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Banerjee P, Sarkar A, Ghosh K, Mazumdar A. A Metagenomic Based Approach on Abundance and Diversity of Bacterial Communities Across the Life Stages of Culicoides peregrinus (Diptera: Ceratopogonidae) a Vector of Bluetongue Virus. JOURNAL OF MEDICAL ENTOMOLOGY 2023; 60:373-383. [PMID: 36744984 DOI: 10.1093/jme/tjad011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Indexed: 06/18/2023]
Abstract
During larval rearing of Culicoides peregrinus Kieffer (Diptera: Ceratopogonidae) it was obligatory to add a small quantity of mud from larval habitat to nutrient broth in culture plates. This initiated microbial growth in rearing plates which facilitated growth and development of immature. The primary aim was to enumerate gut microbial communities across the different life stages of C. peregrinus. Amplicon sequencing of the V3-V4 hypervariable region (16S rDNA) was done on Illumina Miseq platform to detect gut bacterial communities at different life stages, while ITS regions (18S rRNA) were targeted for fungal communities of the 4th instar larvae. The major findings were: 1) Phylum Proteobacteria and Firmicutes were the most abundant throughout the life stages, along with the highest bacterial alpha diversity in the egg, 2) bacterial compositions were similar to laboratory reared and field collected adults, and 3) abundant fungal phyla associated with the larval gut were Ascomycota and Basidiomycota. Furthermore, analyses of the gut microbiome with METAGENassist might be indicative of their likely function in the natural habitat. Abundant gut-associated bacteria and/or fungal genera detected in the present study could be used as dietary supplements to establish laboratory colonies for further vectorial research. While, individual roles of the bacteria or fungi in paratransgenesis are warned for their possible utilization to frame the management strategy in upcoming works.
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Affiliation(s)
- Paramita Banerjee
- Entomology Research Unit, Department of Zoology, The University of Burdwan, Burdwan 713104, West Bengal, India
| | - Ankita Sarkar
- Entomology Research Unit, Department of Zoology, The University of Burdwan, Burdwan 713104, West Bengal, India
| | - Koushik Ghosh
- Aquaculture Laboratory, Department of Zoology, The University of Burdwan, Burdwan 713104, West Bengal, India
| | - Abhijit Mazumdar
- Entomology Research Unit, Department of Zoology, The University of Burdwan, Burdwan 713104, West Bengal, India
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2
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Risely A, Wilhelm K, Clutton-Brock T, Manser MB, Sommer S. Diurnal oscillations in gut bacterial load and composition eclipse seasonal and lifetime dynamics in wild meerkats. Nat Commun 2021; 12:6017. [PMID: 34650048 PMCID: PMC8516918 DOI: 10.1038/s41467-021-26298-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 09/29/2021] [Indexed: 12/27/2022] Open
Abstract
Circadian rhythms in gut microbiota composition are crucial for metabolic function, yet the extent to which they govern microbial dynamics compared to seasonal and lifetime processes remains unknown. Here, we investigate gut bacterial dynamics in wild meerkats (Suricata suricatta) over a 20-year period to compare diurnal, seasonal, and lifetime processes in concert, applying ratios of absolute abundance. We found that diurnal oscillations in bacterial load and composition eclipsed seasonal and lifetime dynamics. Diurnal oscillations were characterised by a peak in Clostridium abundance at dawn, were associated with temperature-constrained foraging schedules, and did not decay with age. Some genera exhibited seasonal fluctuations, whilst others developed with age, although we found little support for microbial senescence in very old meerkats. Strong microbial circadian rhythms in this species may reflect the extreme daily temperature fluctuations typical of arid-zone climates. Our findings demonstrate that accounting for circadian rhythms is essential for future gut microbiome research.
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Affiliation(s)
- Alice Risely
- Institute for Evolutionary Ecology and Conservation Genomics, Ulm, Germany.
| | - Kerstin Wilhelm
- Institute for Evolutionary Ecology and Conservation Genomics, Ulm, Germany
| | - Tim Clutton-Brock
- Large Animal Research Group, Department of Zoology, University of Cambridge, Cambridge, UK
- University of Pretoria, Mammal Research Institute, Pretoria, South Africa
- Kalahari Research Trust, Kuruman River Reserve, Northern Cape, South Africa
| | - Marta B Manser
- University of Pretoria, Mammal Research Institute, Pretoria, South Africa
- Kalahari Research Trust, Kuruman River Reserve, Northern Cape, South Africa
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Simone Sommer
- Institute for Evolutionary Ecology and Conservation Genomics, Ulm, Germany
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3
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Li J, Solhi L, Goddard-Borger ED, Mathieu Y, Wakarchuk WW, Withers SG, Brumer H. Four cellulose-active lytic polysaccharide monooxygenases from Cellulomonas species. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:29. [PMID: 33485381 PMCID: PMC7828015 DOI: 10.1186/s13068-020-01860-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 12/13/2020] [Indexed: 05/10/2023]
Abstract
BACKGROUND The discovery of lytic polysaccharide monooxygenases (LPMOs) has fundamentally changed our understanding of microbial lignocellulose degradation. Cellulomonas bacteria have a rich history of study due to their ability to degrade recalcitrant cellulose, yet little is known about the predicted LPMOs that they encode from Auxiliary Activity Family 10 (AA10). RESULTS Here, we present the comprehensive biochemical characterization of three AA10 LPMOs from Cellulomonas flavigena (CflaLPMO10A, CflaLPMO10B, and CflaLPMO10C) and one LPMO from Cellulomonas fimi (CfiLPMO10). We demonstrate that these four enzymes oxidize insoluble cellulose with C1 regioselectivity and show a preference for substrates with high surface area. In addition, CflaLPMO10B, CflaLPMO10C, and CfiLPMO10 exhibit limited capacity to perform mixed C1/C4 regioselective oxidative cleavage. Thermostability analysis indicates that these LPMOs can refold spontaneously following denaturation dependent on the presence of copper coordination. Scanning and transmission electron microscopy revealed substrate-specific surface and structural morphological changes following LPMO action on Avicel and phosphoric acid-swollen cellulose (PASC). Further, we demonstrate that the LPMOs encoded by Cellulomonas flavigena exhibit synergy in cellulose degradation, which is due in part to decreased autoinactivation. CONCLUSIONS Together, these results advance understanding of the cellulose utilization machinery of historically important Cellulomonas species beyond hydrolytic enzymes to include lytic cleavage. This work also contributes to the broader mapping of enzyme activity in Auxiliary Activity Family 10 and provides new biocatalysts for potential applications in biomass modification.
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Affiliation(s)
- James Li
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
- BioProducts Institute, University of British Columbia, 2385 East Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Laleh Solhi
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
- BioProducts Institute, University of British Columbia, 2385 East Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Ethan D Goddard-Borger
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC, V6T 1Z1, Canada
| | - Yann Mathieu
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
- BioProducts Institute, University of British Columbia, 2385 East Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Warren W Wakarchuk
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - Stephen G Withers
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC, V6T 1Z1, Canada
- BioProducts Institute, University of British Columbia, 2385 East Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada.
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada.
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC, V6T 1Z1, Canada.
- Department of Botany, University of British Columbia, 3200 University Blvd, Vancouver, BC, V6T 1Z4, Canada.
- BioProducts Institute, University of British Columbia, 2385 East Mall, Vancouver, BC, V6T 1Z4, Canada.
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Amino Acids and Ribose: Drivers of Protein and RNA Fermentation by Ingested Bacteria of a Primitive Gut Ecosystem. Appl Environ Microbiol 2019; 85:AEM.01297-19. [PMID: 31324631 PMCID: PMC6752017 DOI: 10.1128/aem.01297-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 07/14/2019] [Indexed: 01/21/2023] Open
Abstract
Animal health is linked to gut ecosystems whose primary function is normally the digestion of dietary matter. Earthworms are representative of one of the oldest known animal lineages and, despite their primitive nature, have unique environmental impact by virtue of their dietary consumption of their habitat, i.e., soil-associated matter. A resident gut community is a hallmark of many gut ecosystems of evolutionarily more advanced animals, but the alimentary canal of earthworms is dominated by ingested transient soil microbes. Protein and RNA are (i) the primary organic components of microbial cells that are subject to lysis during gut passage and (ii) fermentable dietary substrates in the alimentary canal. This study examined the gut-associated fermentation of constituents of these biopolymers to determine how their fermentation is integrated to the microbiological dynamics of the gut and might contribute to earthworm-linked transformations of organic matter in the terrestrial biosphere. Earthworms are among the most primitive animals and are of fundamental importance to the turnover of organic matter in the terrestrial biosphere. These invertebrates ingest materials that are colonized by microbes, some of which are subject to disruption by the crop/gizzard or other lytic events during gut passage. Protein and RNA are dominant polymers of disrupted microbial cells, and these biopolymers facilitate robust fermentations by surviving ingested bacteria. To further resolve these fermentations, amino acids and ribose (as fermentable constituents of protein and RNA, respectively) were evaluated as potential drivers of fermentation in gut content of the model earthworm Lumbricus terrestris (taxa were examined with 16S rRNA-based analyses). Of eight amino acids tested, glutamate, aspartate, and threonine were most stimulatory and yielded dissimilar fermentations facilitated by contrasting taxa (e.g., glutamate stimulated the Fusobacteriaceae and yielded H2 and formate, whereas aspartate stimulated the Aeromonadaceae and yielded succinate and propionate). A marginal Stickland fermentation was associated with the Peptostreptococcaceae and Lachnospiraceae. Ribose fermentation yielded a complex product profile facilitated primarily by the Aeromonadaceae. The transient nature of succinate was linked to its decarboxylation to propionate and the Fusobacteriaceae, whereas the transient nature of formate was linked to formate-hydrogen lyase activity and the Peptostreptococcaceae. These findings reinforce the likelihood that (i) the animal host and hosted fermentative bacteria compete for the constituents of protein and RNA in the alimentary canal and (ii) diverse gut fermenters engaged in the fermentation of these constituents produce products that can be utilized by earthworms. IMPORTANCE Animal health is linked to gut ecosystems whose primary function is normally the digestion of dietary matter. Earthworms are representative of one of the oldest known animal lineages and, despite their primitive nature, have unique environmental impact by virtue of their dietary consumption of their habitat, i.e., soil-associated matter. A resident gut community is a hallmark of many gut ecosystems of evolutionarily more advanced animals, but the alimentary canal of earthworms is dominated by ingested transient soil microbes. Protein and RNA are (i) the primary organic components of microbial cells that are subject to lysis during gut passage and (ii) fermentable dietary substrates in the alimentary canal. This study examined the gut-associated fermentation of constituents of these biopolymers to determine how their fermentation is integrated to the microbiological dynamics of the gut and might contribute to earthworm-linked transformations of organic matter in the terrestrial biosphere.
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Microbial Succession of Anaerobic Chitin Degradation in Freshwater Sediments. Appl Environ Microbiol 2019; 85:AEM.00963-19. [PMID: 31285190 PMCID: PMC6715849 DOI: 10.1128/aem.00963-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 06/29/2019] [Indexed: 12/23/2022] Open
Abstract
Chitin is the most abundant biopolymer in aquatic environments, with a direct impact on the carbon and nitrogen cycles. Despite its massive production as a structural element of crustaceans, insects, or algae, it does not accumulate in sediments. Little is known about its turnover in predominantly anoxic freshwater sediments and the responsible microorganisms. We proved that chitin is readily degraded under anoxic conditions and linked this to a succession of the members of the responsible microbial community over a 43-day period. While Fibrobacteres and Firmicutes members were driving the early and late phases of chitin degradation, respectively, a more diverse community was involved in chitin degradation in the intermediate phase. Entirely different microorganisms responded toward the chitin monomer N-acetylglucosamine, which underscores that soluble monomers are poor and misleading substrates to study polymer-utilizing microorganisms. Our study provides quantitative insights into the microbial ecology driving anaerobic chitin degradation in freshwater sediments. Chitin is massively produced by freshwater plankton species as a structural element of their exoskeleton or cell wall. At the same time, chitin does not accumulate in the predominantly anoxic sediments, underlining its importance as carbon and nitrogen sources for sedimentary microorganisms. We studied chitin degradation in littoral sediment of Lake Constance, Central Europe’s third largest lake. Turnover of the chitin analog methyl-umbelliferyl-N,N-diacetylchitobioside (MUF-DC) was highest in the upper oxic sediment layer, with 5.4 nmol MUF-DC h−1 (g sediment [dry weight])−1. In the underlying anoxic sediment layers, chitin hydrolysis decreased with depth from 1.1 to 0.08 nmol MUF-DC h−1 (g sediment [dry weight])−1. Bacteria involved in chitin degradation were identified by 16S rRNA (gene) amplicon sequencing of anoxic microcosms incubated in the presence of chitin compared to microcosms amended either with N-acetylglucosamine as the monomer of chitin or no substrate. Chitin degradation was driven by a succession of bacteria responding specifically to chitin only. The early phase (0 to 9 days) was dominated by Chitinivibrio spp. (Fibrobacteres). The intermediate phase (9 to 21 days) was characterized by a higher diversity of chitin responders, including, besides Chitinivibrio spp., also members of the phyla Bacteroidetes, Proteobacteria, Spirochaetes, and Chloroflexi. In the late phase (21 to 43 days), the Chitinivibrio populations broke down with a parallel strong increase of Ruminiclostridium spp. (formerly Clostridium cluster III, Firmicutes), which became the dominating chitin responders. Our study provides quantitative insights into anaerobic chitin degradation in lake sediments and linked this to a model of microbial succession associated with this activity. IMPORTANCE Chitin is the most abundant biopolymer in aquatic environments, with a direct impact on the carbon and nitrogen cycles. Despite its massive production as a structural element of crustaceans, insects, or algae, it does not accumulate in sediments. Little is known about its turnover in predominantly anoxic freshwater sediments and the responsible microorganisms. We proved that chitin is readily degraded under anoxic conditions and linked this to a succession of the members of the responsible microbial community over a 43-day period. While Fibrobacteres and Firmicutes members were driving the early and late phases of chitin degradation, respectively, a more diverse community was involved in chitin degradation in the intermediate phase. Entirely different microorganisms responded toward the chitin monomer N-acetylglucosamine, which underscores that soluble monomers are poor and misleading substrates to study polymer-utilizing microorganisms. Our study provides quantitative insights into the microbial ecology driving anaerobic chitin degradation in freshwater sediments.
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Wieczorek AS, Schmidt O, Chatzinotas A, von Bergen M, Gorissen A, Kolb S. Ecological Functions of Agricultural Soil Bacteria and Microeukaryotes in Chitin Degradation: A Case Study. Front Microbiol 2019; 10:1293. [PMID: 31281293 PMCID: PMC6596343 DOI: 10.3389/fmicb.2019.01293] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 05/23/2019] [Indexed: 11/24/2022] Open
Abstract
Chitin provides a valuable carbon and nitrogen source for soil microorganisms and is a major component of particulate organic matter in agricultural soils. To date, there is no information on interaction and interdependence in chitin-degrading soil microbiomes. Since microbial chitin degradation occurs under both oxic and anoxic conditions and both conditions occur simultaneously in soil, the comparison of the active microbiome members under both conditions can reveal key players for the overall degradation in aerated soil. A time-resolved 16S rRNA stable isotope probing experiment was conducted with soil material from the top soil layer of a wheat-covered field. [13CU]-chitin was largely mineralized within 20 days under oxic conditions. Cellvibrio, Massilia, and several Bacteroidetes families were identified as initially active chitin degraders. Subsequently, Planctomycetes and Verrucomicrobia were labeled by assimilation of 13C carbon either from [13CU]-chitin or from 13C-enriched components of primary chitin degraders. Bacterial predators (e.g., Bdellovibrio and Bacteriovorax) were labeled, too, and non-labeled microeukaryotic predators (Alveolata) increased their relative abundance toward the end of the experiment (70 days), indicating that chitin degraders were subject to predation. Trophic interactions differed substantially under anoxic and oxic conditions. Various fermentation types occurred along with iron respiration. While Acidobacteria and Chloroflexi were the first taxa to be labeled, although at a low 13C level, Firmicutes and uncultured Bacteroidetes were predominantly labeled at a much higher 13C level during the later stages, suggesting that the latter two bacterial taxa were mainly responsible for the degradation of chitin and also provided substrates for iron reducers. Eventually, our study revealed that (1) hitherto unrecognized Bacteria were involved in a chitin-degrading microbial food web of an agricultural soil, (2) trophic interactions were substantially shaped by the oxygen availability, and (3) detectable predation was restricted to oxic conditions. The gained insights into trophic interactions foster our understanding of microbial chitin degradation, which is in turn crucial for an understanding of soil carbon dynamics.
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Affiliation(s)
- Adam S Wieczorek
- Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany
| | - Oliver Schmidt
- Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany
| | - Antonis Chatzinotas
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany.,Faculty of Biosciences, Pharmacy and Psychology, Institute of Biochemistry, University of Leipzig, Leipzig, Germany.,Department of Chemistry and Bioscience, University of Aalborg, Aalborg, Denmark
| | | | - Steffen Kolb
- Microbial Biogeochemistry, RA Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany
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Jag V, Poehlein A, Bengelsdorf FR, Daniel R, Dürre P. Genome sequencing and description of Oerskovia enterophila VJag, an agar- and cellulose-degrading bacterium. Stand Genomic Sci 2017; 12:30. [PMID: 28484582 PMCID: PMC5418683 DOI: 10.1186/s40793-017-0244-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 04/27/2017] [Indexed: 01/28/2023] Open
Abstract
A nonmotile, Gram-positive bacterium that shows an elongated and branching cell shape was isolated from soil samples from the botanical garden of Ulm University, Ulm, Germany. Here, the isolation procedure, identification, genome sequencing and metabolic features of the strain are described. Phylogenetic analysis allowed to identify the isolated strain as Oerskovia enterophila. The genus Oerskovia belongs to the family Cellulomonadaceae within the order Actinomycetales. The length of cells of O. enterophila ranges from 1 μm to 15 μm, depending on the growth phase. In the exponential growth phase, cells show an elongated and branching shape, whereas cells break up to round or coccoid elements in the stationary growth phase. The 4,535,074 bp long genome consists of 85 contigs with 3918 protein-coding genes and 57 RNA genes. The isolated strain was shown to degrade numerous complex carbon sources such as cellulose, chitin, and starch, which can be found ubiquitously in nature. Moreover, analysis of the genomic sequence revealed the genetic potential to degrade these compounds.
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Affiliation(s)
- Vanessa Jag
- Institut für Mikrobiologie und Biotechnologie, Universität Ulm, Albert-Einstein-Allee 11, D-89081 Ulm, Germany
| | - Anja Poehlein
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany
| | - Frank R Bengelsdorf
- Institut für Mikrobiologie und Biotechnologie, Universität Ulm, Albert-Einstein-Allee 11, D-89081 Ulm, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany
| | - Peter Dürre
- Institut für Mikrobiologie und Biotechnologie, Universität Ulm, Albert-Einstein-Allee 11, D-89081 Ulm, Germany
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8
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Genome Sequence of the Facultative Anaerobe Oerskovia enterophila DFA-19 (DSM 43852T). GENOME ANNOUNCEMENTS 2016; 4:4/5/e00973-16. [PMID: 27634998 PMCID: PMC5026438 DOI: 10.1128/genomea.00973-16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Here, we report the draft genome sequence of Oerskovia enterophila DFA-19 (DSM 43852T), a facultative anaerobe soil bacterium, which was originally isolated from millipede feces and first described as Promicromonospora enterophila. The genome consists of a circular chromosome comprising approximately 4.65 Mb and 4,044 predicted protein-encoding genes.
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Poulsen HV, Willink FW, Ingvorsen K. Aerobic and anaerobic cellulase production by Cellulomonas uda. Arch Microbiol 2016; 198:725-35. [PMID: 27154570 PMCID: PMC4995238 DOI: 10.1007/s00203-016-1230-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 04/08/2016] [Accepted: 04/25/2016] [Indexed: 10/29/2022]
Abstract
Cellulomonas uda (DSM 20108/ATCC 21399) is one of the few described cellulolytic facultative anaerobes. Based on these characteristics, we initiated a physiological study of C. uda with the aim to exploit it for cellulase production in simple bioreactors with no or sporadic aeration. Growth, cellulase activity and fermentation product formation were evaluated in different media under both aerobic and anaerobic conditions and in experiments where C. uda was exposed to alternating aerobic/anaerobic growth conditions. Here we show that C. uda behaves as a true facultative anaerobe when cultivated on soluble substrates such as glucose and cellobiose, but for reasons unknown cellulase activity is only induced under aerobic conditions on insoluble cellulosic substrates and not under anaerobic conditions. These findings enhance knowledge on the limited number of described facultative cellulolytic anaerobes, and in addition it greatly limits the utility of C. uda as an 'easy to handle' cellulase producer with low aeration demands.
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Affiliation(s)
- Henrik Vestergaard Poulsen
- Department of Bioscience, Section for Microbiology, Aarhus University, Ny Munkegade 116, 8000, Aarhus C, Denmark
| | - Fillip Wolfgang Willink
- Department of Bioscience, Section for Microbiology, Aarhus University, Ny Munkegade 116, 8000, Aarhus C, Denmark
| | - Kjeld Ingvorsen
- Department of Bioscience, Section for Microbiology, Aarhus University, Ny Munkegade 116, 8000, Aarhus C, Denmark.
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Rebollar EA, Hughey MC, Medina D, Harris RN, Ibáñez R, Belden LK. Skin bacterial diversity of Panamanian frogs is associated with host susceptibility and presence of Batrachochytrium dendrobatidis. ISME JOURNAL 2016; 10:1682-95. [PMID: 26744810 DOI: 10.1038/ismej.2015.234] [Citation(s) in RCA: 124] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 10/29/2015] [Accepted: 11/06/2015] [Indexed: 01/06/2023]
Abstract
Symbiotic bacteria on amphibian skin can inhibit growth of the fungus Batrachochytrium dendrobatidis (Bd) that has caused dramatic population declines and extinctions of amphibians in the Neotropics. It remains unclear how the amphibians' skin microbiota is influenced by environmental bacterial reservoirs, host-associated factors such as susceptibility to pathogens, and pathogen presence in tropical amphibians. We sampled skin bacteria from five co-occurring frog species that differ in Bd susceptibility at one Bd-naive site, and sampled one of the non-susceptible species from Bd-endemic and Bd-naive sites in Panama. We hypothesized that skin bacterial communities (1) would be distinct from the surrounding environment regardless of the host habitat, (2) would differ between Bd susceptible and non-susceptible species and (3) would differ on hosts in Bd-naive and Bd-endemic sites. We found that skin bacterial communities were enriched in bacterial taxa that had low relative abundances in the environment. Non-susceptible species had very similar skin bacterial communities that were enriched in particular taxa such as the genera Pseudomonas and Acinetobacter. Bacterial communities of Craugastor fitzingeri in Bd-endemic sites were less diverse than in the naive site, and differences in community structure across sites were explained by changes in relative abundance of specific bacterial taxa. Our results indicate that skin microbial structure was associated with host susceptibility to Bd and might be associated to the history of Bd presence at different sites.
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Affiliation(s)
- Eria A Rebollar
- Department of Biology, James Madison University, Harrisonburg, VA, USA
| | - Myra C Hughey
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Daniel Medina
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Reid N Harris
- Department of Biology, James Madison University, Harrisonburg, VA, USA
| | - Roberto Ibáñez
- Smithsonian Tropical Research Institute, Panama City, Panama
| | - Lisa K Belden
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA.,Smithsonian Tropical Research Institute, Panama City, Panama
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Patil NS, Jadhav JP. Significance of Penicillium ochrochloron chitinase as a biocontrol agent against pest Helicoverpa armigera. CHEMOSPHERE 2015; 128:231-235. [PMID: 25723715 DOI: 10.1016/j.chemosphere.2015.01.038] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2014] [Revised: 01/20/2015] [Accepted: 01/27/2015] [Indexed: 06/04/2023]
Abstract
Penicillium ochrochloron chitinase purified by DEAE-cellulose ion exchange chromatography was evaluated for its antifeedant and growth inhibitory activities against Helicoverpa armigera at different concentrations of 2000, 1000, 500, 250 and 100 U mL(-1). It reduced the successful pupation and increased larval and pupal mortality, adult emergence in a dosage-dependent manner when applied topically. The highest mortalities were recorded for groups treated with 2000 U mL(-1) chitinase activity. The studies showed P.ochrochloron chitinase can affect the growth of H.armigera larvae. Since this insect pest species has developed resistance and resurgence to chemical insecticides, only alternate is the usage of enzyme-based pesticide formulations as an environmentally friendly pest management tool.
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Affiliation(s)
- Nilambari S Patil
- Department of Biotechnology, Shivaji University, Kolhapur 416004, India
| | - Jyoti P Jadhav
- Department of Biotechnology, Shivaji University, Kolhapur 416004, India; Department of Biochemistry, Shivaji University, Kolhapur 416004, India.
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12
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Speers AM, Young JM, Reguera G. Fermentation of glycerol into ethanol in a microbial electrolysis cell driven by a customized consortium. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:6350-8. [PMID: 24802954 DOI: 10.1021/es500690a] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The in situ generation of ethanol from glycerol-containing wastewater shows promise to improve the economics of the biodiesel industry. Consequently, we developed a microbial electrolysis cell (MEC) driven by the synergistic metabolisms of the exoelectrogen Geobacter sulfurreducens and the bacterium Clostridium cellobioparum, which fermented glycerol into ethanol in high yields (90%) and produced fermentative byproducts that served as electron donors for G. sulfurreducens. Syntrophic cooperation stimulated glycerol consumption, ethanol production, and the conversion of fermentation byproducts into cathodic H2 in the MEC. The platform was further improved by adaptively evolving glycerol-tolerant strains with robust growth at glycerol loadings typical of biodiesel wastewater and by increasing the buffering capacity of the anode medium. This resulted in additional increases in glycerol consumption (up to 50 g/L) and ethanol production (up to 10 g/L) at rates that greatly exceeded the capacity of the anode biofilms to concomitantly remove the fermentation byproducts. As a result, 1,3-propanediol was generated as a metabolic sink for electrons not converted into electricity syntrophically. The results highlight the potential of consortia to process glycerol in MECs and provide insights into genetic engineering and system design approaches that can be implemented to further improve MEC performance to satisfy industrial needs.
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Affiliation(s)
- Allison M Speers
- Department of Microbiology and Molecular Genetics, Michigan State University , 6190 Biomedical and Physical Science Building, 567 Wilson Road, East Lansing, Michigan 48824, United States
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Tolonen AC, Cerisy T, El-Sayyed H, Boutard M, Salanoubat M, Church GM. Fungal lysis by a soil bacterium fermenting cellulose. Environ Microbiol 2014; 17:2618-27. [PMID: 24798076 DOI: 10.1111/1462-2920.12495] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2014] [Accepted: 04/26/2014] [Indexed: 11/28/2022]
Abstract
Recycling of plant biomass by a community of bacteria and fungi is fundamental to carbon flow in terrestrial ecosystems. Here we report how the plant fermenting, soil bacterium Clostridium phytofermentans enhances growth on cellulose by simultaneously lysing and consuming model fungi from soil. We investigate the mechanism of fungal lysis to show that among the dozens of different glycoside hydrolases C. phytofermentans secretes on cellulose, the most highly expressed enzymes degrade fungi rather than plant substrates. These enzymes, the GH18 Cphy1799 and Cphy1800, synergize to hydrolyse chitin, a main component of the fungal cell wall. Purified enzymes inhibit fungal growth and mutants lacking either GH18 grow normally on cellulose and other plant substrates, but have a reduced ability to hydrolyse chitinous substrates and fungal hyphae. Thus, C. phytofermentans boosts growth on cellulose by lysing fungi with its most highly expressed hydrolases, highlighting the importance of fungal interactions to the ecology of cellulolytic bacteria.
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Affiliation(s)
- Andrew C Tolonen
- CEA, DSV, IG, Genoscope, Évry, France.,CNRS-UMR8030, Évry, France.,Université d'Évry Val d'Essonne, Évry, France
| | - Tristan Cerisy
- CEA, DSV, IG, Genoscope, Évry, France.,CNRS-UMR8030, Évry, France.,Université d'Évry Val d'Essonne, Évry, France
| | - Hafez El-Sayyed
- CEA, DSV, IG, Genoscope, Évry, France.,CNRS-UMR8030, Évry, France.,Université d'Évry Val d'Essonne, Évry, France
| | | | - Marcel Salanoubat
- CEA, DSV, IG, Genoscope, Évry, France.,CNRS-UMR8030, Évry, France.,Université d'Évry Val d'Essonne, Évry, France
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, MA, USA
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Chen JK, Shen CR, Liu CL. The Characteristics of Chitinase Expression in Aeromonas schubertii. Appl Biochem Biotechnol 2014; 172:3827-34. [DOI: 10.1007/s12010-014-0798-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 02/10/2014] [Indexed: 11/24/2022]
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15
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Macdonald C, Barden S, Foley S. Isolation and characterization of chitin-degrading micro-organisms from the faeces of Goeldi's monkey, Callimico goeldii. J Appl Microbiol 2013; 116:52-9. [DOI: 10.1111/jam.12338] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 08/26/2013] [Accepted: 08/30/2013] [Indexed: 12/01/2022]
Affiliation(s)
- C. Macdonald
- School of Life; Sport & Social Science; Edinburgh Napier University; Edinburgh UK
- Animal Department; Edinburgh Zoo; Edinburgh UK
| | - S. Barden
- School of Life; Sport & Social Science; Edinburgh Napier University; Edinburgh UK
| | - S. Foley
- School of Life; Sport & Social Science; Edinburgh Napier University; Edinburgh UK
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Swiontek Brzezinska M, Jankiewicz U, Burkowska A, Walczak M. Chitinolytic microorganisms and their possible application in environmental protection. Curr Microbiol 2013; 68:71-81. [PMID: 23989799 PMCID: PMC3889922 DOI: 10.1007/s00284-013-0440-4] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 07/05/2013] [Indexed: 11/29/2022]
Abstract
This paper provides a review of the latest research findings on the applications of microbial chitinases to biological control. Microorganisms producing these enzymes can inhibit the growth of many fungal diseases that pose a serious threat to global crop production. Currently, efforts are being made to discover producers of chitinolytic enzymes. The potential exists that natural biofungicides will replace chemical fungicides or will be used to supplement currently used fungicides, which would reduce the negative impact of chemicals on the environment and support the sustainable development of agriculture and forestry.
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Affiliation(s)
- Maria Swiontek Brzezinska
- Department of Environmental Microbiology and Biotechnology, Faculty of Biology and Environmental Protection, Nicolaus Copernicus University, Lwowska 1, 87-100, Toruń, Poland,
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Kaur T, Manhas RK. Antifungal, insecticidal, and plant growth promoting potential of Streptomyces hydrogenans DH16. J Basic Microbiol 2013; 54:1175-85. [PMID: 23765423 DOI: 10.1002/jobm.201300086] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2013] [Accepted: 05/09/2013] [Indexed: 11/11/2022]
Abstract
In the present study, an actinobacterium strain, possessing antagonistic activity against different fungal phytopathogens viz. Colletotrichum acutatum, Cladosporium herbarum, Alternaria brassicicola, Exserohilum sp., Alternaria mali, Colletotrichum gleospoiroides, Alternaria alternata, Cercospora sp., Fusarium oxysporum f.sp. dianthi and Fusarium moniliformae, was isolated from soil and identified as Streptomyces hydrogenans DH16. Application of culture supernatant (5%)/cells (10(7) cfu ml(-1) ), 2 h post inoculation with A. brassicicola (10(5) spores ml(-1) ), resulted in 85.95 and 93.75% suppression of black leaf spot of Raphanus sativus, respectively on detached leaves. Whereas cells/culture supernatant (above 5%) completely suppressed the disease incidence when co inoculated with fungal pathogen. The crude extract containing antifungal components was completely stable at 70 °C for 1 h retaining 90 and 67.67% activity after boiling (for 1 h) and autoclaving (121 °C for 30 min), respectively. No loss in activity was observed when treated with proteinase K and on exposure to sun and UV light and found to be active over a wide range of pH (2 to 14). Bioautography of the solvent extract against test phytopathogens revealed the presence of three active components. Ethyl acetate extract of DH16 also demonstrated insecticidal activity against Spodoptera litura, causing 40% larval mortality and extension of larval period. In addition, it produced 30 µg ml(-1) of Indole Acetic Acid (IAA) in a medium containing tryptophan which promoted lateral root formation in Vigna radiata (green gram). These results indicate that Streptomyces hydrogenans holds the potential to be used as antifungal, insecticidal, and plant growth promoting agent.
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Affiliation(s)
- Talwinder Kaur
- Department of Microbiology, Guru Nanak Dev University, Amritsar, India
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18
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Intriago P. Marine Microorganisms: perspectives for getting involved in cellulosic ethanol. AMB Express 2012; 2:46. [PMID: 22931793 PMCID: PMC3490849 DOI: 10.1186/2191-0855-2-46] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2012] [Accepted: 07/30/2012] [Indexed: 11/10/2022] Open
Abstract
The production of ethanol has been considered as an alternative to replace part of the petroleum derivate. Brazil and the US are the leading producers, but more environmentally friendly alternatives are needed. Lignocellulose has an enormous potential but technology has to be still improve in order to economically produce ethanol. The present paper reviews the potential and problems of this technology and proposes the study of a group of microorganisms with the largest genetic pool, marine microorganism.
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Lethal effect of Streptomyces citreofluorescens against larvae of malaria, filaria and dengue vectors. ASIAN PAC J TROP MED 2012; 5:594-7. [PMID: 22840445 DOI: 10.1016/s1995-7645(12)60123-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2012] [Revised: 05/15/2012] [Accepted: 07/15/2012] [Indexed: 11/22/2022] Open
Abstract
OBJECTIVE To investigate lethal effect of culture filtrates of Streptomyces citreofluorescens (S. citreofluorescens) against Anopheles stephensi (An. stephensi), Culex quinquefasciatus (Cx. quinquefasciatus), and Aedes aegypti (Ae. aegypti) larvae vectors for malaria, filarial and dengue. METHODS The culture filtrates obtained from S. citreofluorescens 2528 was grown in Potato Dextrose Broth (PDB), filtrated and used for the bioassay after a growth of 15 days. RESULTS The results demonstrated that the An. stephensi shows mortalities with LC(50), LC(90) values of first instar 46.8 μL/mL, 79.5 μL/mL, second instar 79.0 μL/mL, 95.6 μL/mL, third instar 79.0 μL/mL, 136.9 μL/mL, and fourth instar 122.6 μL/mL, 174.5 μL/mL. Whereas, The Cx. quinquefasciatus were found effective on first instar 40.0 μL/mL, 138.03 μL/mL, second instar 80.0 μL/mL, 181.97 μL/mL, third instar 100.0 μL/mL, 309.2 μL/mL, and fourth instar 60.0 μL/mL, 169.82 μL/mL. The Ae. aegypti were successfully achieved susceptible with higher concentrations in comparisons of An. stephensi and Cx. quinquefasciatus larvae. These outcomes of the investigations have compared with the Chitinase of Streptomyces griseus (S. griseus) C6137 that shows 90%-95% mortality. CONCLUSIONS These new findings significantly permitted that the culture filtrates of S. citreofluorescens can be used as bacterial larvicides. This is an environmentally safe approach to control the vectors of malaria, dengue and filariasis of tropical areas.
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Young JM, Leschine SB, Reguera G. Reversible control of biofilm formation by Cellulomonas spp. in response to nitrogen availability. Environ Microbiol 2011; 14:594-604. [PMID: 21951594 DOI: 10.1111/j.1462-2920.2011.02596.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jenna M Young
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
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Hunger S, Schmidt O, Hilgarth M, Horn MA, Kolb S, Conrad R, Drake HL. Competing formate- and carbon dioxide-utilizing prokaryotes in an anoxic methane-emitting fen soil. Appl Environ Microbiol 2011; 77:3773-85. [PMID: 21478308 PMCID: PMC3127604 DOI: 10.1128/aem.00282-11] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2011] [Accepted: 03/29/2011] [Indexed: 11/20/2022] Open
Abstract
Methanogenesis in wetlands is dependent on intermediary substrates derived from the degradation of biopolymers. Formate is one such substrate and is stimulatory to methanogenesis and acetogenesis in anoxic microcosms of soil from the fen Schlöppnerbrunnen. Formate dissimilation also yields CO(2) as a potential secondary substrate. The objective of this study was to resolve potential differences between anaerobic formate- and CO(2)-utilizing prokaryotes of this fen by stable isotope probing. Anoxic soil microcosms were pulsed daily with low concentrations of [(13)C]formate or (13)CO(2) (i.e., [(13)C]bicarbonate). Taxa were evaluated by assessment of 16S rRNA genes, mcrA (encoding the alpha-subunit of methyl-coenzyme M reductase), and fhs (encoding formyltetrahydrofolate synthetase). Methanogens, acetogens, and formate-hydrogen lyase-containing taxa appeared to compete for formate. Genes affiliated with Methanocellaceae, Methanobacteriaceae, Acetobacteraceae, and Rhodospirillaceae were (13)C enriched (i.e., labeled) in [(13)C]formate treatments, whereas genes affiliated with Methanosarcinaceae, Conexibacteraceae, and Solirubrobacteraceae were labeled in (13)CO(2) treatments. [(13)C]acetate was enriched in [(13)C]formate treatments, but labeling of known acetogenic taxa was not detected. However, several phylotypes were affiliated with acetogen-containing taxa (e.g., Sporomusa). Methanosaetaceae-affiliated methanogens appeared to participate in the consumption of acetate. Twelve and 58 family-level archaeal and bacterial 16S rRNA phylotypes, respectively, were detected, approximately half of which had no isolated representatives. Crenarchaeota constituted half of the detected archaeal 16S rRNA phylotypes. The results highlight the unresolved microbial diversity of the fen Schlöppnerbrunnen, suggest that differing taxa competed for the same substrate, and indicate that Methanocellaceae, Methanobacteriaceae, Methanosarcinaceae, and Methanosaetaceae were linked to the production of methane, but they do not clearly resolve the taxa responsible for the apparent conversion of formate to acetate.
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MESH Headings
- Anaerobiosis
- Biodiversity
- Carbon Dioxide/metabolism
- Carbon Isotopes/metabolism
- Cluster Analysis
- DNA, Archaeal/chemistry
- DNA, Archaeal/genetics
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Formates/metabolism
- Genes, rRNA
- Methane/metabolism
- Molecular Sequence Data
- Phylogeny
- RNA, Archaeal/genetics
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Soil Microbiology
- Wetlands
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Affiliation(s)
- Sindy Hunger
- Department of Ecological Microbiology, University of Bayreuth, 95440 Bayreuth, Germany
| | - Oliver Schmidt
- Department of Ecological Microbiology, University of Bayreuth, 95440 Bayreuth, Germany
| | - Maik Hilgarth
- Department of Ecological Microbiology, University of Bayreuth, 95440 Bayreuth, Germany
| | - Marcus A. Horn
- Department of Ecological Microbiology, University of Bayreuth, 95440 Bayreuth, Germany
| | - Steffen Kolb
- Department of Ecological Microbiology, University of Bayreuth, 95440 Bayreuth, Germany
| | - Ralf Conrad
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Harold L. Drake
- Department of Ecological Microbiology, University of Bayreuth, 95440 Bayreuth, Germany
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Enzymatic degradation of steam-pretreated Lespedeza stalk (Lespedeza crytobotrya) by cellulosic-substrate induced cellulases. Bioprocess Biosyst Eng 2010; 34:357-65. [DOI: 10.1007/s00449-010-0478-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Accepted: 10/18/2010] [Indexed: 10/18/2022]
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Identification of chitinases Is-chiA and Is-chiB from Isoptericola jiangsuensis CLG and their characterization. Appl Microbiol Biotechnol 2010; 89:705-13. [PMID: 20922373 DOI: 10.1007/s00253-010-2917-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2010] [Revised: 09/07/2010] [Accepted: 09/09/2010] [Indexed: 10/19/2022]
Abstract
A 274-bp conserved fragment of chiA (chiA-CF) was amplified from the genomic DNA of Isoptericola jiangsuensis CLG (DSM 21863, CCTCC AB208287) using the specific PCR primers. Based on chiA-CF sequences, a 5233-bp DNA fragment was obtained by self-formed adaptor PCR. DNA sequencing analysis revealed there were two contiguous open reading frames coding for the precursors of Is-chiA [871 amino acids (aa)] and Is-chiB (561 aa) in the 5233-bp DNA fragment. The Is-chiA and Is-chiB exhibited 58% and 62% identity with ArChiA and ArChiB chitinase from Arthrobacter sp. TAD20, respectively. The Is-chiA and Is-chiB genes were cloned into expression vector pET28a (+) and expressed in Escherichia coli BL21 (DE3) with isopropyl-β-D-thiogalactopyranoside induction. Is-chiA and Is-chiB were 92 kDa and 60 kDa by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and showed chitobiosidase and endochitinase activity, respectively. Is-chiA and Is-chiB were purified by Ni-nitrilotriacetic acid affinity chromatography and the characteristics of both Is-chiA and Is-chiB were studied.
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Lovanh N, Cook KL, Rothrock MJ, Miles DM, Sistani K. Spatial Shifts in Microbial Population Structure Within Poultry Litter Associated with Physicochemical Properties. Poult Sci 2007; 86:1840-9. [PMID: 17704369 DOI: 10.1093/ps/86.9.1840] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Microbial populations within poultry litter have been largely ignored with the exception of potential human or livestock pathogens. A better understanding of the community structure and identity of the microbial populations within poultry litter could aid in the development of management practices that would reduce populations responsible for toxic air emissions and pathogen incidence. In this study, poultry litter air and physical properties were correlated to shifts in microbial community structure as analyzed by principal component analysis (PCA) and measured by denaturing gradient gel electrophoresis (DGGE). Litter samples were taken in a 36-point grid pattern at 5 m across and 12 m down a 146 m x 12.8 m chicken house. At each sample point, physical parameters such as litter moisture, pH, air and litter temperature, and relative humidity were recorded, and samples were taken for molecular analysis. The DGGE analysis showed that the banding pattern of samples from the back and water/feeder areas of poultry house were distinct from those of samples from other areas. There were distinct clusters of banding patterns corresponding to the front, middle front, middle back, back, and waterer/feeder areas. The PCA analysis showed similar cluster patterns, but with more distinct separation of the front and midhouse samples. The PCA analysis also showed that moisture content and litter temperature (accounting for 51.5 and 31.5% of the separation of samples, respectively) play a major role in spatial diversity of microbial community in the poultry house. Based on analysis of DGGE fingerprints and cloned DGGE band sequences, there appear to be differences in the types of microorganisms over the length of the house, which correspond to differences in the physical properties of the litter.
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Affiliation(s)
- N Lovanh
- USDA-ARS, Animal Waste Management Research Unit, Bowling Green, KY 42104, USA.
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Manucharova NA, Yaroslavtsev AM, Senchenko DV, Stepanov AL, Zvyagintsev DG. Microbial transformation of chitin in soil under anaerobic conditions. BIOL BULL+ 2006. [DOI: 10.1134/s1062359006020154] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Lu J, Sanchez S, Hofacre C, Maurer JJ, Harmon BG, Lee MD. Evaluation of broiler litter with reference to the microbial composition as assessed by using 16S rRNA and functional gene markers. Appl Environ Microbiol 2003; 69:901-8. [PMID: 12571010 PMCID: PMC143620 DOI: 10.1128/aem.69.2.901-908.2003] [Citation(s) in RCA: 134] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Very little is known about the microbial composition of animal bedding wastes, including poultry litter, and what is known has been deduced from standard culture methods, by which some fastidious organisms that exist in the environment may not be detected. We evaluated the bacterial composition of poultry litter by using a combination of culture and molecular detection. Total aerobic bacteria in poultry litter were detected by culture at 10(9) CFU/g of material. Enteric bacteria such as Enterococcus spp. and coliforms composed 0.1 and 0.01%, respectively, of the total aerobic cultivatable bacteria in poultry litter; no Salmonella strains were detected by culture. In order to characterize the most abundant bacterial groups, we sequenced 16S ribosomal DNA (rDNA) genes amplified by PCR with microbial community DNA isolated from poultry litter as the template. From the 16S rDNA library, 31 genera were identified. Twelve families or groups were identified with lactobacilli and Salinococcus spp. forming the most abundant groups. In fact, 82% of the total sequences were identified as gram-positive bacteria with 62% of total belonging to low G+C gram-positive groups. In addition to detection of 16S rDNA sequences associated with the expected fecal bacteria present in manure, we detected many bacterial sequences for organisms, such as Globicatella sulfidofaciens, Corynebacterium ammoniagenes, Corynebacterium urealyticum, Clostridium aminovalericum, Arthrobacter sp., and Denitrobacter permanens, that may be involved in the degradation of wood and cycling of nitrogen and sulfur. Several sequences were identified in the library for bacteria associated with disease in humans and poultry such as clostridia, staphylococci, and Bordetella spp. However, specific PCR targeting other human and veterinary pathogens did not detect the presence of Salmonella, pathogenic Escherichia coli, Campylobacter spp., Yersinia spp., Listeria spp., or toxigenic staphylococci. PCR and DNA hybridization revealed the presence of class 1 integrons with gene cassettes that specify resistance to aminoglycosides and chloramphenicol. Only from understanding the microbial community of animal wastes such as poultry litter can we manage animal disease and limit the impact of animal waste on the environment and human and animal health.
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Affiliation(s)
- Jingrang Lu
- Medical Microbiology and Parasitology, College of Veterinary Medicine, The University of Georgia, Athens, Georgia 30602, USA
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