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Aikawa T, Maehara N, Ichihara Y, Masuya H, Nakamura K, Anbutsu H. Cytoplasmic incompatibility in the semivoltine longicorn beetle Acalolepta fraudatrix (Coleoptera: Cerambycidae) double infected with Wolbachia. PLoS One 2022; 17:e0261928. [PMID: 35030199 PMCID: PMC8759696 DOI: 10.1371/journal.pone.0261928] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 12/13/2021] [Indexed: 11/18/2022] Open
Abstract
Wolbachia are obligatory endosymbiotic α-proteobacteria found in many arthropods. They are maternally inherited, and can induce reproductive alterations in the hosts. Despite considerable recent progress in studies on the associations between Wolbachia and various taxonomic groups of insects, none of the researches have revealed the effects of Wolbachia on longicorn beetles as the host insect. Acalolepta fraudatrix is a forest longicorn beetle that is distributed in East Asia. In this study, the relationship between Wolbachia and A. fraudatrix was investigated. Out of two populations of A. fraudatrix screened for Wolbachia using the genes ftsZ, wsp, and 16S rRNA, only one of the populations showed detection of all three genes indicating the presence of Wolbachia. Electron microscopy and fluorescent in situ hybridization also confirmed that the A. fraudatrix population was infected with Wolbachia. Sequencing the wsp genes derived from single insects revealed that two strains of Wolbachia coexisted in the insects based on the detection of two different sequences of the wsp gene. We designated these strains as wFra1 and wFra2. The bacterial titers of wFra1 were nearly 2-fold and 3-fold higher than wFra2 in the testes and ovaries, respectively. The two strains of Wolbachia in the insects were completely eliminated by rearing the insects on artificial diets containing 1% concentration of tetracycline for 1 generation. Reciprocal crosses between Wolbachia-infected and Wolbachia-uninfected A. fraudatrix demonstrated that only eggs produced by the crosses between Wolbachia-infected males and Wolbachia-uninfected females did not hatch, indicating that Wolbachia infecting A. fraudatrix causes cytoplasmic incompatibility in the host insect. This is the first report showing the effect of Wolbachia on reproductive function in a longicorn beetle, A. fraudatrix.
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Affiliation(s)
- Takuya Aikawa
- Tohoku Research Center, Forestry and Forest Products Research Institute, Morioka, Iwate, Japan
- * E-mail:
| | - Noritoshi Maehara
- Department of Forest Entomology, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, Japan
| | - Yu Ichihara
- Kansai Research Center, Forestry and Forest Products Research Institute, Kyoto, Japan
| | - Hayato Masuya
- Department of Mushroom Science and Forest Microbiology, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, Japan
| | - Katsunori Nakamura
- Tohoku Research Center, Forestry and Forest Products Research Institute, Morioka, Iwate, Japan
| | - Hisashi Anbutsu
- Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, Shinjuku-ku, Tokyo, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
- Research Organization for Nano and Life Innovation, Waseda University, Shinjuku-ku, Tokyo, Japan
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Takano SI, Gotoh Y, Hayashi T. "Candidatus Mesenet longicola": Novel Endosymbionts of Brontispa longissima that Induce Cytoplasmic Incompatibility. MICROBIAL ECOLOGY 2021; 82:512-522. [PMID: 33454808 DOI: 10.1007/s00248-021-01686-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 01/06/2021] [Indexed: 06/12/2023]
Abstract
Intracellular bacteria that are mainly transmitted maternally affect their arthropod hosts' biology in various ways. One such effect is known as cytoplasmic incompatibility (CI), and three bacterial species are known to induce CI: Wolbachia, Cardinium hertigii, and a recently found alphaproteobacterial symbiont. To clarify the taxonomic status and provide the foundation for future studies to reveal CI mechanisms and other phenotypes, we investigated genetic and morphological properties of the third CI inducer that we have previously reported inducing CI in the coconut beetle Brontispa longissima. The draft genome of the bacteria was obtained from the oocytes of two isofemale lines of B. longissima infected with the bacteria: one from Japan (GL2) and the other from Vietnam (L5). Genome features of the symbionts (sGL2 and sL5) were highly similar, showing 1.3 Mb in size, 32.1% GC content, and 99.83% average nucleotide sequence. A phylogenetic study based on 43 universal and single-copy phylogenetic marker genes indicates that they formed a distinct clade in the family Anaplasmataceae. 16S rRNA gene sequences indicate that they are different from the closest known relatives, at least at the genus level. Therefore, we propose a new genus and species, "Candidatus Mesenet longicola", for the symbionts of B. longissima. Morphological analyses showed that Ca. M. longicola is an intracellular bacterium that is ellipsoidal to rod-shaped and 0.94 ± 0.26 μm (mean ± SD) in length, and accumulated in the anterior part of the oocyte. Candidates for the Ca. M. longicola genes responsible for CI induction are also described.
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Affiliation(s)
- Shun-Ichiro Takano
- Faculty of Agriculture, Kyushu University, 744 Motooka, Fukuoka, 819-0395, Japan.
| | - Yasuhiro Gotoh
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
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Ün Ç, Schultner E, Manzano-Marín A, Flórez LV, Seifert B, Heinze J, Oettler J. Cytoplasmic incompatibility between Old and New World populations of a tramp ant. Evolution 2021; 75:1775-1791. [PMID: 34047357 DOI: 10.1111/evo.14261] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 04/14/2021] [Accepted: 04/16/2021] [Indexed: 12/21/2022]
Abstract
Reproductive manipulation by endosymbiotic Wolbachia can cause unequal inheritance, allowing the manipulator to spread and potentially impacting evolutionary dynamics in infected hosts. Tramp and invasive species are excellent models to study the dynamics of host-Wolbachia associations because introduced populations often diverge in their microbiomes after colonizing new habitats, resulting in infection polymorphisms between native and introduced populations. Ants are the most abundant group of insects on earth, and numerous ant species are classified as highly invasive. However, little is known about the role of Wolbachia in these ecologically dominant insects. Here, we provide the first description of reproductive manipulation by Wolbachia in an ant. We show that Old and New World populations of the cosmotropic tramp ant Cardiocondyla obscurior harbor distinct Wolbachia strains, and that only the Old World strain manipulates host reproduction by causing cytoplasmic incompatibility (CI) in hybrid crosses. By uncovering a symbiont-induced mechanism of reproductive isolation in a social insect, our study provides a novel perspective on the biology of tramp ants and introduces a new system for studying the evolutionary consequences of CI.
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Affiliation(s)
- Çiğdem Ün
- Zoology/Evolutionary Biology, University of Regensburg, Regensburg, 93053, Germany
| | - Eva Schultner
- Zoology/Evolutionary Biology, University of Regensburg, Regensburg, 93053, Germany
| | - Alejandro Manzano-Marín
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, 1090, Austria
| | - Laura V Flórez
- Institute of Organismic and Molecular Evolution, Evolutionary Ecology Department, Johannes Gutenberg University Mainz, Mainz, 55128, Germany
| | - Bernhard Seifert
- Senckenberg Museum of Natural History Görlitz, Görlitz, 02826, Germany
| | - Jürgen Heinze
- Zoology/Evolutionary Biology, University of Regensburg, Regensburg, 93053, Germany
| | - Jan Oettler
- Zoology/Evolutionary Biology, University of Regensburg, Regensburg, 93053, Germany
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Kopecky J, Samkova Z, Sarikhani E, Kyselková M, Omelka M, Kristufek V, Divis J, Grundmann GG, Moënne-Loccoz Y, Sagova-Mareckova M. Bacterial, archaeal and micro-eukaryotic communities characterize a disease-suppressive or conducive soil and a cultivar resistant or susceptible to common scab. Sci Rep 2019; 9:14883. [PMID: 31619759 PMCID: PMC6796001 DOI: 10.1038/s41598-019-51570-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 09/28/2019] [Indexed: 12/20/2022] Open
Abstract
Control of common scab disease can be reached by resistant cultivars or suppressive soils. Both mechanisms are likely to translate into particular potato microbiome profiles, but the relative importance of each is not known. Here, microbiomes of bulk and tuberosphere soil and of potato periderm were studied in one resistant and one susceptible cultivar grown in a conducive and a suppressive field. Disease severity was suppressed similarly by both means yet, the copy numbers of txtB gene (coding for a pathogenicity determinant) were similar in both soils but higher in periderms of the susceptible cultivar from conducive soil. Illumina sequencing of 16S rRNA genes for bacteria (completed by 16S rRNA microarray approach) and archaea, and of 18S rRNA genes for micro-eukarytes showed that in bacteria, the more important was the effect of cultivar and diversity decreased from resistant cultivar to bulk soil to susceptible cultivar. The major changes occurred in proportions of Actinobacteria, Chloroflexi, and Proteobacteria. In archaea and micro-eukaryotes, differences were primarily due to the suppressive and conducive soil. The effect of soil suppressiveness × cultivar resistance depended on the microbial community considered, but differed also with respect to soil and plant nutrient contents particularly in N, S and Fe.
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Affiliation(s)
- Jan Kopecky
- Crop Research Institute, Epidemiology and Ecology of Microorganisms, Drnovská 509, 161 06, Prague 6, Czech Republic
| | - Zuzana Samkova
- Crop Research Institute, Epidemiology and Ecology of Microorganisms, Drnovská 509, 161 06, Prague 6, Czech Republic
| | - Ensyeh Sarikhani
- Crop Research Institute, Epidemiology and Ecology of Microorganisms, Drnovská 509, 161 06, Prague 6, Czech Republic
| | - Martina Kyselková
- Biology Centre of the Czech Academy of Sciences, v. v. i., Institute of Soil Biology, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
| | - Marek Omelka
- Faculty of Mathematics and Physics, Department of Probability and Mathematical Statistics, Charles University, Sokolovská 83, 186 75, Prague 8, Czech Republic
| | - Vaclav Kristufek
- Biology Centre of the Czech Academy of Sciences, v. v. i., Institute of Soil Biology, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
| | - Jiri Divis
- Faculty of Agriculture, University of South Bohemia, Studentská 13, 370 05, České Budějovice, Czech Republic
| | - Geneviève G Grundmann
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRA, VetAgro Sup, UMR5557 Ecologie Microbienne, F-69622, Villeurbanne, France
| | - Yvan Moënne-Loccoz
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRA, VetAgro Sup, UMR5557 Ecologie Microbienne, F-69622, Villeurbanne, France
| | - Marketa Sagova-Mareckova
- Crop Research Institute, Epidemiology and Ecology of Microorganisms, Drnovská 509, 161 06, Prague 6, Czech Republic. .,Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamycka 129, Prague 6, Czech Republic.
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Distinct Bacterial Consortia Established in ETBE-Degrading Enrichments from a Polluted Aquifer. APPLIED SCIENCES-BASEL 2019. [DOI: 10.3390/app9204247] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Ethyl tert-butyl ether (ETBE) is a gasoline additive that became an important aquifer pollutant. The information about natural bacterial consortia with a capacity for complete ETBE degradation is limited. Here we assess the taxonomical composition of bacterial communities and diversity of the ethB gene (involved in ETBE biodegradation) in ETBE-enrichment cultures that were established from a gasoline-polluted aquifer, either from anoxic ETBE-polluted plume water (PW), or from an upstream non-polluted water (UW). We used a 16S rRNA microarray, and 16S rRNA and ethB gene sequencing. Despite the dissimilar initial chemical conditions and microbial composition, ETBE-degrading consortia were obtained from both PW and UW. The composition of ETBE-enrichment cultures was distinct from their initial water samples, reflecting the importance of the rare biosphere as a reservoir of potential ETBE degraders. No convergence was observed between the enrichment cultures originating from UW and PW, which were dominated by Mesorhizobium and Hydrogenophaga, respectively, indicating that distinct consortia with the same functional properties may be present at one site. Conserved ethB genes were evidenced in both PW and UW ETBE-enrichment cultures and in PW water. Our results suggest that the presence of ethB genes rather than the taxonomical composition of in situ bacterial communities indicate the potential for the ETBE degradation at a given site.
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Abreu F, Leão P, Vargas G, Cypriano J, Figueiredo V, Enrich-Prast A, Bazylinski DA, Lins U. Culture-independent characterization of a novel magnetotactic member affiliated to the Beta class of the Proteobacteria phylum from an acidic lagoon. Environ Microbiol 2019; 20:2615-2624. [PMID: 29806735 DOI: 10.1111/1462-2920.14286] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Revised: 02/08/2018] [Accepted: 03/22/2018] [Indexed: 01/22/2023]
Abstract
Magnetotactic bacteria (MTB) comprise a group of motile microorganisms common in most mesothermal aquatic habitats with pH values around neutrality. However, during the last two decades, a number of MTB from extreme environments have been characterized including: cultured alkaliphilic strains belonging to the Deltaproteobacteria class of the Proteobacteria phylum; uncultured moderately thermophilic strains belonging to the Nitrospirae phylum; cultured and uncultured moderately halophilic or strongly halotolerant bacteria affiliated with the Deltaproteobacteria and Gammaproteobacteria classes and an uncultured psychrophilic species belonging to the Alphaproteobacteria class. Here, we used culture-independent techniques to characterize MTB from an acidic freshwater lagoon in Brazil (pH ∼ 4.4). MTB morphotypes found in this acidic lagoon included cocci, rods, spirilla and vibrioid cells. Magnetite (Fe3 O4 ) was the only mineral identified in magnetosomes of these MTB while magnetite magnetosome crystal morphologies within the different MTB cells included cuboctahedral (present in spirilla), elongated prismatic (present in cocci and vibrios) and bullet-shaped (present in rod-shaped cells). Intracellular pH measurements using fluorescent dyes showed that the cytoplasmic pH was close to neutral in most MTB cells and acidic in some intracellular granules. Based on 16S rRNA gene phylogenetic analyses, some of the retrieved gene sequences belonged to the genus Herbaspirillum within the Betaproteobacteria class of the Proteobacteria phylum. Fluorescent in situ hybridization using a Herbaspirillum-specific probe hybridized with vibrioid MTB in magnetically-enriched samples. Transmission electron microscopy of the Herbaspirillum-like MTB revealed the presence of many intracellular granules and a single chain of elongated prismatic magnetite magnetosomes. Diverse populations of MTB have not seemed to have been described in detail in an acid environment. In addition, this is the first report of an MTB phylogenetically affiliated with Betaproteobacteria class.
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Affiliation(s)
- Fernanda Abreu
- Instituto de Microbiologia Paulo de Góes, Departamento de Microbiologia Geral, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, RJ, Brazil
| | - Pedro Leão
- Instituto de Microbiologia Paulo de Góes, Departamento de Microbiologia Geral, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, RJ, Brazil
| | - Gabriele Vargas
- Instituto de Microbiologia Paulo de Góes, Departamento de Microbiologia Geral, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, RJ, Brazil
| | - Jefferson Cypriano
- Instituto de Microbiologia Paulo de Góes, Departamento de Microbiologia Geral, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, RJ, Brazil
| | - Viviane Figueiredo
- Instituto de Biologia, Departamento de Botânica, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, RJ, Brazil
| | - Alex Enrich-Prast
- Instituto de Biologia, Departamento de Botânica, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, RJ, Brazil.,Department of Thematic Studies - Environmental Change, Linköping University, Linköping, c- 58183, Sweden
| | - Dennis A Bazylinski
- School of Life Sciences, University of Nevada at Las Vegas, Las Vegas, NV, 89154-4004, USA
| | - Ulysses Lins
- Instituto de Microbiologia Paulo de Góes, Departamento de Microbiologia Geral, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, RJ, Brazil
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Carvalho V, Freitas E, Fradinho J, Reis M, Oehmen A. The effect of seed sludge on the selection of a photo-EBPR system. N Biotechnol 2019; 49:112-119. [DOI: 10.1016/j.nbt.2018.10.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 10/10/2018] [Accepted: 10/20/2018] [Indexed: 10/28/2022]
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Correa-Galeote D, Bedmar EJ, Arone GJ. Maize Endophytic Bacterial Diversity as Affected by Soil Cultivation History. Front Microbiol 2018; 9:484. [PMID: 29662471 PMCID: PMC5890191 DOI: 10.3389/fmicb.2018.00484] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 02/28/2018] [Indexed: 11/20/2022] Open
Abstract
The bacterial endophytic communities residing within roots of maize (Zea mays L.) plants cultivated by a sustainable management in soils from the Quechua maize belt (Peruvian Andes) were examined using tags pyrosequencing spanning the V4 and V5 hypervariable regions of the 16S rRNA. Across four replicate libraries, two corresponding to sequences of endophytic bacteria from long time maize-cultivated soils and the other two obtained from fallow soils, 793 bacterial sequences were found that grouped into 188 bacterial operational taxonomic units (OTUs, 97% genetic similarity). The numbers of OTUs in the libraries from the maize-cultivated soils were significantly higher than those found in the libraries from fallow soils. A mean of 30 genera were found in the fallow soil libraries and 47 were in those from the maize-cultivated soils. Both alpha and beta diversity indexes showed clear differences between bacterial endophytic populations from plants with different soil cultivation history and that the soils cultivated for long time requires a higher diversity of endophytes. The number of sequences corresponding to main genera Sphingomonas, Herbaspirillum, Bradyrhizobium and Methylophilus in the maize-cultivated libraries were statistically more abundant than those from the fallow soils. Sequences of genera Dyella and Sreptococcus were significantly more abundant in the libraries from the fallow soils. Relative abundance of genera Burkholderia, candidatus Glomeribacter, Staphylococcus, Variovorax, Bacillus and Chitinophaga were similar among libraries. A canonical correspondence analysis of the relative abundance of the main genera showed that the four libraries distributed in two clearly separated groups. Our results suggest that cultivation history is an important driver of endophytic colonization of maize and that after a long time of cultivation of the soil the maize plants need to increase the richness of the bacterial endophytes communities.
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Affiliation(s)
- David Correa-Galeote
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Agencia Estatal Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Eulogio J Bedmar
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Agencia Estatal Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Gregorio J Arone
- Department of Agricultural Sciences, National University of Huancavelica, Huancavelica, Peru
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Hao DC, Xiao PG. Rhizosphere Microbiota and Microbiome of Medicinal Plants: From Molecular Biology to Omics Approaches. CHINESE HERBAL MEDICINES 2017. [DOI: 10.1016/s1674-6384(17)60097-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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10
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Food Waste to Energy: An Overview of Sustainable Approaches for Food Waste Management and Nutrient Recycling. BIOMED RESEARCH INTERNATIONAL 2017; 2017:2370927. [PMID: 28293629 PMCID: PMC5331173 DOI: 10.1155/2017/2370927] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 12/29/2016] [Accepted: 01/12/2017] [Indexed: 01/06/2023]
Abstract
Food wastage and its accumulation are becoming a critical problem around the globe due to continuous increase of the world population. The exponential growth in food waste is imposing serious threats to our society like environmental pollution, health risk, and scarcity of dumping land. There is an urgent need to take appropriate measures to reduce food waste burden by adopting standard management practices. Currently, various kinds of approaches are investigated in waste food processing and management for societal benefits and applications. Anaerobic digestion approach has appeared as one of the most ecofriendly and promising solutions for food wastes management, energy, and nutrient production, which can contribute to world's ever-increasing energy requirements. Here, we have briefly described and explored the different aspects of anaerobic biodegrading approaches for food waste, effects of cosubstrates, effect of environmental factors, contribution of microbial population, and available computational resources for food waste management researches.
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Michelland R, Thioulouse J, Kyselková M, Grundmann GL. Bacterial Community Structure at the Microscale in Two Different Soils. MICROBIAL ECOLOGY 2016; 72:717-724. [PMID: 27418177 DOI: 10.1007/s00248-016-0810-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 06/27/2016] [Indexed: 06/06/2023]
Abstract
The spatial distributions of bacteria in the soil matrix have a role in ecosystem function, for example, at the small scale, through gene transfer or xenobiotic degradation. Soil bacterial biogeography has been evidenced at the large scale, but data are scarce at the small scale. The objective of this work was to determine the spatial pattern of bacterial diversity, in spatially referenced microsamples, in order to define bacterial community spatial traits. Two soils with different physical structures, moderately aggregated (La Côte St André (LCSA)) or poorly aggregated (La Dombes (LD)), were studied. The spatial distribution of bacteria was studied in microsamples (diameter 3 mm) along 10- and 20-cm transects, with a taxonomic microarray. 16S rRNA gene sequencing was used to further study the spatial characteristics of the microbial communities in LD soil. The frequency-occupancy plot, in the LCSA and LD soils, using microarray and sequencing data, followed Hanski's core-satellite theory. The frequency-occupancy distribution plots obtained in two different soils showed bimodality and indicated that the microscale spatial distributions were different, particularly core taxa percentage. Core taxa are widespread and abundant, while satellite taxa are restricted in their distribution. The spread of satellite taxa was at a distance range larger than 5 cm, whereas the core taxa were distributed in a distance range less than 3 mm. Besides, there was a positive abundancy-occupancy relationship at this fine scale. It may be interesting to further evaluate the role of the different bacterial spatial distributions at the fine scale on soil function.
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Affiliation(s)
- Rory Michelland
- Université de Lyon, 69622, Lyon, France
- Université Lyon 1, Villeurbanne, France
- CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France
| | - Jean Thioulouse
- Université de Lyon, 69622, Lyon, France
- Université Lyon 1, Villeurbanne, France
- CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, France
| | - Martina Kyselková
- Institute of Soil Biology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Genevieve L Grundmann
- Université de Lyon, 69622, Lyon, France.
- Université Lyon 1, Villeurbanne, France.
- CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France.
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Ziegler AS, McIlroy SJ, Larsen P, Albertsen M, Hansen AA, Heinen N, Nielsen PH. Dynamics of the Fouling Layer Microbial Community in a Membrane Bioreactor. PLoS One 2016; 11:e0158811. [PMID: 27399199 PMCID: PMC4939938 DOI: 10.1371/journal.pone.0158811] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 06/22/2016] [Indexed: 11/23/2022] Open
Abstract
Membrane fouling presents the greatest challenge to the application of membrane bioreactor (MBR) technology. Formation of biofilms on the membrane surface is the suggested cause, yet little is known of the composition or dynamics of the microbial community responsible. To gain an insight into this important question, we applied 16S rRNA gene amplicon sequencing with a curated taxonomy and fluorescent in situ hybridization to monitor the community of a pilot-scale MBR carrying out enhanced biological nitrogen and phosphorus removal with municipal wastewater. In order to track the dynamics of the fouling process, we concurrently investigated the communities of the biofilm, MBR bulk sludge, and the conventional activated sludge system used to seed the MBR system over several weeks from start-up. As the biofilm matured the initially abundant betaproteobacterial genera Limnohabitans, Hydrogenophaga and Malikia were succeeded by filamentous Chloroflexi and Gordonia as the abundant species. This study indicates that, although putative pioneer species appear, the biofilm became increasingly similar to the bulk community with time. This suggests that the microbial population in bulk water will largely determine the community structure of the mature biofilm.
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Affiliation(s)
- Anja S. Ziegler
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Simon J. McIlroy
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Poul Larsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Mads Albertsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Aviaja A. Hansen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | | | - Per Halkjær Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
- * E-mail:
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Correa-Galeote D, Bedmar EJ, Fernández-González AJ, Fernández-López M, Arone GJ. Bacterial Communities in the Rhizosphere of Amilaceous Maize (Zea mays L.) as Assessed by Pyrosequencing. FRONTIERS IN PLANT SCIENCE 2016; 7:1016. [PMID: 27524985 PMCID: PMC4966391 DOI: 10.3389/fpls.2016.01016] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 06/27/2016] [Indexed: 05/05/2023]
Abstract
Maize (Zea mays L.) is the staple diet of the native peasants in the Quechua region of the Peruvian Andes who continue growing it in small plots called chacras following ancestral traditions. The abundance and structure of bacterial communities associated with the roots of amilaceous maize has not been studied in Andean chacras. Accordingly, the main objective of this study was to describe the rhizospheric bacterial diversity of amilaceous maize grown either in the presence or the absence of bur clover cultivated in soils from the Quechua maize belt. Three 16S rRNA gene libraries, one corresponding to sequences of bacteria from bulk soil of a chacra maintained under fallow conditions, the second from the rhizosphere of maize-cultivated soils, and the third prepared from rhizospheric soil of maize cultivated in intercropping with bur clover were examined using pyrosequencing tags spanning the V4 and V5 hypervariable regions of the gene. A total of 26031 sequences were found that grouped into 5955 distinct operational taxonomic units which distributed in 309 genera. The numbers of OTUs in the libraries from the maize-cultivated soils were significantly higher than those found in the libraries from bulk soil. One hundred ninety seven genera were found in the bulk soil library and 234 and 203 were in those from the maize and maize/bur clover-cultivated soils. Sixteen out of the 309 genera had a relative abundance higher than 0.5% and the were (in decreasing order of abundance) Gp4, Gp6, Flavobacterium, Subdivision3 genera incertae sedis of the Verrucomicrobia phylum, Gemmatimonas, Dechloromonas, Ohtaekwangia, Rhodoferax, Gaiella, Opitutus, Gp7, Spartobacteria genera incertae sedis, Terrimonas, Gp5, Steroidobacter and Parcubacteria genera incertae sedis. Genera Gp4 and Gp6 of the Acidobacteria, Gemmatimonas and Rhodoferax were the most abundant in bulk soil, whereas Flavobacterium, Dechloromonas and Ohtaekwangia were the main genera in the rhizosphere of maize intercropped with bur clover, and Gp4, Subdivision3 genera incertae sedis of phylum Verrucomicrobia, Gp6 and Rhodoferax were the main genera in the rhizosphere of maize plants. Taken together, our results suggest that bur clover produces specific changes in rhizospheric bacterial diversity of amilaceous maize plants.
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Affiliation(s)
- David Correa-Galeote
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Agencia Estatal Consejo Superior de Investigaciones CientíficasGranada, Spain
- *Correspondence: David Correa-Galeote, Eulogio J. Bedmar,
| | - Eulogio J. Bedmar
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Agencia Estatal Consejo Superior de Investigaciones CientíficasGranada, Spain
- *Correspondence: David Correa-Galeote, Eulogio J. Bedmar,
| | - Antonio J. Fernández-González
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Agencia Estatal Consejo Superior de Investigaciones CientíficasGranada, Spain
| | - Manuel Fernández-López
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Agencia Estatal Consejo Superior de Investigaciones CientíficasGranada, Spain
| | - Gregorio J. Arone
- Department of Agricultural Sciences, National University of HuancavelicaHuancavelica, Peru
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Molecular detection of six (endo-) symbiotic bacteria in Belgian mosquitoes: first step towards the selection of appropriate paratransgenesis candidates. Parasitol Res 2015; 115:1391-9. [DOI: 10.1007/s00436-015-4873-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 12/07/2015] [Indexed: 11/26/2022]
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15
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Rossi P, Ricci I, Cappelli A, Damiani C, Ulissi U, Mancini MV, Valzano M, Capone A, Epis S, Crotti E, Chouaia B, Scuppa P, Joshi D, Xi Z, Mandrioli M, Sacchi L, O'Neill SL, Favia G. Mutual exclusion of Asaia and Wolbachia in the reproductive organs of mosquito vectors. Parasit Vectors 2015; 8:278. [PMID: 25981386 PMCID: PMC4445530 DOI: 10.1186/s13071-015-0888-0] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 05/07/2015] [Indexed: 12/11/2022] Open
Abstract
Background Wolbachia is a group of intracellular maternally inherited bacteria infecting a high number of arthropod species. Their presence in different mosquito species has been largely described, but Aedes aegypti, the main vector of Dengue virus, has never been found naturally infected by Wolbachia. Similarly, malaria vectors and other anophelines are normally negative to Wolbachia, with the exception of an African population where these bacteria have recently been detected. Asaia is an acetic acid bacterium stably associated with several mosquito species, found as a dominant microorganism of the mosquito microbiota. Asaia has been described in gut, salivary glands and in reproductive organs of adult mosquitoes in Ae. aegypti and in anophelines. It has recently been shown that Asaia may impede vertical transmission of Wolbachia in Anopheles mosquitoes. Here we present an experimental study, aimed at determining whether there is a negative interference between Asaia and Wolbachia, for the gonad niche in mosquitoes. Methods Different methods (PCR and qPCR, monoclonal antibody staining and FISH) have been used to address the question of the co-localization and the relative presence/abundance of the two symbionts. PCR and qPCR were performed to qualitatively and quantitatively verify the distribution of Asaia and Wolbachia in different mosquito species/organs. Monoclonal antibody staining and FISH were performed to localize the symbionts in different mosquito species. Results Here we provide evidence that, in Anopheles and in other mosquitoes, there is a reciprocal negative interference between Asaia and Wolbachia symbionts, in terms of the colonization of the gonads. In particular, we have shown that in some mosquito species the presence of one of the symbionts prevented the establishment of the second, while in other systems the symbionts were co-localized, although at reduced densities. Conclusions A mutual exclusion or a competition between Asaia and Wolbachia may contribute to explain the inability of Wolbachia to colonize the female reproductive organs of anophelines, inhibiting its vertical transmission and explaining the absence of Wolbachia infection in Ae. aegypti and in the majority of natural populations of Anopheles mosquitoes. Electronic supplementary material The online version of this article (doi:10.1186/s13071-015-0888-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Paolo Rossi
- Scuola di Bioscienze e Medicina Veterinaria, Università di Camerino, 62032, Camerino, MC, Italy.
| | - Irene Ricci
- Scuola di Bioscienze e Medicina Veterinaria, Università di Camerino, 62032, Camerino, MC, Italy.
| | - Alessia Cappelli
- Scuola di Bioscienze e Medicina Veterinaria, Università di Camerino, 62032, Camerino, MC, Italy.
| | - Claudia Damiani
- Scuola di Bioscienze e Medicina Veterinaria, Università di Camerino, 62032, Camerino, MC, Italy.
| | - Ulisse Ulissi
- Scuola di Bioscienze e Medicina Veterinaria, Università di Camerino, 62032, Camerino, MC, Italy.
| | - Maria Vittoria Mancini
- Scuola di Bioscienze e Medicina Veterinaria, Università di Camerino, 62032, Camerino, MC, Italy.
| | - Matteo Valzano
- Scuola di Bioscienze e Medicina Veterinaria, Università di Camerino, 62032, Camerino, MC, Italy.
| | - Aida Capone
- Scuola di Bioscienze e Medicina Veterinaria, Università di Camerino, 62032, Camerino, MC, Italy.
| | - Sara Epis
- Dipartimento di Scienze Veterinarie e Sanità Pubblica, DIVET, Università degli Studi di Milano, Milan, Italy.
| | - Elena Crotti
- Dipartimento di Scienze per gli Alimenti la Nutrizione e l'Ambiente, DeFENS, Università degli Studi di Milano, Milan, Italy.
| | - Bessem Chouaia
- Dipartimento di Scienze per gli Alimenti la Nutrizione e l'Ambiente, DeFENS, Università degli Studi di Milano, Milan, Italy.
| | - Patrizia Scuppa
- Scuola di Bioscienze e Medicina Veterinaria, Università di Camerino, 62032, Camerino, MC, Italy.
| | - Deepak Joshi
- Department of Microbiology and Molecular Genetic, Michigan State University, Michigan, USA.
| | - Zhiyong Xi
- Department of Microbiology and Molecular Genetic, Michigan State University, Michigan, USA.
| | - Mauro Mandrioli
- Dipartimento di Scienze della Vita, Università di Modena e Reggio Emilia, Modena, Italy.
| | - Luciano Sacchi
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy.
| | - Scott L O'Neill
- School of Biological Sciences, Monash University, Clayton, VIC, Australia.
| | - Guido Favia
- Scuola di Bioscienze e Medicina Veterinaria, Università di Camerino, 62032, Camerino, MC, Italy.
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Raquin V, Valiente Moro C, Saucereau Y, Tran FH, Potier P, Mavingui P. Native Wolbachia from Aedes albopictus Blocks Chikungunya Virus Infection In Cellulo. PLoS One 2015; 10:e0125066. [PMID: 25923352 PMCID: PMC4414612 DOI: 10.1371/journal.pone.0125066] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Accepted: 03/20/2015] [Indexed: 11/19/2022] Open
Abstract
Wolbachia, a widespread endosymbiont of terrestrial arthropods, can protect its host against viral and parasitic infections, a phenotype called "pathogen blocking". However, in some cases Wolbachia may have no effect or even enhance pathogen infection, depending on the host-Wolbachia-pathogen combination. The tiger mosquito Aedes albopictus is naturally infected by two strains of Wolbachia, wAlbA and wAlbB, and is a competent vector for different arboviruses such as dengue virus (DENV) and Chikungunya virus (CHIKV). Interestingly, it was shown in some cases that Ae. albopictus native Wolbachia strains are able to inhibit DENV transmission by limiting viral replication in salivary glands, but no such impact was measured on CHIKV replication in vivo. To better understand the Wolbachia/CHIKV/Ae. albopictus interaction, we generated a cellular model using Ae. albopictus derived C6/36 cells that we infected with the wAlbB strain. Our results indicate that CHIKV infection is negatively impacted at both RNA replication and virus assembly/secretion steps in presence of wAlbB. Using FISH, we observed CHIKV and wAlbB in the same mosquito cells, indicating that the virus is still able to enter the cell in the presence of the bacterium. Further work is needed to decipher molecular pathways involved in Wolbachia-CHIKV interaction at the cellular level, but this cellular model can be a useful tool to study the mechanism behind virus blocking phenotype induced by Wolbachia. More broadly, this underlines that despite Wolbachia antiviral potential other complex interactions occur in vivo to determine mosquito vector competence in Ae. albopictus.
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Affiliation(s)
- Vincent Raquin
- Université de Lyon, UMR 5557 Ecologie Microbienne, CNRS, USC1190 INRA, VetAgro Sup, Université Lyon 1, Villeurbanne, France
- * E-mail: (VR); (PM)
| | - Claire Valiente Moro
- Université de Lyon, UMR 5557 Ecologie Microbienne, CNRS, USC1190 INRA, VetAgro Sup, Université Lyon 1, Villeurbanne, France
| | - Yoann Saucereau
- Université de Lyon, UMR 5557 Ecologie Microbienne, CNRS, USC1190 INRA, VetAgro Sup, Université Lyon 1, Villeurbanne, France
| | - Florence-Hélène Tran
- Université de Lyon, UMR 5557 Ecologie Microbienne, CNRS, USC1190 INRA, VetAgro Sup, Université Lyon 1, Villeurbanne, France
| | - Patrick Potier
- Université de Lyon, UMR 5557 Ecologie Microbienne, CNRS, USC1190 INRA, VetAgro Sup, Université Lyon 1, Villeurbanne, France
| | - Patrick Mavingui
- Université de Lyon, UMR 5557 Ecologie Microbienne, CNRS, USC1190 INRA, VetAgro Sup, Université Lyon 1, Villeurbanne, France
- Université de La Réunion, UMR PIMIT, INSERM U1187, CNRS 9192, IRD 249, Plateforme de Recherche CYROI, Saint-Denis, La Réunion, France
- * E-mail: (VR); (PM)
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17
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Tago K, Itoh H, Kikuchi Y, Hori T, Sato Y, Nagayama A, Okubo T, Navarro R, Aoyagi T, Hayashi K, Hayatsu M. A fine-scale phylogenetic analysis of free-living Burkholderia species in sugarcane field soil. Microbes Environ 2014; 29:434-7. [PMID: 25410730 PMCID: PMC4262370 DOI: 10.1264/jsme2.me14122] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The diversity and abundance of Burkholderia species in sugarcane field soils were investigated by a 16S rRNA gene-based approach using genus-specific primers. A total of 365,721 sequences generated by the Illumina MiSeq platform were assigned to the genus Burkholderia. Nearly 58% of these sequences were placed in a previously defined cluster, including stinkbug symbionts. Quantitative PCR analysis revealed a consistent number of 16S rRNA gene copies for Burkholderia species (107 g−1 soil) across the sampled fields. C/N, pH, and nitrate concentrations were important factors shaping the Burkholderia community structure; however, their impacts were not significant considering the overall genus size.
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Affiliation(s)
- Kanako Tago
- Environmental Biofunction Division, National Institute for Agro-Environmental Sciences
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18
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McIlroy SJ, Starnawska A, Starnawski P, Saunders AM, Nierychlo M, Nielsen PH, Nielsen JL. Identification of active denitrifiers in full-scale nutrient removal wastewater treatment systems. Environ Microbiol 2014; 18:50-64. [DOI: 10.1111/1462-2920.12614] [Citation(s) in RCA: 157] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 08/22/2014] [Indexed: 11/28/2022]
Affiliation(s)
- Simon Jon McIlroy
- Department of Biotechnology, Chemistry and Environmental Engineering; Center for Microbial Communities; Aalborg University; Aalborg Denmark
| | - Anna Starnawska
- Department of Biotechnology, Chemistry and Environmental Engineering; Center for Microbial Communities; Aalborg University; Aalborg Denmark
| | - Piotr Starnawski
- Department of Biotechnology, Chemistry and Environmental Engineering; Center for Microbial Communities; Aalborg University; Aalborg Denmark
| | - Aaron Marc Saunders
- Department of Biotechnology, Chemistry and Environmental Engineering; Center for Microbial Communities; Aalborg University; Aalborg Denmark
| | - Marta Nierychlo
- Department of Biotechnology, Chemistry and Environmental Engineering; Center for Microbial Communities; Aalborg University; Aalborg Denmark
| | - Per Halkjaer Nielsen
- Department of Biotechnology, Chemistry and Environmental Engineering; Center for Microbial Communities; Aalborg University; Aalborg Denmark
| | - Jeppe Lund Nielsen
- Department of Biotechnology, Chemistry and Environmental Engineering; Center for Microbial Communities; Aalborg University; Aalborg Denmark
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Maltz MA, Bomar L, Lapierre P, Morrison HG, McClure EA, Sogin ML, Graf J. Metagenomic analysis of the medicinal leech gut microbiota. Front Microbiol 2014; 5:151. [PMID: 24860552 PMCID: PMC4029005 DOI: 10.3389/fmicb.2014.00151] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 03/21/2014] [Indexed: 12/11/2022] Open
Abstract
There are trillions of microbes found throughout the human body and they exceed the number of eukaryotic cells by 10-fold. Metagenomic studies have revealed that the majority of these microbes are found within the gut, playing an important role in the host's digestion and nutrition. The complexity of the animal digestive tract, unculturable microbes, and the lack of genetic tools for most culturable microbes make it challenging to explore the nature of these microbial interactions within this niche. The medicinal leech, Hirudo verbana, has been shown to be a useful tool in overcoming these challenges, due to the simplicity of the microbiome and the availability of genetic tools for one of the two dominant gut symbionts, Aeromonas veronii. In this study, we utilize 16S rRNA gene pyrosequencing to further explore the microbial composition of the leech digestive tract, confirming the dominance of two taxa, the Rikenella-like bacterium and A. veronii. The deep sequencing approach revealed the presence of additional members of the microbial community that suggests the presence of a moderately complex microbial community with a richness of 36 taxa. The presence of a Proteus strain as a newly identified resident in the leech crop was confirmed using fluorescence in situ hybridization (FISH). The metagenome of this community was also pyrosequenced and the contigs were binned into the following taxonomic groups: Rikenella-like (3.1 MB), Aeromonas (4.5 MB), Proteus (2.9 MB), Clostridium (1.8 MB), Eryspelothrix (0.96 MB), Desulfovibrio (0.14 MB), and Fusobacterium (0.27 MB). Functional analyses on the leech gut symbionts were explored using the metagenomic data and MG-RAST. A comparison of the COG and KEGG categories of the leech gut metagenome to that of other animal digestive-tract microbiomes revealed that the leech digestive tract had a similar metabolic potential to the human digestive tract, supporting the usefulness of this system as a model for studying digestive-tract microbiomes. This study lays the foundation for more detailed metatranscriptomic studies and the investigation of symbiont population dynamics.
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Affiliation(s)
- Michele A Maltz
- Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA
| | - Lindsey Bomar
- Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA
| | - Pascal Lapierre
- Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA
| | - Hilary G Morrison
- Marine Biological Laboratory, The Josephine Bay Paul Center Woods Hole, MA, USA
| | - Emily Ann McClure
- Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA
| | - Mitchell L Sogin
- Marine Biological Laboratory, The Josephine Bay Paul Center Woods Hole, MA, USA
| | - Joerg Graf
- Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA
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20
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Bian G, Joshi D, Dong Y, Lu P, Zhou G, Pan X, Xu Y, Dimopoulos G, Xi Z. Wolbachia invades Anopheles stephensi populations and induces refractoriness to Plasmodium infection. Science 2013; 340:748-51. [PMID: 23661760 DOI: 10.1126/science.1236192] [Citation(s) in RCA: 295] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Wolbachia is a maternally transmitted symbiotic bacterium of insects that has been proposed as a potential agent for the control of insect-transmitted diseases. One of the major limitations preventing the development of Wolbachia for malaria control has been the inability to establish inherited infections of Wolbachia in anopheline mosquitoes. Here, we report the establishment of a stable Wolbachia infection in an important malaria vector, Anopheles stephensi. In A. stephensi, Wolbachia strain wAlbB displays both perfect maternal transmission and the ability to induce high levels of cytoplasmic incompatibility. Seeding of naturally uninfected A. stephensi populations with infected females repeatedly resulted in Wolbachia invasion of laboratory mosquito populations. Furthermore, wAlbB conferred resistance in the mosquito to the human malaria parasite Plasmodium falciparum.
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Affiliation(s)
- Guowu Bian
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
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21
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Walker V, Bruto M, Bellvert F, Bally R, Muller D, Prigent-Combaret C, Moënne-Loccoz Y, Comte G. Unexpected phytostimulatory behavior for Escherichia coli and Agrobacterium tumefaciens model strains. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2013; 26:495-502. [PMID: 23360460 DOI: 10.1094/mpmi-12-12-0298-r] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Plant-beneficial effects of bacteria are often underestimated, especially for well-studied strains associated with pathogenicity or originating from other environments. We assessed the impact of seed inoculation with the emblematic bacterial models Agrobacterium tumefaciens C58 (plasmid-cured) or Escherichia coli K-12 on maize seedlings in nonsterile soil. Compared with the noninoculated control, root biomass (with A. tumefaciens or E. coli) and shoot biomass (with A. tumefaciens) were enhanced at 10 days for 'PR37Y15' but not 'DK315', as found with the phytostimulator Azospirillum brasilense UAP-154 (positive control). In roots as well as in shoots, Agrobacterium tumefaciens and E. coli triggered similar (in PR37Y15) or different (in DK315) changes in the high-performance liquid chromatography profiles of secondary metabolites (especially benzoxazinoids), distinct from those of Azospirillum brasilense UAP-154. Genome sequence analysis revealed homologs of nitrite reductase genes nirK and nirBD and siderophore synthesis genes for Agrobacterium tumefaciens, as well as homologs of nitrite reductase genes nirBD and phosphatase genes phoA and appA in E. coli, whose contribution to phytostimulation will require experimental assessment. In conclusion, the two emblematic bacterial models had a systemic impact on maize secondary metabolism and resulted in unexpected phytostimulation of seedlings in the Azospirillum sp.-responsive cultivar.
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Rungrassamee W, Tosukhowong A, Klanchui A, Maibunkaew S, Plengvidhya V, Karoonuthaisiri N. Development of bacteria identification array to detect lactobacilli in Thai fermented sausage. J Microbiol Methods 2012; 91:341-53. [PMID: 23022427 DOI: 10.1016/j.mimet.2012.09.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2012] [Revised: 09/13/2012] [Accepted: 09/14/2012] [Indexed: 01/11/2023]
Abstract
To improve the quality and safety of food products, there is a need in the food industry for a reliable method for simultaneously monitoring multiple bacterial strains. Microarray technology is a high-throughput screening approach that can provide an alternative for bacteria detection. A total of 164 bacteria-specific probes were designed from 16S rRNA gene sequences to target 12 bacteria species, including lactic acid bacteria and selected food pathogens. After fabrication onto aminosilane-coated slides, hybridization conditions of the array were optimized for high specificity and signal intensities. The array was applied to detect 12 bacteria individually and was specific to all (Lactobacillus plantarum group, L. fermentum, L. brevis, L. delbrueckii, L. casei, L. sakei, Escherichia coli, Staphylococcus aureus, Micrococcus luteus and Listeria monocytogenes) except L. animalis. Multiplex detection using mixed bacteria populations was evaluated and accurate detection was obtained. The feasibility of using the array to detect the target bacteria in food was evaluated with Thai fermented sausages (Nham). Meat samples were collected on days 2, 3 and 7 after natural fermentation, L. plantarum-inoculated fermentation and L. brevis-inoculated fermentation before applying to the array. The naturally-fermented Nham contained L. sakei, L. delbrueckii, L. plantarum and L. fermentum. The L. plantarum-inoculated Nham showed a similar lactic acid bacteria population but the positive signal level for L. plantarum was higher than with natural fermentation. The L. brevis-inoculated Nham contained L. brevis, L. plantarum, L. delbrueckii and L. fermentum. The array was used to monitor bacteria population dynamics during the fermentation process. The naturally-fermented and L. brevis-inoculated samples showed lower positive signal levels of L. plantarum on day 2, but signals gradually increased on days 3 and 7 of the fermentation. In contrast, the L. plantarum-started fermentation showed a higher positive signal level on day 2 than the natural and L. brevis-inoculated samples, and the positive signal level remained high on days 3 and 7. The bacteria identification array was proven to be useful as an alternative method to detect and monitor target bacteria populations during food fermentation.
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Affiliation(s)
- Wanilada Rungrassamee
- Microarray Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), Khlong Luang, Pathum Thani, Thailand.
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Yilmaz LS, Loy A, Wright ES, Wagner M, Noguera DR. Modeling formamide denaturation of probe-target hybrids for improved microarray probe design in microbial diagnostics. PLoS One 2012; 7:e43862. [PMID: 22952791 PMCID: PMC3428302 DOI: 10.1371/journal.pone.0043862] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Accepted: 07/30/2012] [Indexed: 02/01/2023] Open
Abstract
Application of high-density microarrays to the diagnostic analysis of microbial communities is challenged by the optimization of oligonucleotide probe sensitivity and specificity, as it is generally unfeasible to experimentally test thousands of probes. This study investigated the adjustment of hybridization stringency using formamide with the idea that sensitivity and specificity can be optimized during probe design if the hybridization efficiency of oligonucleotides with target and non-target molecules can be predicted as a function of formamide concentration. Sigmoidal denaturation profiles were obtained using fluorescently labeled and fragmented 16S rRNA gene amplicon of Escherichia coli as the target with increasing concentrations of formamide in the hybridization buffer. A linear free energy model (LFEM) was developed and microarray-specific nearest neighbor rules were derived. The model simulated formamide melting with a denaturant m-value that increased hybridization free energy (ΔG°) by 0.173 kcal/mol per percent of formamide added (v/v). Using the LFEM and specific probe sets, free energy rules were systematically established to predict the stability of single and double mismatches, including bulged and tandem mismatches. The absolute error in predicting the position of experimental denaturation profiles was less than 5% formamide for more than 90 percent of probes, enabling a practical level of accuracy in probe design. The potential of the modeling approach for probe design and optimization is demonstrated using a dataset including the 16S rRNA gene of Rhodobacter sphaeroides as an additional target molecule. The LFEM and thermodynamic databases were incorporated into a computational tool (ProbeMelt) that is freely available at http://DECIPHER.cee.wisc.edu.
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Affiliation(s)
- L Safak Yilmaz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America.
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Ding C, He J. Molecular techniques in the biotechnological fight against halogenated compounds in anoxic environments. Microb Biotechnol 2012; 5:347-67. [PMID: 22070763 PMCID: PMC3821678 DOI: 10.1111/j.1751-7915.2011.00313.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Revised: 09/24/2011] [Accepted: 09/28/2011] [Indexed: 11/28/2022] Open
Abstract
Microbial treatment of environmental contamination by anthropogenic halogenated organic compounds has become popular in recent decades, especially in the subsurface environments. Molecular techniques such as polymerase chain reaction-based fingerprinting methods have been extensively used to closely monitor the presence and activities of dehalogenating microbes, which also lead to the discovery of new dehalogenating bacteria and novel functional genes. Nowadays, traditional molecular techniques are being further developed and optimized for higher sensitivity, specificity, and accuracy to better fit the contexts of dehalogenation. On the other hand, newly developed high throughput techniques, such as microarray and next-generation sequencing, provide unsurpassed detection ability, which has enabled large-scale comparative genomic and whole-genome transcriptomic analysis. The aim of this review is to summarize applications of various molecular tools in the field of microbially mediated dehalogenation of various halogenated organic compounds. It is expected that traditional molecular techniques and nucleic-acid-based biomarkers will still be favoured in the foreseeable future because of relative low costs and high flexibility. Collective analyses of metagenomic sequencing data are still in need of information from individual dehalogenating strains and functional reductive dehalogenase genes in order to draw reliable conclusions.
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Affiliation(s)
| | - Jianzhong He
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore 117576
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Zouache K, Michelland RJ, Failloux AB, Grundmann GL, Mavingui P. Chikungunya virus impacts the diversity of symbiotic bacteria in mosquito vector. Mol Ecol 2012; 21:2297-309. [PMID: 22433115 DOI: 10.1111/j.1365-294x.2012.05526.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Mosquitoes transmit numerous arboviruses including dengue and chikungunya virus (CHIKV). In recent years, mosquito species Aedes albopictus has expanded in the Indian Ocean region and was the principal vector of chikungunya outbreaks in La Reunion and neighbouring islands in 2005 and 2006. Vector-associated bacteria have recently been found to interact with transmitted pathogens. For instance, Wolbachia modulates the replication of viruses or parasites. However, there has been no systematic evaluation of the diversity of the entire bacterial populations within mosquito individuals particularly in relation to virus invasion. Here, we investigated the effect of CHIKV infection on the whole bacterial community of Ae. albopictus. Taxonomic microarrays and quantitative PCR showed that members of Alpha- and Gammaproteobacteria phyla, as well as Bacteroidetes, responded to CHIKV infection. The abundance of bacteria from the Enterobacteriaceae family increased with CHIKV infection, whereas the abundance of known insect endosymbionts like Wolbachia and Blattabacterium decreased. Our results clearly link the pathogen propagation with changes in the dynamics of the bacterial community, suggesting that cooperation or competition occurs within the host, which may in turn affect the mosquito traits like vector competence.
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Isolation of bacteria capable of growth with 2-methylisoborneol and geosmin as the sole carbon and energy sources. Appl Environ Microbiol 2011; 78:363-70. [PMID: 22081577 DOI: 10.1128/aem.06333-11] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Using a relatively simple enrichment technique, geosmin and 2-methylisoborneol (MIB)-biodegrading bacteria were isolated from a digestion basin in an aquaculture unit. Comparison of 16S rRNA gene sequences affiliated one of the three isolates with the Gram-positive genus Rhodococcus, while the other two isolates were found to be closely related to the Gram-negative family Comamonadaceae (Variovorax and Comamonas). Growth rates and geosmin and MIB removal rates by the isolates were determined under aerated and nonaerated conditions in mineral medium containing either of the two compounds as the sole carbon and energy source. All isolates exhibited their fastest growth under aerobic conditions, with generation times ranging from 3.1 to 5.7 h, compared to generation times of up to 19.1 h in the nonaerated flasks. Incubation of the isolates with additional carbon sources caused a significant increase in their growth rates, while removal rates of geosmin and MIB were significantly lower than those for incubation with only geosmin or MIB. By fluorescence in situ hybridization, members of the genera Rhodococcus and Comamonas were detected in geosmin- and MIB-enriched sludge from the digestion basin.
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Kopecky J, Kyselkova M, Omelka M, Cermak L, Novotna J, Grundmann GL, Moënne-Loccoz Y, Sagova-Mareckova M. Actinobacterial community dominated by a distinct clade in acidic soil of a waterlogged deciduous forest. FEMS Microbiol Ecol 2011; 78:386-94. [DOI: 10.1111/j.1574-6941.2011.01173.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Revised: 06/22/2011] [Accepted: 07/09/2011] [Indexed: 11/28/2022] Open
Affiliation(s)
- Jan Kopecky
- Crop Research Institute; Prague; Czech Republic
| | | | - Marek Omelka
- Faculty of Mathematics and Physics; Charles University; Prague; Czech Republic
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Temporal development of the infant gut microbiota in immunoglobulin E-sensitized and nonsensitized children determined by the GA-map infant array. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2011; 18:1326-35. [PMID: 21653746 DOI: 10.1128/cvi.00062-11] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
At birth, the human infant gut is sterile, but it becomes fully colonized within a few days. This initial colonization process has a major impact on immune development. Our knowledge about the correlations between aberrant colonization patterns and immunological diseases, however, is limited. The aim of the present work was to develop the GA-map (Genetic Analysis microbiota array platform) infant array and to use this array to compare the temporal development of the gut microbiota in IgE-sensitized and nonsensitized children during the first 2 years of life. The GA-map infant array is composed of highly specific 16S rRNA gene-targeted single nucleotide primer extension (SNuPE) probes, which were designed based on extensive infant 16S rRNA gene sequence libraries. For the clinical screening, we analyzed 216 fecal samples collected from a cohort of 47 infants (16 sensitized and 31 nonsensitized) from 1 day to 2 years of age. The results showed that at a high taxonomic level, Actinobacteria was significantly overrepresented at 4 months while Firmicutes was significantly overrepresented at 1 year for the sensitized children. At a lower taxonomic level, for the sensitized group, we found that Bifidobacterium longum was significantly overrepresented at the age of 1 year and Enterococcus at the age of 4 months. For most phyla, however, there were consistent differences in composition between age groups, irrespective of the sensitization state. The main age patterns were a rapid decrease in staphylococci from 10 days to 4 months and a peak of bifidobacteria and bacteroides at 4 months. In conclusion, our analyses showed consistent microbiota colonization and IgE sensitization patterns that can be important for understanding both normal and diseased immunological development in infants.
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Pereira P, Ibáñez F, Rosenblueth M, Etcheverry M, Martínez-Romero E. Analysis of the Bacterial Diversity Associated with the Roots of Maize (Zea mays L.) through Culture-Dependent and Culture-Independent Methods. ACTA ACUST UNITED AC 2011. [DOI: 10.5402/2011/938546] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The present study investigated bacterial diversity associated with the roots of maize through the use of culture-dependent and culture-independent methods. Bacterial 16S–23S rDNA internal transcribed spacer sequences (ITS) primers were used to amplify sequences obtained directly from the root matrix by Percoll gradient separation. This assay showed that γ-Proteobacteria within Enterobacter, Erwinia, Klebsiella, Pseudomonas, and Stenotrophomonas genera were predominant groups. The culturable component of the bacterial community was also assessed, revealing that the predominant group was Firmicutes, mainly of Bacillus genus, while Achromobacter, Lysinibacillus, and Paenibacillus genera were rarely found in association with the roots. Only two genera within γ-Proteobacteria, Enterobacter and Pseudomonas, were found in the culture collection. Differences in richness and diversity between the rhizospheric and endophytic bacterial communities were also evidenced. The spectrum of bacteria naturally associated with maize roots is wide and the magnitude of such diversity will depend on the methods chosen for analysis. The knowledge of this spectrum will facilitate the search of microorganisms capable of exerting antagonism to diverse pathogens or detecting plant growth enhancers.
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Affiliation(s)
- Paola Pereira
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ruta Nac. 36 Km 601, Río Cuarto, 5800 Córdoba, Argentina
| | - Fernando Ibáñez
- Departamento de Ciencias Naturales, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ruta Nac. 36 Km 601, Río Cuarto, 5800 Córdoba, Argentina
| | - Mónica Rosenblueth
- Centro de Ciencias Genómicas, Programa de Ecología Genómica, Universidad Nacional Autónoma de México, Apartado Postal 565-A, Av. Universidad s/n., Col. Chamilpa, C.P. 62210, Cuernavaca, Morelos, Mexico
| | - Miriam Etcheverry
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ruta Nac. 36 Km 601, Río Cuarto, 5800 Córdoba, Argentina
| | - Esperanza Martínez-Romero
- Centro de Ciencias Genómicas, Programa de Ecología Genómica, Universidad Nacional Autónoma de México, Apartado Postal 565-A, Av. Universidad s/n., Col. Chamilpa, C.P. 62210, Cuernavaca, Morelos, Mexico
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Loy A, Pester M, Steger D. Phylogenetic microarrays for cultivation-independent identification and metabolic characterization of microorganisms in complex samples. Methods Mol Biol 2011; 688:187-206. [PMID: 20938840 DOI: 10.1007/978-1-60761-947-5_13] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
High-throughput sequencing and hybridization technologies promise new insights into the natural diversity and dynamics of microorganisms. Among these new technologies are phylogenetic oligonucleotide microarrays (phylochips) that depend on the standard molecules for taxonomic and environmental studies of microorganisms: the ribosomal RNAs and their encoding genes. The beauty of phylochip hybridization is that a sample can be analyzed with hundreds to thousands of rRNA (gene)-targeted probes simultaneously, lending itself to the efficient diagnosis of many target organisms in many samples. An emerging application of phylochips is the highly parallel analysis of structure-function relationships of microbial community members by employing in vivo substrate-mediated isotope labeling of rRNA (via the isotope array approach). This chapter provides an introduction to phylochip and isotope array analysis and detailed wet-lab protocols for preparation, labeling, and hybridization of target nucleic acids.
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Affiliation(s)
- Alexander Loy
- Department of Microbial Ecology, Faculty of Life Sciences, University of Vienna, Wien, Austria.
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Microorganisms with novel dissimilatory (bi)sulfite reductase genes are widespread and part of the core microbiota in low-sulfate peatlands. Appl Environ Microbiol 2010; 77:1231-42. [PMID: 21169452 DOI: 10.1128/aem.01352-10] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Peatlands of the Lehstenbach catchment (Germany) house as-yet-unidentified microorganisms with phylogenetically novel variants of the dissimilatory (bi)sulfite reductase genes dsrAB. These genes are characteristic of microorganisms that reduce sulfate, sulfite, or some organosulfonates for energy conservation but can also be present in anaerobic syntrophs. However, nothing is currently known regarding the abundance, community dynamics, and biogeography of these dsrAB-carrying microorganisms in peatlands. To tackle these issues, soils from a Lehstenbach catchment site (Schlöppnerbrunnen II fen) from different depths were sampled at three time points over a 6-year period to analyze the diversity and distribution of dsrAB-containing microorganisms by a newly developed functional gene microarray and quantitative PCR assays. Members of novel, uncultivated dsrAB lineages (approximately representing species-level groups) (i) dominated a temporally stable but spatially structured dsrAB community and (ii) represented "core" members (up to 1% to 1.7% relative abundance) of the autochthonous microbial community in this fen. In addition, denaturing gradient gel electrophoresis (DGGE)- and clone library-based comparisons of the dsrAB diversity in soils from a wet meadow, three bogs, and five fens of various geographic locations (distance of ∼1 to 400 km) identified that one Syntrophobacter-related and nine novel dsrAB lineages are widespread in low-sulfate peatlands. Signatures of biogeography in dsrB-based DGGE data were not correlated with geographic distance but could be explained largely by soil pH and wetland type, implying that the distribution of dsrAB-carrying microorganisms in wetlands on the scale of a few hundred kilometers is not limited by dispersal but determined by local environmental conditions.
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Nemir A, David MM, Perrussel R, Sapkota A, Simonet P, Monier JM, Vogel TM. Comparative phylogenetic microarray analysis of microbial communities in TCE-contaminated soils. CHEMOSPHERE 2010; 80:600-607. [PMID: 20444493 DOI: 10.1016/j.chemosphere.2010.03.036] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2009] [Revised: 02/15/2010] [Accepted: 03/28/2010] [Indexed: 05/29/2023]
Abstract
The arrival of chemicals in a soil or groundwater ecosystem could upset the natural balance of the microbial community. Since soil microorganisms are the first to be exposed to the chemicals released into the soil environment, we evaluated the use of a phylogenetic microarray as a bio-indicator of community perturbations due to the exposure to trichloroethylene (TCE). The phylogenetic microarray, which measures the presence of different members of the soil community, was used to evaluate unpolluted soils exposed to TCE as well as to samples from historically TCE polluted sites. We were able to determine an apparent threshold at which the microbial community structure was significantly affected (about 1ppm). In addition, the members of the microbial community most affected were identified. This approach could be useful for assessing environmental impact of chemicals on the biosphere as well as important members of the microbial community involved in TCE degradation.
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Affiliation(s)
- Audra Nemir
- Ecole Centrale de Lyon, Université de Lyon, Ecully, France
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Sapkota AR, Berger S, Vogel TM. Human pathogens abundant in the bacterial metagenome of cigarettes. ENVIRONMENTAL HEALTH PERSPECTIVES 2010; 118:351-6. [PMID: 20064769 PMCID: PMC2854762 DOI: 10.1289/ehp.0901201] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2009] [Accepted: 10/22/2009] [Indexed: 05/21/2023]
Abstract
BACKGROUND Many studies have evaluated chemical, heavy metal, and other abiotic substances present in cigarettes and their roles in the development of lung cancer and other diseases, yet no studies have comprehensively evaluated bacterial diversity of cigarettes and the possible impacts of these microbes on respiratory illnesses in smokers and exposed nonsmokers. OBJECTIVES The goal of this study was to explore the bacterial metagenomes of commercially available cigarettes. METHODS A 16S rRNA-based taxonomic microarray and cloning and sequencing were used to evaluate total bacterial diversity of four brands of cigarettes. Normalized microarray data were compared using principal component analysis and hierarchical cluster analysis to evaluate potential differences in microbial diversity across cigarette brands. RESULTS Fifteen different classes of bacteria and a broad range of potentially pathogenic organisms were detected in all cigarette samples. Most notably, we detected Acinetobacter, Bacillus, Burkholderia, Clostridium, Klebsiella, Pseudomonas aeruginosa, and Serratia in > or = 90% of all cigarette samples. Other pathogenic bacteria detected included Campylobacter, Enterococcus, Proteus, and Staphylococcus. No significant variability in bacterial diversity was observed across the four different cigarette brands. CONCLUSIONS Previous studies have shown that smoking is associated with colonization by pathogenic bacteria and an increased risk of lung infections. However, this is the first study to show that cigarettes themselves could be the direct source of exposure to a wide array of potentially pathogenic microbes among smokers and other people exposed to secondhand smoke. The overall public health implications of these findings are unclear at this time, and future studies are necessary to determine whether bacteria in cigarettes could play important roles in the development of both infectious and chronic respiratory diseases.
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Affiliation(s)
- Amy R Sapkota
- Maryland Institute for Applied Environmental Health, University of Maryland College Park School of Public Health, College Park, Maryland, USA.
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Rudi K, Berg F, Gaustad E, Tannes T, Vatn M. Ratios between Alpha-, Beta- and Gamma-proteobacteria in tap water determined by the ProteoQuant assay. Lett Appl Microbiol 2010; 50:1-6. [DOI: 10.1111/j.1472-765x.2009.02743.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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Franke-Whittle IH, Goberna M, Pfister V, Insam H. Design and development of the ANAEROCHIP microarray for investigation of methanogenic communities. J Microbiol Methods 2009; 79:279-88. [DOI: 10.1016/j.mimet.2009.09.017] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2009] [Revised: 09/18/2009] [Accepted: 09/18/2009] [Indexed: 10/20/2022]
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Iwai S, Kurisu F, Urakawa H, Yagi O, Furumai H. Characterization of monooxygenase gene diversity in benzene-amended soils. Lett Appl Microbiol 2009; 50:138-45. [PMID: 19912525 DOI: 10.1111/j.1472-765x.2009.02764.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIM To understand soil benzene monooxygenase gene diversity by clone library construction and microarray profiling. METHODS AND RESULTS A primer set was designed, and benzene monooxygenase gene diversity was characterized in two benzene-amended soils. The dominant sequence types in the clone libraries were distinct between the two soils, and both sequences were assigned to novel clusters. Monooxygenase gene richness and diversity increased after benzene degradation. Oligonucleotide probes for microarray analysis were designed to detect a number of sequenced clones and reported monooxygenase genes. The microarray detected several genes that were not detected in the clone libraries of the same samples. Six probes were detected in more than one soil. CONCLUSIONS The primer set designed in this study successfully detected diverse benzene monooxygenase genes. The level of diversity may have increased because the degradation of benzene differed from soil to soil. Microarrays have great potential in the comprehensive detection of gene richness as well as the elucidation of key genes for degradation. SIGNIFICANCE AND IMPACT OF THE STUDY This study introduces a new primer set that may be used to identify diverse benzene monooxygenase genes in the environment; moreover, it demonstrates the potential of microarray technology in the profiling of environmental samples.
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Affiliation(s)
- S Iwai
- Department of Urban Engineering, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
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Sanguin H, Sarniguet A, Gazengel K, Moënne-Loccoz Y, Grundmann GL. Rhizosphere bacterial communities associated with disease suppressiveness stages of take-all decline in wheat monoculture. THE NEW PHYTOLOGIST 2009; 184:694-707. [PMID: 19732350 DOI: 10.1111/j.1469-8137.2009.03010.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The decline of take-all disease (Gaeumannomyces graminis var. tritici), which may take place during wheat monocropping, involves plant-protecting, root-colonizing microorganisms. So far, however, most work has focused on antagonistic fluorescent pseudomonads. Our objective was to assess the changes in rhizobacterial community composition during take-all decline of field-grown wheat. The study was based on the development and utilization of a taxonomic 16S rRNA-based microarray of 575 probes, coupled with cloning-sequencing and quantitative PCR. Plots from one experimental field grown with wheat for 1 yr (low level of disease), 5 yr (high level of disease) or 10 yr (low level of disease, suppressiveness reached) were used. Microarray data discriminated between the three stages. The outbreak stage (5 yr) was mainly characterized by the prevalence of Proteobacteria, notably Pseudomonas (Gammaproteobacteria), Nitrosospira (Betaproteobacteria), Rhizobacteriaceae, Sphingomonadaceae, Phyllobacteriaceae (Alphaproteobacteria), as well as Bacteroidetes and Verrucomicrobia. By contrast, suppressiveness (10 yr) correlated with the prevalence of a broader range of taxa, which belonged mainly to Acidobacteria, Planctomycetes, Nitrospira, Chloroflexi, Alphaproteobacteria (notably Azospirillum) and Firmicutes (notably Thermoanaerobacter). In conclusion, take-all decline correlated with multiple changes in rhizobacterial community composition, far beyond the sole case of pseudomonads.
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Affiliation(s)
- H Sanguin
- Université de Lyon, F-69003, Lyon, France
- Université Lyon 1, F-69003 Villeurbanne, France
- CNRS, UMR5557, Ecologie Microbienne, F-69622 Villeurbanne, France
| | - A Sarniguet
- INRA, Agrocampus Ouest, Université Rennes 1, UMR 1099 BiO3P 'Biologie des Organismes et des Populations appliquée à la Protection des Plantes', F-35653 Le Rheu, France
| | - K Gazengel
- INRA, Agrocampus Ouest, Université Rennes 1, UMR 1099 BiO3P 'Biologie des Organismes et des Populations appliquée à la Protection des Plantes', F-35653 Le Rheu, France
| | - Y Moënne-Loccoz
- Université de Lyon, F-69003, Lyon, France
- Université Lyon 1, F-69003 Villeurbanne, France
- CNRS, UMR5557, Ecologie Microbienne, F-69622 Villeurbanne, France
| | - G L Grundmann
- Université de Lyon, F-69003, Lyon, France
- Université Lyon 1, F-69003 Villeurbanne, France
- CNRS, UMR5557, Ecologie Microbienne, F-69622 Villeurbanne, France
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Kyselková M, Kopecký J, Frapolli M, Défago G, Ságová-Marecková M, Grundmann GL, Moënne-Loccoz Y. Comparison of rhizobacterial community composition in soil suppressive or conducive to tobacco black root rot disease. THE ISME JOURNAL 2009; 3:1127-38. [PMID: 19554036 DOI: 10.1038/ismej.2009.61] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Work on soils suppressive to Thielaviopsis basicola-mediated tobacco black root rot has focused on antagonistic pseudomonads to date. The role of non-Pseudomonas rhizosphere populations has been neglected, and whether they differ in black root rot-suppressive versus -conducive soils is unknown. To assess this possibility, tobacco was grown in a suppressive and a conducive soil of similar physicochemical properties, and rhizobacterial community composition was compared using a 16S rRNA taxonomic microarray. The microarray contains 1033 probes and targets 19 bacterial phyla. Among them, 398 probes were designed for Proteobacteria, Firmicutes, Actinomycetes, Cyanobacteria and Bacteroidetes genera/species known to include strains relevant for plant protection or plant growth promotion. Hierarchical clustering as well as principal component analysis of microarray data discriminated clearly between black root rot-suppressive and -conducive soils. In contrast, T. basicola inoculation had no impact on rhizobacterial community composition. In addition to fluorescent Pseudomonas, the taxa Azospirillum, Gluconacetobacter, Burkholderia, Comamonas and Sphingomonadaceae, which are known to comprise strains with plant-beneficial properties, were more prevalent in the suppressive soil. Mycobacterium, Bradyrhizobium, Rhodobacteraceae, Rhodospirillum and others were more prevalent in the conducive soil. For selected taxa, microarray results were largely corroborated by quantitative PCR and cloning/sequencing. In conclusion, this work identified novel bacterial taxa that could serve as indicators of disease suppressiveness in soil-quality assessments, and it extends the range of bacterial taxa hypothesized to participate in black root rot suppression.
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Duc L, Neuenschwander S, Rehrauer H, Wagner U, Sobek J, Schlapbach R, Zeyer J. Development and experimental validation of anifHoligonucleotide microarray to study diazotrophic communities in a glacier forefield. Environ Microbiol 2009; 11:2179-89. [DOI: 10.1111/j.1462-2920.2009.01945.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Persistent Wolbachia and cultivable bacteria infection in the reproductive and somatic tissues of the mosquito vector Aedes albopictus. PLoS One 2009; 4:e6388. [PMID: 19633721 PMCID: PMC2712238 DOI: 10.1371/journal.pone.0006388] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2009] [Accepted: 06/25/2009] [Indexed: 11/25/2022] Open
Abstract
Background Commensal and symbiotic microbes have a considerable impact on the behavior of many arthropod hosts, including hematophagous species that transmit pathogens causing infectious diseases to human and animals. Little is known about the bacteria associated with mosquitoes other than the vectorized pathogens. This study investigated Wolbachia and cultivable bacteria that persist through generations in Ae. albopictus organs known to host transmitted arboviruses, such as dengue and chikungunya. Methodology/Principal Findings We used culturing, diagnostic and quantitative PCR, as well as in situ hybridization, to detect and locate bacteria in whole individual mosquitoes and in dissected tissues. Wolbachia, cultivable bacteria of the genera Acinetobacter, Comamonas, Delftia and Pseudomonas co-occurred and persisted in the bodies of both males and females of Ae. albopictus initially collected in La Réunion during the chikungunya outbreak, and maintained as colonies in insectaries. In dissected tissues, Wolbachia and the cultivable Acinetobacter can be detected in the salivary glands. The other bacteria are commonly found in the gut. Quantitative PCR estimates suggest that Wolbachia densities are highest in ovaries, lower than those of Acinetobacter in the gut, and approximately equal to those of Acinetobacter in the salivary glands. Hybridization using specific fluorescent probes successfully localized Wolbachia in all germ cells, including the oocytes, and in the salivary glands, whereas the Acinetobacter hybridizing signal was mostly located in the foregut and in the anterior midgut. Conclusions/Significance Our results show that Proteobacteria are distributed in the somatic and reproductive tissues of mosquito where transmissible pathogens reside and replicate. This location may portend the coexistence of symbionts and pathogens, and thus the possibility that competition or cooperation phenomena may occur in the mosquito vector Ae. albopictus. Improved understanding of the vectorial system, including the role of bacteria in the vector's biology and competence, could have major implications for understanding viral emergences and for disease control.
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Schönmann S, Loy A, Wimmersberger C, Sobek J, Aquino C, Vandamme P, Frey B, Rehrauer H, Eberl L. 16S rRNA gene-based phylogenetic microarray for simultaneous identification of members of the genus Burkholderia. Environ Microbiol 2009; 11:779-800. [PMID: 19396938 DOI: 10.1111/j.1462-2920.2008.01800.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
For cultivation-independent and highly parallel analysis of members of the genus Burkholderia, an oligonucleotide microarray (phylochip) consisting of 131 hierarchically nested 16S rRNA gene-targeted oligonucleotide probes was developed. A novel primer pair was designed for selective amplification of a 1.3 kb 16S rRNA gene fragment of Burkholderia species prior to microarray analysis. The diagnostic performance of the microarray for identification and differentiation of Burkholderia species was tested with 44 reference strains of the genera Burkholderia, Pandoraea, Ralstonia and Limnobacter. Hybridization patterns based on presence/absence of probe signals were interpreted semi-automatically using the novel likelihood-based strategy of the web-tool Phylo- Detect. Eighty-eight per cent of the reference strains were correctly identified at the species level. The evaluated microarray was applied to investigate shifts in the Burkholderia community structure in acidic forest soil upon addition of cadmium, a condition that selected for Burkholderia species. The microarray results were in agreement with those obtained from phylogenetic analysis of Burkholderia 16S rRNA gene sequences recovered from the same cadmiumcontaminated soil, demonstrating the value of the Burkholderia phylochip for determinative and environmental studies.
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Affiliation(s)
- Susan Schönmann
- Institute of Plant Biology, Department of Microbiology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
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Composition of bacterial communities associated with natural and laboratory populations of Asobara tabida infected with Wolbachia. Appl Environ Microbiol 2009; 75:3755-64. [PMID: 19376923 DOI: 10.1128/aem.02964-08] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Asobara tabida wasps are fly endoparasitoids that naturally harbor three Wolbachia strains, which induce cytoplasmic incompatibility and control oogenesis. To investigate whether other bacteria play a role in wasp biology, we surveyed the bacterial communities of wild A. tabida populations originating from different regions of France and of laboratory colonies using PCR-denaturing gradient gel electrophoresis and culture methods. Proteobacteria and Firmicutes were found to be the main phyla represented in these populations. Among these were several cultured and uncultured representatives of the genera Acetobacter, Acidomonas, Bacillus, Brevibacillus, Duganella, Herbaspirillum, Pseudomonas, Staphylococcus, and Streptococcus. In addition to Wolbachia, wild individuals harbored Rickettsia, which tended to be lost when insects were reared in the laboratory. The antibiotic treatment used to generate wasp sublines singly infected with Wolbachia also affected the overall bacterial composition, with most fingerprint sequences being characteristic of the family Enterobacteriaceae. We also screened for potentially heritable endosymbionts by PCR and fluorescence in situ hybridization in stable laboratory lines, with only Wolbachia being consistently found in wasp ovaries.
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Franke-Whittle IH, Knapp BA, Fuchs J, Kaufmann R, Insam H. Application of COMPOCHIP microarray to investigate the bacterial communities of different composts. MICROBIAL ECOLOGY 2009; 57:510-521. [PMID: 18818861 DOI: 10.1007/s00248-008-9435-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2008] [Accepted: 07/31/2008] [Indexed: 05/26/2023]
Abstract
A microarray spotted with 369 different 16S rRNA gene probes specific to microorganisms involved in the degradation process of organic waste during composting was developed. The microarray was tested with pure cultures, and of the 30,258 individual probe-target hybridization reactions performed, there were only 188 false positive (0.62%) and 22 false negative signals (0.07%). Labeled target DNA was prepared by polymerase chain reaction amplification of 16S rRNA genes using a Cy5-labeled universal bacterial forward primer and a universal reverse primer. The COMPOCHIP microarray was applied to three different compost types (green compost, manure mix compost, and anaerobic digestate compost) of different maturity (2, 8, and 16 weeks), and differences in the microorganisms in the three compost types and maturity stages were observed. Multivariate analysis showed that the bacterial composition of the three composts was different at the beginning of the composting process and became more similar upon maturation. Certain probes (targeting Sphingobacterium, Actinomyces, Xylella/Xanthomonas/Stenotrophomonas, Microbacterium, Verrucomicrobia, Planctomycetes, Low G + C and Alphaproteobacteria) were more influential in discriminating between different composts. Results from denaturing gradient gel electrophoresis supported those of microarray analysis. This study showed that the COMPOCHIP array is a suitable tool to study bacterial communities in composts.
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Ward BB. PHYTOPLANKTON COMMUNITY COMPOSITION AND GENE EXPRESSION OF FUNCTIONAL GENES INVOLVED IN CARBON AND NITROGEN ASSIMILATION(1). JOURNAL OF PHYCOLOGY 2008; 44:1490-1503. [PMID: 27039863 DOI: 10.1111/j.1529-8817.2008.00594.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A functional gene microarray was developed and used to investigate phytoplankton community composition and gene expression in the English Channel. Genes encoding the CO2 -fixation enzyme RUBISCO (rbcL) and the nitrate assimilation enzyme nitrate reductase (NR) representing several major groups of phytoplankton were included as oligonucleotide probes on the "phytoarray." Five major groups of eukaryotic phytoplankton that possess the Type 1D rbcL gene were detected, both in terms of presence (DNA) and activity (rbcL gene expression). Changes in relative signal intensity among the Type 1D rbcL probes indicated a shift from diatom dominance in the spring bloom to dominance by haptophytes and flagellates later in the summer. Because of the limitations of a smaller database, NR probes detected fewer groups, but due to the greater diversity among known NR sequences, NR probes provided higher phylogenetic resolution than did rbcL probes and identified two uncultivated diatom phylotypes as the most abundant (DNA) and active (NR gene expression) in field samples. Unidentified chlorophytes and the diatom Phaeodactylum tricornutum Bohlin were detected at both the DNA and cDNA (gene expression) levels. The reproducibility of the array was evaluated in several ways, and future directions for further improvement of probe development and sensitivity are outlined. The phytoarray provides a relatively high-resolution, high-throughput approach to assessing phytoplankton community composition in marine environments.
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Affiliation(s)
- B B Ward
- Department of Geosciences, Princeton University, Princeton, New Jersey 08544, USA
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Aittamaa M, Somervuo P, Pirhonen M, Mattinen L, Nissinen R, Auvinen P, Valkonen JPT. Distinguishing bacterial pathogens of potato using a genome-wide microarray approach. MOLECULAR PLANT PATHOLOGY 2008; 9:705-17. [PMID: 19018999 PMCID: PMC6640225 DOI: 10.1111/j.1364-3703.2008.00482.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
A set of 9676 probes was designed for the most harmful bacterial pathogens of potato and tested in a microarray format. Gene-specific probes could be designed for all genes of Pectobacterium atrosepticum, c. 50% of the genes of Streptomyces scabies and c. 30% of the genes of Clavibacter michiganensis ssp. sepedonicus utilizing the whole-genome sequence information available. For Streptomyces turgidiscabies, 226 probes were designed according to the sequences of a pathogenicity island containing important virulence genes. In addition, probes were designed for the virulence-associated nip (necrosis-inducing protein) genes of P. atrosepticum, P. carotovorum and Dickeya dadantii and for the intergenic spacer (IGS) sequences of the 16S-23S rRNA gene region. Ralstonia solanacearum was not included in the study, because it is a quarantine organism and is not presently found in Finland, but a few probes were also designed for this species. The probes contained on average 40 target-specific nucleotides and were synthesized on the array in situ, organized as eight sub-arrays with an identical set of probes which could be used for hybridization with different samples. All bacteria were readily distinguished using a single channel system for signal detection. Nearly all of the c. 1000 probes designed for C. michiganensis ssp. sepedonicus, c. 50% and 40% of the c. 4000 probes designed for the genes of S. scabies and P. atrosepticum, respectively, and over 100 probes for S. turgidiscabies showed significant signals only with the respective species. P. atrosepticum, P. carotovorum and Dickeya strains were all detected with 110 common probes. By contrast, the strains of these species were found to differ in their signal profiles. Probes targeting the IGS region and nip genes could be used to place strains of Dickeya to two groups, which correlated with differences in virulence. Taken together, the approach of using a custom-designed, genome-wide microarray provided a robust means for distinguishing the bacterial pathogens of potato.
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Affiliation(s)
- M Aittamaa
- Department of Applied Biology, PO Box 27, FIN-00014 University of Helsinki, Finland
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Rehrauer H, Schonmann S, Eberl L, Schlapbach R. PhyloDetect: a likelihood-based strategy for detecting microorganisms with diagnostic microarrays. Bioinformatics 2008; 24:i83-9. [DOI: 10.1093/bioinformatics/btn269] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Loy A, Arnold R, Tischler P, Rattei T, Wagner M, Horn M. probeCheck--a central resource for evaluating oligonucleotide probe coverage and specificity. Environ Microbiol 2008; 10:2894-8. [PMID: 18647333 PMCID: PMC2613240 DOI: 10.1111/j.1462-2920.2008.01706.x] [Citation(s) in RCA: 162] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The web server probeCheck, freely accessible at http://www.microbial-ecology.net/probecheck, provides a pivotal forum for rapid specificity and coverage evaluations of probes and primers against selected databases of phylogenetic and functional marker genes. Currently, 24 widely used sequence collections including the Ribosomal Database Project (RDP) II, Greengenes, SILVA and the Functional Gene Pipeline/Repository can be queried. For this purpose, probeCheck integrates a new online version of the popular ARB probe match tool with free energy (ΔG) calculations for each perfectly matched and mismatched probe-target hybrid, allowing assessment of the theoretical binding stabilities of oligo-target and non-target hybrids. For each output sequence, the accession number, the GenBank taxonomy and a link to the respective entry at GenBank, EMBL and, if applicable, the query database are displayed. Filtering options allow customizing results on the output page. In addition, probeCheck is linked with probe match tools of RDP II and Greengenes, NCBI blast, the Oligonucleotide Properties Calculator, the two-state folding tool of the DINAMelt server and the rRNA-targeted probe database probeBase. Taken together, these features provide a multifunctional platform with maximal flexibility for the user in the choice of databases and options for the evaluation of published and newly developed probes and primers.
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Affiliation(s)
- Alexander Loy
- Department of Microbial Ecology, Universität Wien, Althanstrasse 14, A-1090 Wien, Austria
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Development of a 16S rRNA gene-based prototype microarray for the detection of selected actinomycetes genera. Antonie van Leeuwenhoek 2008; 94:439-53. [PMID: 18600470 DOI: 10.1007/s10482-008-9261-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2008] [Accepted: 06/05/2008] [Indexed: 10/21/2022]
Abstract
Actinomycetes are known for their secondary metabolites, which have been successfully used as drugs in human and veterinary medicines. However, information on the distribution of this group of Gram-positive bacteria in diverse ecosystems and a comprehension of their activities in ecosystem processes are still scarce. We have developed a 16S rRNA-based taxonomic microarray that targets key actinomycetes at the genus level. In total, 113 actinomycete 16S rRNA probes, corresponding to 55 of the 202 described genera, were designed. The microarray accuracy was evaluated by comparing signal intensities with probe/target-weighted mismatch values and the Gibbs energy of the probe/target duplex formation by hybridizing 17 non-actinomycete and 29 actinomycete strains/clones with the probe set. The validation proved that the probe set was specific, with only 1.3% of false results. The incomplete coverage of actinomycetes by a genus-specific probe was caused by the limited number of 16S rRNA gene sequences in databases or insufficient 16S rRNA gene polymorphism. The microarray enabled discrimination between actinomycete communities from three forest soil samples collected at one site. Cloning and sequencing of 16S rRNA genes from one of the soil samples confirmed the microarray results. We propose that this newly constructed microarray will be a valuable tool for genus-level comparisons of actinomycete communities in various ecological conditions.
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Frapolli M, Moënne-Loccoz Y, Meyer J, Défago G. A new DGGE protocol targeting 2,4-diacetylphloroglucinol biosynthetic gene phlD from phylogenetically contrasted biocontrol pseudomonads for assessment of disease-suppressive soils. FEMS Microbiol Ecol 2008; 64:468-81. [PMID: 18393988 DOI: 10.1111/j.1574-6941.2008.00471.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
In the rhizosphere, biocontrol pseudomonads producing 2,4-diacetylphloroglucinol (Phl) can protect plants from soil-borne pathogens. DGGE of phlD has been proposed to monitor these bacteria, but two distinct protocols were needed for analysis of both the 'Pseudomonas fluorescens' species complex and the strains from rrs restriction group ARDRA-1. Here, a single DGGE protocol performed on 668-bp GC-clamp-containing phlD amplicons was effective with both types of pseudomonads, and 36 reference biocontrol strains from the 'P. fluorescens' complex or group ARDRA-1 gave a total of 11 distinct DGGE bands. phlD amplicons with at least two to seven nucleotidic differences could be discriminated, and the discrimination level was similar to that of phlD restriction analysis with four enzymes. Multiple phlD-DGGE bands were obtained when studying rhizosphere soil containing indigenous phlD+ pseudomonads, and phlD diversity was higher when DGGE was implemented after incubation of tobacco rhizosphere extracts in semi-selective medium (MPN approach) in comparison with approaches based on direct analysis of rhizosphere DNA extracts or assessment of phlD+colonies. phlD-DGGE profiles differed for a soil suppressive and a soil conducive to black root rot of tobacco, and each soil yielded new phlD sequences. In conclusion, this DGGE protocol was useful for monitoring indigenous rhizosphere consortia of phlD+ pseudomonads.
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Affiliation(s)
- Michele Frapolli
- Plant Pathology Group, Institute of Integrative Biology, Swiss Federal Institute of Technology (ETH), Zurich, Switzerland
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Ludwig W. Reprint of “Nucleic acid techniques in bacterial systematics and identification" [Int. J. Food Microbiol., 120 (2007) 225–236]. Int J Food Microbiol 2008; 125:I-XII. [DOI: 10.1016/s0168-1605(08)00293-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2007] [Revised: 05/08/2007] [Accepted: 06/04/2007] [Indexed: 10/22/2022]
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