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Zhang Y, Ma J, O'Connor P, Zhu YG. Microbial communities on biodegradable plastics under different fertilization practices in farmland soil microcosms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 809:152184. [PMID: 34890659 DOI: 10.1016/j.scitotenv.2021.152184] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/28/2021] [Accepted: 11/30/2021] [Indexed: 06/13/2023]
Abstract
Plastic mulching is a common practice in agricultural systems and is often combined with fertilization. Biodegradable plastics (BPs) are becoming an alternative to non-biodegradable plastics (non-BPs) for soil mulching. However, the effects of fertilization on the microbial communities on BPs remain unclear. Here, we explored the responses of the plastisphere to different fertilization practices in soil-based microcosms containing three BPs: polylactic acid (PLA), poly (butylene succinate) (PBS), and poly (butylene-adipate-co-terephthalate) (PBAT), and one non-BP (low-density polyethylene, LDPE). The 16S and ITS rRNA gene-based Illumina sequencing method were used to identify the bacterial and fungal communities on the plastics and in the soils. Microbial community structure on BPs was significantly different from that in soils and on LDPE. The predicted functional profiles of bacteria on BPs, especially PBAT, were distinct from those in soils. The plastisphere communities on BPs were dominated by microbes adapted to access and utilize carbon sources compared with of the communities on LDPE. Application of manure increased the alpha diversity of bacterial communities on BPs but decreased it on LDPE. The structure of bacterial communities on BPs changed with the application of manure. Our research establishes the baseline dynamics of plastisphere communities on BPs in soils.
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Affiliation(s)
- Yu Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Ma
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, Ningbo Urban Environment Observation and Research Station-NUEORS, Institute of Urban Environment, Chinese Academy of Sciences, Ningbo 315800, China.
| | - Patrick O'Connor
- Centre for Global Food and Resources, University of Adelaide, Adelaide 5005, Australia
| | - Yong-Guan Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
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Abstract
Manganese is among Earth’s most abundant elements. Its oxidation had long been theorized1, yet undemonstrated2–4, to fuel chemolithoautotrophic microbial growth. Here, an enrichment culture exhibiting Mn(II)-oxidation-dependent, exponential growth was refined to a two species co-culture. Oxidation required viable bacteria at permissive temperatures, resulting in the generation of small Mn oxide nodules to which the cells associated. The majority member of the culture, ‘Candidatus Manganitrophus noduliformans’, affiliates within phylum Nitrospirae (Nitrospirota) but is distantly related to known Nitrospira and Leptospirillum species. The minority member has been isolated, but does not oxidise Mn(II) alone. Stable isotope probing revealed Mn(II)-oxidation-dependent, 13CO2-fixation into cellular biomass. Transcriptomics reveals candidate pathways for coupling extracellular manganese oxidation to aerobic energy conservation and to autotrophic CO2-fixation. These findings expand the known diversity of inorganic metabolisms supporting life, while completing a biogeochemical energy cycle for manganese5,6, one that may interface with other major global elemental cycles.
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A selective genome-guided method for environmental Burkholderia isolation. J Ind Microbiol Biotechnol 2019; 46:345-362. [PMID: 30680473 DOI: 10.1007/s10295-018-02121-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 12/19/2018] [Indexed: 12/31/2022]
Abstract
The genus Burkholderia is an emerging source of novel natural products chemistry, yet to date few methods exist for the selective isolation of strains of this genus from the environment. More broadly, tools to efficiently design selection media for any given genus would be of significant value to the natural products and microbiology communities. Using a modification of the recently published SMART protocol, we have developed a two-stage isolation protocol for strains from the genus Burkholderia. This method uses a combination of selective agar isolation media and multiplexed PCR profiling to derive Burkholderia strains from environmental samples with 95% efficiency. Creation of this new method paves the way for the systematic exploration of natural products chemistry from this important genus and offers new insight into potential methods for selective isolation method development for other priority genera.
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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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Greuter D, Loy A, Horn M, Rattei T. probeBase--an online resource for rRNA-targeted oligonucleotide probes and primers: new features 2016. Nucleic Acids Res 2016; 44:D586-9. [PMID: 26586809 PMCID: PMC4702872 DOI: 10.1093/nar/gkv1232] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 10/27/2015] [Accepted: 10/30/2015] [Indexed: 12/29/2022] Open
Abstract
probeBase http://www.probebase.net is a manually maintained and curated database of rRNA-targeted oligonucleotide probes and primers. Contextual information and multiple options for evaluating in silico hybridization performance against the most recent rRNA sequence databases are provided for each oligonucleotide entry, which makes probeBase an important and frequently used resource for microbiology research and diagnostics. Here we present a major update of probeBase, which was last featured in the NAR Database Issue 2007. This update describes a complete remodeling of the database architecture and environment to accommodate computationally efficient access. Improved search functions, sequence match tools and data output now extend the opportunities for finding suitable hierarchical probe sets that target an organism or taxon at different taxonomic levels. To facilitate the identification of complementary probe sets for organisms represented by short rRNA sequence reads generated by amplicon sequencing or metagenomic analysis with next generation sequencing technologies such as Illumina and IonTorrent, we introduce a novel tool that recovers surrogate near full-length rRNA sequences for short query sequences and finds matching oligonucleotides in probeBase.
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Affiliation(s)
- Daniel Greuter
- Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, A-1090 Wien, Austria
| | - Alexander Loy
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, A-1090 Wien, Austria
| | - Matthias Horn
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, A-1090 Wien, Austria
| | - Thomas Rattei
- Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, A-1090 Wien, Austria
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6
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Tago K, Okubo T, Itoh H, Kikuchi Y, Hori T, Sato Y, Nagayama A, Hayashi K, Ikeda S, Hayatsu M. Insecticide-degrading Burkholderia symbionts of the stinkbug naturally occupy various environments of sugarcane fields in a Southeast island of Japan. Microbes Environ 2014; 30:29-36. [PMID: 25736865 PMCID: PMC4356461 DOI: 10.1264/jsme2.me14124] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 10/11/2014] [Indexed: 11/16/2022] Open
Abstract
The stinkbug Cavelerius saccharivorus, which harbors Burkholderia species capable of degrading the organophosphorus insecticide, fenitrothion, has been identified on a Japanese island in farmers' sugarcane fields that have been exposed to fenitrothion. A clearer understanding of the ecology of the symbiotic fenitrothion degraders of Burkholderia species in a free-living environment is vital for advancing our knowledge on the establishment of degrader-stinkbug symbiosis. In the present study, we analyzed the composition and abundance of degraders in sugarcane fields on the island. Degraders were recovered from field samples without an enrichment culture procedure. Degrader densities in the furrow soil in fields varied due to differences in insecticide treatment histories. Over 99% of the 659 isolated degraders belonged to the genus Burkholderia. The strains related to the stinkbug symbiotic group predominated among the degraders, indicating a selection for this group in response to fenitrothion. Degraders were also isolated from sugarcane stems, leaves, and rhizosphere in fields that were continuously exposed to fenitrothion. Their density was lower in the plant sections than in the rhizosphere. A phylogenetic analysis of 16S rRNA gene sequences demonstrated that most of the degraders from the plants and rhizosphere clustered with the stinkbug symbiotic group, and some were identical to the midgut symbionts of C. saccharivorus collected from the same field. Our results confirmed that plants and the rhizosphere constituted environmental reservoirs for stinkbug symbiotic degraders. To the best of our knowledge, this is the first study to investigate the composition and abundance of the symbiotic fenitrothion degraders of Burkholderia species in farmers' fields.
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Affiliation(s)
- Kanako Tago
- Environmental Biofunction Division, National Institute for Agro-Environmental Sciences3–1–3 Kannondai, Tsukuba, Ibaraki 305–8604Japan
| | - Takashi Okubo
- Environmental Biofunction Division, National Institute for Agro-Environmental Sciences3–1–3 Kannondai, Tsukuba, Ibaraki 305–8604Japan
| | - Hideomi Itoh
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) Hokkaido2–17–2–1 Tsukisamu-higashi, Toyohira-ku, Sapporo, Hokkaido 062–8517Japan
| | - Yoshitomo Kikuchi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) Hokkaido2–17–2–1 Tsukisamu-higashi, Toyohira-ku, Sapporo, Hokkaido 062–8517Japan
| | - Tomoyuki Hori
- Research Institute for Environmental Management Technology, AISTTsukuba, Ibaraki 305–8569Japan
| | - Yuya Sato
- Research Institute for Environmental Management Technology, AISTTsukuba, Ibaraki 305–8569Japan
| | - Atsushi Nagayama
- Okinawa Prefectural Agricultural Research CenterItoman, Okinawa 901–0336Japan
| | - Kentaro Hayashi
- Environmental Biofunction Division, National Institute for Agro-Environmental Sciences3–1–3 Kannondai, Tsukuba, Ibaraki 305–8604Japan
| | - Seishi Ikeda
- Memuro Research Station, Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization9–4 Shinsei Minami, Memuro-cho, Kasai-gun, Hokkaido 082–0081Japan
| | - Masahito Hayatsu
- Environmental Biofunction Division, National Institute for Agro-Environmental Sciences3–1–3 Kannondai, Tsukuba, Ibaraki 305–8604Japan
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7
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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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8
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Bragina A, Cardinale M, Berg C, Berg G. Vertical transmission explains the specific Burkholderia pattern in Sphagnum mosses at multi-geographic scale. Front Microbiol 2013; 4:394. [PMID: 24391630 PMCID: PMC3866706 DOI: 10.3389/fmicb.2013.00394] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 12/03/2013] [Indexed: 11/13/2022] Open
Abstract
The betaproteobacterial genus Burkholderia is known for its versatile interactions with its hosts that can range from beneficial to pathogenic. A plant-beneficial-environmental (PBE) Burkholderia cluster was recently separated from the pathogen cluster, yet still little is known about burkholderial diversity, distribution, colonization, and transmission patterns on plants. In our study, we applied a combination of high-throughput molecular and microscopic methods to examine the aforementioned factors for Burkholderia communities associated with Sphagnum mosses - model plants for long-term associations - in Austrian and Russian bogs. Analysis of 16S rRNA gene amplicons libraries revealed that most of the Burkholderia are part of the PBE group, but a minor fraction was closely related to B. glathei and B. andropogonis from the pathogen cluster. Notably, Burkholderia showed highly similar composition patterns for each moss species independent of the geographic region, and Burkholderia-specific fluorescent in situ hybridization of Sphagnum gametophytes exhibited similar colonization patterns in different Sphagnum species at multi-geographic scales. To explain these patterns, we compared the compositions of the surrounding water, gametophyte-, and sporophyte-associated microbiome at genus level and discovered that Burkholderia were present in the Sphagnum sporophyte and gametophyte, but were absent in the flark water. Therefore, Burkholderia is a part of the core microbiome transmitted from the moss sporophyte to the gametophyte. This suggests a vertical transmission of Burkholderia strains, and thus underlines their importance for the plants themselves.
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Affiliation(s)
- Anastasia Bragina
- Institute of Environmental Biotechnology, Graz University of TechnologyGraz, Austria
| | - Massimiliano Cardinale
- Institute of Environmental Biotechnology, Graz University of TechnologyGraz, Austria
- Institute of Plant Sciences, Karl-Franzens University of GrazGraz, Austria
| | - Christian Berg
- Institute of Plant Sciences, Karl-Franzens University of GrazGraz, Austria
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of TechnologyGraz, Austria
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9
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Stopnisek N, Bodenhausen N, Frey B, Fierer N, Eberl L, Weisskopf L. Genus-wide acid tolerance accounts for the biogeographical distribution of soil Burkholderia populations. Environ Microbiol 2013; 16:1503-12. [PMID: 23945027 DOI: 10.1111/1462-2920.12211] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 07/04/2013] [Accepted: 07/10/2013] [Indexed: 11/30/2022]
Abstract
Bacteria belonging to the genus Burkholderia are highly versatile with respect to their ecological niches and lifestyles, ranging from nodulating tropical plants to causing melioidosis and fatal infections in cystic fibrosis patients. Despite the clinical importance and agronomical relevance of Burkholderia species, information about the factors influencing their occurrence, abundance and diversity in the environment is scarce. Recent findings have demonstrated that pH is the main predictor of soil bacterial diversity and community structure, with the highest diversity observed in neutral pH soils. As many Burkholderia species have been isolated from low pH environments, we hypothesized that acid tolerance may be a general feature of this genus, and pH a good predictor of their occurrence in soils. Using a combination of environmental surveys at trans-continental and local scales, as well as in vitro assays, we show that, unlike most bacteria, Burkholderia species have a competitive advantage in acidic soils, but are outcompeted in alkaline soils. Physiological assays and diversity analysis based on 16S rRNA clone libraries demonstrate that pH tolerance is a general phenotypic trait of the genus Burkholderia. Our results provide a basis for building a predictive understanding of the biogeographical patterns exhibited by Burkholderia sp.
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Affiliation(s)
- Nejc Stopnisek
- Institute of Plant Biology, University of Zurich, Zürich, CH-8008, Switzerland; Swiss Federal Research Station for Agronomy and Nature, Agroscope Reckenholz-Tänikon, Zürich, CH-8046, Switzerland
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10
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Schwager S, Lumjiaktase P, Stöckli M, Weisskopf L, Eberl L. The genetic basis of cadmium resistance of Burkholderia cenocepacia. ENVIRONMENTAL MICROBIOLOGY REPORTS 2012; 4:562-568. [PMID: 23760902 DOI: 10.1111/j.1758-2229.2012.00372.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Revised: 07/13/2012] [Accepted: 07/16/2012] [Indexed: 06/02/2023]
Abstract
Burkholderia species are highly resistant to heavy metals (HMs), yet their resistance mechanisms are largely unknown. In this study we screened 5000 mini-Tn5 transposon insertion mutants of Burkholderia cenocepacia H111 for loss of cadmium tolerance. Of the four genes identified three affected outer membrane biogenesis and integrity or DNA repair. The fourth gene, BCAE0587, encoded a P1-type ATPase belonging to the CadA family of HM exporters. CadA-deficient strains lost the ability to grow in the presence of cadmium, zinc and lead, whereas resistance to nickel, copper and cobalt was not affected. Expression studies using a transcriptional fusion of the cadA promoter to gfp confirmed this specificity, as induction was only observed in presence of cadmium, zinc and lead. The promoter activity was found to be highest at neutral pH with an activation threshold of 30 nM cadmium. Inoculation of the HM-hyperaccumulating plant Arabidopsis halleri with a RFP-marked derivative of B. cenocepacia H111 containing the PcadA -gfp fusion demonstrated the applicability of this biosensor for monitoring cadmium at the single cell level in a natural environment.
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Affiliation(s)
- Stephan Schwager
- Department of Microbiology, Institute of Plant Biology, University of Zurich, Zurich, Switzerland
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11
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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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12
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Dugat-Bony E, Peyretaillade E, Parisot N, Biderre-Petit C, Jaziri F, Hill D, Rimour S, Peyret P. Detecting unknown sequences with DNA microarrays: explorative probe design strategies. Environ Microbiol 2011; 14:356-71. [PMID: 21895914 DOI: 10.1111/j.1462-2920.2011.02559.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Designing environmental DNA microarrays that can be used to survey the extreme diversity of microorganisms existing in nature, represents a stimulating challenge in the field of molecular ecology. Indeed, recent efforts in metagenomics have produced a substantial amount of sequence information from various ecosystems, and will continue to accumulate large amounts of sequence data given the qualitative and quantitative improvements in the next-generation sequencing methods. It is now possible to take advantage of these data to develop comprehensive microarrays by using explorative probe design strategies. Such strategies anticipate genetic variations and thus are able to detect known and unknown sequences in environmental samples. In this review, we provide a detailed overview of the probe design strategies currently available to construct both phylogenetic and functional DNA microarrays, with emphasis on those permitting the selection of such explorative probes. Furthermore, exploration of complex environments requires particular attention on probe sensitivity and specificity criteria. Finally, these innovative probe design approaches require exploiting newly available high-density microarray formats.
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Affiliation(s)
- Eric Dugat-Bony
- Clermont Université, Université Blaise Pascal, Laboratoire Microorganismes: Génome et Environnement, Clermont-Ferrand, France
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13
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Eissler T, Hodges CP, Meier H. PTPan--overcoming memory limitations in oligonucleotide string matching for primer/probe design. ACTA ACUST UNITED AC 2011; 27:2797-805. [PMID: 21856736 DOI: 10.1093/bioinformatics/btr483] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
MOTIVATION Nucleic acid diagnostics has high demands for non-heuristic exact and approximate oligonucleotide string matching concerning in silico primer/probe design in huge nucleic acid sequence collections. Unfortunately, public sequence repositories grow much faster than computer hardware performance and main memory capacity do. This growth imposes severe problems on existing oligonucleotide primer/probe design applications necessitating new approaches based on space-efficient indexing structures. RESULTS We developed PTPan (spoken Peter Pan, 'PT' is for Position Tree, the earlier name of suffix trees), a space-efficient indexing structure for approximate oligonucleotide string matching in nucleic acid sequence data. Based on suffix trees, it combines partitioning, truncation and a new suffix tree stream compression to deal with large amounts of aligned and unaligned data. PTPan operates efficiently in main memory and on secondary storage, balancing between memory consumption and runtime during construction and application. Based on PTPan, applications supporting similarity search and primer/probe design have been implemented, namely FindFamily, ProbeMatch and ProbeDesign. All three use a weighted Levenshtein distance metric for approximative queries to find and rate matches with indels as well as substitutions. We integrated PTPan in the worldwide used software package ARB to demonstrate usability and performance. Comparing PTPan and the original ARB index for the very large ssu-rRNA database SILVA, we recognized a shorter construction time, extended functionality and dramatically reduced memory requirements at the price of expanded, but very reasonable query times. PTPan enables indexing of huge nucleic acid sequence collections at reasonable application response times. Not being limited by main memory, PTPan constitutes a major advancement regarding rapid oligonucleotide string matching in primer/probe design now and in the future facing the enormous growth of molecular sequence data. AVAILABILITY Supplementary Material, PTPan stand-alone library and ARB-PTPan binary on http://ptpan.lrr.in.tum.de/. CONTACT meierh@in.tum.de SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Tilo Eissler
- Department of Informatics, Technische Universität München, Boltzmannstrasse 3, 85748 Garching, Germany
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14
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Steger D, Berry D, Haider S, Horn M, Wagner M, Stocker R, Loy A. Systematic spatial bias in DNA microarray hybridization is caused by probe spot position-dependent variability in lateral diffusion. PLoS One 2011; 6:e23727. [PMID: 21858215 PMCID: PMC3157431 DOI: 10.1371/journal.pone.0023727] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2011] [Accepted: 07/26/2011] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The hybridization of nucleic acid targets with surface-immobilized probes is a widely used assay for the parallel detection of multiple targets in medical and biological research. Despite its widespread application, DNA microarray technology still suffers from several biases and lack of reproducibility, stemming in part from an incomplete understanding of the processes governing surface hybridization. In particular, non-random spatial variations within individual microarray hybridizations are often observed, but the mechanisms underpinning this positional bias remain incompletely explained. METHODOLOGY/PRINCIPAL FINDINGS This study identifies and rationalizes a systematic spatial bias in the intensity of surface hybridization, characterized by markedly increased signal intensity of spots located at the boundaries of the spotted areas of the microarray slide. Combining observations from a simplified single-probe block array format with predictions from a mathematical model, the mechanism responsible for this bias is found to be a position-dependent variation in lateral diffusion of target molecules. Numerical simulations reveal a strong influence of microarray well geometry on the spatial bias. CONCLUSIONS Reciprocal adjustment of the size of the microarray hybridization chamber to the area of surface-bound probes is a simple and effective measure to minimize or eliminate the diffusion-based bias, resulting in increased uniformity and accuracy of quantitative DNA microarray hybridization.
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Affiliation(s)
- Doris Steger
- Department of Microbial Ecology, Vienna Ecology Center, Faculty of Life Sciences, University of Vienna, Wien, Austria
| | - David Berry
- Department of Microbial Ecology, Vienna Ecology Center, Faculty of Life Sciences, University of Vienna, Wien, Austria
| | - Susanne Haider
- Department of Microbial Ecology, Vienna Ecology Center, Faculty of Life Sciences, University of Vienna, Wien, Austria
| | - Matthias Horn
- Department of Microbial Ecology, Vienna Ecology Center, Faculty of Life Sciences, University of Vienna, Wien, Austria
| | - Michael Wagner
- Department of Microbial Ecology, Vienna Ecology Center, Faculty of Life Sciences, University of Vienna, Wien, Austria
| | - Roman Stocker
- Ralph M. Parsons Laboratory, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Alexander Loy
- Department of Microbial Ecology, Vienna Ecology Center, Faculty of Life Sciences, University of Vienna, Wien, Austria
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15
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Bader KC, Grothoff C, Meier H. Comprehensive and relaxed search for oligonucleotide signatures in hierarchically clustered sequence datasets. Bioinformatics 2011; 27:1546-54. [PMID: 21471017 DOI: 10.1093/bioinformatics/btr161] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION PCR, hybridization, DNA sequencing and other important methods in molecular diagnostics rely on both sequence-specific and sequence group-specific oligonucleotide primers and probes. Their design depends on the identification of oligonucleotide signatures in whole genome or marker gene sequences. Although genome and gene databases are generally available and regularly updated, collections of valuable signatures are rare. Even for single requests, the search for signatures becomes computationally expensive when working with large collections of target (and non-target) sequences. Moreover, with growing dataset sizes, the chance of finding exact group-matching signatures decreases, necessitating the application of relaxed search methods. The resultant substantial increase in complexity is exacerbated by the dearth of algorithms able to solve these problems efficiently. RESULTS We have developed CaSSiS, a fast and scalable method for computing comprehensive collections of sequence- and sequence group-specific oligonucleotide signatures from large sets of hierarchically clustered nucleic acid sequence data. Based on the ARB Positional Tree (PT-)Server and a newly developed BGRT data structure, CaSSiS not only determines sequence-specific signatures and perfect group-covering signatures for every node within the cluster (i.e. target groups), but also signatures with maximal group coverage (sensitivity) within a user-defined range of non-target hits (specificity) for groups lacking a perfect common signature. An upper limit of tolerated mismatches within the target group, as well as the minimum number of mismatches with non-target sequences, can be predefined. Test runs with one of the largest phylogenetic gene sequence datasets available indicate good runtime and memory performance, and in silico spot tests have shown the usefulness of the resulting signature sequences as blueprints for group-specific oligonucleotide probes. AVAILABILITY Software and Supplementary Material are available at http://cassis.in.tum.de/.
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Affiliation(s)
- Kai Christian Bader
- Services Department of Informatics, Technische Universität München, Boltzmannstrasse 3, 85748 Garching, Germany
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Huang YJ, Nelson CE, Brodie EL, Desantis TZ, Baek MS, Liu J, Woyke T, Allgaier M, Bristow J, Wiener-Kronish JP, Sutherland ER, King TS, Icitovic N, Martin RJ, Calhoun WJ, Castro M, Denlinger LC, Dimango E, Kraft M, Peters SP, Wasserman SI, Wechsler ME, Boushey HA, Lynch SV. Airway microbiota and bronchial hyperresponsiveness in patients with suboptimally controlled asthma. J Allergy Clin Immunol 2010; 127:372-381.e1-3. [PMID: 21194740 DOI: 10.1016/j.jaci.2010.10.048] [Citation(s) in RCA: 515] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2010] [Revised: 10/08/2010] [Accepted: 10/27/2010] [Indexed: 02/01/2023]
Abstract
BACKGROUND Improvement in lung function after macrolide antibiotic therapy has been attributed to reduction in bronchial infection by specific bacteria. However, the airway might be populated by a more diverse microbiota, and clinical features of asthma might be associated with characteristics of the airway microbiota present. OBJECTIVE We sought to determine whether relationships exist between the composition of the airway bacterial microbiota and clinical features of asthma using culture-independent tools capable of detecting the presence and relative abundance of most known bacteria. METHODS In this pilot study bronchial epithelial brushings were collected from 65 adults with suboptimally controlled asthma participating in a multicenter study of the effects of clarithromycin on asthma control and 10 healthy control subjects. A combination of high-density 16S ribosomal RNA microarray and parallel clone library-sequencing analysis was used to profile the microbiota and examine relationships with clinical measurements. RESULTS Compared with control subjects, 16S ribosomal RNA amplicon concentrations (a proxy for bacterial burden) and bacterial diversity were significantly higher among asthmatic patients. In multivariate analyses airway microbiota composition and diversity were significantly correlated with bronchial hyperresponsiveness. Specifically, the relative abundance of particular phylotypes, including members of the Comamonadaceae, Sphingomonadaceae, Oxalobacteraceae, and other bacterial families were highly correlated with the degree of bronchial hyperresponsiveness. CONCLUSION The composition of bronchial airway microbiota is associated with the degree of bronchial hyperresponsiveness among patients with suboptimally controlled asthma. These findings support the need for further functional studies to examine the potential contribution of members of the airway microbiota in asthma pathogenesis.
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Affiliation(s)
- Yvonne J Huang
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of California, San Francisco, Calif, USA
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