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Kovács B, Andreolli M, Lampis S, Biró B, Kotroczó Z. Bacterial Community Structure Responds to Soil Management in the Rhizosphere of Vine Grape Vineyards. BIOLOGY 2024; 13:254. [PMID: 38666866 PMCID: PMC11048173 DOI: 10.3390/biology13040254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024]
Abstract
The microbial communities of the rhizospheres of vineyards have been subject to a considerable body of research, but it is still unclear how the applied soil cultivation methods are able to change the structure, composition, and level of diversity of their communities. Rhizosphere samples were collected from three neighbouring vineyards with the same time of planting and planting material (rootstock: Teleki 5C; Vitis vinifera: Müller Thurgau). Our objective was to examine the diversity occurring in bacterial community structures in vineyards that differ only in the methods of tillage procedure applied, namely intensive (INT), extensive (EXT), and abandoned (AB). For that we took samples from two depths (10-30 cm (shallow = S) and 30-50 cm (deep = D) of the grape rhizosphere in each vineyard and the laboratory and immediately prepared the slices of the roots for DNA-based analysis of the bacterial communities. Bacterial community structure was assessed by means of PCR-DGGE analysis carried out on the v3 region of 16S rRNA gene. Based on the band composition of the DGGE profiles thus obtained, the diversity of the microbial communities was evaluated and determined by the Shannon-Weaver index (H'). Between the AB and EXT vineyards at the S depth, the similarity of the community structure was 55%; however, the similarity of the D samples was more than 80%, while the difference between the INT samples and the other two was also higher than 80%. Based on our results, we can conclude that intensive cultivation strongly affects the structure and diversity of the bacterial community.
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Affiliation(s)
- Barnabás Kovács
- Institute of Viticulture and Enology, Hungarian University of Agriculture and Life Sciences, 8360 Keszthely, Hungary
| | - Marco Andreolli
- Department of Biotechnology & Verona University Culture Collection-Department of Biotechnology (VUCC-DBT), University of Verona, 37134 Verona, Italy; (M.A.); (S.L.)
| | - Silvia Lampis
- Department of Biotechnology & Verona University Culture Collection-Department of Biotechnology (VUCC-DBT), University of Verona, 37134 Verona, Italy; (M.A.); (S.L.)
| | - Borbála Biró
- Department of Agro-Environmental Studies, Hungarian University of Agriculture and Life Sciences, 1118 Budapest, Hungary; (B.B.); (Z.K.)
| | - Zsolt Kotroczó
- Department of Agro-Environmental Studies, Hungarian University of Agriculture and Life Sciences, 1118 Budapest, Hungary; (B.B.); (Z.K.)
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2
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Li X, Yang F, Zhao J, Ge F. Mapping the knowledge domain of microbial desulfurization application in fuels and ores for sustainable industry. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:113151-113174. [PMID: 37853221 DOI: 10.1007/s11356-023-30236-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 09/29/2023] [Indexed: 10/20/2023]
Abstract
Direct application of high-sulfur fuels and ores can cause environmental pollution (such as air pollution and acid rain) and, in serious cases, endanger human health and contribute to property damage. In the background of preserving the environment, microbial desulfurization technologies for high-sulfur fuels and ores are rapidly developed. This paper aims to reveal the progress of microbial desulfurization research on fuels and ores using bibliometric analysis. 910 publications on microbial desulfurization of fuels and ores from web core databases were collected in this work, spanning 39 years. Through 910 retrieved documents, collaborative networks of authors, institutions and countries were mapped by this work, the sources of highly cited articles and cited documents were statistically analyzed, and keyword development from different perspectives was discussed. The results of the study provide a reference for microbial desulfurization research and benefit environmental protection and energy green applications.
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Affiliation(s)
- Xin Li
- College of Environment and Safety Engineering, Fuzhou University, Fuzhou, 350116, China
| | - Fuqiang Yang
- College of Environment and Safety Engineering, Fuzhou University, Fuzhou, 350116, China.
- Fujian Provincial Key Laboratory of Remote Sensing of Soil Erosion and Disaster Prevention, Fuzhou University, No. 2 Xueyuan Road, University Town, Fuzhou, 350116, Fujian Province, China.
| | - Jiale Zhao
- College of Environment and Safety Engineering, Fuzhou University, Fuzhou, 350116, China
| | - Fanliang Ge
- College of Environment and Safety Engineering, Fuzhou University, Fuzhou, 350116, China
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3
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Tan KY, Deng S, Tan TK, Hari R, Sitam FT, Othman RY, Wong KT, Mohidin TBM, Choo SW. Genome sequence analysis of Malayan pangolin ( Manis javanica) forensic samples reveals the presence of Paraburkholderia fungorum sequences. PeerJ 2023; 11:e16002. [PMID: 37810781 PMCID: PMC10559893 DOI: 10.7717/peerj.16002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 08/09/2023] [Indexed: 10/10/2023] Open
Abstract
Background The Malayan pangolin (Manis javanica) is a placental mammal and is listed as Critically Endangered on the IUCN Red List of Threatened Species. Most previous attempts to breed pangolins in captivity have met with little success because of dietary issues, infections, and other complications, although a previous study reported breeding pangolins in captivity to the third generation. In our previous pangolin genome sequencing data analysis, we obtained a considerable amount of bacterial DNA from a pregnant female Malayan pangolin (named "UM3"), which was likely infected by Paraburkholderia fungorum-an agent of biodegradation and bioremediation in agriculture. Methodology Here, we further confirmed and characterized this bacterial species using PCR, histological staining, whole-genome sequencing, and bioinformatics approaches. PCR assays with in-house designed primer sets and 16S universal primers showed clear positive bands in the cerebrum, cerebellum, lung, and blood of UM3 suggesting that UM3 might have developed septicaemia. Histological staining showed the presence of Gram-negative rod-shaped bacteria in the pangolin brain and lungs, indicating the colonization of the bacteria in these two organs. In addition, PCR screening of UM3's fetal tissues revealed the presence of P. fungorum in the gastrocnemius muscle, but not in other tissues that we examined. We also sequenced and reconstructed the genome of pangolin P. fungorum, which has a genome size of 7.7 Mbps. Conclusion Our study is the first to present detailed evidence of the presence of P. fungorum in a pangolin and her fetus (although preliminary results were presented in our previous article). Here, we raise the concern that P. fungorum may potentially infect humans, especially YOPI (young, old, pregnant, and immunocompromised) people. Therefore, caution should be exercised when using this bacterial species as biodegradation or bioremediation agents in agriculture.
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Affiliation(s)
- Ka Yun Tan
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Siwei Deng
- College of Science and Technology, Wenzhou-Kean University, Wenzhou, Zhejiang, China
| | - Tze King Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Ranjeev Hari
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Frankie Thomas Sitam
- National Wildlife Forensic Laboratory, Department of Wildlife and National Parks (PERHILITAN), Kuala Lumpur, Malaysia
| | - Rofina Yasmin Othman
- Centre for Research in Biotechnology for Agriculture (CEBAR), University of Malaya, Kuala Lumpur, Malaysia
| | - Kum Thong Wong
- Department of Pathology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | | | - Siew Woh Choo
- College of Science and Technology, Wenzhou-Kean University, Wenzhou, Zhejiang, China
- Zhejiang Bioinformatics International Science and Technology Cooperation Center, Wenzhou, Zhejiang, China
- Wenzhou Municipal Key Laboratory for Applied Biomedical and Biopharmaceutical Informatics, Wenzhou, Zhejiang, China
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4
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Andreolli M, Lampis S, Tosi L, Marano V, Zapparoli G. Fungicide sensitivity of grapevine bacteria with plant growth-promoting traits and antagonistic activity as non-target microorganisms. World J Microbiol Biotechnol 2023; 39:121. [PMID: 36929028 PMCID: PMC10020324 DOI: 10.1007/s11274-023-03569-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 03/07/2023] [Indexed: 03/18/2023]
Abstract
This study evaluates the capacity of commercial formulations of synthetic fungicides to inhibit grapevine bacterial growth when sprayed on vineyards to control diseases, such as downy mildew, powdery mildew and secondary rots. Fungicide sensitivity plate assays were carried out on bacteria isolated from vineyards that were also identified and characterized for their plant growth-promoting (PGP) traits and antifungal activity. The high taxonomic variability of bacteria screened with different chemical classes of fungicides is one new finding of this study. Seven out of 11 fungicides were able to inhibit the growth of bacteria at a concentration corresponding to the maximum dose allowed by law in spray treatments of vineyards. Bacterial sensitivity to each fungicide varied greatly. Many sensitive isolates displayed PGP traits and/or antagonistic activity. This study shows the potential impact of fungicidal treatments on grapevine bacterial microbiota. The involvement of bacteria beneficial to the growth and health of plants underlines the importance of this investigation. Our data reveal that the control of a certain disease may be possible using fungicides that have no or low impact on natural non-target microbiota. Understanding the action mechanisms of the active ingredients in these products is a priority for the development of new eco-friendly pesticides.
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Affiliation(s)
- Marco Andreolli
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, Verona, 37134, Italy
| | - Silvia Lampis
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, Verona, 37134, Italy
| | - Lorenzo Tosi
- AGREA Centro Studi, San Giovanni Lupatoto, Italy
| | - Viviana Marano
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, Verona, 37134, Italy
| | - Giacomo Zapparoli
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, Verona, 37134, Italy.
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Keaney D, Lucey B, Quinn N, Finn K. The Effects of Freeze-Thaw and UVC Radiation on Microbial Survivability in a Selected Mars-like Environment. Microorganisms 2022; 10:microorganisms10030576. [PMID: 35336151 PMCID: PMC8956125 DOI: 10.3390/microorganisms10030576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/23/2022] [Accepted: 03/04/2022] [Indexed: 02/06/2023] Open
Abstract
The purpose of this study was to determine survivability of Escherichia coli, Deinococcus radiodurans and Paraburkholderia fungorum under Mars-simulated conditions for freeze-thawing (−80 °C to +30 °C) and UV exposure alone and in combination. E. coli ATCC 25922, D. radiodurans and P. fungorum remained viable following 20 successive freeze-thaw cycles, exhibiting viabilities of 2.3%, 96% and 72.6%, respectively. E. coli ATCC 9079 was non-recoverable by cycle 9. When exposed to UV irradiation, cells withstood doses of 870 J/m2 (E. coli ATCC 25922), 200 J/m2 (E. coli ATCC 9079), 50,760 J/m2 (D. radiodurans) and 44,415 J/m2 (P. fungorum). Data suggests P. fungorum is highly UV-resistant. Combined freeze-thawing with UV irradiation showed freezing increased UV resistance in E. coli ATCC 25922, E. coli DSM 9079 and D. radiodurans by 6-fold, 30-fold and 1.2-fold, respectively. Conversely, freezing caused P. fungorum to exhibit a 1.75-fold increase in UV susceptibility. Strain-dependent experimentation demonstrated that freezing increases UV resistance and prolongs survival. These findings suggest that exposure to short wavelength UV rays (254 nm) and temperature cycles resembling the daily fluctuating conditions on Mars do not significantly affect survival of D. radiodurans, P. fungorum and E. coli ATCC 25922 following 20 days of exposure.
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Affiliation(s)
- Daniel Keaney
- Department of Biological Sciences, Munster Technological University, Bishopstown, T12 P928 Cork, Ireland; (D.K.); (B.L.)
| | - Brigid Lucey
- Department of Biological Sciences, Munster Technological University, Bishopstown, T12 P928 Cork, Ireland; (D.K.); (B.L.)
| | - Noreen Quinn
- Department of Mathematics, Munster Technological University, Bishopstown, T12 P928 Cork, Ireland;
| | - Karen Finn
- Department of Analytical, Biopharmaceutical and Medical Sciences, Galway-Mayo Institute of Technology, Old Dublin Road, H91 T8NW Galway, Ireland
- Correspondence:
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Soil Characteristics Constrain the Response of Microbial Communities and Associated Hydrocarbon Degradation Genes during Phytoremediation. Appl Environ Microbiol 2021; 87:AEM.02170-20. [PMID: 33097512 DOI: 10.1128/aem.02170-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 10/18/2020] [Indexed: 12/21/2022] Open
Abstract
Rhizodegradation is a promising cleanup technology where microorganisms degrade soil contaminants in the rhizosphere. A symbiotic relationship is expected to occur between plant roots and soil microorganisms in contaminated soils that enhances natural microbial degradation. However, little is known about how different initial microbiotas influence the rhizodegradation outcome. Recent studies have hinted that soil initial diversity has a determining effect on the outcome of contaminant degradation. To test this, we either planted (P) or not (NP) balsam poplars (Populus balsamifera) in two soils of contrasting diversity (agricultural and forest) that were contaminated or not with 50 mg kg-1 of phenanthrene (PHE). The DNA from the rhizosphere of the P and the bulk soil of the NP pots was extracted and the bacterial genes encoding the 16S rRNA, the PAH ring-hydroxylating dioxygenase alpha subunits (PAH-RHDα) of Gram-positive and Gram-negative bacteria, and the fungal ITS region were sequenced to characterize the microbial communities. The abundances of the PAH-RHDα genes were quantified by real-time quantitative PCR. Plant presence had a significant effect on PHE degradation only in the forest soil, whereas both NP and P agricultural soils degraded the same amount of PHE. Fungal communities were mainly affected by plant presence, whereas bacterial communities were principally affected by the soil type, and upon contamination the dominant PAH-degrading community was similarly constrained by soil type. Our results highlight the crucial importance of soil microbial and physicochemical characteristics in the outcome of rhizoremediation.IMPORTANCE Polycyclic aromatic hydrocarbons (PAH) are a group of organic contaminants that pose a risk to ecosystems' health. Phytoremediation is a promising biotechnology with the potential to restore PAH-contaminated soils. However, some limitations prevent it from becoming the remediation technology of reference, despite being environmentally friendlier than mainstream physicochemical alternatives. Recent reports suggest that the original soil microbial diversity is the key to harnessing the potential of phytoremediation. Therefore, this study focused on determining the effect of two different soil types in the fate of phenanthrene (a polycyclic aromatic hydrocarbon) under balsam poplar remediation. Poplar increased the degradation of phenanthrene in forest, but not in agricultural soil. The fungi were affected by poplars, whereas total bacteria and specific PAH-degrading bacteria were constrained by soil type, leading to different degradation patterns between soils. These results highlight the importance of performing preliminary microbiological studies of contaminated soils to determine whether plant presence could improve remediation rates or not.
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7
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Biodegradation of selected hydrocarbons by novel bacterial strains isolated from contaminated Arabian Gulf sediment. Sci Rep 2020; 10:21846. [PMID: 33318512 PMCID: PMC7736303 DOI: 10.1038/s41598-020-78733-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Accepted: 11/11/2020] [Indexed: 01/05/2023] Open
Abstract
Three strains of novel bacteria were isolated from oil-contaminated sediment from the Arabian Gulf (Brevibacillus brevis T2C2008, Proteus mirabilis T2A12001, and Rhodococcus quinshengi TA13008). The isolated strains were tested for their degrading efficacy of low and high molecular hydrocarbon (naphthalene and pyrene). The efficacy of the two-hydrocarbon degradation by the isolates bacterial was determined at a temperature of 25 °C and 37 °C and pH of 5.0 and 9.0. In inoculated media at 37 °C, Rhodococcus qinshengi fully metabolized naphthalene and degrade 56% of pyrene. Brevibacillus brevis break down over 80% of naphthalene at room temperatures (25 °C). However, it was found that P. mirabilis and R. qinshengi biodegraded nearly 94% of naphthalene in the incubated media. The capacity for pyrene and naphthalene degradation in varying pH and temperature conditions was shown to be significant in Rhodococcus qinshengi because of its mineralization exceeding 50% across the tested pH and temperature. This implies that the isolated strains are ideal for biodegradation of contaminated sediment with naphthalene and pyrene.
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8
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Tan KY, Dutta A, Tan TK, Hari R, Othman RY, Choo SW. Comprehensive genome analysis of a pangolin-associated Paraburkholderia fungorum provides new insights into its secretion systems and virulence. PeerJ 2020; 8:e9733. [PMID: 32953261 PMCID: PMC7474880 DOI: 10.7717/peerj.9733] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 07/25/2020] [Indexed: 12/26/2022] Open
Abstract
Background Paraburkholderia fungorum (P. fungorum) is a Gram-negative environmental species that has been commonly used as a beneficial microorganism in agriculture as an agent for biocontrol and bioremediation. Its use in agriculture is controversial as many people believe that it could harm human health; however, there is no clear evidence to support. Methodology The pangolin P. fungorum (pangolin Pf) genome has a genomic size of approximately 7.7 Mbps with N50 of 69,666 bps. Our study showed that pangolin Pf is a Paraburkholderia fungorum supported by evidence from the core genome SNP-based phylogenetic analysis and the ANI analysis. Functional analysis has shown that the presence of a considerably large number of genes related to stress response, virulence, disease, and defence. Interestingly, we identified different types of secretion systems in the genome of pangolin Pf, which are highly specialized and responsible for a bacterium’s response to its environment and in physiological processes such as survival, adhesion, and adaptation. The pangolin Pf also shared some common virulence genes with the known pathogenic member of the Burkholderiales. These genes play important roles in adhesion, motility, and invasion. Conclusion This study may provide better insights into the functions, secretion systems and virulence of this pangolin-associated bacterial strain. The addition of this genome sequence is also important for future comparative analysis and functional work of P. fungorum.
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Affiliation(s)
- Ka Yun Tan
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur, Malaysia.,Genome Informatics Research Laboratory, Centre for Research in Biotechnology for Agriculture (CEBAR), High Impact Research Building, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Avirup Dutta
- Genome Informatics Research Laboratory, Centre for Research in Biotechnology for Agriculture (CEBAR), High Impact Research Building, Universiti Malaya, Kuala Lumpur, Malaysia.,Current affiliation: The Novo Nordisk Foundation Center for Basic Metabolic Research, Human Genomics and Metagenomics in Metabolism, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tze King Tan
- Genome Informatics Research Laboratory, Centre for Research in Biotechnology for Agriculture (CEBAR), High Impact Research Building, Universiti Malaya, Kuala Lumpur, Malaysia.,Current affiliation: Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Ranjeev Hari
- Genome Informatics Research Laboratory, Centre for Research in Biotechnology for Agriculture (CEBAR), High Impact Research Building, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Rofina Y Othman
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur, Malaysia.,Centre for Research in Biotechnology for Agriculture (CEBAR), Level 3, Research Management & Innovation Complex, Universiti Malaya, Copenhagen, Kuala Lumpur, Malaysia
| | - Siew Woh Choo
- College of Science and Technology, Wenzhou-Kean University, Wenzhou, Zhejiang Province, China
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Madhaiyan M, See-Too WS, Ee R, Saravanan VS, Wirth JS, Alex THH, Lin C, Kim SJ, Weon HY, Kwon SW, Whitman WB, Ji L. Chitinasiproducens palmae gen. nov., sp. nov., a new member of the family Burkholderiaceae isolated from leaf tissues of oil palm (Elaeis guineensis Jacq.). Int J Syst Evol Microbiol 2020; 70:2640-2647. [DOI: 10.1099/ijsem.0.004084] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
A Gram-stain-negative, aerobic, rod-shaped, leaf-associated bacterium, designated JS23T, was isolated from surface-sterilized leaf tissue of an oil palm grown in Singapore and was investigated by polyphasic taxonomy. Phylogenetic analyses based on 16S rRNA gene sequences and 180 conserved genes in the genome of several members of
Burkholderiaceae
revealed that strain JS23T formed a distinct evolutionary lineage independent of other taxa within the family
Burkholderiaceae
. The predominant ubiquinone was Q-8. The primary polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, and an unidentified aminophospholipid. The major fatty acids were C16 : 0, summed feature 3 (C16 : 1
ω7c /C16 : 1
ω6c) and summed feature 8 (C18 : 1
ω7c /C18 : 1
ω6c). The size of the genome is 5.36 Mbp with a DNA G+C content of 66.2 mol%. Genomic relatedness measurements such as average nucleotide identity, genome-to-genome distance and digital DNA–DNA hybridization clearly distinguished strain JS23T from the closely related genera
Burkholderia
,
Caballeronia
,
Mycetohabitans
,
Mycoavidus
,
Pandoraea
,
Paraburkholderia
,
Robbsia
and
Trinickia
. Furthermore, average amino acid identity values and the percentages of conserved proteins, 56.0–68.4 and 28.2–45.5, respectively, were well below threshold values for genus delineation and supported the assignment of JS23T to a novel genus. On the basis of the phylogenetic, biochemical, chemotaxonomic and phylogenomic evidence, strain JS23T is proposed to represent a novel species of a new genus within the family
Burkholderiaceae
, for which the name Chitinasiproducens palmae gen. nov., sp. nov., is proposed with the type strain of JS23T (= DSM 27307T=KACC 17592T).
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Affiliation(s)
- Munusamy Madhaiyan
- Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604, Singapore
| | - Wah-Seng See-Too
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Robson Ee
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | | | - Joseph S. Wirth
- Department of Microbiology, 527 Biological Sciences Building, University of Georgia, Athens, GA 30602-2605, USA
| | - Tan Hian Hwee Alex
- Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604, Singapore
| | - Cai Lin
- Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604, Singapore
| | - Soo-Jin Kim
- Agricultural Microbiology Division, National Institute of Agricultural Science, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Hang-Yeon Weon
- Agricultural Microbiology Division, National Institute of Agricultural Science, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Soon-Wo Kwon
- Agricultural Microbiology Division, National Institute of Agricultural Science, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - William B. Whitman
- Department of Microbiology, 527 Biological Sciences Building, University of Georgia, Athens, GA 30602-2605, USA
| | - Lianghui Ji
- Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604, Singapore
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Lorenzini M, Zapparoli G. Epiphytic bacteria from withered grapes and their antagonistic effects on grape-rotting fungi. Int J Food Microbiol 2019; 319:108505. [PMID: 31911210 DOI: 10.1016/j.ijfoodmicro.2019.108505] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 12/05/2019] [Accepted: 12/28/2019] [Indexed: 11/25/2022]
Abstract
The bacterial community in the surface of withered grapes, which are partially dehydrated in the post-harvest period to produce Italian passito wine, has been seldom investigated. Fifty epiphytic bacterial strains isolated from withered berries were identified and characterized. Genera such as Bacillus, Brevibacillus, Curtobacterium, Micrococcus, Pseudomonas and Staphylococcus have been identified by comparative sequence and phylogenetic analyses of 16S rRNA gene sequences. Bacillus was predominant and several taxa within this genus have been recognized. All isolates were characterized by PCR fingerprinting and assayed for osmotic tolerance, motility and antifungal activity. Several Bacillus strains displayed antagonistic effects on grape-rotting fungi such as Botrytis cinerea, Penicillium expansum and Aspergillus uvarum. The other strains were weakly or non-antagonistic on these fungi. Assay on antagonistic interactions among bacteria was also carried out. Bacillus strains, which exhibit swimming and swarming motility, have the potential to colonize the grape surface and to compete with their neighbours for space and resources. The occurrence of these isolates could reduce the contamination of fungal pathogens during grape withering. Epiphytic antagonistic bacteria could potentially be of interest for fungal biocontrol in the post-harvest processing of fruit and vegetables.
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Affiliation(s)
- Marilinda Lorenzini
- Dipartimento di Biotecnologie, Università degli Studi di Verona, 37134 Verona, Italy
| | - Giacomo Zapparoli
- Dipartimento di Biotecnologie, Università degli Studi di Verona, 37134 Verona, Italy.
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Lemmel F, Maunoury-Danger F, Leyval C, Cébron A. DNA stable isotope probing reveals contrasted activity and phenanthrene-degrading bacteria identity in a gradient of anthropized soils. FEMS Microbiol Ecol 2019; 95:5626340. [PMID: 31730156 DOI: 10.1093/femsec/fiz181] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 11/13/2019] [Indexed: 11/13/2022] Open
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous soil organic pollutants. Although PAH-degrading bacteria are present in almost all soils, their selection and enrichment have been shown in historically high PAH contaminated soils. We can wonder if the effectiveness of PAH biodegradation and the PAH-degrading bacterial diversity differ among soils. The stable isotope probing (SIP) technique with 13C-phenanthrene (PHE) as a model PAH was used to: (i) compare for the first time a range of 10 soils with various PAH contamination levels, (ii) determine their PHE-degradation efficiency and (iii) identify the active PHE-degraders using 16S rRNA gene amplicon sequencing from 13C-labeled DNA. Surprisingly, the PHE degradation rate was not directly correlated to the initial level of total PAHs and phenanthrene in the soils, but was mostly explained by the initial abundance and richness of soil bacterial communities. A large diversity of PAH-degrading bacteria was identified for seven of the soils, with differences among soils. In the soils where the PHE degradation activities were the higher, Mycobacterium species were always the dominant active PHE degraders. A positive correlation between PHE-degradation level and the diversity of active PHE-degraders (Shannon index) supported the hypothesis that cooperation between strains led to a more efficient PAH degradation.
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Affiliation(s)
- Florian Lemmel
- Université de Lorraine, CNRS, LIEC UMR7360, Faculté des Sciences et Technologies, Bd des Aiguillettes, BP70239, 54506 Vandoeuvre-les-Nancy, France
| | - Florence Maunoury-Danger
- Université de Lorraine, CNRS, LIEC UMR7360, Campus Bridoux, Avenue du général Delestraint, 57070 Metz, France
| | - Corinne Leyval
- Université de Lorraine, CNRS, LIEC UMR7360, Faculté des Sciences et Technologies, Bd des Aiguillettes, BP70239, 54506 Vandoeuvre-les-Nancy, France
| | - Aurélie Cébron
- Université de Lorraine, CNRS, LIEC UMR7360, Faculté des Sciences et Technologies, Bd des Aiguillettes, BP70239, 54506 Vandoeuvre-les-Nancy, France
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12
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Liu XX, Hu X, Cao Y, Pang WJ, Huang JY, Guo P, Huang L. Biodegradation of Phenanthrene and Heavy Metal Removal by Acid-Tolerant Burkholderia fungorum FM-2. Front Microbiol 2019; 10:408. [PMID: 30930861 PMCID: PMC6427951 DOI: 10.3389/fmicb.2019.00408] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 02/18/2019] [Indexed: 11/13/2022] Open
Abstract
Phenanthrene (PHE) is a common pollutant of acidic and non-acidic environments that is recalcitrant to biodegradation. Herein, Burkholderia fungorum FM-2 (GenBank accession no. KM263605) was isolated from oil-contaminated soil in Xinjiang and characterized morphologically, physiologically, and phylogenetically. Environmental parameters including PHE concentration, pH, temperature, and salinity were optimized, and heavy metal tolerance was investigated. The MIC of strain FM-2 tolerant to Pb(II) and Cd(II) was 50 and 400 mg L−1, respectively, while the MIC of Zn(II) was >1,200 mg L−1. Atypically for a B. fungorum strain, FM-2 utilized PHE (300 mg L−1) as a sole carbon source over a wide pH range (between pH 3 and 9). PHE and heavy metal metabolism were assessed using gas chromatography (GC), inductively coupled plasma optical emission spectroscopy (ICP-OES), scanning electron microscopy-energy dispersive X-ray spectroscopy (SEM-EDS), Fourier-transform infrared (FTIR) spectroscopy and ultraviolet (UV) absorption spectrometry. The effects of heavy metals on the bioremediation of PHE in soil were investigated, and the findings suggest that FM-2 has potential for combined bioremediation of soils co-contaminated with PHE and heavy metals.
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Affiliation(s)
- Xin-Xin Liu
- Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, College of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin, China
| | - Xin Hu
- Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, College of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin, China
| | - Yue Cao
- Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, College of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin, China
| | - Wen-Jing Pang
- Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, College of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin, China
| | - Jin-Yu Huang
- Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, College of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin, China
| | - Peng Guo
- Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, College of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin, China
| | - Lei Huang
- Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, College of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin, China
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13
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Lee Y, Lee Y, Jeon CO. Biodegradation of naphthalene, BTEX, and aliphatic hydrocarbons by Paraburkholderia aromaticivorans BN5 isolated from petroleum-contaminated soil. Sci Rep 2019; 9:860. [PMID: 30696831 PMCID: PMC6351602 DOI: 10.1038/s41598-018-36165-x] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 11/16/2018] [Indexed: 11/09/2022] Open
Abstract
To isolate bacteria responsible for the biodegradation of naphthalene, BTEX (benzene, toluene, ethylbenzene, and o-, m-, and p-xylene), and aliphatic hydrocarbons in petroleum-contaminated soil, three enrichment cultures were established using soil extract as the medium supplemented with naphthalene, BTEX, or n-hexadecane. Community analyses showed that Paraburkholderia species were predominant in naphthalene and BTEX, but relatively minor in n-hexadecane. Paraburkholderia aromaticivorans BN5 was able to degrade naphthalene and all BTEX compounds, but not n-hexadecane. The genome of strain BN5 harbors genes encoding 29 monooxygenases including two alkane 1-monooxygenases and 54 dioxygenases, indicating that strain BN5 has versatile metabolic capabilities, for diverse organic compounds: the ability of strain BN5 to degrade short chain aliphatic hydrocarbons was verified experimentally. The biodegradation pathways of naphthalene and BTEX compounds were bioinformatically predicted and verified experimentally through the analysis of their metabolic intermediates. Some genomic features including the encoding of the biodegradation genes on a plasmid and the low sequence homologies of biodegradation-related genes suggest that biodegradation potentials of strain BN5 may have been acquired via horizontal gene transfers and/or gene duplication, resulting in enhanced ecological fitness by enabling strain BN5 to degrade all compounds including naphthalene, BTEX, and short aliphatic hydrocarbons in contaminated soil.
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Affiliation(s)
- Yunho Lee
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Yunhee Lee
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea.
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14
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Anticandidal Potential of Endophytic Bacteria Isolated from Dryopteris Uniformis (Makino). Jundishapur J Microbiol 2018. [DOI: 10.5812/jjm.69878] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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15
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Bassene H, Niang EHA, Fenollar F, Dipankar B, Doucouré S, Ali E, Michelle C, Raoult D, Sokhna C, Mediannikov O. 16S Metagenomic Comparison of Plasmodium falciparum-Infected and Noninfected Anopheles gambiae and Anopheles funestus Microbiota from Senegal. Am J Trop Med Hyg 2018; 99:1489-1498. [PMID: 30350766 DOI: 10.4269/ajtmh.18-0263] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
In the context of the pre-elimination of malaria, biological control may provide an alternative or additional tool to current malaria control strategies. During their various stages of development, mosquitoes undergo subsequent changes in their associated microbiota, depending on their environment and nutritional status. Although Anopheles gambiae s.l. and Anopheles funestus are the two major malaria vectors in Senegal, the composition of their microbiota is not yet well known. In this study, we explored the microbiota of mosquitoes naturally infected or not by Plasmodium falciparum (Pf) using the 16S ribosomal RNA gene-based bacterial metagenomic approach. In both vector species, the microbiota was more diverse in Pf-infected samples than in the noninfected ones, although the total number of reads appeared to be higher in noninfected mosquitoes. Overall, the microbiota was different between the two vector species. Noteworthy, the bacterial microbiota was significantly different between Pf-positive and Pf-negative groups whatever the species, but was similar between individuals of the same infection status within a species. Overall, the phylum of Proteobacteria was the most predominant in both species, with bacteria of the genus Burkholderia outweighing the others in noninfected vectors. The presence of some specific bacterial species such as Asaia bogorensis, Enterobacter cloacae, Burkholderia fungorum, and Burkholderia cepacia was also observed in Pf-free samples only. These preliminary observations pave the way for further characterization of the mosquito microbiota to select promising bacterial candidates for potential use in an innovative approach to controlling malaria and overcoming the challenges to achieving a malaria-free world.
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Affiliation(s)
- Hubert Bassene
- Aix Marseille Université, IRD, Assistance Publique-Hopitaux Marseille, Service de Santé des Armées, Vecteurs-Infections Tropicales et Méditerranéennes (VITROME), Marseille, France.,Vecteurs-Infections Tropicales et Méditerranéennes (VITROME), Campus International Université Cheikh Anta Diop-Institut de Recherche pour le Développement, Dakar, Sénégal
| | - El Hadji Amadou Niang
- Aix Marseille Université, IRD, AP-HM, Microbes, Evolution, Phylogeny and Infection (MEPHI), Marseille, France.,Laboratoire d'Ecologie Vectorielle et Parasitaire (LEVP), Faculté des Sciences et Techniques, Université Cheikh Anta Diop (UCAD) de Dakar, Dakar, Sénégal.,Vecteurs-Infections Tropicales et Méditerranéennes (VITROME), Campus International Université Cheikh Anta Diop-Institut de Recherche pour le Développement, Dakar, Sénégal
| | - Florence Fenollar
- Aix Marseille Université, IRD, Assistance Publique-Hopitaux Marseille, Service de Santé des Armées, Vecteurs-Infections Tropicales et Méditerranéennes (VITROME), Marseille, France
| | - Bachar Dipankar
- Aix Marseille Université, IRD, AP-HM, Microbes, Evolution, Phylogeny and Infection (MEPHI), Marseille, France
| | - Souleymane Doucouré
- Aix Marseille Université, IRD, Assistance Publique-Hopitaux Marseille, Service de Santé des Armées, Vecteurs-Infections Tropicales et Méditerranéennes (VITROME), Marseille, France.,Vecteurs-Infections Tropicales et Méditerranéennes (VITROME), Campus International Université Cheikh Anta Diop-Institut de Recherche pour le Développement, Dakar, Sénégal
| | - Essoham Ali
- Laboratoire d'Études et de Recherche en Statistique et Développement (LERSTAD), Université Gaston Berger de Saint Louis, St. Louis, Sénégal
| | - Caroline Michelle
- Aix Marseille Université, IRD, AP-HM, Microbes, Evolution, Phylogeny and Infection (MEPHI), Marseille, France
| | - Didier Raoult
- Aix Marseille Université, IRD, AP-HM, Microbes, Evolution, Phylogeny and Infection (MEPHI), Marseille, France
| | - Cheikh Sokhna
- Aix Marseille Université, IRD, Assistance Publique-Hopitaux Marseille, Service de Santé des Armées, Vecteurs-Infections Tropicales et Méditerranéennes (VITROME), Marseille, France.,Vecteurs-Infections Tropicales et Méditerranéennes (VITROME), Campus International Université Cheikh Anta Diop-Institut de Recherche pour le Développement, Dakar, Sénégal
| | - Oleg Mediannikov
- Aix Marseille Université, IRD, AP-HM, Microbes, Evolution, Phylogeny and Infection (MEPHI), Marseille, France
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16
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Martínez I, El-Said Mohamed M, Santos VE, García JL, García-Ochoa F, Díaz E. Metabolic and process engineering for biodesulfurization in Gram-negative bacteria. J Biotechnol 2017; 262:47-55. [PMID: 28947364 DOI: 10.1016/j.jbiotec.2017.09.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 09/08/2017] [Accepted: 09/09/2017] [Indexed: 11/19/2022]
Abstract
Microbial desulfurization or biodesulfurization (BDS) is an attractive low-cost and environmentally friendly complementary technology to the hydrotreating chemical process based on the potential of certain bacteria to specifically remove sulfur from S-heterocyclic compounds of crude fuels that are recalcitrant to the chemical treatments. The 4S or Dsz sulfur specific pathway for dibenzothiophene (DBT) and alkyl-substituted DBTs, widely used as model S-heterocyclic compounds, has been extensively studied at the physiological, biochemical and genetic levels mainly in Gram-positive bacteria. Nevertheless, several Gram-negative bacteria have been also used in BDS because they are endowed with some properties, e.g., broad metabolic versatility and easy genetic and genomic manipulation, that make them suitable chassis for systems metabolic engineering strategies. A high number of recombinant bacteria, many of which are Pseudomonas strains, have been constructed to overcome the major bottlenecks of the desulfurization process, i.e., expression of the dsz operon, activity of the Dsz enzymes, retro-inhibition of the Dsz pathway, availability of reducing power, uptake-secretion of substrate and intermediates, tolerance to organic solvents and metals, and other host-specific limitations. However, to attain a BDS process with industrial applicability, it is necessary to apply all the knowledge and advances achieved at the genetic and metabolic levels to the process engineering level, i.e., kinetic modelling, scale-up of biphasic systems, enhancing mass transfer rates, biocatalyst separation, etc. The production of high-added value products derived from the organosulfur material present in oil can be regarded also as an economically viable process that has barely begun to be explored.
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Affiliation(s)
- I Martínez
- Environmental Biology Department, Biological Research Center (CIB-CSIC), 28040 Madrid, Spain
| | - M El-Said Mohamed
- Research and Development Center, Saudi Aramco, Dhahran, Saudi Arabia
| | - V E Santos
- Chemical Engineering Department, Complutense University of Madrid, 28040 Madrid Spain
| | - J L García
- Environmental Biology Department, Biological Research Center (CIB-CSIC), 28040 Madrid, Spain; Institute for Integrative Systems Biology (I2SysBio) (University of Valencia-CSIC), 46980 Paterna Valencia, Spain
| | - F García-Ochoa
- Chemical Engineering Department, Complutense University of Madrid, 28040 Madrid Spain
| | - E Díaz
- Environmental Biology Department, Biological Research Center (CIB-CSIC), 28040 Madrid, Spain.
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17
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Joshi DR, Zhang Y, Gao Y, Liu Y, Yang M. Biotransformation of nitrogen- and sulfur-containing pollutants during coking wastewater treatment: Correspondence of performance to microbial community functional structure. WATER RESEARCH 2017; 121:338-348. [PMID: 28570873 DOI: 10.1016/j.watres.2017.05.045] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 05/18/2017] [Accepted: 05/21/2017] [Indexed: 06/07/2023]
Abstract
Although coking wastewater is generally considered to contain high concentration of nitrogen- and sulfur-containing pollutants, the biotransformation processes of these compounds have not been well understood. Herein, a high throughput functional gene array (GeoChip 5.0) in combination with Illumina MiSeq sequencing of the 16S rRNA gene were used to identify microbial functional traits and their role in biotransformation of nitrogen- and sulfur-containing compounds in a bench-scale aerobic coking wastewater treatment system operated for 488 days. Biotransformation of nitrogen and sulfur-containing pollutants deteriorated when pH of the bioreactor was increased to >8.0, and the microbial community functional structure was significantly associated with pH (Mantels test, P < 0.05). The release of ammonia nitrogen and sulfate was correlated with both the taxonomic and functional microbial community structure (P < 0.05). Considering the abundance and correlation with the release of ammonia nitrogen and sulfate, aromatic dioxygenases (e.g. xylXY, nagG), nitrilases (e.g. nhh, nitrilase), dibenzothiophene oxidase (DbtAc), and thiocyanate hydrolase (scnABC) were important functional genes for biotransformation of nitrogen- and sulfur-containing pollutants. Functional characterization of taxa and network analysis suggested that Burkholderiales, Actinomycetales, Rhizobiales, Pseudomonadales, and Hydrogenophiliales (Thiobacillus) were key functional taxa. Variance partitioning analysis showed that pH and influent ammonia nitrogen jointly explained 25.9% and 35.5% of variation in organic pollutant degrading genes and microbial community structure, respectively. This study revealed a linkage between microbial community functional structure and the likely biotransformation of nitrogen- and sulfur-containing pollutants, along with a suitable range of pH (7.0-7.5) for stability of the biological system treating coking wastewater.
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Affiliation(s)
- Dev Raj Joshi
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu Zhang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Yinxin Gao
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuan Liu
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Min Yang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China
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18
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Shah A, Hassan QP, Mushtaq S, Shah AM, Hussain A. Chemoprofile and functional diversity of fungal and bacterial endophytes and role of ecofactors - A review. J Basic Microbiol 2017; 57:814-826. [PMID: 28737000 DOI: 10.1002/jobm.201700275] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 06/18/2017] [Accepted: 06/25/2017] [Indexed: 11/08/2022]
Abstract
Endophytes represent a hidden world within plants. Almost all plants that are studied harbor one or more endophytes, which help their host to survive against pathogens and changing adverse environmental conditions. Fungal and bacterial endophytes with distinct ecological niches show important biological activities and ecological functions. Their unique physiological and biochemical characteristics lead to the production of niche specific secondary metabolites that may have pharmacological potential. Identification of specific secondary metabolites in adverse environment can also help us in understanding mechanisms of host tolerance against stress condition such as biological invasions, salt, drought, temperature. These metabolites include micro as well as macromolecules, which they produce through least studied yet surprising mechanisms like xenohormesis, toxin-antitoxin system, quorum sensing. Therefore, future studies should focus on unfolding all the underlying molecular mechanisms as well as the impact of physical and biochemical environment of a specific host over endophytic function and metabolite elicitation. Need of the hour is to reshape the focus of research over endophytes and scientifically drive their ecological role toward prospective pharmacological as well as eco-friendly biological applications. This may help to manage these endophytes especially from untapped ecoregions as a useful undying biological tool to meet the present challenges as well as lay a strong and logical basis for any impending challenges.
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Affiliation(s)
- Aiyatullah Shah
- Biotechnology Division, Indian Institute of Integrative Medicine, Sanat Nagar, Srinagar, India.,Academy of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, India
| | - Qazi Parvaiz Hassan
- Biotechnology Division, Indian Institute of Integrative Medicine, Sanat Nagar, Srinagar, India.,Academy of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, India
| | - Saleem Mushtaq
- Biotechnology Division, Indian Institute of Integrative Medicine, Sanat Nagar, Srinagar, India
| | - Aabid Manzoor Shah
- Biotechnology Division, Indian Institute of Integrative Medicine, Sanat Nagar, Srinagar, India.,Academy of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, India
| | - Aehtesham Hussain
- Biotechnology Division, Indian Institute of Integrative Medicine, Sanat Nagar, Srinagar, India.,Academy of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, India
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19
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Akita H, Kimura ZI, Yusoff MZM, Nakashima N, Hoshino T. Identification and characterization of Burkholderia multivorans CCA53. BMC Res Notes 2017; 10:249. [PMID: 28683814 PMCID: PMC5501517 DOI: 10.1186/s13104-017-2565-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 06/26/2017] [Indexed: 01/30/2023] Open
Abstract
Objective A lignin-degrading bacterium, Burkholderia sp. CCA53, was previously isolated from leaf soil. The purpose of this study was to determine phenotypic and biochemical features of Burkholderia sp. CCA53. Results Multilocus sequence typing (MLST) analysis based on fragments of the atpD, gltD, gyrB, lepA, recA and trpB gene sequences was performed to identify Burkholderia sp. CCA53. The MLST analysis revealed that Burkholderia sp. CCA53 was tightly clustered with B. multivorans ATCC BAA-247T. The quinone and cellular fatty acid profiles, carbon source utilization, growth temperature and pH were consistent with the characteristics of B. multivorans species. Burkholderia sp. CCA53 was therefore identified as B. multivorans CCA53.
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Affiliation(s)
- Hironaga Akita
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-0046, Japan.
| | - Zen-Ichiro Kimura
- Department of Civil and Environmental Engineering, National Institute of Technology, Kure College, 2-2-11 Aga-minami, Kure, Hiroshima, 737-8506, Japan
| | - Mohd Zulkhairi Mohd Yusoff
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-0046, Japan.,Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Nobutaka Nakashima
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo, Hokkaido, 062-8517, Japan.,Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 2-12-1-M6-5 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Tamotsu Hoshino
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-0046, Japan.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo, Hokkaido, 062-8517, Japan
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20
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Oyehan TA, Al-Thukair AA. Isolation and characterization of PAH-degrading bacteria from the Eastern Province, Saudi Arabia. MARINE POLLUTION BULLETIN 2017; 115:39-46. [PMID: 27912917 DOI: 10.1016/j.marpolbul.2016.11.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 10/25/2016] [Accepted: 11/06/2016] [Indexed: 06/06/2023]
Abstract
Contaminated sediment samples were collected from the Eastern Province, Saudi Arabia for isolation of pyrene- and phenanthrene-degrading bacteria by enrichment method. Four isolates were morphologically characterized as Gram-negative rod strains and 16S rRNA sequence analysis revealed the isolates as closely related to Pseudomonas aeruginosa, P. citronellolis, Ochrobactrum intermedium and Cupriavidus taiwanensis. Degradation of the polycyclic aromatic hydrocarbons (PAHs) by the latter three strains was investigated in liquid cultures. Results of concentration reduction analyzed with gas chromatography show that P. citronellolis_LB was efficient in removing phenanthrene, degrading 94% of 100ppm in 15days while O. intermedium_BC1 was more efficient in pyrene-removal, degrading 62% in 2weeks. Furthermore, bacterial growth assessment using optical density and population counts revealed the latter as more suitable for microbial growth analysis in PAH-containing cultures. In conclusion, the isolated bacterial strains could be further developed for efficient use in biodegradation of PAH.
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Affiliation(s)
- Tajudeen A Oyehan
- Environmental Sciences Program of Earth Sciences Dept., King Fahd University of Petroleum & Minerals, Dhahran 31261, Saudi Arabia
| | - Assad A Al-Thukair
- Life Sciences Dept., King Fahd University of Petroleum & Minerals, Dhahran 31261, Saudi Arabia.
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21
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Brock DA, Callison WÉ, Strassmann JE, Queller DC. Sentinel cells, symbiotic bacteria and toxin resistance in the social amoeba Dictyostelium discoideum. Proc Biol Sci 2017; 283:rspb.2015.2727. [PMID: 27097923 DOI: 10.1098/rspb.2015.2727] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 03/29/2016] [Indexed: 01/16/2023] Open
Abstract
The social amoeba Dictyostelium discoideum is unusual among eukaryotes in having both unicellular and multicellular stages. In the multicellular stage, some cells, called sentinels, ingest toxins, waste and bacteria. The sentinel cells ultimately fall away from the back of the migrating slug, thus removing these substances from the slug. However, some D. discoideum clones (called farmers) carry commensal bacteria through the multicellular stage, while others (called non-farmers) do not. Farmers profit from their beneficial bacteria. To prevent the loss of these bacteria, we hypothesize that sentinel cell numbers may be reduced in farmers, and thus farmers may have a diminished capacity to respond to pathogenic bacteria or toxins. In support, we found that farmers have fewer sentinel cells compared with non-farmers. However, farmers produced no fewer viable spores when challenged with a toxin. These results are consistent with the beneficial bacteria Burkholderia providing protection against toxins. The farmers did not vary in spore production with and without a toxin challenge the way the non-farmers did, which suggests the costs of Burkholderia may be fixed while sentinel cells may be inducible. Therefore, the costs for non-farmers are only paid in the presence of the toxin. When the farmers were cured of their symbiotic bacteria with antibiotics, they behaved just like non-farmers in response to a toxin challenge. Thus, the advantages farmers gain from carrying bacteria include not just food and protection against competitors, but also protection against toxins.
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Affiliation(s)
- Debra A Brock
- Department of Biology, Washington University in Saint Louis, Campus Box 1137, One Brookings Drive, Saint Louis, MO, USA
| | - W Éamon Callison
- Department of Biology, Washington University in Saint Louis, Campus Box 1137, One Brookings Drive, Saint Louis, MO, USA
| | - Joan E Strassmann
- Department of Biology, Washington University in Saint Louis, Campus Box 1137, One Brookings Drive, Saint Louis, MO, USA
| | - David C Queller
- Department of Biology, Washington University in Saint Louis, Campus Box 1137, One Brookings Drive, Saint Louis, MO, USA
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22
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Khoei NS, Lampis S, Zonaro E, Yrjälä K, Bernardi P, Vallini G. Insights into selenite reduction and biogenesis of elemental selenium nanoparticles by two environmental isolates of Burkholderia fungorum. N Biotechnol 2016; 34:1-11. [PMID: 27717878 DOI: 10.1016/j.nbt.2016.10.002] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 07/11/2016] [Accepted: 10/03/2016] [Indexed: 11/30/2022]
Abstract
Microorganisms capable of transforming toxic selenium oxyanions into non-toxic elemental selenium (Se°) may be considered as biocatalysts for the production of selenium nanoparticles (SeNPs), eventually exploitable in different biotechnological applications. Two Burkholderia fungorum strains (B. fungorum DBT1 and B. fungorum 95) were monitored during their growth for both capacity and efficiency of selenite (SeO32-) reduction and elemental selenium formation. Both strains are environmental isolates in origin: B. fungorum DBT1 was previously isolated from an oil refinery drainage, while B. fungorum 95 has been enriched from inner tissues of hybrid poplars grown in a soil contaminated by polycyclic aromatic hydrocarbons. Our results showed that B. fungorum DBT1 is able to reduce 0.5mM SeO32- to Se° when cultured aerobically in liquid medium at 27°C, while B. fungorum 95 can reduce more than 1mM SeO32- to Se° within 96h under the same growth conditions, with the appearance of SeNPs in cultures of both bacterial strains. Biogenic SeNPs were spherical, with pH-dependent charge and an average hydrodynamic diameter of 170nm and 200nm depending on whether they were produced by B. fungorum 95 or B. fungorum DBT1, respectively. Electron microscopy analyses evidenced that Se nanoparticles occurred intracellularly and extracellularly. The mechanism of SeNPs formation can be tentatively attributed to cytoplasmic enzymatic activation mediated by electron donors. Biogenic nanoparticles were then probably released outside the bacterial cells as a consequence of a secretory process or cell lysis. Nevertheless, formation of elemental selenium nanoparticles under aerobic conditions by B. fungorum DBT1 and B. fungorum 95 is likely due to intracellular reduction mechanisms. Biomedical and other high tech sectors might exploit these biogenic nanoparticles in the near future, once fully characterized and tested for their multiple properties.
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Affiliation(s)
- Nazanin Seyed Khoei
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy.
| | - Silvia Lampis
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy.
| | - Emanuele Zonaro
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Kim Yrjälä
- MEM-group, Department of Biosciences, University of Helsinki, 00014 Helsinki, Finland
| | - Paolo Bernardi
- Department of Neurological and Movement Sciences, University of Verona, Strada Le Grazie 8, 37134 Verona, Italy
| | - Giovanni Vallini
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
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Khoei NS, Andreolli M, Lampis S, Vallini G, Turner RJ. A comparison of the response of twoBurkholderia fungorumstrains grown as planktonic cells versus biofilm to dibenzothiophene and select polycyclic aromatic hydrocarbons. Can J Microbiol 2016; 62:851-860. [DOI: 10.1139/cjm-2016-0160] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In natural environments, bacteria often exist in close association with surfaces and interfaces by establishing biofilms. Here, we report on the ability of Burkholderia fungorum strains DBT1 and 95 to survive in high concentrations of hydrocarbons, and we compare their growth as a biofilm vs. planktonic cells. The 2 compounds tested were dibenzothiophene (DBT) and a mixture of naphthalene, phenanthrene, and pyrene (5:2:1) as representative compounds of thiophenes and polycyclic aromatic hydrocarbons (PAHs), respectively. The results showed that both strains were able to degrade DBT and to survive in the presence of up to a 2000 mg·L−1concentration of this compound both as a biofilm and as free-living cells. Moreover, B. fungorum DBT1 showed reduced tolerance towards the mixed PAHs (2000 mg·L−1naphthalene, 800 mg·L−1phenanthrene, and 400 mg·L−1pyrene) both as a biofilm and as free-living cells. Conversely, biofilms of B. fungorum 95 enhanced resistance against these toxic compounds compared with planktonic cells (P < 0.05). Visual observation through confocal laser scanning microscopy showed that exposure of biofilms to DBT and PAHs altered their structure: high concentrations of DBT triggered an aggregation of biofilm cells. These findings provide new perspectives on the effectiveness of using DBT-degrading bacterial strains in bioremediation of hydrocarbon-contaminated sites.
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Affiliation(s)
- Nazanin Seyed Khoei
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Marco Andreolli
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Silvia Lampis
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Giovanni Vallini
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Raymond J. Turner
- Biofilm Research Group, Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
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Andreolli M, Lampis S, Brignoli P, Vallini G. Trichoderma longibrachiatum Evx1 is a fungal biocatalyst suitable for the remediation of soils contaminated with diesel fuel and polycyclic aromatic hydrocarbons. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:9134-9143. [PMID: 26832871 DOI: 10.1007/s11356-016-6167-6] [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: 08/27/2015] [Accepted: 01/22/2016] [Indexed: 06/05/2023]
Abstract
Trichoderma sp. strain Evx1 was isolated from a semi-deciduous forest soil in Southern Italy. It decolorizes polynuclear organic dyes and tolerates high concentrations of phenanthrene, anthracene, fluoranthene, and pyrene. The ability of this ascomycete fungus to degrade polycyclic aromatic hydrocarbons was verified in vitro and confirmed by its strong phenoloxidase activity in the presence of gallic acid. Phylogenetic characterization of Trichoderma sp. Evx1 positioned this strain within the species Trichoderma longibrachiatum. The potential use of this species for the bioremediation of contaminated environmental matrices was tested by inoculating diesel-spiked soil with a dense mycelial suspension. The biodegradation percentage of the C12-40 hydrocarbon fraction in the inoculated soil rose to 54.2 ± 1.6 %, much higher than that in non-inoculated soil or soil managed solely by a combination of watering and aeration. The survival and persistence of T. longibrachiatum Evx1 throughout the bioremediation trial was monitored by PCR-DGGE analysis. The fungal strain was still present in the soil 30 days after bioaugmentation. These findings indicate that T. longibrachiatum Evx1 may be a suitable inoculum in bioremediation protocols for the reclamation of soils contaminated by complex mixtures of hydrocarbons.
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Affiliation(s)
- Marco Andreolli
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Silvia Lampis
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy.
| | | | - Giovanni Vallini
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy.
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Andreolli M, Lampis S, Zapparoli G, Angelini E, Vallini G. Diversity of bacterial endophytes in 3 and 15 year-old grapevines of Vitis vinifera cv. Corvina and their potential for plant growth promotion and phytopathogen control. Microbiol Res 2016; 183:42-52. [DOI: 10.1016/j.micres.2015.11.009] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 11/22/2015] [Indexed: 11/28/2022]
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Yang L, Poles MA, Fisch GS, Ma Y, Nossa C, Phelan JA, Pei Z. HIV-induced immunosuppression is associated with colonization of the proximal gut by environmental bacteria. AIDS 2016; 30:19-29. [PMID: 26731752 DOI: 10.1097/qad.0000000000000935] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
OBJECTIVES To evaluate the impact of HIV infection on colonization resistance in the proximal gut. DESIGN It was a case-control study. METHODS We contrasted microbiota composition between eight HIV-1-infected patients and eight HIV-negative controls to characterize community alteration and detect exogenous bacteria in the esophagus, stomach, and duodenum, as well as the mouth using a universal 16s ribosomal RNA gene survey and correlated the findings with HIV serostatus and peripheral blood T-cell counts. RESULTS HIV infection was associated with an enrichment of Proteobacteria (P=0.020) and depletion of Firmicutes (P = 0.005) in the proximal gut. In particular, environmental species Burkholderia fungorum and Bradyrhizobium pachyrhizi colonized the duodenum of HIV patients who had abnormal blood CD4 T-cell counts but were absent in HIV-negative controls or HIV patients whose CD4 cell counts were normal. The two species coexisted and exhibited a decreasing trend proximally toward the stomach and esophagus and were virtually absent in the mouth. B. fungorum always outnumbered B. pachyrhizi in a ratio of approximately 15 to 1 regardless of the body sites (P < 0.0001, r = 0.965). Their abundance was inversely correlated with CD4 cell counts (P = 0.004) but not viral load. Overgrowth of potential opportunistic pathogens for example, Prevotella, Fusobacterium, and Ralstonia and depletion of beneficial bacteria, for example, Lactobacillus was also observed in HIV patients. CONCLUSIONS The colonization of the duodenum by environmental bacteria reflects loss of colonization resistance in HIV infection. Their correlation with CD4 cell counts suggests that compromised immunity could be responsible for the observed invasion by exogenous microbes.
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Draft Genome Sequence of Burkholderia cordobensis Type Strain LMG 27620, Isolated from Agricultural Soils in Argentina. GENOME ANNOUNCEMENTS 2015; 3:3/5/e01238-15. [PMID: 26494680 PMCID: PMC4616187 DOI: 10.1128/genomea.01238-15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
ABSTRACT
Bacteria of the genus
Burkholderia
are commonly found in diverse ecological niches in nature. We report here the draft genome sequence of
Burkholderia cordobensis
type strain LMG 27620, isolated from agricultural soil in Córdoba, Argentina. This strain harbors several genes involved in chitin utilization and phenol degradation, which make it an interesting candidate for biocontrol purposes and xenobiotic degradation in polluted environments.
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Andreolli M, Lampis S, Brignoli P, Vallini G. Bioaugmentation and biostimulation as strategies for the bioremediation of a burned woodland soil contaminated by toxic hydrocarbons: a comparative study. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2015; 153:121-131. [PMID: 25688477 DOI: 10.1016/j.jenvman.2015.02.007] [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: 09/29/2014] [Revised: 01/13/2015] [Accepted: 02/08/2015] [Indexed: 06/04/2023]
Abstract
In this work, the natural attenuation strategy (no soil amendments done) was compared with two different bioremediation approaches, namely bioaugmentation through soil inoculation with a suspension of Trichoderma sp. mycelium and biostimulation by soil addition with a microbial growth promoting formulation, in order to verify the effectiveness of these methods in terms of degradation efficiency towards toxic hydrocarbons, with particular attention to the high molecular weight (HMW) fraction, in a forest area impacted by recent wildfire in Northern Italy. The area under investigation, divided into three parcels, was monitored to figure out the dynamics of decay in soil concentration of C₁₂₋₄₀ hydrocarbons (including isoalkanes, cycloalkanes, alkyl-benzenes and alkyl-naphthalenes besides PAHs) and low molecular weight (LMW) PAHs, following the adoption of the foregoing different remediation strategies. Soil hydrocarbonoclastic potential was even checked by characterizing the autochthonous microbial cenoses. Field experiments proved that the best performance in the abatement of HMW hydrocarbons was reached 60 days after soil treatment through the biostimulation protocol, when about 70% of the initial concentration of HMW hydrocarbons was depleted. Within the same time, about 55% degradation was obtained with the bioaugmentation protocol, whilst natural attenuation allowed only a 45% removal of the starting C12-40 hydrocarbon fraction. Therefore, biostimulation seems to significantly reduce the time required for the remediation, most likely because of the enhancement of microbial degradation through the improvement of nutrient balance in the burned soil.
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Affiliation(s)
- Marco Andreolli
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Silvia Lampis
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy.
| | | | - Giovanni Vallini
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy.
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Koribanics NM, Tuorto SJ, Lopez-Chiaffarelli N, McGuinness LR, Häggblom MM, Williams KH, Long PE, Kerkhof LJ. Spatial distribution of an uranium-respiring betaproteobacterium at the Rifle, CO field research site. PLoS One 2015; 10:e0123378. [PMID: 25874721 PMCID: PMC4395306 DOI: 10.1371/journal.pone.0123378] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 02/13/2015] [Indexed: 11/21/2022] Open
Abstract
The Department of Energy’s Integrated Field-Scale Subsurface Research Challenge Site (IFRC) at Rifle, Colorado was created to address the gaps in knowledge on the mechanisms and rates of U(VI) bioreduction in alluvial sediments. Previous studies at the Rifle IFRC have linked microbial processes to uranium immobilization during acetate amendment. Several key bacteria believed to be involved in radionuclide containment have been described; however, most of the evidence implicating uranium reduction with specific microbiota has been indirect. Here, we report on the cultivation of a microorganism from the Rifle IFRC that reduces uranium and appears to utilize it as a terminal electron acceptor for respiration with acetate as electron donor. Furthermore, this bacterium constitutes a significant proportion of the subsurface sediment community prior to biostimulation based on TRFLP profiling of 16S rRNA genes. 16S rRNA gene sequence analysis indicates that the microorganism is a betaproteobacterium with a high similarity to Burkholderia fungorum. This is, to our knowledge, the first report of a betaproteobacterium capable of uranium respiration. Our results indicate that this microorganism occurs commonly in alluvial sediments located between 3-6 m below ground surface at Rifle and may play a role in the initial reduction of uranium at the site.
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Affiliation(s)
- Nicole M. Koribanics
- Inst. of Marine and Coastal Science, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Steven J. Tuorto
- Inst. of Marine and Coastal Science, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Nora Lopez-Chiaffarelli
- Inst. of Marine and Coastal Science, Rutgers University, New Brunswick, New Jersey, United States of America
- Dept. of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Lora R. McGuinness
- Inst. of Marine and Coastal Science, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Max M. Häggblom
- Dept. of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Kenneth H. Williams
- Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Philip E. Long
- Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Lee J. Kerkhof
- Inst. of Marine and Coastal Science, Rutgers University, New Brunswick, New Jersey, United States of America
- * E-mail:
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Draft Genome Sequence of Burkholderia sordidicola S170, a Potential Plant Growth Promoter Isolated from Coniferous Forest Soil in the Czech Republic. GENOME ANNOUNCEMENTS 2014; 2:2/4/e00810-14. [PMID: 25125648 PMCID: PMC4132624 DOI: 10.1128/genomea.00810-14] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Burkholderia species are key players in the accumulation of carbon from cellulose decomposition in coniferous forest ecosystems. We report here the draft genome of Burkholderia sordidicola strain S170, containing features associated with known genes involved in plant growth promotion, the biological control of plant diseases, and green remediation technologies.
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Jain CK, Gupta M, Prasad Y, Wadhwa G, Sharma SK. Homology modeling and protein engineering of alkane monooxygenase in Burkholderia thailandensis MSMB121: in silico insights. J Mol Model 2014; 20:2340. [PMID: 24990796 DOI: 10.1007/s00894-014-2340-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Accepted: 06/08/2014] [Indexed: 12/23/2022]
Abstract
The degradation of hydrocarbons plays an important role in the eco-balancing of petroleum products, pesticides and other toxic products in the environment. The degradation of hydrocarbons by microbes such as Geobacillus thermodenitrificans, Burkhulderia, Gordonia sp. and Acinetobacter sp. has been studied intensively in the literature. The present study focused on the in silico protein engineering of alkane monooxygenase (ladA)-a protein involved in the alkane degradation pathway. We demonstrated the improvement in substrate binding energy with engineered ladA in Burkholderia thailandensis MSMB121. We identified an ortholog of ladA monooxygenase found in B. thailandensis MSMB121, and showed it to be an enzyme involved in an alkane degradation pathway studied extensively in Geobacillus thermodenitrificans. Homology modeling of the three-dimensional structure of ladA was performed with a crystal structure (protein databank ID: 3B9N) as a template in MODELLER 9v11, and further validated using PROCHECK, VERIFY-3D and WHATIF tools. Specific amino acids were substituted in the region corresponding to amino acids 305-370 of ladA protein, resulting in an enhancement of binding energy in different alkane chain molecules as compared to wild protein structures in the docking experiments. The substrate binding energy with the protein was calculated using Vina (Implemented in VEGAZZ). Molecular dynamics simulations were performed to study the dynamics of different alkane chain molecules inside the binding pockets of wild and mutated ladA. Here, we hypothesize an improvement in binding energies and accessibility of substrates towards engineered ladA enzyme, which could be further facilitated for wet laboratory-based experiments for validation of the alkane degradation pathway in this organism.
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Affiliation(s)
- Chakresh Kumar Jain
- Department of Biotechnology, Jaypee Institute of Information Technology, A-10, Sector-62, NOIDA, Uttar Pradesh, 201307, India,
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Andreolli M, Lampis S, Poli M, Gullner G, Biró B, Vallini G. Endophytic Burkholderia fungorum DBT1 can improve phytoremediation efficiency of polycyclic aromatic hydrocarbons. CHEMOSPHERE 2013; 92:688-94. [PMID: 23706896 DOI: 10.1016/j.chemosphere.2013.04.033] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 04/11/2013] [Accepted: 04/12/2013] [Indexed: 05/22/2023]
Abstract
Burkholderia fungorum DBT1 is a bacterial strain isolated from an oil refinery discharge and capable of transforming dibenzothiophene, phenanthrene, naphthalene, and fluorene. In order to evaluate the influence of a policyclic aromatic hydrocarbon (PAH)-transforming bacterial strain on the phytoremediation of organic contaminants, B. fungorum DBT1 was inoculated into hybrid poplar (Populus deltoides×Populus nigra). The poplar plants were grown for 18-wk with or without naphthalene, phenanthrene, fluorene and dibenzothiophene (488mgkg(-1) soil each) in non-sterile sand-peat substrate. Evidences were gained that B. fungorum DBT1 was present in high concentration in poplar root tissues (2.9-9.5×10(3)CFUg(-1)), while the strain was not detected in stem, leaves and rhizosphere. When poplar was planted in uncontaminated substrate, the infection caused negative effects on biomass index, leaves and stem dry weight, without showing however any disease symptoms. On the other hand, plants inoculated with the strain DBT1 resulted in better tolerance against the toxic effects of PAHs, in terms of root dry weight. Although the presence of plants acted as the main effective treatment for PAH dissipation (82-87%), the inoculum with DBT1 strain lead to the highest PAH abatement (up to 99%). In the present study, an environmental isolate with proper metabolic features was demonstrated to be possibly suitable as a poplar endophyte for improving microbe-assisted phytoremediation in PAH contaminated matrices.
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Affiliation(s)
- Marco Andreolli
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
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Piccoli S, Andreolli M, Giorgetti A, Zordan F, Lampis S, Vallini G. Identification of aldolase and ferredoxin reductase within the dbt
operon of Burkholderia fungorum
DBT1. J Basic Microbiol 2013; 54:464-9. [DOI: 10.1002/jobm.201200408] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 02/07/2013] [Indexed: 11/09/2022]
Affiliation(s)
- Stefano Piccoli
- Department of Biotechnology; University of Verona; Strada Le Grazie 15 37134 Verona Italy
| | - Marco Andreolli
- Department of Biotechnology; University of Verona; Strada Le Grazie 15 37134 Verona Italy
| | - Alejandro Giorgetti
- Department of Biotechnology; University of Verona; Strada Le Grazie 15 37134 Verona Italy
| | - Fabio Zordan
- Department of Biotechnology; University of Verona; Strada Le Grazie 15 37134 Verona Italy
| | - Silvia Lampis
- Department of Biotechnology; University of Verona; Strada Le Grazie 15 37134 Verona Italy
| | - Giovanni Vallini
- Department of Biotechnology; University of Verona; Strada Le Grazie 15 37134 Verona Italy
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Martin F, Malagnoux L, Violet F, Jakoncic J, Jouanneau Y. Diversity and catalytic potential of PAH-specific ring-hydroxylating dioxygenases from a hydrocarbon-contaminated soil. Appl Microbiol Biotechnol 2012; 97:5125-35. [PMID: 22903320 DOI: 10.1007/s00253-012-4335-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Revised: 07/20/2012] [Accepted: 07/21/2012] [Indexed: 10/28/2022]
Abstract
Ring-hydroxylating dioxygenases (RHDs) catalyze the initial oxidation step of a range of aromatic hydrocarbons including polycyclic aromatic hydrocarbons (PAHs). As such, they play a key role in the bacterial degradation of these pollutants in soil. Several polymerase chain reaction (PCR)-based methods have been implemented to assess the diversity of RHDs in soil, allowing limited sequence-based predictions on RHD function. In the present study, we developed a method for the isolation of PAH-specific RHD gene sequences of Gram-negative bacteria, and for analysis of their catalytic function. The genomic DNA of soil PAH degraders was labeled in situ by stable isotope probing, then used to PCR amplify sequences specifying the catalytic domain of RHDs. Sequences obtained fell into five clusters phylogenetically linked to RHDs from either Sphingomonadales or Burkholderiales. However, two clusters comprised sequences distantly related to known RHDs. Some of these sequences were cloned in-frame in place of the corresponding region of the phnAIa gene from Sphingomonas CHY-1 to generate hybrid genes, which were expressed in Escherichia. coli as chimerical enzyme complexes. Some of the RHD chimeras were found to be competent in the oxidation of two- and three-ring PAHs, but other appeared unstable. Our data are interpreted in structural terms based on 3D modeling of the catalytic subunit of hybrid RHDs. The strategy described herein might be useful for exploring the catalytic potential of the soil metagenome and recruit RHDs with new activities from uncultured soil bacteria.
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Affiliation(s)
- Florence Martin
- Laboratoire de Chimie et Biologie des Métaux, CEA, DSV, 38054 Grenoble Cedex 9, France
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Hunter WJ, Shaner DL. Removing Hexazinone from Groundwater with Microbial Bioreactors. Curr Microbiol 2012; 64:405-11. [DOI: 10.1007/s00284-012-0086-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Accepted: 01/11/2012] [Indexed: 10/14/2022]
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