151
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An oligarchic microbial assemblage in the anoxic bottom waters of a volcanic subglacial lake. ISME JOURNAL 2008; 3:486-97. [DOI: 10.1038/ismej.2008.124] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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152
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Abstract
Most bacteria are recalcitrant to traditional cultivation in the laboratory. The soil substrate membrane system provides a simulated environment for the cultivation of previously undescribed soil bacteria as microcolonies. The system uses a polycarbonate membrane as a solid support for growth and soil extract as the substrate. Diverse microcolonies can be visualized using total bacterial staining combined with fluorescence in situ hybridization (FISH) after 7-10-d incubation. Molecular typing shows that the majority of microcolony-forming bacteria recovered using this protocol were resistant to growth using standard methods. The protocol takes <4 h of bench time over the 10-d period.
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153
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Riesenfeld CS, Murray AE, Baker BJ. Characterization of the microbial community and polyketide biosynthetic potential in the palmerolide-producing tunicate Synoicum adareanum. JOURNAL OF NATURAL PRODUCTS 2008; 71:1812-1818. [PMID: 18950228 DOI: 10.1021/np800287n] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Palmerolide A (1) is a macrolide isolated from the Antarctic tunicate Synoicum adareanum that is of interest due to its potential as an antimelanoma drug. Biosynthesis is predicted to occur via a hybrid PKS-NRPS pathway within S. adareanum, but the identity of the palmerolide-producing organism (host or putative host-associated microorganism) has not been established. Microscopic observation revealed a dense microbial community inside the tunicate, and evidence from 16S rRNA gene DGGE profiles and clone library sequences suggests that the bacterial community has moderate phylogenetic complexity. The alpha and gamma classes of Proteobacteria account for ∼75% of the cloned 16S rRNA genes, and the majority of these sequences are affiliated with the genera Pseudovibrio and Microbulbifer. DNA sequences encoding type I PKS ketosynthase (KS) domains were detected by PCR. The S. adareanum KS sequences, which affiliate with the trans-AT clade, are similar to portions of PKS proteins that lack integrated acyltransferase domains in pathways for generating bioactive polyketide compounds, including bryostatin, leinamycin, and pederin.
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154
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Xia Y, Kong Y, Nielsen PH. In situ detection of starch-hydrolyzing microorganisms in activated sludge. FEMS Microbiol Ecol 2008; 66:462-71. [DOI: 10.1111/j.1574-6941.2008.00559.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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155
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Kong Y, Xia Y, Nielsen PH. Activity and identity of fermenting microorganisms in full-scale biological nutrient removing wastewater treatment plants. Environ Microbiol 2008; 10:2008-19. [DOI: 10.1111/j.1462-2920.2008.01617.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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156
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Microbial ecology of the equine hindgut during oligofructose-induced laminitis. ISME JOURNAL 2008; 2:1089-100. [DOI: 10.1038/ismej.2008.67] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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157
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Kong Y, Xia Y, Nielsen JL, Nielsen PH. Structure and function of the microbial community in a full-scale enhanced biological phosphorus removal plant. MICROBIOLOGY-SGM 2008; 153:4061-4073. [PMID: 18048920 DOI: 10.1099/mic.0.2007/007245-0] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The structure and function of the microbial community in a full-scale enhanced biological phosphorus removal wastewater treatment plant (WWTP; Skagen) were investigated using the full-cycle rRNA approach, combined with ecophysiological studies. A total of 87 16S rRNA gene sequences were retrieved, and 78 operational taxonomic units were identified. Novel oligonucleotide probes were designed, and quantitative fluorescence in situ hybridization revealed that six hitherto undescribed probe-defined groups within the phylum Bacteroidetes (two groups), and classes Betaproteobacteria (two groups) and Gammaproteobacteria (two groups), were relatively abundant (>1% of total biovolume) in the Skagen WWTP and 10 other full-scale WWTPs with biological P removal. The most abundant was a group of rod-shaped Bacteroidetes attached to filamentous bacteria, which is distantly related to the genus Haliscomenobacter of the family Saprospiraceae, and comprised 9-19% of the bacterial biovolume in all the WWTPs investigated. The other five probe-defined groups were found in all WWTPs, but they were less abundant (1-6%). Two groups had a glycogen-accumulating phenotype and one Dechloromonas-related group had a polyphosphate-accumulating phenotype, and they were potentially all involved in denitrification. In total, about 81% of all bacteria hybridizing with the general eubacterial probe were detected in the Skagen WWTP by using clone- or group-specific probes, indicating that most members of the microbial community had been identified.
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Affiliation(s)
- Yunhong Kong
- Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, DK-9000 Aalborg, Denmark
| | - Yun Xia
- Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, DK-9000 Aalborg, Denmark
| | - Jeppe Lund Nielsen
- Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, DK-9000 Aalborg, Denmark
| | - Per Halkjær Nielsen
- Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, DK-9000 Aalborg, Denmark
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158
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Identification and ecophysiological characterization of epiphytic protein-hydrolyzing saprospiraceae ("Candidatus Epiflobacter" spp.) in activated sludge. Appl Environ Microbiol 2008; 74:2229-38. [PMID: 18263744 DOI: 10.1128/aem.02502-07] [Citation(s) in RCA: 131] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The identity and ecophysiology of a group of uncultured protein-hydrolyzing epiphytic rods attached to filamentous bacteria in activated sludge from nutrient removal plants were investigated by using the full-cycle rRNA approach combined with microautoradiography and histochemical staining. The epiphytic group consists of three closely related clusters, each containing 11 to 16 clones. The closest related cultured isolate is the type strain Haliscomenobacter hydrossis (ATCC 27775) (<87% similarity) in the family Saprospiraceae of the phylum Bacteroidetes. Oligonucleotide probes at different hierarchical levels were designed for each cluster and used for ecophysiological studies. All three clusters behaved similarly in their physiology and were specialized in protein hydrolysis and used amino acids as energy and carbon sources. They were not involved in denitrification. No storage of polyphosphate and polyhydroxyalkanoates was found. They all colonized probe-defined filamentous bacteria belonging to the phyla Chloroflexi, Proteobacteria, and candidate phylum TM7, with the exception of cluster 1, which did not colonize TM7 filaments. The three epiphytic clusters were all widespread in domestic and industrial wastewater treatment plants with or without biological phosphorus removal, constituting, in total, up to 9% of the bacterial biovolume. A new genus, "Candidatus Epiflobacter," is proposed for this epiphytic group in activated-sludge treatment plants, where it presumably plays an important role in protein degradation.
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159
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Talbot G, Topp E, Palin MF, Massé DI. Evaluation of molecular methods used for establishing the interactions and functions of microorganisms in anaerobic bioreactors. WATER RESEARCH 2008; 42:513-37. [PMID: 17719078 DOI: 10.1016/j.watres.2007.08.003] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2006] [Revised: 07/31/2007] [Accepted: 08/01/2007] [Indexed: 05/16/2023]
Abstract
Molecular techniques have unveiled the complexity of the microbial consortium in anaerobic bioreactors and revealed the presence of several uncultivated species. This paper presents a review of the panoply of classical and recent molecular approaches and multivariate analyses that have been, or might be used to establish the interactions and functions of these anaerobic microorganisms. Most of the molecular approaches used so far are based on the analysis of small subunit ribosomal RNA but recent studies also use quantification of functional gene expressions. There are now several studies that have developed quantitative real-time PCR assays to investigate methanogens. With a view to improving the stability and performance of bioreactors, monitoring with molecular methods is also discussed. Advances in metagenomics and proteomics will lead to the development of promising lab-on chip technologies for cost-effective monitoring.
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Affiliation(s)
- G Talbot
- Dairy and Swine Research and Development Centre, Agriculture and Agri-Food Canada, 2000 College Street, Sherbrooke, Quebec, Canada J1M 0C8.
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160
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Amyloid-like adhesins produced by floc-forming and filamentous bacteria in activated sludge. Appl Environ Microbiol 2008; 74:1517-26. [PMID: 18192426 DOI: 10.1128/aem.02274-07] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Amyloid proteins (fimbriae or other microbial surface-associated structures) are expressed by many types of bacteria, not yet identified, in biofilms from various habitats, where they likely are of key importance to biofilm formation and biofilm properties. As these amyloids are potentially of great importance to the floc properties in activated sludge wastewater treatment plants (WWTP), the abundance of amyloid adhesins in activated sludge flocs from different WWTP and the identity of bacteria producing these were investigated. Amyloid adhesins were quantified using a combination of conformationally specific antibodies targeting amyloid fibrils, propidium iodide to target all fixed bacterial cells, confocal laser scanning microscopy, and digital image analysis. The biovolume fraction containing amyloid adhesins ranged from 10 to 40% in activated sludge from 10 different WWTP. The identity of bacteria producing amyloid adhesins was determined using fluorescence in situ hybridization with oligonucleotide probes in combination with antibodies or thioflavin T staining. Among the microcolony-forming bacteria, amyloids were primarily detected among Alpha- and Betaproteobacteria and Actinobacteria. A more detailed analysis revealed that many denitrifiers (from Thauera, Azoarcus, Zoogloea, and Aquaspirillum-related organisms) and Actinobacteria-related polyphosphate-accumulating organisms most likely produced amyloid adhesins, whereas nitrifiers did not. Many filamentous bacteria also expressed amyloid adhesins, including several Alphaproteobacteria (e.g., Meganema perideroedes), some Betaproteobacteria (e.g., Aquaspirillum-related filaments), Gammaproteobacteria (Thiothrix), Bacteroidetes, Chloroflexi (e.g., Eikelboom type 1851), and some foam-forming Actinobacteria (e.g., Gordonia amarae). The results show that amyloid adhesins were an abundant component of activated sludge extracellular polymeric substances and seem to have unexpected, divers functions.
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161
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Affiliation(s)
- Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
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162
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Microbial Diversity, Life Strategies, and Adaptation to Life in Extreme Soils. SOIL BIOLOGY 2008. [DOI: 10.1007/978-3-540-74231-9_2] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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163
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Müller E, Schade M, Lemmer H. Filamentous scum bacteria in activated sludge plants: detection and identification quality by conventional activated sludge microscopy versus fluorescence in situ hybridization. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2007; 79:2274-2286. [PMID: 17966695 DOI: 10.2175/106143007x183943] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Detection of filamentous bacteria morphotypes involved in scum formation in activated sludge wastewater treatment plants by conventional sludge microscopy is often doomed to fail because of morphological and taxonomical variations. The aim of this study is to compare detection, identification, and quantification quality of filamentous "scum bacteria" found by conventional activated sludge microscopy and fluorescence in situ hybridization (FISH). In the case of filamentous Microthrix parvicella and Eikelboom morphotypes 1863 and 1851, conventional activated sludge microscopy and FISH results correspond well. In contrast, conventional activated sludge microscopy overlooks nocardioform actinomycete and type 1863 single cells. On the other hand, FISH underestimates filamentous nocardioform actinomycetes and morphotypes 0041/0675 or 0092 because of insufficient cell wall permeability or because of their taxonomic variability, with a resulting inadequacy of previously published probes. Nostocoida limicola morphotype results are still inconclusive because of low bacteria numbers being available in situ and the enormous taxonomic variability within this group.
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Affiliation(s)
- Elisabeth Müller
- Institute of Water Quality Control, Technical University of Munich, Garching, Germany.
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164
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Yan S, Subramanian B, Surampalli RY, Narasiah S, Tyagi RD. Isolation, Characterization, and Identification of Bacteria from Activated Sludge and Soluble Microbial Products in Wastewater Treatment Systems. ACTA ACUST UNITED AC 2007. [DOI: 10.1061/(asce)1090-025x(2007)11:4(240)] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
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165
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Milinovich GJ, Trott DJ, Burrell PC, Croser EL, Al Jassim RAM, Morton JM, van Eps AW, Pollitt CC. Fluorescence in situ hybridization analysis of hindgut bacteria associated with the development of equine laminitis. Environ Microbiol 2007; 9:2090-100. [PMID: 17635552 DOI: 10.1111/j.1462-2920.2007.01327.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Carbohydrate-induced laminitis in horses is characterized by marked changes in the composition of the hindgut microbiota, from a predominantly Gram-negative population to one dominated by Gram-positive bacteria. The objective of this study was to monitor changes in the relative abundance of selected hindgut bacteria that have previously been implicated in the pathophysiology of equine laminitis using fluorescence in situ hybridization (FISH). Caecal cannulae were surgically implanted in five Standardbred horses and laminitis induced by oral administration of a bolus dose of oligofructose. Caecal fluid and faecal specimens were collected over a 48 h period at 2 to 4 h intervals post-oligofructose administration and subjected to FISH using probes specific for nine bacterial groups to determine changes in their relative abundance compared with total bacteria hybridizing to the generic EUBMIX probe. Additionally, hoof biopsies were taken over the course of the experiment at 6 h intervals and evaluated for histopathological changes consistent with laminitis, allowing changes in hindgut microbiota to be correlated with the onset of lesions in the foot. Of the microorganisms specifically targeted, streptococci of the Streptococcus bovis/equinus complex were the only bacteria that consistently proliferated in both caecal fluid and faeces immediately before the onset of histological signs of laminitis. Furthermore, lactobacilli, Enterobacteriaceae, Allisonella histaminiformans, enterococci, Bacteroides fragilis, Mitsuokella jalaludinii and Clostridium difficile did not establish significant populations in the hindgut before the onset of equine laminitis.
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Affiliation(s)
- Gabriel J Milinovich
- Australian Equine Laminitis Research Unit, School of Veterinary Science, The University of Queensland, Brisbane, Qld, Australia.
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166
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Connon SA, Lester ED, Shafaat HS, Obenhuber DC, Ponce A. Bacterial diversity in hyperarid Atacama Desert soils. ACTA ACUST UNITED AC 2007. [DOI: 10.1029/2006jg000311] [Citation(s) in RCA: 131] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | | | | | | | - Adrian Ponce
- Jet Propulsion Laboratory; Pasadena California USA
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167
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Marcy Y, Ouverney C, Bik EM, Lösekann T, Ivanova N, Martin HG, Szeto E, Platt D, Hugenholtz P, Relman DA, Quake SR. Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth. Proc Natl Acad Sci U S A 2007; 104:11889-94. [PMID: 17620602 PMCID: PMC1924555 DOI: 10.1073/pnas.0704662104] [Citation(s) in RCA: 441] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We have developed a microfluidic device that allows the isolation and genome amplification of individual microbial cells, thereby enabling organism-level genomic analysis of complex microbial ecosystems without the need for culture. This device was used to perform a directed survey of the human subgingival crevice and to isolate bacteria having rod-like morphology. Several isolated microbes had a 16S rRNA sequence that placed them in candidate phylum TM7, which has no cultivated or sequenced members. Genome amplification from individual TM7 cells allowed us to sequence and assemble >1,000 genes, providing insight into the physiology of members of this phylum. This approach enables single-cell genetic analysis of any uncultivated minority member of a microbial community.
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Affiliation(s)
- Yann Marcy
- *Department of Bioengineering, Stanford University, and Howard Hughes Medical Institute, Stanford, CA 94305
| | - Cleber Ouverney
- Department of Biological Sciences, San Jose State University, San Jose, CA 95192
| | - Elisabeth M. Bik
- Department of Microbiology and Immunology, and Department of Medicine, Stanford University, Stanford, CA 94305
- Veterans Affairs Palo Alto Health Care System, Palo Alto, CA 94304; and
| | - Tina Lösekann
- Department of Microbiology and Immunology, and Department of Medicine, Stanford University, Stanford, CA 94305
- Veterans Affairs Palo Alto Health Care System, Palo Alto, CA 94304; and
| | - Natalia Ivanova
- Department of Energy Joint Genome Institute, Walnut Creek, CA 94598
| | | | - Ernest Szeto
- Department of Energy Joint Genome Institute, Walnut Creek, CA 94598
| | - Darren Platt
- Department of Energy Joint Genome Institute, Walnut Creek, CA 94598
| | | | - David A. Relman
- Department of Microbiology and Immunology, and Department of Medicine, Stanford University, Stanford, CA 94305
- Veterans Affairs Palo Alto Health Care System, Palo Alto, CA 94304; and
| | - Stephen R. Quake
- *Department of Bioengineering, Stanford University, and Howard Hughes Medical Institute, Stanford, CA 94305
- **To whom correspondence should be addressed. E-mail:
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168
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Thiel V, Leininger S, Schmaljohann R, Brümmer F, Imhoff JF. Sponge-specific bacterial associations of the Mediterranean sponge Chondrilla nucula (Demospongiae, Tetractinomorpha). MICROBIAL ECOLOGY 2007; 54:101-11. [PMID: 17364249 DOI: 10.1007/s00248-006-9177-y] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2006] [Revised: 09/07/2006] [Accepted: 10/05/2006] [Indexed: 05/14/2023]
Abstract
A stable and specific bacterial community was shown to be associated with the Mediterranean sponge Chondrilla nucula. The associated bacterial communities were demonstrated to be highly similar for all studied specimens regardless of sampling time and geographical region. In addition, analysis of 16S rDNA clone libraries revealed three constantly C. nucula-associated bacterial phylotypes belonging to the Acidobacteria, the Gamma- and Deltaproteobacteria present in sponge specimens from two Mediterranean regions with distinct water masses (Ligurian Sea and Adriatic Sea). For the first time, candidate division TM7 bacteria were found in marine sponges. A major part (79%) of the C. nucula-derived 16S rDNA sequences were closely related to other sponge-associated bacteria. Phylogenetic analysis identified 14 16S rRNA gene sequence clusters, seven of which consisted of exclusively sponge-derived sequences, whereas the other seven clusters contained additional environmental sequences. This study adds to a growing database on the stability and variability of microbial consortia associated with marine sponges.
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Affiliation(s)
- Vera Thiel
- Leibniz-Institut für Meereswissenschaften, IFM-GEOMAR, Düsternbrooker Weg 20, 24105, Kiel, Germany
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169
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Kim GT, Webster G, Wimpenny JWT, Kim BH, Kim HJ, Weightman AJ. Bacterial community structure, compartmentalization and activity in a microbial fuel cell. J Appl Microbiol 2007; 101:698-710. [PMID: 16907820 DOI: 10.1111/j.1365-2672.2006.02923.x] [Citation(s) in RCA: 141] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AIMS To characterize bacterial populations and their activities within a microbial fuel cell (MFC), using cultivation-independent and cultivation approaches. METHODS AND RESULTS Electron microscopic observations showed that the fuel cell electrode had a microbial biofilm attached to its surface with loosely associated microbial clumps. Bacterial 16S rRNA gene libraries were constructed and analysed from each of four compartments within the fuel cell: the planktonic community; the membrane biofilm; bacterial clumps (BC) and the anode biofilm. Results showed that the bacterial community structure varied significantly between these compartments. It was observed that Gammaproteobacteria phylotypes were present at higher numbers within libraries from the BC and electrode biofilm compared with other parts of the fuel cell. Community structure of the MFC determined by analyses of bacterial 16S rRNA gene libraries and anaerobic cultivation showed excellent agreement with community profiles from denaturing gradient gel electrophoresis (DGGE) analysis. CONCLUSIONS Members of the family Enterobacteriaceae, such as Klebsiella sp. and Enterobacter sp. and other Gammaproteobacteria with Fe(III)-reducing and electrochemical activity had a significant potential for energy generation in this system. SIGNIFICANCE AND IMPACT OF THE STUDY This study has shown that electrochemically active bacteria can be enriched using an electrochemical fuel cell.
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Affiliation(s)
- G T Kim
- Cardiff School of Biosciences, Cardiff University, Cardiff, UK.
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170
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DeSantis TZ, Brodie EL, Moberg JP, Zubieta IX, Piceno YM, Andersen GL. High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment. MICROBIAL ECOLOGY 2007; 53:371-83. [PMID: 17334858 DOI: 10.1007/s00248-006-9134-9] [Citation(s) in RCA: 238] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2006] [Accepted: 06/20/2006] [Indexed: 05/14/2023]
Abstract
Molecular approaches aimed at detection of a broad-range of prokaryotes in the environment routinely rely on classifying heterogeneous 16S rRNA genes amplified by polymerase chain reaction (PCR) using primers with broad specificity. The general method of sampling and categorizing DNA has been to clone then sequence the PCR products. However, the number of clones required to adequately catalog the majority of taxa in a sample is unwieldy. Alternatively, hybridizing target sequences to a universal 16S rRNA gene microarray may provide a more rapid and comprehensive view of prokaryotic community composition. This study investigated the breadth and accuracy of a microarray in detecting diverse 16S rRNA gene sequence types compared to clone-and-sequencing using three environmental samples: urban aerosol, subsurface soil, and subsurface water. PCR products generated from universal 16S rRNA gene-targeted primers were classified by using either the clone-and-sequence method or by hybridization to a novel high-density microarray of 297,851 probes complementary to 842 prokaryotic subfamilies. The three clone libraries comprised 1391 high-quality sequences. Approximately 8% of the clones could not be placed into a known subfamily and were considered novel. The microarray results confirmed the majority of clone-detected subfamilies and additionally demonstrated greater amplicon diversity extending into phyla not observed by the cloning method. Sequences matching operational taxonomic units within the phyla Nitrospira, Planctomycetes, and TM7, which were uniquely detected by the array, were verified with specific primers and subsequent amplicon sequencing. Subfamily richness detected by the array corresponded well with nonparametric richness predictions extrapolated from clone libraries except in the water community where clone-based richness predictions were greatly exceeded. It was concluded that although the microarray is unreliable in identifying novel prokaryotic taxa, it reveals greater diversity in environmental samples than sequencing a typically sized clone library. Furthermore, the microarray allowed samples to be rapidly evaluated with replication, a significant advantage in studies of microbial ecology.
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Affiliation(s)
- Todd Z DeSantis
- Lawrence Berkeley National Laboratory, Center for Environmental Biotechnology, 1 Cyclotron Road, Mail Stop 70A-3317, Berkeley, CA 94720, USA
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171
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Ohkuma M, Sato T, Noda S, Ui S, Kudo T, Hongoh Y. The candidate phylum 'Termite Group 1' of bacteria: phylogenetic diversity, distribution, and endosymbiont members of various gut flagellated protists. FEMS Microbiol Ecol 2007; 60:467-76. [PMID: 17391329 DOI: 10.1111/j.1574-6941.2007.00311.x] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The candidate phylum 'Termite Group 1' (TG1) of bacteria, which is abundant in termite guts but has no culturable representative, was investigated with respect to the in situ localization, distribution, and diversity. Based on the 16S rRNA gene sequence analyses and FISH in termite guts, a number of lineages of TG1 members were identified as endosymbionts of a variety of gut flagellated protists from the orders Trichonymphida, Cristamonadida, and Oxymonadida that are mostly unique to termites. However, the survey in various environments using specific PCR primers revealed that TG1 members were also present in termites, a cockroach, and the bovine rumen that typically lack these protist orders. Most of the TG1 members from gut flagellates, termites, cockroaches, and the rumen formed a monophyletic subcluster that showed a shallow branching pattern in the phylogenetic tree, suggesting their recent diversification. Although endosymbionts of the same protist genera tended to be closely related, the endosymbiont lineages were often independent of the higher level classifications of their host protist and were dispersed in the phylogenetic tree. It appears that their cospeciation is not the sole rule for the diversification of TG1 members of endosymbionts.
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Affiliation(s)
- Moriya Ohkuma
- Environmental Molecular Biology Laboratory, RIKEN, Saitama, Japan.
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172
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Podar M, Abulencia CB, Walcher M, Hutchison D, Zengler K, Garcia JA, Holland T, Cotton D, Hauser L, Keller M. Targeted access to the genomes of low-abundance organisms in complex microbial communities. Appl Environ Microbiol 2007; 73:3205-14. [PMID: 17369337 PMCID: PMC1907129 DOI: 10.1128/aem.02985-06] [Citation(s) in RCA: 151] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Current metagenomic approaches to the study of complex microbial consortia provide a glimpse into the community metabolism and occasionally allow genomic assemblies for the most abundant organisms. However, little information is gained for the members of the community present at low frequencies, especially those representing yet-uncultured taxa, which include the bulk of the diversity present in most environments. Here we used phylogenetically directed cell separation by fluorescence in situ hybridization and flow cytometry, followed by amplification and sequencing of a fraction of the genomic DNA of several bacterial cells that belong to the TM7 phylum. Partial genomic assembly allowed, for the first time, a look into the evolution and potential metabolism of a soil representative from this group of organisms for which there are no species in stable laboratory cultures. Genomic reconstruction from targeted cells of uncultured organisms isolated directly from the environment represents a powerful approach to access any specific members of a community and an alternative way to assess the community's metabolic potential.
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173
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Xia Y, Kong Y, Nielsen PH. In situ detection of protein-hydrolysing microorganisms in activated sludge. FEMS Microbiol Ecol 2007; 60:156-65. [PMID: 17313663 DOI: 10.1111/j.1574-6941.2007.00279.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Protein hydrolysis plays an important role in the transformation of organic matter in activated sludge wastewater treatment plants, but no information is currently available regarding the identity and ecophysiology of protein-hydrolysing organisms (PHOs). In this study, fluorescence in situ enzyme staining with casein and bovine serum albumin conjugated with BODIPY dye was applied and optimized to label PHOs in activated sludge plants. A strong fluorescent labeling of the surface of microorganisms expressing protease activity was achieved. Metabolic inhibitors were applied to inhibit the metabolic activity to prevent uptake of the fluorescent hydrolysates by oligopeptide-consuming bacteria. In five full-scale, nutrient-removing activated sludge plants examined, the dominant PHOs were always different morphotypes of filamentous bacteria and the epiflora attached to many of these. The PHOs were identified by FISH using a range of available oligonucleotide probes. The filamentous PHOs belonged to the candidate phylum TM7, the phylum Chloroflexi and the class Betaproteobacteria. In total they comprised 1-5% of the bacterial biovolume. Most of the epiflora-PHOs hybridized with probe SAP-309 targeting Saprospiraceae in the phylum Bacteroidetes and accounted for 8-12% of the total bacterial biovolume in most plants and were thus an important and dominant part of the microbial communities.
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Affiliation(s)
- Yun Xia
- Department of Biotechnology, Chemistry and Environmental Engineering, Section of Environmental Engineering, Aalborg University, Sohngaardsholmsvej 57, DK-9000 Aalborg, Denmark
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174
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Mosier AC, Murray AE, Fritsen CH. Microbiota within the perennial ice cover of Lake Vida, Antarctica. FEMS Microbiol Ecol 2007; 59:274-88. [PMID: 17092309 DOI: 10.1111/j.1574-6941.2006.00220.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Lake Vida, located in the McMurdo Dry Valleys, Antarctica, is an 'ice-sealed' lake with approximately 19 m of ice covering a highly saline water column (approximately 245 ppt). The lower portions of the ice cover and the lake beneath have been isolated from the atmosphere and land for circa 2800 years. Analysis of microbial assemblages within the perennial ice cover of the lake revealed a diverse array of bacteria and eukarya. Bacterial and eukaryal denaturing gradient gel electrophoresis phylotype profile similarities were low (<59%) between all of the depths compared (five depths spanning 11 m of the ice cover), with the greatest differences occurring between surface and deep ice. The majority of bacterial 16S rRNA gene sequences in the surface ice were related to Actinobacteria (42%) while Gammaproteobacteria (52%) dominated the deep ice community. Comparisons of assemblage composition suggest differences in ice habitability and organismal origin in the upper and lower portions of ice cover. Specifically, the upper ice cover microbiota likely reflect the modern day transport and colonization of biota from the terrestrial landscape, whereas assemblages in the deeper ice are more likely to be persistent remnant biota that originated from the ancient liquid water column of the lake that froze.
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Affiliation(s)
- Annika C Mosier
- Desert Research Institute, Division of Earth and Ecosystem Sciences, Reno, NV 89512, USA
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175
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Hao CB, Zhang HX, Bai ZH, Hu Q, Zhang BG. A novel acidophile community populating waste ore deposits at an acid mine drainage site. J Environ Sci (China) 2007; 19:444-450. [PMID: 17915708 DOI: 10.1016/s1001-0742(07)60074-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Waste ore samples (pH 3.0) were collected at an acid mine drainage (AMD) site in Anhui, China. The present acidophilic microbial community in the waste ore was studied with 16S rRNA gene clone library and denaturing gradient gel electrophoresis (DGGE). Eighteen different clones were identified and affiliated with Actinobacteria, low G + C Gram-positives, Thermomicrobia, Acidobacteria, Proteobacteria, candidate division TM7, and Planctomycetes. Phylogenetic analysis of 16S rRNA gene sequences revealed a diversity of acidophiles in the samples that were mostly novel. It is unexpected that the moderately thermophilic acidophiles were abundant in the acidic ecosystem and may play a great role in the generation of AMD. The result of DGGE was consistent with that of clone library analysis. These findings help in the better understanding of the generation mechanism of AMD and in developing a more efficient method to control AMD.
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Affiliation(s)
- Chun-bo Hao
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
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176
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Loy A, Maixner F, Wagner M, Horn M. probeBase--an online resource for rRNA-targeted oligonucleotide probes: new features 2007. Nucleic Acids Res 2006; 35:D800-4. [PMID: 17099228 PMCID: PMC1669758 DOI: 10.1093/nar/gkl856] [Citation(s) in RCA: 369] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
probeBase is a curated database of annotated rRNA-targeted oligonucleotide probes and supporting information. Rapid access to probe, microarray and reference data is achieved by powerful search tools and via different lists that are based on selected categories such as functional or taxonomic properties of the target organism(s) or the hybridization format (fluorescence in situ hybridization or microarray) in which the probes were applied. Additional information on probe coverage and specificity is available through direct submissions of probe sequences from probeBase to RDP-II and Greengenes, two major rRNA sequence databases. A freely editable user comments field for each probe entry allows any user to add, modify or remove information or to report errors in real-time. probeBase entries increased from 700 to more than 1200 during the past three years. Several options for submission of single probes or entire probe sets, even prior to publication of newly developed probes, should further contribute to keeping probeBase an up-to-date and useful resource. probeBase is freely accessible at http://www.microbial-ecology.net/probebase. Email correspondence can be addressed to probebase@microbial-ecology.net.
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Affiliation(s)
| | | | | | - Matthias Horn
- To whom correspondence should be addressed: Tel: +43 1 4277 54393; Fax: +43 1 4277 54389;
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177
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Affiliation(s)
- Anne C R Tanner
- Department of Molecular Genetics, The Forsyth Institute, Boston, Massachusetts, USA
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178
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Seasonal variation of snow microbial community structure in the East Rongbuk glacier, Mt. Everest. Sci Bull (Beijing) 2006. [DOI: 10.1007/s11434-006-1476-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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179
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Radeva G, Selenska-Pobell S. Bacterial diversity in water samples from uranium wastes as demonstrated by 16S rDNA and ribosomal intergenic spacer amplification retrievals. Can J Microbiol 2006; 51:910-23. [PMID: 16333330 DOI: 10.1139/w05-082] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Bacterial diversity was assessed in water samples collected from several uranium mining wastes in Ger many and in the United States by using 16S rDNA and ribosomal intergenic spacer amplification retrievals. The results obtained using the 16S rDNA retrieval showed that the samples collected from the uranium mill tailings of Schlema/Alberoda, Germany, were predominated by Nitrospina-like bacteria, whereas those from the mill tailings of Shiprock, New Mexico, USA, were predominated by gamma-Pseudomonas and Frauteria spp. Additional smaller populations of the Cytophaga-Flavobacterium-Bacteroides group and alpha- and delta-Proteobacteria were identified in the Shiprock samples as well. Proteobacteria and Cytophaga-Flavobacterium-Bacteroides were also found in the third uranium mill tailings studied, Gittersee/Coschütz, Germany, but the groups of the predominant clones were rather small. Most of the clones of the Gittersee/Coschütz samples represented individual sequences, which indicates a high level of bacterial diversity. The samples from the fourth uranium waste studied, Steinsee Deponie B1, Germany, were predominantly occupied by Acinetobacter spp. The ribosomal intergenic spacer amplification retrieval provided results complementary to those obtained by the 16S rDNA analyses. For instance, in the Shiprock samples, an additional predominant bacterial group was identified and affiliated with Nitrosomonas sp., whereas in the Gittersee/Coschütz samples, anammox populations were identified that were not retrieved by the applied 16S rDNA approach.
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MESH Headings
- Bacteria/classification
- Bacteria/genetics
- Bacteria/isolation & purification
- Bacteroides/classification
- Bacteroides/isolation & purification
- Biodiversity
- Cytophaga/classification
- Cytophaga/isolation & purification
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- DNA, Ribosomal Spacer/chemistry
- DNA, Ribosomal Spacer/genetics
- Flavobacterium/classification
- Flavobacterium/isolation & purification
- Germany
- Industrial Waste
- Molecular Sequence Data
- Phylogeny
- Polymerase Chain Reaction
- Polymorphism, Restriction Fragment Length
- Proteobacteria/classification
- Proteobacteria/isolation & purification
- Pseudomonas/classification
- Pseudomonas/cytology
- Pseudomonas/isolation & purification
- RNA, Ribosomal, 16S/genetics
- Radioactive Pollutants
- Sequence Analysis, DNA
- United States
- Uranium
- Waste Disposal, Fluid
- Water Microbiology
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Affiliation(s)
- Galina Radeva
- Institute of Radiochemistry, Forschungszentrum Rossendorf, D-10314 Dresden, Germany.
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180
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Hao C, Zhang H, Haas R, Bai Z, Zhang B. A Novel Community of Acidophiles in an Acid Mine Drainage Sediment. World J Microbiol Biotechnol 2006. [DOI: 10.1007/s11274-006-9188-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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181
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Milinovich GJ, Trott DJ, Burrell PC, van Eps AW, Thoefner MB, Blackall LL, Al Jassim RAM, Morton JM, Pollitt CC. Changes in equine hindgut bacterial populations during oligofructose-induced laminitis. Environ Microbiol 2006; 8:885-98. [PMID: 16623745 DOI: 10.1111/j.1462-2920.2005.00975.x] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In the horse, carbohydrate overload is thought to play an integral role in the onset of laminitis by drastically altering the profile of bacterial populations in the hindgut. The objectives of this study were to develop and validate microbial ecology methods to monitor changes in bacterial populations throughout the course of experimentally induced laminitis and to identify the predominant oligofructose-utilizing organisms. Laminitis was induced in five horses by administration of oligofructose. Faecal specimens were collected at 8 h intervals from 72 h before to 72 h after the administration of oligofructose. Hindgut microbiota able to utilize oligofructose were enumerated throughout the course of the experiment using habitat-simulating medium. Isolates were collected and representatives identified by 16S rRNA gene sequencing. The majority of these isolates collected belonged to the genus Streptococcus, 91% of which were identified as being most closely related to Streptococcus infantarius ssp. coli. Furthermore, S. infantarius ssp. coli was the predominant oligofructose-utilizing organism isolated before the onset of lameness. Fluorescence in situ hybridization probes developed to specifically target the isolated Streptococcus spp. demonstrated marked population increases between 8 and 16 h post oligofructose administration. This was followed by a rapid population decline which corresponded with a sharp decline in faecal pH and subsequently lameness at 24-32 h post oligofructose administration. This research suggests that streptococci within the Streptococcus bovis/equinus complex may be involved in the series of events which precede the onset of laminitis in the horse.
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Affiliation(s)
- G J Milinovich
- Australian Equine Laminitis Research Unit, School of Veterinary Science, The University of Queensland, Queensland, Australia.
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182
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Yasumoto-Hirose M, Nishijima M, Ngirchechol MK, Kanoh K, Shizuri Y, Miki W. Isolation of marine bacteria by in situ culture on media-supplemented polyurethane foam. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2006; 8:227-37. [PMID: 16763938 DOI: 10.1007/s10126-005-5015-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2005] [Accepted: 09/18/2005] [Indexed: 05/10/2023]
Abstract
Polyurethane foam (PUF) supplemented with various agar media was used in situ to trap marine bacteria and it consequently provided a substrate on which they could be cultivated while exposed to natural seawater in the coral reef area. The bacterial population on the PUF blocks was analyzed by denaturing gradient gel electrophoresis (DGGE) of polymerase chain reaction (PCR)-amplified 16S rDNA fragments. Changing the composition of the cultivation medium in the PUF blocks and selecting different sampling sites resulted in different bacteria being detected on the PUF blocks. For example, iron-utilizing (IU) bacteria, siderophore-producing (SP) bacteria, and petroleum-degrading (PD) bacteria were isolated from PUF blocks and it was discovered that IU and SP contained iron and PD contained hydrocarbon. This method opens up the possibility for isolating novel and useful marine bacteria.
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Affiliation(s)
- Mina Yasumoto-Hirose
- Marine Biotechnology Institute (MBI), 3-75-1 Heita, Kamaishi-shi, Iwate, 026-0001, Japan
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183
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Bertin L, Colao MC, Ruzzi M, Marchetti L, Fava F. Performances and microbial features of an aerobic packed-bed biofilm reactor developed to post-treat an olive mill effluent from an anaerobic GAC reactor. Microb Cell Fact 2006; 5:16. [PMID: 16595023 PMCID: PMC1501037 DOI: 10.1186/1475-2859-5-16] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2006] [Accepted: 04/05/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Olive mill wastewater (OMW) is the aqueous effluent of olive oil producing processes. Given its high COD and content of phenols, it has to be decontaminated before being discharged. Anaerobic digestion is one of the most promising treatment process for such an effluent, as it combines high decontamination efficiency with methane production. The large scale anaerobic digestion of OMWs is normally conducted in dispersed-growth reactors, where however are generally achieved unsatisfactory COD removal and methane production yields. The possibility of intensifying the performance of the process using a packed bed biofilm reactor, as anaerobic treatment alternative, was demonstrated. Even in this case, however, a post-treatment step is required to further reduce the COD. In this work, a biological post-treatment, consisting of an aerobic biological "Manville" silica bead-packed bed aerobic reactor, was developed, tested for its ability to complete COD removal from the anaerobic digestion effluents, and characterized biologically through molecular tools. RESULTS The aerobic post-treatment was assessed through a 2 month-continuous feeding with the digested effluent at 50.42 and 2.04 gl(-1)day(-1) of COD and phenol loading rates, respectively. It was found to be a stable process, able to remove 24 and 39% of such organic loads, respectively, and to account for 1/4 of the overall decontamination efficiency displayed by the anaerobic-aerobic integrated system when fed with an amended OMW at 31.74 and 1.70 gl(-1)day(-1) of COD and phenol loading rates, respectively. Analysis of 16S rRNA gene sequences of biomass samples from the aerobic reactor biofilm revealed that it was colonized by Rhodobacterales, Bacteroidales, Pseudomonadales, Enterobacteriales, Rhodocyclales and genera incertae sedis TM7. Some taxons occurring in the influent were not detected in the biofilm, whereas others, such as Paracoccus, Pseudomonas, Acinetobacter and Enterobacter, enriched significantly in the biofilter throughout the treatment. CONCLUSION The silica-bead packed bed biofilm reactor developed and characterized in this study was able to significantly decontaminate anaerobically digested OMWs. Therefore, the application of an integrated anaerobic-aerobic process resulted in an improved system for valorization and decontamination of OMWs.
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Affiliation(s)
- Lorenzo Bertin
- DICASM, Faculty of Engineering, University of Bologna, viale Risorgimento 2, I-40136 Bologna, Italy
| | - Maria Chiara Colao
- DABAC, University of Tuscia, Via C. de Lellis, snc. I-01100 Viterbo, Italy
| | - Maurizio Ruzzi
- DABAC, University of Tuscia, Via C. de Lellis, snc. I-01100 Viterbo, Italy
| | - Leonardo Marchetti
- DICASM, Faculty of Engineering, University of Bologna, viale Risorgimento 2, I-40136 Bologna, Italy
| | - Fabio Fava
- DICASM, Faculty of Engineering, University of Bologna, viale Risorgimento 2, I-40136 Bologna, Italy
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184
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Lahtinen T, Kosonen M, Tiirola M, Vuento M, Oker-Blom C. Diversity of bacteria contaminating paper machines. J Ind Microbiol Biotechnol 2006; 33:734-40. [PMID: 16520979 DOI: 10.1007/s10295-006-0105-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2005] [Accepted: 02/06/2006] [Indexed: 10/24/2022]
Abstract
Formation of microbial biofilms and slimes is a general and serious problem in the operation of paper machines. Studies of microbial populations in paper machine-derived biofilms have been conducted using standard microbiological procedures; however, the bacterial genera present in this type of samples as well as their diversity are quite poorly known. Here, the bacterial diversity of 38 process water and 22 biofilm samples from four different Finnish paper machines were analyzed by length heterogeneity analysis of PCR-amplified 16S ribosomal DNA (LH-PCR). In addition, sequencing of the amplified 16S rRNA gene from 69 clones was conducted for characterization of the bacterial genera present in biofilm and slime samples. The LH-PCR profiles of both the free-living (process waters) and immobilized (biofilms) bacteria were diverse at all stages of the papermaking process. Out of the 69 sequenced clones, 44 belonged to alpha-Proteobacteria, most of which were close to the nitrogen-fixing root nodule genera Sinorhizobium, Rhizobium and Azorhizobium. Other clones were assigned to beta- and gamma-Proteobacteria and the phylum Bacteroidetes. In addition, eight of the clones were assigned to a yet uncultivated phylum, TM7. Finally, epifluorescence microscopy revealed that Gram-negative bacteria were predominant in both the biofilm (65%) and process water (54%) samples and a small coccoid cell morphology was most common in all samples. Together, our results show that the analysis of microbial samples from paper machines using modern molecular biology techniques adds valuable information and should, therefore, be useful as a more specific and sensitive microbiological method for the paper industry. This information could further be applied, e.g., in the development of more specific and environmental friendly antimicrobial agents for paper mills.
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Affiliation(s)
- Tomi Lahtinen
- NanoScience Center, Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
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185
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Janssen PH. Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Appl Environ Microbiol 2006; 72:1719-28. [PMID: 16517615 PMCID: PMC1393246 DOI: 10.1128/aem.72.3.1719-1728.2006] [Citation(s) in RCA: 885] [Impact Index Per Article: 49.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Peter H Janssen
- Department of Microbiology and Immunology, University of Melbourne, Victoria, Australia.
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186
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Ferrari BC, Binnerup SJ, Gillings M. Microcolony cultivation on a soil substrate membrane system selects for previously uncultured soil bacteria. Appl Environ Microbiol 2006; 71:8714-20. [PMID: 16332866 PMCID: PMC1317317 DOI: 10.1128/aem.71.12.8714-8720.2005] [Citation(s) in RCA: 133] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Traditional microbiological methods of cultivation recover less than 1% of the total bacterial species, and the culturable portion of bacteria is not representative of the total phylogenetic diversity. Classical cultivation strategies are now known to supply excessive nutrients to a system and therefore select for fast-growing bacteria that are capable of colony or biofilm formation. New approaches to the cultivation of bacteria which rely on growth in dilute nutrient media or simulated environments are beginning to address this problem of selection. Here we describe a novel microcultivation method for soil bacteria that mimics natural conditions. Our soil slurry membrane system combines a polycarbonate membrane as a growth support and soil extract as the substrate. The result is abundant growth of uncharacterized bacteria as microcolonies. By combining microcultivation with fluorescent in situ hybridization, previously "unculturable" organisms belonging to cultivated and noncultivated divisions, including candidate division TM7, can be identified by fluorescence microscopy. Successful growth of soil bacteria as microcolonies confirmed that the missing culturable majority may have a growth strategy that is not observed when traditional cultivation indicators are used.
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Affiliation(s)
- Belinda C Ferrari
- Department of Biological Sciences, Division of Environmental and Life Sciences, Macquarie University, Sydney 2109, NSW, Australia.
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187
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Paster BJ, Russell MK, Alpagot T, Lee AM, Boches SK, Galvin JL, Dewhirst FE. Bacterial diversity in necrotizing ulcerative periodontitis in HIV-positive subjects. ACTA ACUST UNITED AC 2005; 7:8-16. [PMID: 16013212 DOI: 10.1902/annals.2002.7.1.8] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND Necrotizing ulcerative periodontitis (NUP) is a painful and potentially debilitating affliction that affects about 2% to 6% of HIV-positive subjects. NUP may be caused by specific microorganisms that are presently unknown or by microbial species not usually thought to cause periodontal infections. The purpose of this study was to define the bacterial species associated with NUP in HIV-positive patients. METHODS 16S rRNA bacterial genes of DNA isolated from subgingival plaque of 8 HIV-positive subjects with NUP were amplified by polymerase chain reaction (PCR) and cloned into Escherichia coli. The sequences of cloned inserts were used to determine species identity or closest relatives by comparison with known sequences. The microbial profiles in subgingival plaque of subjects with NUP, chronic periodontitis, and periodontal health were compared using a battery of over 200 oligonucleotide probes in a PCR-based, reverse-capture, checkerboard DNA-DNA hybridization assay. RESULTS Sequence analysis of over 400 clones revealed 108 species; 65 were "uncultivable" phylotypes, of which 26 were novel to NUP subjects. Species or phylotypes most commonly detected were Bulleidia extructa, Dialister, Fusobacterium, Selenomonas, Peptostreptococcus, Veillonella, and the phylum TM7. Based on sequence analysis and checkerboard analysis, NUP did not possess the classical periodontal pathogens such as Porphyromonas gingivalis. Otherwise, the microbial profiles of NUP and periodontitis had many similarities. The microbial profiles of subgingival plaque from periodontally healthy subjects were different and less complex in comparison to the profiles of both disease groups. CONCLUSIONS Certain species appear to be associated with health and periodontal diseases. The putative pathogens associated with periodontal disease in HIV-negative subjects are not associated with NUP in HIV-positive subjects.
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Affiliation(s)
- Bruce J Paster
- Department of Molecular Genetics, The Forsyth Institute, Boston, Massachusetts 02115, USA.
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188
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Godon JJ, Morinière J, Moletta M, Gaillac M, Bru V, Delgènes JP. Rarity associated with specific ecological niches in the bacterial world: the 'Synergistes' example. Environ Microbiol 2005; 7:213-24. [PMID: 15658988 DOI: 10.1111/j.1462-2920.2004.00693.x] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The 'Synergistes' group, which apparently represents an as yet unnamed division of the bacteria, was explored in 93 anaerobic environments (guts, soils, digestors, etc.). From 16S rDNA gene-targeted polymerase chain reaction (PCR) assays, this group appeared to be present in 90% of the anaerobic microbial ecosystems analysed. The phylogeny of 103 16S rDNA sequences from 30 ecosystems showed a strong link between 16S rDNA sequences and given ecosystems. 'Synergistes' 16S rDNA sequences from animal sources (termites, guinea pigs, pigs, birds, etc.) formed clustered phylogenetical groups. 'Synergistes' groups were also associated either with anaerobic digestors and soils or with thermophilic conditions. Sequences available from the DNA database were consistent with the results. These results show the wide diversity of the 'Synergistes' division as well as the specific ecological niche of each 16S rDNA sequences.
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Affiliation(s)
- Jean-Jacques Godon
- Laboratoire de Biotechnologie de l'Environnement, INRA, Avenue des Etangs, 11100 Narbonne, France.
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189
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Connon SA, Tovanabootr A, Dolan M, Vergin K, Giovannoni SJ, Semprini L. Bacterial community composition determined by culture-independent and -dependent methods during propane-stimulated bioremediation in trichloroethene-contaminated groundwater. Environ Microbiol 2005; 7:165-78. [PMID: 15658984 DOI: 10.1111/j.1462-2920.2004.00680.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An in situ co-metabolic air sparging (CAS) study was carried out at McClellan Air Force Base (MAFB), Sacramento, CA, USA, in a trichloroethene- (TCE) and cis-dichloroethene (cis-DCE)-contaminated aquifer where one test zone received 2% propane in air and the other served as a control and received only air. As part of that study, bacterial population shifts were evaluated by length heterogeneity polymerase chain reaction (LH-PCR). The results showed that an organism(s) that had a fragment size of 385 bp was positively correlated with propane removal rates. The 385 bp fragment consisted of up to 83% of the total fragments in the analysis when propane removal rates peaked. A 16S rRNA clone library made from the bacteria sampled from the propane-sparged groundwater included clones of a TM7 division bacterium that had a 385 bp LH-PCR fragment; no other bacterial species with this fragment size were detected. Both propane removal rates and the 385 bp LH-PCR fragment decreased as nitrate levels in the groundwater decreased. Extinction culturing in natural unamended groundwater medium was used to assess the bacterial diversity of the culturable fraction of microorganisms in both CAS and air-sparged groundwater and to bring novel species into culture for further study. The dominant cultures acquired from the CAS groundwater were from the Herbaspirillum/Oxalobacter clade. The dominant cultures from the air-sparged groundwater were from a novel beta-Proteobacterial clade, which we named after isolate HTCC333.
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MESH Headings
- Bacteria/classification
- Bacteria/cytology
- Bacteria/isolation & purification
- Bacterial Physiological Phenomena
- Biodegradation, Environmental
- Biodiversity
- DNA Fingerprinting
- DNA, Bacterial/analysis
- DNA, Bacterial/chemistry
- DNA, Bacterial/isolation & purification
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/isolation & purification
- Gene Library
- Genes, rRNA
- Herbaspirillum
- Molecular Sequence Data
- Nitrates/metabolism
- Oxalobacter formigenes
- Phylogeny
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Trichloroethylene/metabolism
- Water Microbiology
- Water Pollution, Chemical
- Water Purification/methods
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Affiliation(s)
- Stephanie A Connon
- Microbiology Department, Oregon State University, 202 Apperson Hall, Corvallis, OR 97331, USA
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190
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Lemmer H, Lind G, Müller E, Schade M. Non-famous Scum Bacteria: Biological Characterization and Troubleshooting. ACTA ACUST UNITED AC 2005. [DOI: 10.1002/aheh.200400567] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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191
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Siyambalapitiya N, Blackall LL. Discrepancies in the widely applied GAM42a fluorescence in situ hybridisation probe forGammaproteobacteria. FEMS Microbiol Lett 2005; 242:367-73. [PMID: 15621461 DOI: 10.1016/j.femsle.2004.11.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2004] [Revised: 10/25/2004] [Accepted: 11/02/2004] [Indexed: 10/26/2022] Open
Abstract
A bacterial culture collection of 104 strains was obtained from an activated sludge wastewater treatment plant to pursue studies into microbial flocculation. Characterisation of the culture collection using a polyphasic approach indicated seven isolates, phylogenetically affiliated with the deep-branching Xanthomonas group of the class Gammaproteobacteria, were unable to hybridise the GAM42a fluorescence in situ hybridisation (FISH) probe for Gammaproteobacteria. The sequence of the GAM42a probe target region in the 23S rRNA gene of these isolates was determined to have mismatches to GAM42a. Probes perfectly targeting the mismatches (GAM42a_T1038_G1031, and GAM42a_T1038 and GAM42a_A1041_A1040) were synthesised, and used in conjunction with GAM42a in FISH to study the Gammaproteobacteria community structure in one full-scale activated sludge plant. Several bacteria in the activated sludge biomass bound the modified probes demonstrating their presence and the fact that these Gammaproteobacteria have been overlooked in community structure analyses of activated sludge.
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Affiliation(s)
- Nishanthi Siyambalapitiya
- Advanced Wastewater Management Centre, The University of Queensland, St. Lucia, 4072, Queensland, Australia
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192
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Munson MA, Banerjee A, Watson TF, Wade WG. Molecular analysis of the microflora associated with dental caries. J Clin Microbiol 2004; 42:3023-9. [PMID: 15243054 PMCID: PMC446285 DOI: 10.1128/jcm.42.7.3023-3029.2004] [Citation(s) in RCA: 254] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Molecular techniques have revealed many novel, presumed unculturable, taxa in oral infections. The aim of this study was to characterize the bacterial community of the middle and advancing front of carious dental lesions by cultural and molecular analyses. Samples were collected with a hand excavator from five teeth with carious lesions involving dentine. Samples were cultured on blood agar and Rogosa agar incubated in air plus 5% CO(2) and on fastidious anaerobe agar anaerobically. DNA was also extracted directly from the samples and 16S rRNA genes were amplified by PCR with universal primers. PCR products were singularized by cloning, and the cloned inserts and cultured isolates were identified by 16S rRNA gene sequence analysis. We identified 95 taxa among the 496 isolates and 1,577 clones sequenced; 44 taxa were detected by the molecular method alone; 31 taxa were previously undescribed. Only three taxa, Streptococcus mutans, Rothia dentocariosa, and an unnamed Propionibacterium sp., were found in all five samples. The predominant taxa by anaerobic cultivation were the novel Propionibacterium sp. (18%), Olsenella profusa (14%), and Lactobacillus rhamnosus (8%). The predominant taxa in the molecular analysis were Streptococcus mutans (16%), Lactobacillus gasseri/johnsonii (13%), and Lactobacillus rhamnosus (8%). There was no significant difference between the compositions of the microflora in the middle and advancing front samples (P < 0.05, Wilcoxon matched pairs, signed ranks test). In conclusion, combined cultural and molecular analyses have shown that a diverse bacterial community is found in dentinal caries and that numerous novel taxa are present.
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Affiliation(s)
- M A Munson
- Infection Research Group, The Dental Institute, King's College London, United Kingdom
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193
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Mummey DL, Stahl PD. Analysis of soil whole- and inner-microaggregate bacterial communities. MICROBIAL ECOLOGY 2004; 48:41-50. [PMID: 15085298 DOI: 10.1007/s00248-003-1000-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2002] [Accepted: 02/14/2003] [Indexed: 05/03/2023]
Abstract
Although soil structure largely determines energy flows and the distribution and composition of soil microhabitats, little is known about how microbial community composition is influenced by soil structural characteristics and organic matter compartmentalization dynamics. A UV irradiation-based procedure was developed to specifically isolate inner-microaggregate microbial communities, thus providing the means to analyze these communities in relation to their environment. Whole- and inner-microaggregate fractions of undisturbed soil and soils reclaimed after disturbance by surface coal mining were analyzed using 16S rDNA terminal restriction fragment polymorphism (T-RFLP) and sequence analyses to determine salient bacterial community structural characteristics. We hypothesized that inner-microaggregate environments select for definable microbial communities and that, due to their sequestered environment, inner-microaggregate communities would not be significantly impacted by disturbance. However, T-RFLP analysis indicated distinct differences between bacterial populations of inner-microaggregates of undisturbed and reclaimed soils. While both undisturbed and reclaimed inner-microaggregate bacterial communities were found dominated by Actinobacteria, undisturbed soils contained only Actinobacteridae, while in inner-microaggregates of reclaimed soils Rubrobacteridae predominate. Spatial stratification of division-level lineages within microaggregates was also evidenced, with Proteobacteria clones being prevalent in libraries derived from whole microaggregates. The fractionation methods employed in this study therefore represent a valuable tool for defining relationships between biodiversity and soil structure.
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Affiliation(s)
- D L Mummey
- Department of Renewable Resources, University of Wyoming, P.O. 3354, Laramie, Wyoming 82070, USA.
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194
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Thomsen TR, Nielsen JL, Ramsing NB, Nielsen PH. Micromanipulation and further identification of FISH-labelled microcolonies of a dominant denitrifying bacterium in activated sludge. Environ Microbiol 2004; 6:470-9. [PMID: 15049920 DOI: 10.1111/j.1462-2920.2004.00580.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The activated sludge process relies on the formation of strong microbial flocs. The knowledge about dominant floc-forming bacteria is at present very limited, especially from a phylogenetic perspective. In this study, numerous microcolonies in the activated sludge flocs were found to be targeted by a Betaproteobacteria-group-specific oligonucleotide probe using fluorescence in situ hybridization (FISH). Some of these were micromanipulated and further identified by reverse transcriptase polymerase chain reaction (RT-PCR) and sequencing to belong to the Aquaspirillum genus in the Neisseriaceae family. A specific oligonucleotide probe, Aqs997, was designed to target the identified bacteria. A survey in nine different wastewater treatment plants with nutrient removal (WWTP) showed a high abundance of bacteria hybridizing to the oligonucleotide probe developed. Microautoradiography (MAR) combined with FISH on activated sludge incubated with radiolabelled substrate showed uptake of substrate with oxygen, nitrate and nitrite as electron acceptor demonstrating a denitrifying potential of the bacteria investigated. The Aquaspirillum-related bacteria seemed to be abundant denitrifiers in WWTPs with nitrogen removal and they were particularly numerous in plants mainly receiving domestic wastewater, where they constituted up to 30% of all bacteria.
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Affiliation(s)
- T R Thomsen
- Department of Life Sciences, Aalborg University, Sohngaardsholmsvej 57, DK-9000 Aalborg, Denmark
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195
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Nemergut DR, Martin AP, Schmidt SK. Integron diversity in heavy-metal-contaminated mine tailings and inferences about integron evolution. Appl Environ Microbiol 2004; 70:1160-8. [PMID: 14766601 PMCID: PMC348930 DOI: 10.1128/aem.70.2.1160-1168.2004] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Integrons are horizontal gene transfer (HGT) systems containing elements necessary for site-specific recombination and expression of foreign DNA. The overall phylogenetic distribution of integrons and range of genes that can be transferred by integrons are unknown. This report contains an exploration of integrons in an environmental microbial community and an investigation of integron evolution. First, using culture-independent techniques, we explored the diversity of integrons and integron-transferred genes in heavy-metal-contaminated mine tailings. Using degenerate primers, we amplified integron integrase genes from the tailings. We discovered 14 previously undescribed integrase genes, including six novel gene lineages. In addition, we found 11 novel gene cassettes in this sample. One of the gene cassettes that we sequenced is similar to a gene that codes for a step in a pathway for nitroaromatic catabolism, a group of compounds associated with mining activity. This suggests that integrons may be important for gene transfer in response to selective pressures other than the presence of antibiotics. We also investigated the evolution of integrons by statistically comparing the phylogenies of 16S rRNA and integrase genes from the same organisms, using sequences from GenBank and various sequencing projects. We found significant differences between the organismal (16S rRNA) and integrase trees, and we suggest that these differences may be due to HGT.
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Affiliation(s)
- D R Nemergut
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado 80309, USA
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196
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Fieseler L, Horn M, Wagner M, Hentschel U. Discovery of the novel candidate phylum "Poribacteria" in marine sponges. Appl Environ Microbiol 2004; 70:3724-32. [PMID: 15184179 PMCID: PMC427773 DOI: 10.1128/aem.70.6.3724-3732.2004] [Citation(s) in RCA: 247] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2003] [Accepted: 02/23/2004] [Indexed: 11/20/2022] Open
Abstract
Marine sponges (Porifera) harbor large amounts of commensal microbial communities within the sponge mesohyl. We employed 16S rRNA gene library construction using specific PCR primers to provide insights into the phylogenetic identity of an abundant sponge-associated bacterium that is morphologically characterized by the presence of a membrane-bound nucleoid. In this study, we report the presence of a previously unrecognized evolutionary lineage branching deeply in the domain Bacteria that is moderately related to the Planctomycetes, Verrucomicrobia, and Chlamydia lines of decent. Because members of this lineage showed <75% 16S rRNA gene sequence similarity to known bacterial phyla, we suggest the status of a new candidate phylum, named "Poribacteria", to acknowledge the affiliation of the new bacterium with sponges. The affiliation of the morphologically conspicuous sponge bacterium with the novel phylogenetic lineage was confirmed by fluorescence in situ hybridization with newly designed probes targeting different sites of the poribacterial 16S rRNA. Consistent with electron microscopic observations of cell compartmentalization, the fluorescence signals appeared in a ring-shaped manner. PCR screening with "Poribacteria"-specific primers gave positive results for several other sponge species, while samples taken from the environment (seawater, sediments, and a filter-feeding tunicate) were PCR negative. In addition to a report for Planctomycetes, this is the second report of cell compartmentalization, a feature that was considered exclusive to the eukaryotic domain, in prokaryotes.
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Affiliation(s)
- Lars Fieseler
- Zentrum für Infektionsforschung, Universität Würzburg, D-97070 Wuerzburg, Germany
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197
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Lipson DA, Schmidt SK. Seasonal changes in an alpine soil bacterial community in the colorado rocky mountains. Appl Environ Microbiol 2004; 70:2867-79. [PMID: 15128545 PMCID: PMC404381 DOI: 10.1128/aem.70.5.2867-2879.2004] [Citation(s) in RCA: 160] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2003] [Accepted: 01/02/2004] [Indexed: 11/20/2022] Open
Abstract
The period when the snowpack melts in late spring is a dynamic time for alpine ecosystems. The large winter microbial community begins to turn over rapidly, releasing nutrients to plants. Past studies have shown that the soil microbial community in alpine dry meadows of the Colorado Rocky Mountains changes in biomass, function, broad-level structure, and fungal diversity between winter and early summer. However, little specific information exists on the diversity of the alpine bacterial community or how it changes during this ecologically important period. We constructed clone libraries of 16S ribosomal DNA from alpine soil collected in winter, spring, and summer. We also cultivated bacteria from the alpine soil and measured the seasonal abundance of selected cultured isolates in hybridization experiments. The uncultured bacterial communities changed between seasons in diversity and abundance within taxa. The Acidobacterium division was most abundant in the spring. The winter community had the highest proportion of Actinobacteria and members of the Cytophaga/Flexibacter/Bacteroides (CFB) division. The summer community had the highest proportion of the Verrucomicrobium division and of beta-PROTEOBACTERIA: As a whole, alpha-Proteobacteria were equally abundant in all seasons, although seasonal changes may have occurred within this group. A number of sequences from currently uncultivated divisions were found, including two novel candidate divisions. The cultured isolates belonged to the alpha-, beta-, and gamma-Proteobacteria, the Actinobacteria, and the CFB groups. The only uncultured sequences that were closely related to the isolates were from winter and spring libraries. Hybridization experiments showed that actinobacterial and beta-proteobacterial isolates were most abundant during winter, while the alpha- and gamma-proteobacterial isolates tested did not vary significantly. While the cultures and clone libraries produced generally distinct groups of organisms, the two approaches gave consistent accounts of seasonal changes in microbial diversity.
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Affiliation(s)
- David A Lipson
- Department of Biology, San Diego State University, San Diego, California 92182-4614, USA.
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198
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Burrell PC, O'Sullivan C, Song H, Clarke WP, Blackall LL. Identification, detection, and spatial resolution of Clostridium populations responsible for cellulose degradation in a methanogenic landfill leachate bioreactor. Appl Environ Microbiol 2004; 70:2414-9. [PMID: 15066839 PMCID: PMC383074 DOI: 10.1128/aem.70.4.2414-2419.2004] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2003] [Accepted: 12/18/2003] [Indexed: 11/20/2022] Open
Abstract
An anaerobic landfill leachate bioreactor was operated with crystalline cellulose and sterile landfill leachate until a steady state was reached. Cellulose hydrolysis, acidogenesis, and methanogenesis were measured. Microorganisms attached to the cellulose surfaces were hypothesized to be the cellulose hydrolyzers. 16S rRNA gene clone libraries were prepared from this attached fraction and also from the mixed fraction (biomass associated with cellulose particles and in the planktonic phase). Both clone libraries were dominated by Firmicutes phylum sequences (100% of the attached library and 90% of the mixed library), and the majority fell into one of five lineages of the clostridia. Clone group 1 (most closely related to Clostridium stercorarium), clone group 2 (most closely related to Clostridium thermocellum), and clone group 5 (most closely related to Bacteroides cellulosolvens) comprised sequences in Clostridium group III. Clone group 3 sequences were in Clostridium group XIVa (most closely related to Clostridium sp. strain XB90). Clone group 4 sequences were affiliated with a deeply branching clostridial lineage peripherally associated with Clostridium group VI. This monophyletic group comprises a new Clostridium cluster, designated cluster VIa. Specific fluorescence in situ hybridization (FISH) probes for the five groups were designed and synthesized, and it was demonstrated in FISH experiments that bacteria targeted by the probes for clone groups 1, 2, 4, and 5 were very abundant on the surfaces of the cellulose particles and likely the key cellulolytic microorganisms in the landfill bioreactor. The FISH probe for clone group 3 targeted cells in the planktonic phase, and these organisms were hypothesized to be glucose fermenters.
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Affiliation(s)
- P C Burrell
- School of Molecular and Microbial Sciences. School of Engineering, The University of Queensland, St. Lucia 4072, Australia
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199
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López-García P, Duperron S, Philippot P, Foriel J, Susini J, Moreira D. Bacterial diversity in hydrothermal sediment and epsilonproteobacterial dominance in experimental microcolonizers at the Mid-Atlantic Ridge. Environ Microbiol 2004; 5:961-76. [PMID: 14510850 DOI: 10.1046/j.1462-2920.2003.00495.x] [Citation(s) in RCA: 164] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report here a molecular survey based on 16S rRNA genes of the bacterial diversity found in two deep-sea vent niches at the Mid-Atlantic Ridge: hydrothermal sediment (Rainbow site), and microcolonizers made of three different substrates (organic-rich, iron-rich and pumice) that were exposed for 15 days to a vent emission. Bacterial diversity in sediment samples was scattered through many bacterial divisions. The most abundant and diverse environmental sequences (phylotypes) in our libraries corresponded to the Gammaproteobacteria, followed by the Acidobacteria. We detected members of all the subdivisions within the Proteobacteria. Myxobacterial lineages were the most represented within the delta subdivision. Phylotypes ascribing to the Cytophaga-Flavobacterium-Bacteroides, Planctomycetales, high and low G + C Gram-positives, Nitrospirae, and the candidate division TM7 were also identified. Compared to this broad taxonomic coverage, microcolonizers were almost exclusively colonized by epsilonproteobacteria, although these exhibited considerable morphological and phylogenetic in-group diversity. No specificity for any of the substrates tested was seen. This observation further supports the idea of the ecological dominance of epsilonproteobacteria in the fluid-seawater interface environment. Because oxidation of reduced S species and/or sulphur-reduction is thought to be essential for their energetic metabolism in these areas, we mapped different oxidation states of S in individual bacterial filaments from the iron-rich microcolonizer. For this, we used high-resolution, non-destructive synchrotron micro-X-ray Absorption Near-Edge Spectroscopy (micro-XANES), which revealed the co-existence of different S oxidation states, from sulphide to sulphate, at the level of individual cells. This suggests that these cells were metabolizing sulphur in situ.
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Affiliation(s)
- Purificación López-García
- UMR CNRS 8079, Ecologie, Systématique et Evolution, Université Paris-Sud, bâtiment 360, 91405 Orsay Cedex, France
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200
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Stoeck T, Fowle WH, Epstein SS. Methodology of protistan discovery: from rRNA detection to quality scanning electron microscope images. Appl Environ Microbiol 2004; 69:6856-63. [PMID: 14602650 PMCID: PMC262282 DOI: 10.1128/aem.69.11.6856-6863.2003] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Each year, thousands of new protistan 18S rRNA sequences are detected in environmental samples. Many of these sequences are molecular signatures of new protistan species, classes, and/or kingdoms that have never been seen before. The main goal of this study was to enable visualization of these novel organisms and to conduct quality ultrastructural examination. We achieved this goal by modifying standard procedures for cell fixation, fluorescence in situ hybridization, and scanning electron microscopy (SEM) and by making these methodologies work in concert. As a result, the same individual cell can now be detected by 18S rRNA-targeted fluorochrome-labeled probes and then viewed by SEM to reveal its diagnostic morphological characteristics. The method was successfully tested on a wide range of protists (alveolates, stramenopiles, kinetoplastids, and cryptomonads). The new methodology thus opens a way for fine microscopy studies of many organisms previously known exclusively by their 18S rRNA sequences.
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Affiliation(s)
- Thorsten Stoeck
- Marine Science Center, Northeastern University, East Point, Nahant, Massachusetts 01908, USA
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