C from younger soils to older soils. Total numbers of culturable bacteria in the soils cultured at 25°C were significantly positively correlated to the soil total N, organic C, and soil water content, as well as the activities of soil urease, sucrase, dehydrogenase, catalase, and polyphenol oxidase. We have obtained 224 isolates from the glacier forefield soils. The isolates were clustered into 28 groups by amplified ribosomal DNA restriction analysis (ARDRA). Among them, 27 groups and 25 groups were obtained from the soils at 25°C and at 4°C incubation temperatures, respectively. These groups are affiliated with 18 genera that belong to six taxa, viz, Actinobacteria, Gammaproteobacteria, Bacteroidetes, Firmicutes, Alphaproteobacteria, and Betaproteobacteria. The dominant taxa were Actinobacteria, Gammaproteobacteria, and Bacteroidetes in all the samples. The abundance and the diversity of the genera isolated at 25°C incubation temperature were greater than that at 4°C.
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Martin F, Torelli S, Le Paslier D, Barbance A, Martin-Laurent F, Bru D, Geremia R, Blake G, Jouanneau Y. Betaproteobacteria dominance and diversity shifts in the bacterial community of a PAH-contaminated soil exposed to phenanthrene. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2012; 162:345-353. [PMID: 22243884 DOI: 10.1016/j.envpol.2011.11.032] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Revised: 11/12/2011] [Accepted: 11/22/2011] [Indexed: 05/31/2023]
Abstract
In this study, the PAH-degrading bacteria of a constructed wetland collecting road runoff has been studied through DNA stable isotope probing. Microcosms were spiked with (13)C-phenanthrene at 34 or 337 ppm, and bacterial diversity was monitored over a 14-day period. At 337 ppm, PAH degraders became dominated after 5 days by Betaproteobacteria, including novel Acidovorax, Rhodoferax and Hydrogenophaga members, and unknown bacteria related to Rhodocyclaceae. The prevalence of Betaproteobacteria was further demonstrated by phylum-specific quantitative PCR, and was correlated with a burst of phenanthrene mineralization. Striking shifts in the population of degraders were observed after most of the phenanthrene had been removed. Soil exposed to 34 ppm phenanthrene showed a similar population of degraders, albeit only after 14 days. Results demonstrate that specific Betaproteobacteria are involved in the main response to soil PAH contamination, and illustrate the potential of SIP approaches to investigate PAH biodegradation in soil.
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Affiliation(s)
- Florence Martin
- CEA, DSV, iRTSV, Laboratoire de Chimie et Biologie des Métaux, Grenoble, France
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Bacchetti De Gregoris T, Aldred N, Clare AS, Burgess JG. Improvement of phylum- and class-specific primers for real-time PCR quantification of bacterial taxa. J Microbiol Methods 2011; 86:351-6. [PMID: 21704084 DOI: 10.1016/j.mimet.2011.06.010] [Citation(s) in RCA: 293] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Accepted: 06/10/2011] [Indexed: 12/28/2022]
Abstract
Mapping the distribution of phylogenetically distinct bacteria in natural environments is of primary importance to an understanding of ecological dynamics. Here we present a quantitative PCR (qPCR) assay for the analysis of higher taxa composition in natural communities that advances previously available methods by allowing quantification of several taxa during the same qPCR run. Existing primers targeting the 16S rRNA gene specific for Firmicutes, Actinobacteria, Bacteroidetes and for the α and γ subdivisions of the Proteobacteria were improved by largely increasing the coverage of the taxon they target without diminishing their specificity. The qPCR assay was validated in vitro testing artificial mixtures of 16S rRNA sequences and used to characterise the composition of natural communities developing in young marine biofilms. The possible contribution of the proposed technique in revealing ecological dynamics affecting higher bacterial taxa is discussed.
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Affiliation(s)
- Tristano Bacchetti De Gregoris
- School of Marine Science and Technology, Ridley Building, Newcastle University, Newcastle upon Tyne NE1 7RU, England, UK
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