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Remenyik J, Csige L, Dávid P, Fauszt P, Szilágyi-Rácz AA, Szőllősi E, Bacsó ZR, Szepsy Jnr I, Molnár K, Rácz C, Fidler G, Kállai Z, Stündl L, Dobos AC, Paholcsek M. Exploring the interplay between the core microbiota, physicochemical factors, agrobiochemical cycles in the soil of the historic tokaj mád wine region. PLoS One 2024; 19:e0300563. [PMID: 38626236 PMCID: PMC11020696 DOI: 10.1371/journal.pone.0300563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 02/29/2024] [Indexed: 04/18/2024] Open
Abstract
A Hungarian survey of Tokaj-Mád vineyards was conducted. Shotgun metabarcoding was applied to decipher the microbial-terroir. The results of 60 soil samples showed that there were three dominant fungal phyla, Ascomycota 66.36% ± 15.26%, Basidiomycota 18.78% ± 14.90%, Mucoromycota 11.89% ± 8.99%, representing 97% of operational taxonomic units (OTUs). Mutual interactions between microbiota diversity and soil physicochemical parameters were revealed. Principal component analysis showed descriptive clustering patterns of microbial taxonomy and resistance gene profiles in the case of the four historic vineyards (Szent Tamás, Király, Betsek, Nyúlászó). Linear discriminant analysis effect size was performed, revealing pronounced shifts in community taxonomy based on soil physicochemical properties. Twelve clades exhibited the most significant shifts (LDA > 4.0), including the phyla Verrucomicrobia, Bacteroidetes, Chloroflexi, and Rokubacteria, the classes Acidobacteria, Deltaproteobacteria, Gemmatimonadetes, and Betaproteobacteria, the order Sphingomonadales, Hypomicrobiales, as well as the family Sphingomonadaceae and the genus Sphingomonas. Three out of the four historic vineyards exhibited the highest occurrences of the bacterial genus Bradyrhizobium, known for its positive influence on plant development and physiology through the secretion of steroid phytohormones. During ripening, the taxonomical composition of the soil fungal microbiota clustered into distinct groups depending on altitude, differences that were not reflected in bacteriomes. Network analyses were performed to unravel changes in fungal interactiomes when comparing postveraison and preharvest samples. In addition to the arbuscular mycorrhiza Glomeraceae, the families Mycosphaerellacae and Rhyzopodaceae and the class Agaricomycetes were found to have important roles in maintaining soil microbial community resilience. Functional metagenomics showed that the soil Na content stimulated several of the microbiota-related agrobiogeochemical cycles, such as nitrogen and sulphur metabolism; steroid, bisphenol, toluene, dioxin and atrazine degradation and the synthesis of folate.
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Affiliation(s)
- Judit Remenyik
- Center for Complex Systems and Microbiome Innovations, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Debrecen, Hungary
| | - László Csige
- Research Laboratory and Wine Academy of Mad, University of Debrecen, Mád, Hungary
| | - Péter Dávid
- Center for Complex Systems and Microbiome Innovations, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Debrecen, Hungary
| | - Péter Fauszt
- Center for Complex Systems and Microbiome Innovations, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Debrecen, Hungary
| | - Anna Anita Szilágyi-Rácz
- Center for Complex Systems and Microbiome Innovations, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Debrecen, Hungary
| | - Erzsébet Szőllősi
- Center for Complex Systems and Microbiome Innovations, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Debrecen, Hungary
| | - Zsófia Réka Bacsó
- Research Laboratory and Wine Academy of Mad, University of Debrecen, Mád, Hungary
| | - István Szepsy Jnr
- Research Laboratory and Wine Academy of Mad, University of Debrecen, Mád, Hungary
| | - Krisztina Molnár
- Centre for Precision Farming R&D Services, Faculty of Agriculture, Food Science and Environmental Management, University of Debrecen, Debrecen, Hungary
| | - Csaba Rácz
- Centre for Precision Farming R&D Services, Faculty of Agriculture, Food Science and Environmental Management, University of Debrecen, Debrecen, Hungary
| | - Gábor Fidler
- Center for Complex Systems and Microbiome Innovations, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Debrecen, Hungary
| | - Zoltán Kállai
- Department of Genetics and Applied Microbiology, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
| | - László Stündl
- Institute of Food Technology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Debrecen, Hungary
| | - Attila Csaba Dobos
- Centre for Precision Farming R&D Services, Faculty of Agriculture, Food Science and Environmental Management, University of Debrecen, Debrecen, Hungary
| | - Melinda Paholcsek
- Center for Complex Systems and Microbiome Innovations, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Debrecen, Hungary
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Su RR, Pan BQ, Luo YX, Zheng XL, Lu W, Wang XY. Characterization of bacterial diversity and screening of cellulose-degrading bacteria in the gut system of Glenea cantor (Fabricius) larvae. Front Bioeng Biotechnol 2024; 12:1340168. [PMID: 38456003 PMCID: PMC10919226 DOI: 10.3389/fbioe.2024.1340168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 02/01/2024] [Indexed: 03/09/2024] Open
Abstract
The intestinal bacteria of longhorn beetles would be ideal targets for pest control and lignocellulosic resources by destroying or exploiting their cellulose-degrading function. This article aims to investigate the diversity and community structure of intestinal bacteria the oligophagous longhorn beetle Glenea cantor. Additionally, it seeks to identify the presence of lignocellulose-degrading bacteria in the gut, and explore their role in consuming host kapok trees Bombax malabaricum. In this study, the bacterial community from G. cantor was examined by Illumina sequencing of 16S ribosomal RNA (rRNA) targeting the V3 and V4 regions. A total of 563,201 valid sequences and 814 OTUs were obtained. The dominant phyla were Proteobacteria, and the dominant genera were Acinetobacter and Lactococcus. The analysis of microbial diversity revealed a high bacterial diversity in the samples, with the gut bacteria playing a crucial role in the physiological activities of the host, particularly, 9 genera of intestinal bacteria with cellulose degradation function were found, highlighting their vital role in cellulose degradation. Five strains of cellulose-degrading bacteria, belonging to the genus Pseudomonas, were obtained from the intestinal tract of G. cantor larvae using traditional isolation and culture techniques as well as 16S rDNA sequencing. Among these strains, A4 exhibited a cellulase activity of 94.42 ± 0.42 U/mL, while A5 displayed the highest filter paper enzyme activity of 127.46 ± 3.54 U/mL. These results offered valuable insights into potential targets for pest control through internal attack digestion and cellulose-degrading bacteria in longhorn beetles.
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Affiliation(s)
| | | | | | | | | | - Xiao-Yun Wang
- Guangxi Key Laboratory of Agric-Environment and Agric-Products Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, China
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Herrera-Calderon AC, Leal L, Suárez-Bautista JD, Manotas-Viloria HS, Muñoz-García A, Franco D, Arenas NE, Vanegas J. Metagenomic and genomic analysis of heavy metal-tolerant and -resistant bacteria in resource islands in a semi-arid zone of the Colombian Caribbean. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:5596-5609. [PMID: 38127234 PMCID: PMC10799150 DOI: 10.1007/s11356-023-30253-w] [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: 06/20/2023] [Accepted: 09/29/2023] [Indexed: 12/23/2023]
Abstract
Bacteria from resource islands can adapt to different extreme conditions in semi-arid regions. We aimed to determine the potential resistance and tolerance to heavy metals from the bacterial community under the canopy of three resource islands in a semi-arid zone of the Colombian Caribbean. Total DNA was extracted from soil and through a metagenomics approach, we identified genes related to heavy metal tolerance and resistance under the influence of drought and humidity conditions, as well as the presence or absence of vegetation. We characterized the genomes of bacterial isolates cultivated in the presence of four heavy metals. The abundances of genes related to heavy metal resistance and tolerance were favored by soil moisture and the presence of vegetation. We observed a high abundance of resistance genes (60.4%) for Cu, Zn, and Ni, while 39.6% represented tolerance. These genes positively correlated with clay and silt content, and negatively correlated with sand content. Resistance and tolerance were associated with detoxification mechanisms involving oxidoreductase enzymes, metalloproteases, and hydrolases, as well as transmembrane proteins involved in metal transport such as efflux pumps and ion transmembrane transporters. The Bacillus velezensis C3-3 and Cytobacillus gottheilii T106 isolates showed resistance to 5 mM of Cd, Co, Mn, and Ni through detoxification genes associated with ABC pumps, metal transport proteins, ion antiporter proteins, and import systems, among others. Overall, these findings highlight the potential of bacteria from resource islands in bioremediation processes of soils contaminated with heavy metals.
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Affiliation(s)
| | - Leslie Leal
- Department of Biological and Environmental Sciences, Universidad Jorge Tadeo Lozano, Bogotá, Colombia
| | | | | | | | - Diego Franco
- Faculty of Biology, Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
| | - Nelson Enrique Arenas
- Faculty of Sciences, Department of Biology, Universidad Antonio Nariño, Bogotá, Colombia
| | - Javier Vanegas
- Faculty of Sciences, Department of Biology, Universidad Antonio Nariño, Bogotá, Colombia.
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Brescia F, Sillo F, Franchi E, Pietrini I, Montesano V, Marino G, Haworth M, Zampieri E, Fusini D, Schillaci M, Papa R, Santamarina C, Vita F, Chitarra W, Nerva L, Petruzzelli G, Mennone C, Centritto M, Balestrini R. The 'microbiome counterattack': Insights on the soil and root-associated microbiome in diverse chickpea and lentil genotypes after an erratic rainfall event. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:459-483. [PMID: 37226644 PMCID: PMC10667653 DOI: 10.1111/1758-2229.13167] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 05/05/2023] [Indexed: 05/26/2023]
Abstract
Legumes maintain soil fertility thanks to their associated microbiota but are threatened by climate change that causes soil microbial community structural and functional modifications. The core microbiome associated with different chickpea and lentil genotypes was described after an unexpected climatic event. Results showed that chickpea and lentil bulk soil microbiomes varied significantly between two sampling time points, the first immediately after the rainfall and the second 2 weeks later. Rhizobia were associated with the soil of the more productive chickpea genotypes in terms of flower and fruit number. The root-associated bacteria and fungi were surveyed in lentil genotypes, considering that several parcels showed disease symptoms. The metabarcoding analysis revealed that reads related to fungal pathogens were significantly associated with one lentil genotype. A lentil core prokaryotic community common to all genotypes was identified as well as a genotype-specific one. A higher number of specific bacterial taxa and an enhanced tolerance to fungal diseases characterized a lentil landrace compared to the commercial varieties. This outcome supported the hypothesis that locally adapted landraces might have a high recruiting efficiency of beneficial soil microbes.
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Affiliation(s)
- Francesca Brescia
- Institute for Sustainable Plant ProtectionNational Research Council of ItalyTurinItaly
| | - Fabiano Sillo
- Institute for Sustainable Plant ProtectionNational Research Council of ItalyTurinItaly
| | - Elisabetta Franchi
- Eni S.p.A.R&D Environmental & Biological LaboratoriesSan Donato MilaneseItaly
| | - Ilaria Pietrini
- Eni S.p.A.R&D Environmental & Biological LaboratoriesSan Donato MilaneseItaly
| | - Vincenzo Montesano
- Institute for Sustainable Plant ProtectionNational Research Council of ItalyBernalda (MT)Italy
| | - Giovanni Marino
- Institute for Sustainable Plant ProtectionNational Research Council of ItalySesto FiorentinoItaly
| | - Matthew Haworth
- Institute for Sustainable Plant ProtectionNational Research Council of ItalySesto FiorentinoItaly
| | - Elisa Zampieri
- Institute for Sustainable Plant ProtectionNational Research Council of ItalyTurinItaly
| | - Danilo Fusini
- Eni S.p.A.R&D Environmental & Biological LaboratoriesSan Donato MilaneseItaly
| | - Martino Schillaci
- Institute for Sustainable Plant ProtectionNational Research Council of ItalyTurinItaly
| | - Roberto Papa
- Department of Agricultural, Food and Environmental SciencesPolytechnic University of MarcheAnconaItaly
| | - Chiara Santamarina
- Department of Agricultural, Food and Environmental SciencesPolytechnic University of MarcheAnconaItaly
| | - Federico Vita
- Department of Bioscience, Biotechnology and EnvironmentUniversity of Bari Aldo MoroBariItaly
| | - Walter Chitarra
- Research Centre for Viticulture and EnologyCouncil for Agricultural Research and EconomicsConeglianoItaly
| | - Luca Nerva
- Research Centre for Viticulture and EnologyCouncil for Agricultural Research and EconomicsConeglianoItaly
| | | | - Carmelo Mennone
- Azienda Pantanello, ALSIA Research Center Metapontum AgrobiosBernalda (MT)Italy
| | - Mauro Centritto
- Institute for Sustainable Plant ProtectionNational Research Council of ItalySesto FiorentinoItaly
- ENI‐CNR Water Research Center ‘Hypatia of Alexandria’ALSIA Research Center Metapontum AgrobiosBernaldaItaly
| | - Raffaella Balestrini
- Institute for Sustainable Plant ProtectionNational Research Council of ItalyTurinItaly
- ENI‐CNR Water Research Center ‘Hypatia of Alexandria’ALSIA Research Center Metapontum AgrobiosBernaldaItaly
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5
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Ventorino V, La Storia A, Robertiello A, Corsi S, Romano I, Sannino L, Pepe O. Fungal Biodeterioration and Preservation of Miniature Artworks. J Fungi (Basel) 2023; 9:1054. [PMID: 37998860 PMCID: PMC10672278 DOI: 10.3390/jof9111054] [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: 09/20/2023] [Revised: 10/20/2023] [Accepted: 10/23/2023] [Indexed: 11/25/2023] Open
Abstract
The study of biodeterioration is an important issue to allow the best conservation and prevent the decay of cultural heritage and artworks. In Naples (Italy), a particular museum (Museodivino) preserves the miniature artworks representing Dante's Divine Comedy and Nativity scenes, executed with organic-based materials in walnut and clay shells. Since they showed putative signs of biodeterioration, the first aim of this study was to verify the presence of microbial colonization. A culture-dependent approach and molecular biology allowed us to isolate and identify the sole fungal strain Aspergillus NCCD (Nativity and Dante's Divine Comedy) belonging to the A. sydowii sub-clade. Based on this result, a sustainable and eco-friendly approach was applied to find a method to preserve the miniature artwork by contrasting the growth of the strain NCCD. Several essential oils used as a natural biocide were tested against Aspergillus strain NCCD belonging to the A. sydowii subclade to determine their potential antimicrobial activity. Results revealed that basil, cloves, fennel, and thyme essential oils exerted antifungal activity, although their effect depended also on the concentration used. Moreover, anoxic treatment and the control of the relative humidity were used in the presence of thyme, in vitro, and in vivo assays to define the impact on fungal growth. No fungal development was detected in vivo in the shells treated with thyme essential oil at high relative humidity after 60 days of incubation at 28 °C. These results highlighted that although relative humidity was the major factor affecting the development of the strain Aspergillus NDDC, the application of thyme in an anaerobic environment is essential in contrasting the fungal growth. Identifying the biodeterioration agent allowed us to plan an eco-friendly, non-destructive approach to be successfully used to guarantee the conditions suitable for conserving miniature artwork.
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Affiliation(s)
- Valeria Ventorino
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, 80055 Portici, Italy; (V.V.); (A.L.S.); (A.R.); (I.R.)
| | - Antonietta La Storia
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, 80055 Portici, Italy; (V.V.); (A.L.S.); (A.R.); (I.R.)
| | - Alessandro Robertiello
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, 80055 Portici, Italy; (V.V.); (A.L.S.); (A.R.); (I.R.)
| | | | - Ida Romano
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, 80055 Portici, Italy; (V.V.); (A.L.S.); (A.R.); (I.R.)
| | - Luigi Sannino
- SIB Società Italiana di Biotecnologie, 80055 Naples, Italy;
| | - Olimpia Pepe
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, 80055 Portici, Italy; (V.V.); (A.L.S.); (A.R.); (I.R.)
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Zhao N, Cao R, Han J, Wang S, Xu H, Wang J, Huang T, Wen G. The change of amino acids samples under metalimnetic oxygen minimum condition: Characterization and mechanism. JOURNAL OF HAZARDOUS MATERIALS 2023; 445:130591. [PMID: 37055995 DOI: 10.1016/j.jhazmat.2022.130591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/28/2022] [Accepted: 12/08/2022] [Indexed: 06/19/2023]
Abstract
The metalimnetic oxygen minimum (MOM) is a common anaerobic phenomenon that occur between 5.00 and 40.00 m of reservoirs. Amino acids (AAs) are widely found in water, but their change in MOM remain unclear. In this study, four AAs with different side chain groups were selected to explore the change of their samples and related disinfection by-products formation potential (DBPFPs) under MOM condition. The results showed that the final degradation rate of dissolved organic carbon and dissolved organic nitrogen of four AAs samples were 11.71%-59.87% and 26.50%-100.00% under MOM condition. Aspartic acid samples were the easiest to be degraded, whereas glycine samples were the opposite. While the total fluorescence intensity increased by 6.30%-113.40% for the appearance of tryptophan-like substance. The total DBPFPs of glutamic acid, arginine and aspartic acid samples were finally decreased by 4.73%, 8.00% and 98.88% (glycine sample increased by 2.30 times). Compared with the surface condition, the degradation of AAs samples and the change of DBPFPs were significantly inhibited under MOM condition. In addition, the diversities of bacterial communities were significantly reduced under MOM condition, which was very unfavorable to the degradation of AAs samples, and in turn affected the control of DBPs and deteriorated the water quality.
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Affiliation(s)
- Na Zhao
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an 710055, PR China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, PR China
| | - Ruihua Cao
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an 710055, PR China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, PR China
| | - Jingru Han
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an 710055, PR China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, PR China
| | - Shuo Wang
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an 710055, PR China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, PR China
| | - Huining Xu
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an 710055, PR China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, PR China
| | - Jingyi Wang
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an 710055, PR China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, PR China
| | - Tinglin Huang
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an 710055, PR China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, PR China
| | - Gang Wen
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an 710055, PR China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, PR China.
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Dong X, Ji J, Zhang S, Peng D, Wang Y, Zhang L, Li J, Wang G. Study on a Low-temperature Cellulose-degrading Strain: Fermentation Optimization, Straw Degradation, and the Effect of Fermentation Broth on Seed Growth. BIOTECHNOL BIOPROC E 2022. [DOI: 10.1007/s12257-021-0265-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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8
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Hossain L, Ledesma RMB, Tanner J, Garnier G. Effect of crosslinking on nanocellulose superabsorbent biodegradability. CARBOHYDRATE POLYMER TECHNOLOGIES AND APPLICATIONS 2022. [DOI: 10.1016/j.carpta.2022.100199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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9
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Mendes-Silva TDCD, Vidal EE, de Souza RDFR, Schmidt KDC, Mendes PVD, da Silva Andrade RF, da Silva Oliveira FG, de Lucena BTL, de Oliveira MBM, dos Santos Correia MT, da Silva MV. Production of carotenoid sarcinaxanthin by Kocuria palustris isolated from Northeastern Brazil Caatinga soil and their antioxidant and photoprotective activities. ELECTRON J BIOTECHN 2021. [DOI: 10.1016/j.ejbt.2021.05.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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Effects of Atrazine on Chernozem Microbial Communities Evaluated by Traditional Detection and Modern Sequencing Technology. Microorganisms 2021; 9:microorganisms9091832. [PMID: 34576727 PMCID: PMC8464665 DOI: 10.3390/microorganisms9091832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/24/2021] [Accepted: 08/26/2021] [Indexed: 11/16/2022] Open
Abstract
Atrazine is a long residual herbicide commonly used in maize fields. Although atrazine can effectively control weeds and improve crop yield, long-term application leads to continuous pollution in the agricultural ecological environment, especially in the soil ecosystem, and its impact on soil microorganisms is still not clear. Four methods were used in the experiment to clarify the effect of atrazine on the bacterial populations of cultivated soil layers of chernozem in a cold region in different periods: high-performance liquid chromatography (HPLC), colorimetry, microplate, and high-throughput sequencing. The level of residual atrazine in cold chernozem decreased from 4.645 to 0.077 mg/kg soil over time, and the residue gradually leached into deep soil and then decreased after accumulating to a maximum value. Atrazine significantly affected the activities of urease and polyphenol oxidase activity in the soil layers at different periods but had no significant effect on sucrase and phosphatase activity. Atrazine significantly reduced the diversity of microbial carbon source utilization and total activity in soil layers of 0-10 and 20-30 cm but only reduced the diversity of microbial carbon source utilization in the 10-20 cm layer. Atrazine had no significant effect on bacterial populations (10-12 phyla, 29-34 genera), but had a slight effect on the relative abundance of various groups. Atrazine significantly reduced the diversity of bacterial populations in cultivated soil layers of chernozem in a cold region, and the diversity of bacterial populations decreased with decreased residue. This lays a foundation for guiding the safe use of herbicides on farmland in Northeast China.
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Pham VHT, Ahn JY, Ro YH, Ravindran B, Kim JS, Chang SW, Shim JH, Chung WJ. The efficiency of potential food waste-degrading bacteria under harsh conditions. J Appl Microbiol 2021; 132:340-350. [PMID: 33900007 DOI: 10.1111/jam.15119] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 04/02/2021] [Accepted: 04/21/2021] [Indexed: 11/27/2022]
Abstract
AIMS Investigate the impact of highly adapted bacterial strains and their ability in waste degradation under a wide range of temperatures. METHODS AND RESULTS Bacteria isolated from soil and food waste were grown in various media under fluctuated temperatures. After screening for organic compound degradation, the seven strongest bacterial strains have been selected for further experiments. Their enzyme activities were expressed in terms of the size of the hydrolysis zone in a wide temperature range of 2.5-70 ºC. The enzyme production assay was carried out for each protease, cellulase, and amylase. The waste degradation was determined with a maximum 80% decrease in the volume of food waste in 21 days compared to the control in lab-scale with enriched bacterial cultures and soil bacteria as additives at room temperature around 18 ºC-20 ºC. CONCLUSION These seven bacteria are promising candidates for food waste biodegradation in composting especially in the winter without heating expense for maintaining ambient temperature. SIGNIFICANCE AND IMPACT OF THE STUDY It is necessary to coax the uncultured bacteria from the various environments into the laboratory for investigating their valuable functions. Herein, using enrichment culture of consortium and additive of soil have illustrated the significant mean in food waste degradation.
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Affiliation(s)
- Van Hong Thi Pham
- Environmental Remediation Laboratory, Department of Environmental Energy Engineering, Kyonggi University, South Korea
| | - Jeong Yoon Ahn
- Environmental Remediation Laboratory, Department of Environmental Energy Engineering, Kyonggi University, South Korea
| | - Yeon Hee Ro
- Environmental Remediation Laboratory, Department of Environmental Energy Engineering, Kyonggi University, South Korea
| | - Balasubramani Ravindran
- Environmental Remediation Laboratory, Department of Environmental Energy Engineering, Kyonggi University, South Korea
| | - Jai Soo Kim
- Microbial Ecology Laboratory, Department of Life Science, Kyonggi University, South Korea
| | - Soon Woong Chang
- Environmental Remediation Laboratory, Department of Environmental Energy Engineering, Kyonggi University, South Korea
| | - Jea Hong Shim
- Fertilizer Resources Lab, Soil and Fertilizer Management Division, National Institute of Agricultural Science, Rural Development Administration
| | - Woo Jin Chung
- Environmental Remediation Laboratory, Department of Environmental Energy Engineering, Kyonggi University, South Korea
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Steiner E, Margesin R. Production and partial characterization of a crude cold-active cellulase (CMCase) from Bacillus mycoides AR20-61 isolated from an Alpine forest site. ANN MICROBIOL 2020. [DOI: 10.1186/s13213-020-01607-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Purpose
To evaluate the production of a cold-active CMCase (endoglucanase) by Bacillus mycoides AR20-61 isolated from Alpine forest soil and to characterize the crude enzyme.
Methods
After studying the effect of cultivation parameters (medium composition, temperature, NaCl concentration, pH) on bacterial growth and enzyme production, the crude enzyme was characterized with regard to the effect of pH, temperature, and inhibitors on enzyme activity and stability.
Result
Optimum growth and enzyme production occurred at 20–25 °C, pH 7, and 1–1.5% (w/v) CMC. Despite high biomass production over the whole growth temperature range (10–35 °C), enzyme production was low at 10 and 35 °C. CMC concentration had a minor effect on growth, independent of the growth temperature, but a significant effect on CMCase production at temperatures ≥ 20 °C. The crude enzyme was active over a broad temperature range (0–60 °C); the apparent optimum temperature for activity was at 40–50 °C. The cultivation temperature influenced the effect of temperature on enzyme activity and stability. A significantly higher thermosensitivity of the enzyme produced at a cultivation temperature of 10 °C compared to that produced at 25 °C was noted at 50 and 65 °C. The enzyme was highly active over a pH range of 4–6 and showed optimum activity at pH 5. No activity was lost after 60 min of incubation at 30 °C and pH 4–9. The CMCase was resistant against a number of monovalent and divalent metal ions, metal-chelating agents, and phenol.
Conclusion
The CMCase produced by the studied strain is characterized by high activities in the low temperature range (down to 0 °C) and acidic pH range, high stability over a broad pH range, and high resistance against a number of effectors. Our results also demonstrate the different, independent roles of temperature in bacterial growth, enzyme production, nutrient requirements during enzyme production, and enzyme characteristics regarding thermosensitivity, which has not yet been described for cellulases.
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Wei M, Liu H, Chen J, Xu C, Li J, Xu P, Sun Z. Effects of aerosol pollution on PM 2.5-associated bacteria in typical inland and coastal cities of northern China during the winter heating season. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 262:114188. [PMID: 32126435 DOI: 10.1016/j.envpol.2020.114188] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 02/13/2020] [Accepted: 02/13/2020] [Indexed: 05/14/2023]
Abstract
Frequent heavy aerosol pollution occurs during the winter heating season in northern China. Here, we characterized the airborne bacterial community structure and concentration, during typical pollution episodes that occurred during the winter heating season of 2017-2018 in Jinan and Weihai. During this heating season, five and four heavy pollution episodes were observed in Jinan and Weihai, respectively. Compared with December and January, pollution episodes in March were significantly affected by sand dust events. Higher Bacillales were identified in the March samples from Jinan, indicating that sand dust influences bacterial communities. During similar pollution episodes, air pollution in the coastal city of Weihai was lower than the inland city of Jinan. The predominant bacteria included Staphylococcus, Cyanobacteria, Lactobacillus, Deinococcus, Enbydrobacter, Ralstonia, Bacillus, Comamonas, and Sphingomonas. These predominant bacteria are mainly from Proteobacteria, Firmicutes, Cyanobacteria, Actinobacteria, and Bacteroidetes phyla. Bacterial concentration showed significant variation with increased airborne pollutants. The highest concentration appeared during moderate pollution (up to 106 cells/m3), whereas bacterial concentration decreased during heavy and severe pollution (105 cells/m3), which may be related to toxic effects of high pollutant concentrations during heavy or severe pollution. Community structure variation indicated that Cyanobacterial genera were dominant in clean or slight pollution. With increased PM2.5, Staphylococcus increased and became the most abundant bacteria in moderate pollution (up to 40%). During heavy or severe pollution, bacteria that are adaptable to harsh or extreme environments predominate, such as Deinococcus and Bacillus. In the assessment of health risks from air pollution, the bioaerosols risks must consider. Additionally, although most microbial genera are similar between the two cities, there are important differences associated with pollution level. During air pollution regulation in different regions with varied geographical and climatic conditions, bioaerosol pollution difference is an unignored factor.
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Affiliation(s)
- Min Wei
- College of Geography and Environment, Shandong Normal University, Jinan, 250014, China; Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP(3)), Fudan Tyndall Centre, Department of Environmental Science & Engineering, Fudan University, Shanghai, 200433, China.
| | - Houfeng Liu
- College of Geography and Environment, Shandong Normal University, Jinan, 250014, China; Center for Environmental Technology and Policy Research, Shandong Normal University, Jinan, 250014, China
| | - Jianmin Chen
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP(3)), Fudan Tyndall Centre, Department of Environmental Science & Engineering, Fudan University, Shanghai, 200433, China
| | - Caihong Xu
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP(3)), Fudan Tyndall Centre, Department of Environmental Science & Engineering, Fudan University, Shanghai, 200433, China
| | - Jie Li
- College of Geography and Environment, Shandong Normal University, Jinan, 250014, China
| | - Pengju Xu
- College of Geography and Environment, Shandong Normal University, Jinan, 250014, China
| | - Ziwen Sun
- Center for Environmental Technology and Policy Research, Shandong Normal University, Jinan, 250014, China
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Zhang P, Huang P, Xu X, Sun H, Jiang B, Liao Y. Spectroscopic and molecular characterization of biochar-derived dissolved organic matter and the associations with soil microbial responses. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 708:134619. [PMID: 31791751 DOI: 10.1016/j.scitotenv.2019.134619] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 09/20/2019] [Accepted: 09/21/2019] [Indexed: 06/10/2023]
Abstract
Dissolved organic matter (DOM) released from biochar can influence the microbial community structure, but the inherent mechanism associated with the structure of biochar-derived DOM remains insufficiently elucidated. In this study, the spectroscopic characteristics and molecular structures of biochar-derived DOM were studied, and the microbial responses to biochar-derived DOM were explored. With increasing biochar pyrolysis temperature (PT), the molecular weight and proportions of aliphatic and fulvic acid-like compounds in the biochar-derived DOM decrease along with an reduction in the amount of DOM released from the biochars, but the proportions of combustion-derived condensed polycyclic aromatics and humic acid-like and soluble microbial byproduct-like compounds increased. Accordingly, the humification index, H/C and (O + N)/C values also decreased. The spectroscopic characteristics of biochar-derived DOM were distinct from those of natural substrates. Moreover, the DOM extracted from biochar raw materials contained a high proportion of aliphatic compounds, while the DOM derived from high-PT biochars (500 °C) had similar characteristics to fulvic acid-like and soluble microbial byproduct-like compounds. The microbial abundance and community structure varied in different DOM solutions. The relative abundances (RAs) of eight genera (e.g. Dyadobacter, Sphingobacterium and Novosphingobium) had significantly positive correlations with the content of aliphatic compounds, while RAs of seven genera (e.g. Methylotenera, Acinetobacter and Reyranella) had significant positive correlations with the content of high-aromatic combustion-derived condensed polycyclic aromatics. These results are helpful for obtaining a deep understanding of the potential influences of various types of biochar-derived DOM on terrestrial and aquatic microbiology.
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Affiliation(s)
- Peng Zhang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Peng Huang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Xuejing Xu
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Hongwen Sun
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China.
| | - Bin Jiang
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Yuhong Liao
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
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15
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Dash PK, Bhattacharyya P, Shahid M, Roy PS, Padhy SR, Swain CK, Kumar U, Kumar A, Gautam P, Lal B, Panneerselvam P, Nayak AK. Structural diversity and efficacy of culturable cellulose decomposing bacteria isolated from rice-pulse resource conservation practices. J Basic Microbiol 2019; 59:963-978. [PMID: 31410860 DOI: 10.1002/jobm.201900275] [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: 05/27/2019] [Revised: 07/20/2019] [Accepted: 07/25/2019] [Indexed: 11/07/2022]
Abstract
The diversity of cellulolytic bacteria from the rice-pulse system can be sourced for identification of efficient cellulose decomposing microbial strains. In the present study, the abundance, structural diversity, and cellulolytic potential of the culturable bacterial community were studied in 5-year old rice-pulse system under different resource conservation technologies. Higher cellulose (68% more) and xylanase (35% more) activities were observed under zero tilled soil. The populations of cellulolytic bacteria were significantly higher (44%) in zero tillage (ZT) treatment than those of conventional practice. Results revealed that the cellulolytic bacterial diversity was found to be significantly higher under ZT practice, but the present population may not be sufficient for effective recycling of organic wastes in this system. Out of 290 bacterial isolates, 20 isolates had significantly higher cellulolytic activities, of which the top three superior isolates were received from ZT practice. The cellulolytic bacterial diversity based on 16S rDNA sequencing data revealed that the Firmicutes was the most dominant phyla and the Bacillus spp. were the common genus, the observation also showed that there were 17 different haplotypes were recorded among 20 isolates of cellulolytic bacteria. The present findings indicated that long-term ZT in the rice-pulse system could be a unique source for efficient cellulose decomposing bacteria and further the efficient bacterial strains isolated from this system can be used as efficient bioinoculants for in situ as well as ex-situ decomposition of rice straw particularly in conservation agriculture.
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Affiliation(s)
- Pradeep Kumar Dash
- Division of Crop Production, ICAR-National Rice Research Institute, Cuttack, Odisha, India
| | - Pratap Bhattacharyya
- Division of Crop Production, ICAR-National Rice Research Institute, Cuttack, Odisha, India
| | - Mohammad Shahid
- Division of Crop Production, ICAR-National Rice Research Institute, Cuttack, Odisha, India
| | - Pritesh Sunder Roy
- Division of Crop Production, ICAR-National Rice Research Institute, Cuttack, Odisha, India
| | - Soumya Ranjan Padhy
- Division of Crop Production, ICAR-National Rice Research Institute, Cuttack, Odisha, India
| | - Chinmaya Kumar Swain
- Division of Crop Production, ICAR-National Rice Research Institute, Cuttack, Odisha, India
| | - Upendra Kumar
- Division of Crop Production, ICAR-National Rice Research Institute, Cuttack, Odisha, India
| | - Anjani Kumar
- Division of Crop Production, ICAR-National Rice Research Institute, Cuttack, Odisha, India
| | - Priyanka Gautam
- Division of Crop Production, ICAR-National Rice Research Institute, Cuttack, Odisha, India
| | - Banawari Lal
- Division of Crop Production, ICAR-National Rice Research Institute, Cuttack, Odisha, India
| | | | - Amaresh Kumar Nayak
- Division of Crop Production, ICAR-National Rice Research Institute, Cuttack, Odisha, India
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16
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Olaniyi OO, Yang K, Zhu YG, Cui L. Heavy water-labeled Raman spectroscopy reveals carboxymethylcellulose-degrading bacteria and degradation activity at the single-cell level. Appl Microbiol Biotechnol 2018; 103:1455-1464. [DOI: 10.1007/s00253-018-9459-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 10/13/2018] [Accepted: 10/16/2018] [Indexed: 01/19/2023]
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17
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Cold survival strategies for bacteria, recent advancement and potential industrial applications. Arch Microbiol 2018; 201:1-16. [PMID: 30478730 DOI: 10.1007/s00203-018-1602-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 11/04/2018] [Accepted: 11/24/2018] [Indexed: 12/12/2022]
Abstract
Microorganisms have evolved themselves to thrive under various extreme environmental conditions such as extremely high or low temperature, alkalinity, and salinity. These microorganisms adapted several metabolic processes to survive and reproduce efficiently under such extreme environments. As the major proportion of earth is covered with the cold environment and is exploited by human beings, these sites are not pristine anymore. Human interventions are a great reason for disturbing the natural biogeochemical cycles in these regions. The survival strategies of these organisms have shown great potential for helping us to restore these pristine sites and the use of isolated cold-adapted enzymes from these organisms has also revolutionized various industrial products. This review gives you the insight of psychrophilic enzyme adaptations and their industrial applications.
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18
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Thakur V, Kumar V, Kumar S, Singh D. Diverse culturable bacterial communities with cellulolytic potential revealed from pristine habitat in Indian trans-Himalaya. Can J Microbiol 2018; 64:798-808. [DOI: 10.1139/cjm-2017-0754] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The Pangi–Chamba Himalaya (PCH) region is very pristine, unique, and virgin niche for bioresource exploration. In the current study, for the first time, the bacterial diversity of this region was investigated for potential cellulose degraders. A total of 454 pure bacterial isolates were obtained from diverse sites in the PCH region, and 111 isolates were further selected for 16S rDNA characterization based on ARDRA grouping. The identified bacteria belonged to 28 genera representing four phyla: Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes. Pseudomonas was most abundant genus, followed by Bacillus, Geobacillus, Arthrobacter, Paenibacillus, and Flavobacterium. In addition, six putative novel bacteria (based on 16S rDNA sequence similarity) and thermophiles from non-thermogenic sites were also reported for the first time. Screening for cellulose degradation ability on carboxymethyl cellulose plates revealed that 70.92% of bacteria were cellulolytic. The current study reports diverse bacterial genera (Arthrobacter, Paenibacillus, Chryseobacterium, Pedobacter, Streptomyces, Agromyces, Flavobacterium, and Pseudomonas) with high capacity for cellulose hydrolysis and cellulolytic functionality at wide pH and temperature not previously reported in the literature. Diverse bacterial genera with high cellulolytic activity in broad pH and temperature range provide opportunity to develop a bioprocess for efficient pretreatment of lignocellulosic biomass, which is currently being investigated.
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Affiliation(s)
- Vikas Thakur
- Biotechnology Division, CSIR – Institute of Himalayan Bioresource Technology, Post Box No. 6, Palampur-176 061, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR – Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Vijay Kumar
- Biotechnology Division, CSIR – Institute of Himalayan Bioresource Technology, Post Box No. 6, Palampur-176 061, Himachal Pradesh, India
| | - Sanjay Kumar
- Biotechnology Division, CSIR – Institute of Himalayan Bioresource Technology, Post Box No. 6, Palampur-176 061, Himachal Pradesh, India
| | - Dharam Singh
- Biotechnology Division, CSIR – Institute of Himalayan Bioresource Technology, Post Box No. 6, Palampur-176 061, Himachal Pradesh, India
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19
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Trubl G, Jang HB, Roux S, Emerson JB, Solonenko N, Vik DR, Solden L, Ellenbogen J, Runyon AT, Bolduc B, Woodcroft BJ, Saleska SR, Tyson GW, Wrighton KC, Sullivan MB, Rich VI. Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing. mSystems 2018; 3:e00076-18. [PMID: 30320215 PMCID: PMC6172770 DOI: 10.1128/msystems.00076-18] [Citation(s) in RCA: 137] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Accepted: 08/24/2018] [Indexed: 01/10/2023] Open
Abstract
Rapidly thawing permafrost harbors ∼30 to 50% of global soil carbon, and the fate of this carbon remains unknown. Microorganisms will play a central role in its fate, and their viruses could modulate that impact via induced mortality and metabolic controls. Because of the challenges of recovering viruses from soils, little is known about soil viruses or their role(s) in microbial biogeochemical cycling. Here, we describe 53 viral populations (viral operational taxonomic units [vOTUs]) recovered from seven quantitatively derived (i.e., not multiple-displacement-amplified) viral-particle metagenomes (viromes) along a permafrost thaw gradient at the Stordalen Mire field site in northern Sweden. Only 15% of these vOTUs had genetic similarity to publicly available viruses in the RefSeq database, and ∼30% of the genes could be annotated, supporting the concept of soils as reservoirs of substantial undescribed viral genetic diversity. The vOTUs exhibited distinct ecology, with different distributions along the thaw gradient habitats, and a shift from soil-virus-like assemblages in the dry palsas to aquatic-virus-like assemblages in the inundated fen. Seventeen vOTUs were linked to microbial hosts (in silico), implicating viruses in infecting abundant microbial lineages from Acidobacteria, Verrucomicrobia, and Deltaproteobacteria, including those encoding key biogeochemical functions such as organic matter degradation. Thirty auxiliary metabolic genes (AMGs) were identified and suggested virus-mediated modulation of central carbon metabolism, soil organic matter degradation, polysaccharide binding, and regulation of sporulation. Together, these findings suggest that these soil viruses have distinct ecology, impact host-mediated biogeochemistry, and likely impact ecosystem function in the rapidly changing Arctic. IMPORTANCE This work is part of a 10-year project to examine thawing permafrost peatlands and is the first virome-particle-based approach to characterize viruses in these systems. This method yielded >2-fold-more viral populations (vOTUs) per gigabase of metagenome than vOTUs derived from bulk-soil metagenomes from the same site (J. B. Emerson, S. Roux, J. R. Brum, B. Bolduc, et al., Nat Microbiol 3:870-880, 2018, https://doi.org/10.1038/s41564-018-0190-y). We compared the ecology of the recovered vOTUs along a permafrost thaw gradient and found (i) habitat specificity, (ii) a shift in viral community identity from soil-like to aquatic-like viruses, (iii) infection of dominant microbial hosts, and (iv) carriage of host metabolic genes. These vOTUs can impact ecosystem carbon processing via top-down (inferred from lysing dominant microbial hosts) and bottom-up (inferred from carriage of auxiliary metabolic genes) controls. This work serves as a foundation which future studies can build upon to increase our understanding of the soil virosphere and how viruses affect soil ecosystem services.
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Affiliation(s)
- Gareth Trubl
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Ho Bin Jang
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Simon Roux
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Joanne B. Emerson
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Natalie Solonenko
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Dean R. Vik
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Lindsey Solden
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Jared Ellenbogen
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | | | - Benjamin Bolduc
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Ben J. Woodcroft
- Australian Centre for Ecogenomics, The University of Queensland, St. Lucia, Queensland, Australia
| | - Scott R. Saleska
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, USA
| | - Gene W. Tyson
- Australian Centre for Ecogenomics, The University of Queensland, St. Lucia, Queensland, Australia
| | - Kelly C. Wrighton
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Matthew B. Sullivan
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, Ohio, USA
| | - Virginia I. Rich
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
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20
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Yadav S, Dubey SK. Cellulose degradation potential of Paenibacillus lautus strain BHU3 and its whole genome sequence. BIORESOURCE TECHNOLOGY 2018; 262:124-131. [PMID: 29702421 DOI: 10.1016/j.biortech.2018.04.067] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 04/15/2018] [Accepted: 04/17/2018] [Indexed: 06/08/2023]
Abstract
The aim of this work was to study cellulose degradation and whole genome sequence of Paenibacillus lautus BHU3 isolate. The 16S rRNA gene sequence analysis revealed genetic relatedness (99%) of Iso 7 with Paenibacillus lautus, Iso 8 with Paenibacillus lactis, and Iso 9 with Bacillus amyloliquefaciens. Clear zone formation followed by CMCase and FPase assays exhibited cellulolytic potential in the order: P. lautus > P. lactis > B. amyloliquefaciens. The most potent isolate, Paenibacillus lautus strain BHU3 was subjected to whole genome analysis with reference to the genomic basis of cellulose degradation. Results showed that P. lautus strain BHU3 contains 6234 protein coding genes of which, 316 were associated with the carbohydrate metabolism. Further, genomic CAZymes analysis indicated that the P. lautus strain BHU3 comprising a range of glycoside hydrolase (GH) family genes (143), may play the vital role(s) in enhancing the cellulolytic attributes, and could be the useful tool for lignocellulosic biomass degradation and waste management.
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Affiliation(s)
- Suman Yadav
- Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Suresh Kumar Dubey
- Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India.
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21
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Schmid CAO, Schröder P, Armbruster M, Schloter M. Organic Amendments in a Long-term Field Trial-Consequences for the Bulk Soil Bacterial Community as Revealed by Network Analysis. MICROBIAL ECOLOGY 2018; 76:226-239. [PMID: 29188301 DOI: 10.1007/s00248-017-1110-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 11/13/2017] [Indexed: 05/09/2023]
Abstract
This study intended to elucidate the long-term effects of organic soil amendments on bacterial co-occurrence in bulk soil with and without addition of mineral fertiliser. Previous research mostly neglected the bacterial co-occurrence structure and focussed mainly on the parameters species diversity and abundance changes of species. Here we present a systematic comparison of two frequently used soil amendments, manure and straw, with regard to their impact on bacterial co-occurrence in a long-term field trial in Speyer, Germany. The approach involved 16S amplicon sequencing in combination with a bacterial network analysis, comparing the different fertiliser regimes. The results show an increase of bacterial diversity as well as an accumulation of bacteria of the order Bacillales in plots fertilised with manure compared to a control treatment. In the straw-amended plots neither an increase in diversity was found nor were indicative species detectable. Furthermore, network analysis revealed a clear impact of mineral fertiliser addition on bacterial co-occurrence structure. Most importantly, both organic amendments increased network complexity irrespective of mineral fertilisation regime. At the same time, the effects of manure and straw exhibited differences that might be explained by differences in their nutritional/chemical contents. It is concluded that bacterial interactions are a crucial parameter for the assessment of amendment effects regarding soil health and sustainability.
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Affiliation(s)
- Christoph A O Schmid
- Helmholtz Zentrum München GmbH, Research Unit for Comparative Microbiome Analysis, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Peter Schröder
- Helmholtz Zentrum München GmbH, Research Unit for Comparative Microbiome Analysis, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany.
| | | | - Michael Schloter
- Helmholtz Zentrum München GmbH, Research Unit for Comparative Microbiome Analysis, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
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22
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Borbón-García A, Reyes A, Vives-Flórez M, Caballero S. Captivity Shapes the Gut Microbiota of Andean Bears: Insights into Health Surveillance. Front Microbiol 2017; 8:1316. [PMID: 28751883 PMCID: PMC5507997 DOI: 10.3389/fmicb.2017.01316] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 06/29/2017] [Indexed: 12/31/2022] Open
Abstract
The Andean bear is an endemic species of the tropical Andes who has an almost exclusively plant-based diet. Since herbivorous mammals do not carry enzymes for fiber degradation, the establishment of symbiosis with cellulolytic microorganisms in their gastrointestinal (GI) tract is necessary to help them fulfill their nutritional needs. Furthermore, as described for other mammals, a stable, diverse, and balanced gut microbial composition is an indicator of a healthy status of the host; under disturbances this balance can be lost, leading to potential diseases of the host. The goal of this study was to describe the gut microbiota of wild and captive Andean bears and determine how habitat status influences the composition and diversity of the gut symbiotic community. Fecal samples from wild (n = 28) and captive (n = 8) Andean bears were collected in "Reserva Pantano de Martos" and "Fundación Bioandina", Colombia. Composition and diversity analyses were performed using amplicons from the V4 region of the 16S rDNA gene sequenced using the Ion PGM platform. PICRUSt algorithm was applied to predict the gene content of the gut microbiome of wild and captive Andean bears. A total of 5,411 and 838 OTUs were identified for wild and captive bears, respectively. Captive bears contained a lower number of bacterial phyla (n = 7) compared to wild individuals (n = 9). Proteobacteria (59.03%) and Firmicutes (14.03%) were the phyla that contributed the most to differences between wild and captive bears (overall dissimilarity = 87.72%). At family level, Enterobacteriaceae drove the main differences between the two groups (13.7%). PICRUSt metagenomics predictions suggested a similar pattern of relative abundance of gene families associated with the metabolism of carbohydrates across samples in wild individuals, despite the taxonomic differences of their gut microbiota. Captivity alters the availability and diversity of food resources, which likely reduces microbiota richness and diversity compared to wild individuals. Further considerations should be taken into account for nutritional schemes improving ex-situ conservation and its potential as a surveillance tool of endangered populations of wild Andean bears.
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Affiliation(s)
- Andrea Borbón-García
- Research Group on Computational Biology and Microbial Ecology, Department of Biological Sciences, Universidad de los AndesBogotá, Colombia.,Max Planck Tandem Group in Computational Biology, Universidad de los AndesBogotá, Colombia.,Laboratorio de Ecología Molecular de Vertebrados Acuáticos, Department of Biological Sciences, Universidad de los AndesBogotá, Colombia
| | - Alejandro Reyes
- Research Group on Computational Biology and Microbial Ecology, Department of Biological Sciences, Universidad de los AndesBogotá, Colombia.,Max Planck Tandem Group in Computational Biology, Universidad de los AndesBogotá, Colombia.,Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint LouisMO, United States
| | - Martha Vives-Flórez
- Centro de Investigaciones Microbiológicas, Department of Biological Sciences, Universidad de los AndesBogotá, Colombia
| | - Susana Caballero
- Laboratorio de Ecología Molecular de Vertebrados Acuáticos, Department of Biological Sciences, Universidad de los AndesBogotá, Colombia
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Isolation of a Cellulolytic Bacterium from the Lonar Soda Lake and Genomic Analysis of it. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2017. [DOI: 10.22207/jpam.11.2.54] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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24
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Wilhelm RC, Cardenas E, Leung H, Szeitz A, Jensen LD, Mohn WW. Long-Term Enrichment of Stress-Tolerant Cellulolytic Soil Populations following Timber Harvesting Evidenced by Multi-Omic Stable Isotope Probing. Front Microbiol 2017; 8:537. [PMID: 28443069 PMCID: PMC5386986 DOI: 10.3389/fmicb.2017.00537] [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: 02/07/2017] [Accepted: 03/14/2017] [Indexed: 12/23/2022] Open
Abstract
Soil management is vital for maintaining the productivity of commercial forests, yet the long-term impact of timber harvesting on soil microbial communities remains largely a matter of conjecture. Decomposition of plant biomass, comprised mainly of lignocellulose, has a broad impact on nutrient cycling, microbial activity and physicochemical characteristics of soil. At "Long-term Soil Productivity Study" sites in California dominated by Ponderosa pine, we tested whether clear-cut timber harvesting, accompanied by varying degrees of organic matter (OM) removal, affected the activity and structure of the cellulose-degrading microbial populations 16 years after harvesting. Using a variety of experimental approaches, including stable isotope probing with 13C-labeled cellulose in soil microcosms, we demonstrated that harvesting led to a decrease in net respiration and cellulolytic activity. The decrease in cellulolytic activity was associated with an increased relative abundance of thermophilic, cellulolytic fungi (Chaetomiaceae), coupled with a decreased relative abundance of cellulolytic bacteria, particularly members of Opitutaceae, Caulobacter, and Streptomycetaceae. In general, harvesting led to an increase in stress-tolerant taxa (i.e., also non-cellulolytic taxa), though our results indicated that OM retention mitigated population shifts via buffering against abiotic changes. Stable-isotope probing improved shotgun metagenome assembly by 20-fold and enabled the recovery of 10 metagenome-assembled genomes of cellulolytic bacteria and fungi. Our study demonstrates the putative cellulolytic activity of a number of uncultured taxa and highlights the mineral soil layer as a reservoir of uncharacterized diversity of cellulose-degraders. It also and contributes to a growing body of research showing persistent changes in microbial community structure in the decades following forest harvesting.
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Affiliation(s)
- Roland C. Wilhelm
- Department of Microbiology and Immunology, Life Sciences Institute, University of British ColumbiaVancouver, BC, Canada
| | - Erick Cardenas
- Department of Microbiology and Immunology, Life Sciences Institute, University of British ColumbiaVancouver, BC, Canada
| | - Hilary Leung
- Department of Microbiology and Immunology, Life Sciences Institute, University of British ColumbiaVancouver, BC, Canada
| | - András Szeitz
- Pharmaceutical Analytical Suite, Faculty of Pharmaceutical Sciences, University of British ColumbiaVancouver, BC, Canada
| | - Lionel D. Jensen
- Department of Microbiology and Immunology, Life Sciences Institute, University of British ColumbiaVancouver, BC, Canada
| | - William W. Mohn
- Department of Microbiology and Immunology, Life Sciences Institute, University of British ColumbiaVancouver, BC, Canada
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Gadow SI, Jiang H, Li YY. Characterization and potential of three temperature ranges for hydrogen fermentation of cellulose by means of activity test and 16s rRNA sequence analysis. BIORESOURCE TECHNOLOGY 2016; 209:80-89. [PMID: 26954308 DOI: 10.1016/j.biortech.2016.02.098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 02/19/2016] [Accepted: 02/22/2016] [Indexed: 06/05/2023]
Abstract
A series of standardized activity experiments were performed to characterize three different temperature ranges of hydrogen fermentation from different carbon sources. 16S rRNA sequences analysis showed that the bacteria were close to Enterobacter genus in the mesophilic mixed culture (MMC) and Thermoanaerobacterium genus in the thermophilic and hyper-thermophilic mixed cultures (TMC and HMC). The MMC was able to utilize the glucose and cellulose to produce methane gas within a temperature range between 25 and 45 °C and hydrogen gas from 35 to 60°C. While, the TMC and HMC produced only hydrogen gas at all temperature ranges and the highest activity of 521.4mlH2/gVSSd was obtained by TMC. The thermodynamic analysis showed that more energy is consumed by hydrogen production from cellulose than from glucose. The experimental results could help to improve the economic feasibility of cellulosic biomass energy using three-phase technology to produce hythane.
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Affiliation(s)
- Samir I Gadow
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Sendai 9808579, Japan; Department of Agricultural Microbiology, Agriculture and Biology Research Division, National Research Centre, Dokki, Cairo 12622, Egypt
| | - Hongyu Jiang
- Department of Environmental Science, Graduate School of Environmental Studies, Tohoku University, Sendai 9808579, Japan
| | - Yu-You Li
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Sendai 9808579, Japan; Department of Environmental Science, Graduate School of Environmental Studies, Tohoku University, Sendai 9808579, Japan.
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26
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Chen WM, Chen YL, Sheu SY. Flavobacterium brevivitae sp. nov., isolated from river water. Int J Syst Evol Microbiol 2016; 66:1705-1712. [DOI: 10.1099/ijsem.0.000928] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Wen-Ming Chen
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung Marine University, No. 142, Hai-Chuan Rd. Nan-Tzu, Kaohsiung City 811, Taiwan
| | - Yi-Ling Chen
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung Marine University, No. 142, Hai-Chuan Rd. Nan-Tzu, Kaohsiung City 811, Taiwan
| | - Shih-Yi Sheu
- Department of Marine Biotechnology, National Kaohsiung Marine University, No. 142, Hai-Chuan Rd. Nan-Tzu, Kaohsiung City 811, Taiwan
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27
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Abstract
Members of the family Bacillaceae are among the most robust bacteria on Earth, which is mainly due to their ability to form resistant endospores. This trait is believed to be the key factor determining the ecology of these bacteria. However, they also perform fundamental roles in soil ecology (i.e., the cycling of organic matter) and in plant health and growth stimulation (e.g., via suppression of plant pathogens and phosphate solubilization). In this review, we describe the high functional and genetic diversity that is found within the Bacillaceae (a family of low-G+C% Gram-positive spore-forming bacteria), their roles in ecology and in applied sciences related to agriculture. We then pose questions with respect to their ecological behavior, zooming in on the intricate social behavior that is becoming increasingly well characterized for some members of Bacillaceae. Such social behavior, which includes cell-to-cell signaling via quorum sensing or other mechanisms (e.g., the production of extracellular hydrolytic enzymes, toxins, antibiotics and/or surfactants) is a key determinant of their lifestyle and is also believed to drive diversification processes. It is only with a deeper understanding of cell-to-cell interactions that we will be able to understand the ecological and diversification processes of natural populations within the family Bacillaceae. Ultimately, the resulting improvements in understanding will benefit practical efforts to apply representatives of these bacteria in promoting plant growth as well as biological control of plant pathogens.
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28
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Premalatha N, Gopal NO, Jose PA, Anandham R, Kwon SW. Optimization of cellulase production by Enhydrobacter sp. ACCA2 and its application in biomass saccharification. Front Microbiol 2015; 6:1046. [PMID: 26500615 PMCID: PMC4597110 DOI: 10.3389/fmicb.2015.01046] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 09/14/2015] [Indexed: 11/13/2022] Open
Abstract
Cellulase finds use in saccharification of lignocellulosic agroresidues to fermentable sugars which can be used for production of commercially important metabolites. This study reports endoglucanase (CMCase) production by Enhydrobacter sp. ACCA2. The CMCase activity of the strain ACCA2 was successively improved by optimization of range of physical and nutritional parameter in a set of non-statistical and statistical experiments. Initial non-statistical selection of carbon source, incubation time, temperature and pH resulted in 1.07 fold increase of CMCase activity. In a subsequent statistical method, response surface methodology, optimization of medium components such as carboxymethylcellulose, peptone, NaCl, MgSO4, K2HPO4, and (NH4)2SO4 yielded further increase up to 2.39 fold CMCase activity. The cellulolytic potential was evaluated in biomass saccharification with different plant materials and the results revealed that the enzyme produced by strain may have significant commercial values for industrial saccharification process. Moreover, this is the first report of cellulase production by an Enhydrobacter spp.
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Affiliation(s)
- Nagaiah Premalatha
- Department of Agricultural Microbiology, Agricultural College and Research Institute, Tamil Nadu Agricultural University Madurai, India
| | - Nellaiappan O Gopal
- Department of Agricultural Microbiology, Agricultural College and Research Institute, Tamil Nadu Agricultural University Madurai, India
| | - Polpass Arul Jose
- Department of Agricultural Microbiology, Agricultural College and Research Institute, Tamil Nadu Agricultural University Madurai, India
| | - Rangasamy Anandham
- Department of Agricultural Microbiology, Agricultural College and Research Institute, Tamil Nadu Agricultural University Madurai, India
| | - Soon-Wo Kwon
- Korean Agricultural Culture Collection, National Academy of Agricultural Science, Rural Development Administration Jeonju, South Korea
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29
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Pinheiro GL, Correa RF, Cunha RS, Cardoso AM, Chaia C, Clementino MM, Garcia ES, de Souza W, Frasés S. Isolation of aerobic cultivable cellulolytic bacteria from different regions of the gastrointestinal tract of giant land snail Achatina fulica. Front Microbiol 2015; 6:860. [PMID: 26347735 PMCID: PMC4542579 DOI: 10.3389/fmicb.2015.00860] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 08/06/2015] [Indexed: 11/22/2022] Open
Abstract
The enzymatic hydrolysis of cellulose by cellulases is one of the major limiting steps in the conversion of lignocellulosic biomass to yield bioethanol. To overcome this hindrance, significant efforts are underway to identify novel cellulases. The snail Achatina fulica is a gastropod with high cellulolytic activity, mainly due to the abundance of glycoside hydrolases produced by both the animal and its resident microbiota. In this study, we partially assessed the cellulolytic aerobic bacterial diversity inside the gastrointestinal tract of A. fulica by culture-dependent methods and evaluated the hydrolytic repertoire of the isolates. Forty bacterial isolates were recovered from distinct segments of the snail gut and identified to the genus level by 16S rRNA gene sequence analysis. Additional phenotypic characterization was performed using biochemical tests provided by the Vitek2 identification system. The overall enzymatic repertoire of the isolated strains was investigated by enzymatic plate assays, containing the following substrates: powdered sugarcane bagasse, carboxymethylcellulose (CMC), p-nitrophenyl-β-D-glucopyranoside (pNPG), p-nitrophenyl-β-D-cellobioside (pNPC), 4-methylumbelliferyl-β-D-glucopyranoside (MUG), 4-methylumbelliferyl-β-D-cellobioside (MUC), and 4-methylumbelliferyl-β-D-xylopyranoside (MUX). Our results indicate that the snail A. fulica is an attractive source of cultivable bacteria that showed to be valuable resources for the production of different types of biomass-degrading enzymes.
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Affiliation(s)
- Guilherme L Pinheiro
- Diretoria de Metrologia Aplicada às Ciências da Vida, Instituto Nacional de Metrologia, Qualidade e Tecnologia Rio de Janeiro, Brazil ; Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro Rio de Janeiro, Brazil
| | - Raquel F Correa
- Diretoria de Metrologia Aplicada às Ciências da Vida, Instituto Nacional de Metrologia, Qualidade e Tecnologia Rio de Janeiro, Brazil
| | - Raquel S Cunha
- Diretoria de Metrologia Aplicada às Ciências da Vida, Instituto Nacional de Metrologia, Qualidade e Tecnologia Rio de Janeiro, Brazil
| | - Alexander M Cardoso
- Diretoria de Metrologia Aplicada às Ciências da Vida, Instituto Nacional de Metrologia, Qualidade e Tecnologia Rio de Janeiro, Brazil ; Centro Universitário Estadual da Zona Oeste, Unidade Universitária de Biologia Rio de Janeiro, Brazil
| | - Catia Chaia
- Departamento de Microbiologia, Instituto Nacional de Controle da Qualidade em Saúde, Fundação Oswaldo Cruz Rio de Janeiro, Brazil
| | - Maysa M Clementino
- Departamento de Microbiologia, Instituto Nacional de Controle da Qualidade em Saúde, Fundação Oswaldo Cruz Rio de Janeiro, Brazil
| | - Eloi S Garcia
- Diretoria de Metrologia Aplicada às Ciências da Vida, Instituto Nacional de Metrologia, Qualidade e Tecnologia Rio de Janeiro, Brazil ; Departamento de Bioquímica e Biologia Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz Rio de Janeiro, Brazil
| | - Wanderley de Souza
- Diretoria de Metrologia Aplicada às Ciências da Vida, Instituto Nacional de Metrologia, Qualidade e Tecnologia Rio de Janeiro, Brazil ; Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro Rio de Janeiro, Brazil
| | - Susana Frasés
- Diretoria de Metrologia Aplicada às Ciências da Vida, Instituto Nacional de Metrologia, Qualidade e Tecnologia Rio de Janeiro, Brazil ; Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro Rio de Janeiro, Brazil
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30
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Exploring the microbiota dynamics related to vegetable biomasses degradation and study of lignocellulose-degrading bacteria for industrial biotechnological application. Sci Rep 2015; 5:8161. [PMID: 25641069 PMCID: PMC4648445 DOI: 10.1038/srep08161] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 01/06/2015] [Indexed: 12/31/2022] Open
Abstract
The aims of this study were to evaluate the microbial diversity of different lignocellulosic biomasses during degradation under natural conditions and to isolate, select, characterise new well-adapted bacterial strains to detect potentially improved enzyme-producing bacteria. The microbiota of biomass piles of Arundo donax, Eucalyptus camaldulensis and Populus nigra were evaluated by high-throughput sequencing. A highly complex bacterial community was found, composed of ubiquitous bacteria, with the highest representation by the Actinobacteria, Proteobacteria, Bacteroidetes and Firmicutes phyla. The abundances of the major and minor taxa retrieved during the process were determined by the selective pressure produced by the lignocellulosic plant species and degradation conditions. Moreover, cellulolytic bacteria were isolated using differential substrates and screened for cellulase, cellobiase, xylanase, pectinase and ligninase activities. Forty strains that showed multienzymatic activity were selected and identified. The highest endo-cellulase activity was seen in Promicromonospora sukumoe CE86 and Isoptericola variabilis CA84, which were able to degrade cellulose, cellobiose and xylan. Sixty-two percent of bacterial strains tested exhibited high extracellular endo-1,4-ß-glucanase activity in liquid media. These approaches show that the microbiota of lignocellulosic biomasses can be considered an important source of bacterial strains to upgrade the feasibility of lignocellulose conversion for the ‘greener' technology of second-generation biofuels.
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31
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Isolation and identification of a cellulolytic bacterium from the Tibetan pig's intestine and investigation of its cellulase production. ELECTRON J BIOTECHN 2014. [DOI: 10.1016/j.ejbt.2014.08.002] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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32
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FATIMAH FATIMAH, ZAENAL MUSTOPA APON, KUSNANDARSYAH IQBAL. Identification and characterization of virulence factor of several Indonesian Xanthomonas oryzae pv. oryzae. MICROBIOLOGY INDONESIA 2014. [DOI: 10.5454/mi.8.3.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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33
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Isolation, screening, and identification of cellulolytic bacteria from natural reserves in the subtropical region of China and optimization of cellulase production by Paenibacillus terrae ME27-1. BIOMED RESEARCH INTERNATIONAL 2014; 2014:512497. [PMID: 25050355 PMCID: PMC4090499 DOI: 10.1155/2014/512497] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 05/08/2014] [Indexed: 11/17/2022]
Abstract
From different natural reserves in the subtropical region of China, a total of 245 aerobic bacterial strains were isolated on agar plates containing sugarcane bagasse pulp as the sole carbon source. Of the 245 strains, 22 showed hydrolyzing zones on agar plates containing carboxymethyl cellulose after Congo-red staining. Molecular identification showed that the 22 strains belonged to 10 different genera, with the Burkholderia genus exhibiting the highest strain diversity and accounting for 36.36% of all the 22 strains. Three isolates among the 22 strains showed higher carboxymethyl cellulase (CMCase) activity, and isolate ME27-1 exhibited the highest CMCase activity in liquid culture. The strain ME27-1 was identified as Paenibacillus terrae on the basis of 16S rRNA gene sequence analysis as well as physiological and biochemical properties. The optimum pH and temperature for CMCase activity produced by the strain ME27-1 were 5.5 and 50°C, respectively, and the enzyme was stable at a wide pH range of 5.0–9.5. A 12-fold improvement in the CMCase activity (2.08 U/mL) of ME27-1 was obtained under optimal conditions for CMCase production. Thus, this study provided further information about the diversity of cellulose-degrading bacteria in the subtropical region of China and found P. terrae ME27-1 to be highly cellulolytic.
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34
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Melo IS, Zucchi TD, Silva RE, Vilela ESD, Sáber ML, Rosa LH, Pellizari VH. Isolation and characterization of cellulolytic bacteria from the Stain house Lake, Antarctica. Folia Microbiol (Praha) 2014; 59:303-6. [PMID: 24442675 DOI: 10.1007/s12223-013-0295-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 12/11/2013] [Indexed: 11/29/2022]
Abstract
The main aim was to evaluate the occurrence of cellulolytic bacteria from the Stain house Lake, located at Admiralty Bay, Antarctica. Thick cotton string served as a cellulose bait for the isolation of bacteria. A total of 52 bacterial isolates were recovered and tested for their cellulase activity, and two of them, isolates CMAA 1184 and CMAA 1185, showed significant cellulolytic activity on carboxymethylcellulose agar plates. Phylogenetic analysis placed the isolates into the Bacillus 16S ribosomal RNA gene subclade. Both isolates produced a cold-active cellulase which may play a crucial role in this extreme environment.
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Affiliation(s)
- Itamar S Melo
- Embrapa Environment, CP 69, 13820-000, Jaguariúna, São Paulo, Brazil,
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35
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de Carvalho CCCR, Caramujo MJ. Bacterial diversity assessed by cultivation-based techniques shows predominance ofStaphylococccusspecies on coins collected in Lisbon and Casablanca. FEMS Microbiol Ecol 2013; 88:26-37. [DOI: 10.1111/1574-6941.12266] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Revised: 11/25/2013] [Accepted: 11/26/2013] [Indexed: 11/30/2022] Open
Affiliation(s)
- Carla C. C. R. de Carvalho
- IBB-Institute for Biotechnology and Bioengineering; Centre for Biological and Chemical Engineering; Department of Bioengineering; Instituto Superior Técnico; Universidade de Lisboa; Lisbon Portugal
| | - Maria José Caramujo
- Centre for Environmental Biology; Faculty of Sciences; Universidade de Lisboa; Lisbon Portugal
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36
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Rajaei S, Heidari R, Shahbani Zahiri H, Sharifzadeh S, Torktaz I, Akbari Noghabi K. A novel cold-adapted pullulanase fromExiguobacteriumsp. SH3: Production optimization, purification, and characterization. STARCH-STARKE 2013. [DOI: 10.1002/star.201300030] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Sarah Rajaei
- Department of Molecular Genetics; National Institute of Genetic Engineering and Biotechnology (NIGEB); Tehran Iran
| | - Reza Heidari
- Department of Molecular Genetics; National Institute of Genetic Engineering and Biotechnology (NIGEB); Tehran Iran
| | - Hossein Shahbani Zahiri
- Department of Molecular Genetics; National Institute of Genetic Engineering and Biotechnology (NIGEB); Tehran Iran
| | - Sara Sharifzadeh
- Department of Molecular Genetics; National Institute of Genetic Engineering and Biotechnology (NIGEB); Tehran Iran
| | - Ibrahim Torktaz
- Department of Molecular Genetics; National Institute of Genetic Engineering and Biotechnology (NIGEB); Tehran Iran
| | - Kambiz Akbari Noghabi
- Department of Molecular Genetics; National Institute of Genetic Engineering and Biotechnology (NIGEB); Tehran Iran
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37
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Di Maiuta N, Schwarzentruber P, Schenker M, Schoelkopf J. Microbial population dynamics in the faeces of wood-eating loricariid catfishes. Lett Appl Microbiol 2013; 56:401-7. [DOI: 10.1111/lam.12061] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Revised: 02/15/2013] [Accepted: 02/19/2013] [Indexed: 11/30/2022]
Affiliation(s)
- N. Di Maiuta
- Omya Development AG; R&D-Microbiology; Oftringen Switzerland
| | | | - M. Schenker
- Omya Development AG; R&D-Surface Chemistry; Oftringen Switzerland
| | - J. Schoelkopf
- Omya Development AG; R&D-Surface Chemistry; Oftringen Switzerland
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38
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Rodrigues DF, Jaisi DP, Elimelech M. Toxicity of functionalized single-walled carbon nanotubes on soil microbial communities: implications for nutrient cycling in soil. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2013; 47:625-633. [PMID: 23205469 DOI: 10.1021/es304002q] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Culture-dependent and -independent methods were employed to determine the impact of carboxyl-functionalized single-walled carbon nanotubes (SWNTs) on fungal and bacterial soil microbial communities. Soil samples were exposed to 0 (control), 250, and 500 μg of SWNTs per gram of soil. Aliquots of soil were sampled for up to 14 days for culture-dependent analyses, namely, plate count agar and bacterial community level physiological profiles, and culture-independent analyses, namely, quantitative real-time polymerase chain reaction (qPCR), mutliplex-terminal restriction fragment length polymorphism (M-TRFLP), and clone libraries. Results from culture-independent and -dependent methods show that the bacterial soil community is transiently affected by the presence of SWNTs. The major impact of SWNTs on bacterial community was observed after 3 days of exposure, but the bacterial community completely recovered after 14 days. However, no recovery of the fungal community was observed for the duration of the experiment. Physiological and DNA microbial community analyses suggest that fungi and bacteria involved in carbon and phosphorus biogeochemical cycles can be adversely affected by the presence of SWNTs. This study suggests that high concentrations of SWNTs can have widely varying effects on microbial communities and biogeochemical cycling of nutrients in soils.
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Affiliation(s)
- Debora F Rodrigues
- Department of Civil and Environmental Engineering, University of Houston, Houston, Texas 77204-5003, United States.
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