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Panchami PS, Geetha Thanuja K, Karthikeyan S. Isolation and Characterization of Indigenous Plant Growth-Promoting Rhizobacteria (PGPR) from Cardamom Rhizosphere. Curr Microbiol 2020; 77:2963-2981. [PMID: 32681313 DOI: 10.1007/s00284-020-02116-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 07/06/2020] [Indexed: 01/27/2023]
Abstract
The present study was conducted to explore the native plant growth-promoting (PGP) bacteria from cardamom rhizosphere in few districts of Kerala and Tamilnadu under cardamom cultivation. The isolates obtained were screened for their PGP characteristics and their beneficial effect on cardamom was evaluated. Of the total 88 isolates, ten were screened as promising based on their performance in growth promoting attributes such as production of indole acetic acid, gibberellic acid, siderophore, hydrogen cyanide, heavy metal tolerance and antibiotic resistance. Diazotrophy of the screened isolates were tested by nitrogenase assay and evaluated using the diversity of nif genes. Genetic analysis was carried out to assess the phylogenetic relationship using 16S rRNA sequencing. The phylogenetic analysis exhibited clear clustering of isolates into three phyla namely Firmicutes, Actinobacteria and γ-proteobacteria. Majority of the isolates were grouped into Bacillus and Pseudomonas at genus level. Three different plant inoculation study at nursery and field level, viz., Bacillus subtilis TAUC1, Bacillus subtilis TAUC2 and Pseudomonas putida TAUC10. The combined inoculation of bioinoculants were superior over individual inoculation with respect to growth, soil and plant nutrient content, biochemical constituents, rhizosphere population, soil enzyme activities and yield. Hence the present study reveals the potential effect of PGPR for bioinoculant production for enhancing growth and development of cardamom under field conditions.
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Affiliation(s)
- Pottekkat Sidharthan Panchami
- Department of Agricultural Microbiology, Directorate of Natural Resource Management, Tamil Nadu Agricultural University, Coimbatore, India
| | - Kalyanasundaram Geetha Thanuja
- Department of Agricultural Microbiology, Directorate of Natural Resource Management, Tamil Nadu Agricultural University, Coimbatore, India
| | - Subburamu Karthikeyan
- Department of Agricultural Microbiology, Directorate of Natural Resource Management, Tamil Nadu Agricultural University, Coimbatore, India. .,Department of Renewable Energy Engineering, Tamil Nadu Agricultural University, Coimbatore, India.
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2
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Tu Q, Lin L, Cheng L, Deng Y, He Z. NCycDB: a curated integrative database for fast and accurate metagenomic profiling of nitrogen cycling genes. Bioinformatics 2019; 35:1040-1048. [PMID: 30165481 DOI: 10.1093/bioinformatics/bty741] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 08/06/2018] [Accepted: 08/23/2018] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION The nitrogen (N) cycle is a collection of important biogeochemical pathways in the Earth ecosystem and has gained extensive foci in ecology and environmental studies. Currently, shotgun metagenome sequencing has been widely applied to explore gene families responsible for N cycle processes. However, there are problems in applying publically available orthology databases to profile N cycle gene families in shotgun metagenomes, such as inefficient database searching, unspecific orthology groups and low coverage of N cycle genes and/or gene (sub)families. RESULTS To solve these issues, this study built a manually curated integrative database (NCycDB) for fast and accurate profiling of N cycle gene (sub)families from shotgun metagenome sequencing data. NCycDB contains a total of 68 gene (sub)families and covers eight N cycle processes with 84 759 and 219 146 representative sequences at 95 and 100% identity cutoffs, respectively. We also identified 1958 homologous orthology groups and included corresponding sequences in the database to avoid false positive assignments due to 'small database' issues. We applied NCycDB to characterize N cycle gene (sub)families in 52 shotgun metagenomes from the Global Ocean Sampling expedition. Further analysis showed that the structure and composition of N cycle gene families were most strongly correlated with latitude and temperature. NCycDB is expected to facilitate N cycle studies via shotgun metagenome sequencing approaches in various environments. The framework developed in this study can be served as a good reference to build similar knowledge-based functional gene databases in various processes and pathways. AVAILABILITY AND IMPLEMENTATION NCycDB database files are available at https://github.com/qichao1984/NCyc. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Qichao Tu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Lu Lin
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Lei Cheng
- Department of Ecology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ye Deng
- Research Center for Eco-Environmental Science, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Zhili He
- Department of Environmental Science, School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, Guangdong, China.,Department of Agriculture, College of Agriculture, Hunan Agricultural University, Changsha, China
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3
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Hirokawa Y, Kanesaki Y, Arai S, Saruta F, Hayashihara K, Murakami A, Shimizu K, Honda H, Yoshikawa H, Hanai T. Mutations responsible for alcohol tolerance in the mutant of Synechococcus elongatus PCC 7942 (SY1043) obtained by single-cell screening system. J Biosci Bioeng 2018; 125:572-577. [DOI: 10.1016/j.jbiosc.2017.11.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 11/10/2017] [Accepted: 11/27/2017] [Indexed: 11/28/2022]
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Yoo K, Lee TK, Choi EJ, Yang J, Shukla SK, Hwang SI, Park J. Molecular approaches for the detection and monitoring of microbial communities in bioaerosols: A review. J Environ Sci (China) 2017; 51:234-247. [PMID: 28115135 DOI: 10.1016/j.jes.2016.07.002] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 07/04/2016] [Accepted: 07/08/2016] [Indexed: 05/21/2023]
Abstract
Bioaerosols significantly affect atmospheric processes while they undergo long-range vertical and horizontal transport and influence atmospheric chemistry and physics and climate change. Accumulating evidence suggests that exposure to bioaerosols may cause adverse health effects, including severe disease. Studies of bioaerosols have primarily focused on their chemical composition and largely neglected their biological composition and the negative effects of biological composition on ecosystems and human health. Here, current molecular methods for the identification, quantification, and distribution of bioaerosol agents are reviewed. Modern developments in environmental microbiology technology would be favorable in elucidation of microbial temporal and spatial distribution in the atmosphere at high resolution. In addition, these provide additional supports for growing evidence that microbial diversity or composition in the bioaerosol is an indispensable environmental aspect linking with public health.
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Affiliation(s)
- Keunje Yoo
- Department of Civil and Environmental Engineering, Yonsei University, Seoul 03722, South Korea; Division of Natural Resources Conservation, Korea Environment Institute, Sejong-si 30147, South Korea
| | - Tae Kwon Lee
- Department of Environmental Engineering, Yonsei University, Wonju 26493, South Korea
| | - Eun Joo Choi
- Department of Systems Biology, Yonsei University, Seoul 03722, South Korea
| | - Jihoon Yang
- Division of Natural Resources Conservation, Korea Environment Institute, Sejong-si 30147, South Korea
| | - Sudheer Kumar Shukla
- Department of Built and Natural Environment, Caledonian College of Engineering, Sultanate of Oman
| | - Sang-Il Hwang
- Division of Natural Resources Conservation, Korea Environment Institute, Sejong-si 30147, South Korea
| | - Joonhong Park
- Department of Civil and Environmental Engineering, Yonsei University, Seoul 03722, South Korea.
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5
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Saha C, Mukherjee G, Agarwal-Banka P, Seal A. A consortium of non-rhizobial endophytic microbes from Typha angustifolia functions as probiotic in rice and improves nitrogen metabolism. PLANT BIOLOGY (STUTTGART, GERMANY) 2016; 18:938-946. [PMID: 27453497 DOI: 10.1111/plb.12485] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Accepted: 07/19/2016] [Indexed: 06/06/2023]
Abstract
Endophytic microbes isolated from plants growing in nutrient-deficient environments often possess properties that improve nutrition of agriculturally important plants. A consortium of non-rhizobial endophytic microbes isolated from a macrophyte Typha angustifolia growing in the marginal wetlands associated with a Uranium mine was characterized for their beneficial effect on rice and the mechanisms of growth promotion were investigated. The microbes were identified and characterized for their potential plant growth promoting (PGP) properties. Effect of these microbes on nitrogen (N)-metabolism of rice was tested as Typha endophytes were predominantly (N)-fixing. Relative N-use efficiency and expression of genes involved in N-uptake and assimilation were investigated in treated plants. Evidence of horizontal gene transfer (HGT) of dinitrogen reductase gene was observed within the consortium from a Pseudomonas stutzeri strain. The consortium behaved as plant probiotic and showed substantial growth benefits to Typha, their natural host as well as to rice. Typha endophytes colonized rice endosphere significantly increasing biomass, shoot length and chlorophyll content in rice plants both under N-sufficient and N-deficient conditions. N-uptake and assimilation genes were upregulated in plants treated with the endophytes even after three weeks post infection. Our results suggested, HGT of nitrogen-fixation trait to be highly prevalent among endophytes isolated from nutrient-poor habitats of the uranium mine. A long-term nitrogen deficiency response in the treated plants was elicited by the consortium improving N-uptake, assimilation and relative N-use efficiency of rice plants. This appeared to be at least one of the main strategies of plant growth promotion.
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Affiliation(s)
- C Saha
- Department of Biotechnology, Dr. B. C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, Kolkata, India
| | - G Mukherjee
- Department of Biotechnology, Dr. B. C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, Kolkata, India
| | | | - A Seal
- Department of Biotechnology, Dr. B. C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, Kolkata, India.
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Tanasupawat S, Takehana T, Yoshida S, Hiraga K, Oda K. Ideonella sakaiensis sp. nov., isolated from a microbial consortium that degrades poly(ethylene terephthalate). Int J Syst Evol Microbiol 2016; 66:2813-2818. [PMID: 27045688 DOI: 10.1099/ijsem.0.001058] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic, non-spore-forming, rod-shaped bacterium, designed strain 201-F6T, was isolated from a microbial consortium that degrades poly(ethylene terephthalate) (PET) collected in Sakai city, Japan, and was characterized on the basis of a polyphasic taxonomic study. The cells were motile with a polar flagellum. The strain contained cytochrome oxidase and catalase. It grew within the pH range 5.5-9.0 (optimally at pH 7-7.5) and at 15-42 ºC (optimally at 30-37 ºC). The major isoprenoid quinone was ubiquinone with eight isoprene units (Q-8). C16 : 0, C17 : 0 cyclo, C18 :1ω7c and C12 : 0 2-OH were the predominant cellular fatty acids. The major polar lipids were phosphatidylethanolamine, lyso-phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The G+C content of genomic DNA was 70.4 mol%. Phylogenetic analysis using the 16S rRNA gene sequences showed that strain 201-F6T was affiliated to the genus Ideonella, and was closely related to Ideonella dechloratans LMG 28178T (97.7 %) and Ideonella azotifigens JCM 15503T (96.6 %). Strain 201-F6T could be clearly distinguished from the related species of the genus Ideonella by its physiological and biochemical characteristics as well as by its phylogenetic position and DNA-DNA relatedness. Therefore, the strain represents a novel species of the genus Ideonella, for which the name Ideonella sakaiensis sp. nov. (type strain 201-F6T=NBRC 110686T=TISTR 2288T) is proposed.
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Affiliation(s)
- Somboon Tanasupawat
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Toshihiko Takehana
- Life Science Materials Laboratory, ADEKA Corporation, 7-2-34 Higashiogu, Arakawa-ku, Tokyo 116-8553, Japan
| | - Shosuke Yoshida
- Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Kazumi Hiraga
- Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Kohei Oda
- Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
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Sakrouhi I, Belfquih M, Sbabou L, Moulin P, Bena G, Filali-Maltouf A, Le Quéré A. Recovery of symbiotic nitrogen fixing acacia rhizobia from Merzouga Desert sand dunes in South East Morocco – Identification of a probable new species of Ensifer adapted to stressed environments. Syst Appl Microbiol 2016; 39:122-31. [DOI: 10.1016/j.syapm.2016.01.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 11/17/2015] [Accepted: 01/14/2016] [Indexed: 10/22/2022]
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Engene N. Caldora penicillata gen. nov., comb. nov. (cyanobacteria), a pantropical marine species with biomedical relevance. JOURNAL OF PHYCOLOGY 2015; 51:670-81. [PMID: 26327714 PMCID: PMC4551411 DOI: 10.1111/jpy.12309] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Many tropical marine cyanobacteria are prolific producers of bioactive secondary metabolites with ecological relevance and promising pharmaceutical applications. One species of chemically rich, tropical marine cyanobacteria that was previously identified as Symploca hydnoides or Symploca sp. corresponds to the traditional taxonomic definition of Phormidium penicillatum. In this study, we clarified the taxonomy of this biomedically and ecologically important cyanobacterium by comparing recently collected specimens with the original type material and the taxonomic description of P. penicillatum. Molecular phylogenetic analyses of the 16S rRNA gene and the 16S-23S internal transcribed spacer regions showed that P. penicillatum formed an independent clade sister to the genus Symploca, and distantly related to Phormidium and Lyngbya. We propose the new genus Caldora for this clade, with Caldora penicillata comb. nov. as the type species and designate as the epitype the recently collected strain FK13-1. Furthermore, the production of bioactive secondary metabolites among various geographically dispersed collections of C. penicillata showed that this species consistently produced the metabolite dolastatin 10 and/or the related compound symplostatin 1, which appear to be robust autapomorphic characters and chemotaxonomic markers for this taxon.
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Affiliation(s)
- Niclas Engene
- Department of Biological Sciences, Florida International University, Miami, FL 33199, USA
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9
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Brown SM, Jenkins BD. Profiling gene expression to distinguish the likely active diazotrophs from a sea of genetic potential in marine sediments. Environ Microbiol 2014; 16:3128-42. [PMID: 24447468 PMCID: PMC4231279 DOI: 10.1111/1462-2920.12403] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Accepted: 01/12/2014] [Indexed: 11/29/2022]
Abstract
Nitrogen (N) cycling microbial communities in marine sediments are extremely diverse, and it is unknown whether this diversity reflects extensive functional redundancy. Sedimentary denitrifiers remove significant amounts of N from the coastal ocean and diazotrophs are typically regarded as inconsequential. Recently, N fixation has been shown to be a potentially important source of N in estuarine and continental shelf sediments. Analysis of expressed genes for nitrite reductase (nirS) and a nitrogenase subunit (nifH) was used to identify the likely active denitrifiers and nitrogen fixers in surface sediments from different seasons in Narragansett Bay (Rhode Island, USA). The overall diversity of diazotrophs expressing nifH decreased along the estuarine gradient from the estuarine head to an offshore continental shelf site. Two groups of sequences related to anaerobic sulphur/iron reducers and sulphate reducers dominated libraries of expressed nifH genes. Quantitative polymerase chain reaction (qPCR) and quantitative reverse transcription polymerase chain reaction (qRT-PCR) data shows the highest abundance of both groups at a mid bay site, and the highest nifH expression at the head of the estuary, regardless of season. Several potential environmental factors, including water temperature, oxygen concentration and metal contamination, may influence the abundance and nifH expression of these two bacterial groups.
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Affiliation(s)
- S M Brown
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, RI, USA
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10
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Abell GCJ, Robert SS, Frampton DMF, Volkman JK, Rizwi F, Csontos J, Bodrossy L. High-throughput analysis of ammonia oxidiser community composition via a novel, amoA-based functional gene array. PLoS One 2012; 7:e51542. [PMID: 23284709 PMCID: PMC3526613 DOI: 10.1371/journal.pone.0051542] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Accepted: 11/08/2012] [Indexed: 11/17/2022] Open
Abstract
Advances in microbial ecology research are more often than not limited by the capabilities of available methodologies. Aerobic autotrophic nitrification is one of the most important and well studied microbiological processes in terrestrial and aquatic ecosystems. We have developed and validated a microbial diagnostic microarray based on the ammonia-monooxygenase subunit A (amoA) gene, enabling the in-depth analysis of the community structure of bacterial and archaeal ammonia oxidisers. The amoA microarray has been successfully applied to analyse nitrifier diversity in marine, estuarine, soil and wastewater treatment plant environments. The microarray has moderate costs for labour and consumables and enables the analysis of hundreds of environmental DNA or RNA samples per week per person. The array has been thoroughly validated with a range of individual and complex targets (amoA clones and environmental samples, respectively), combined with parallel analysis using traditional sequencing methods. The moderate cost and high throughput of the microarray makes it possible to adequately address broader questions of the ecology of microbial ammonia oxidation requiring high sample numbers and high resolution of the community composition.
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Affiliation(s)
- Guy C J Abell
- CSIRO Marine and Atmospheric Research and Wealth from Oceans National Research Flagship, Hobart, Tasmania, Australia
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11
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Nostrand JDV, He Z, Zhou J. Use of functional gene arrays for elucidating in situ biodegradation. Front Microbiol 2012; 3:339. [PMID: 23049526 PMCID: PMC3448134 DOI: 10.3389/fmicb.2012.00339] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 09/03/2012] [Indexed: 12/18/2022] Open
Abstract
Microarrays have revolutionized the study of microbiology by providing a high-throughput method for examining thousands of genes with a single test and overcome the limitations of many culture-independent approaches. Functional gene arrays (FGA) probe a wide range of genes involved in a variety of functions of interest to microbial ecology (e.g., carbon degradation, N fixation, metal resistance) from many different microorganisms, cultured and uncultured. The most comprehensive FGA to date is the GeoChip array, which targets tens of thousands of genes involved in the geochemical cycling of carbon, nitrogen, phosphorus, and sulfur, metal resistance and reduction, energy processing, antibiotic resistance and contaminant degradation as well as phylogenetic information (gyrB). Since the development of GeoChips, many studies have been performed using this FGA and have shown it to be a powerful tool for rapid, sensitive, and specific examination of microbial communities in a high-throughput manner. As such, the GeoChip is well-suited for linking geochemical processes with microbial community function and structure. This technology has been used successfully to examine microbial communities before, during, and after in situ bioremediation at a variety of contaminated sites. These studies have expanded our understanding of biodegradation and bioremediation processes and the associated microorganisms and environmental conditions responsible. This review provides an overview of FGA development with a focus on the GeoChip and highlights specific GeoChip studies involving in situ bioremediation.
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Affiliation(s)
- Joy D Van Nostrand
- Institute for Environmental Genomics, University of Oklahoma Norman, OK, USA ; Department of Microbiology and Plant Biology, University of Oklahoma Norman, OK, USA
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He Z, Van Nostrand JD, Zhou J. Applications of functional gene microarrays for profiling microbial communities. Curr Opin Biotechnol 2012; 23:460-6. [PMID: 22226464 DOI: 10.1016/j.copbio.2011.12.021] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Revised: 11/23/2011] [Accepted: 12/19/2011] [Indexed: 10/14/2022]
Abstract
Functional gene arrays (FGAs) have been considered as a specific, sensitive, quantitative, and high throughput metagenomic tool to detect, monitor and characterize microbial communities. Especially GeoChips, the most comprehensive FGAs have been applied to analyze the functional diversity, composition, structure, and metabolic potential or activity of a variety of microbial communities from different habitats, such as aquatic ecosystems, soils, contaminated sites, extreme environments, and bioreactors. FGAs are able to address fundamental questions related to global change, bioremediation, land use, human health, and ecological theories, and link the microbial community structure to environmental properties and ecosystem functioning. This review focuses on applications of FGA technology for profiling microbial communities, including target preparation, hybridization and data processing, and data analysis. We also discuss challenges and future directions of FGA applications.
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Affiliation(s)
- Zhili He
- Institute for Environmental Genomics, Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA
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He Z, Deng Y, Zhou J. Development of functional gene microarrays for microbial community analysis. Curr Opin Biotechnol 2011; 23:49-55. [PMID: 22100036 DOI: 10.1016/j.copbio.2011.11.001] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Revised: 10/31/2011] [Accepted: 11/01/2011] [Indexed: 01/21/2023]
Abstract
Functional gene arrays (FGAs) are a special type of microarrays containing probes for key genes involved in microbial functional processes, such as biogeochemical cycling of carbon, nitrogen, sulfur, phosphorus and metals, virulence and antibiotic resistance, biodegradation of environmental contaminants, and stress responses. FGAs have been demonstrated to be a specific, sensitive, and quantitative tool for rapid analysis of microbial communities from different habitats, such as waters, soils, extreme environments, bioreactors, and human microbiomes. In this review, we first summarize currently reported FGAs, and then focus on the FGA development. We will also discuss several key issues of FGA technology as well as challenges and directions in future FGA development.
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Affiliation(s)
- Zhili He
- Institute for Environmental Genomics, Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA.
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14
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Sato A, Watanabe T, Unno Y, Purnomo E, Osaki M, Shinano T. Analysis of diversity of diazotrophic bacteria associated with the rhizosphere of a tropical Arbor, Melastoma malabathricum L. Microbes Environ 2011; 24:81-7. [PMID: 21566359 DOI: 10.1264/jsme2.me08565] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The diversity of diazotrophic bacteria in the rhizosphere of Melastoma malabathricum L. was investigated by cloning-sequencing of the nifH gene directly amplified from DNA extracted from soil. Samples were obtained from the rhizosphere and bulk soil of M. malabathricum growing in three different soil types (acid sulfate, peat and sandy clay soils) located very close to each other in south Kalimantan, Indonesia. Six clone libraries were constructed, generated from bulk and rhizosphere soil samples, and 300 nifH clones were produced, then assembled into 29 operational taxonomic units (OTUs) based on percent identity values. Our results suggested that nifH gene diversity is mainly dependent on soil properties, and did not differ remarkably between the rhizosphere and bulk soil of M. malabathricum except in acid sulfate soil. In acid sulfate soil, as the Shannon diversity index was lower in rhizosphere than in bulk soil, it is suggested that particular bacterial species might accumulate in the rhizosphere.
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Affiliation(s)
- Atsuya Sato
- Graduate School of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kitaku, Sapporo 060-8589, Japan
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15
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Fernandez C, Farías L, Ulloa O. Nitrogen fixation in denitrified marine waters. PLoS One 2011; 6:e20539. [PMID: 21687726 PMCID: PMC3110191 DOI: 10.1371/journal.pone.0020539] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Accepted: 05/04/2011] [Indexed: 11/19/2022] Open
Abstract
Nitrogen fixation is an essential process that biologically transforms atmospheric dinitrogen gas to ammonia, therefore compensating for nitrogen losses occurring via denitrification and anammox. Currently, inputs and losses of nitrogen to the ocean resulting from these processes are thought to be spatially separated: nitrogen fixation takes place primarily in open ocean environments (mainly through diazotrophic cyanobacteria), whereas nitrogen losses occur in oxygen-depleted intermediate waters and sediments (mostly via denitrifying and anammox bacteria). Here we report on rates of nitrogen fixation obtained during two oceanographic cruises in 2005 and 2007 in the eastern tropical South Pacific (ETSP), a region characterized by the presence of coastal upwelling and a major permanent oxygen minimum zone (OMZ). Our results show significant rates of nitrogen fixation in the water column; however, integrated rates from the surface down to 120 m varied by ∼30 fold between cruises (7.5±4.6 versus 190±82.3 µmol m−2 d−1). Moreover, rates were measured down to 400 m depth in 2007, indicating that the contribution to the integrated rates of the subsurface oxygen-deficient layer was ∼5 times higher (574±294 µmol m−2 d−1) than the oxic euphotic layer (48±68 µmol m−2 d−1). Concurrent molecular measurements detected the dinitrogenase reductase gene nifH in surface and subsurface waters. Phylogenetic analysis of the nifH sequences showed the presence of a diverse diazotrophic community at the time of the highest measured nitrogen fixation rates. Our results thus demonstrate the occurrence of nitrogen fixation in nutrient-rich coastal upwelling systems and, importantly, within the underlying OMZ. They also suggest that nitrogen fixation is a widespread process that can sporadically provide a supplementary source of fixed nitrogen in these regions.
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Affiliation(s)
- Camila Fernandez
- Departamento de Oceanografía and Centro de Investigación Oceanográfica en el Pacífico Sur-Oriental (COPAS), Universidad de Concepción, Concepción, Chile.
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Pathak A, Shanker R, Garg SK, Manickam N. Profiling of biodegradation and bacterial 16S rRNA genes in diverse contaminated ecosystems using 60-mer oligonucleotide microarray. Appl Microbiol Biotechnol 2011; 90:1739-54. [DOI: 10.1007/s00253-011-3268-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2011] [Revised: 03/16/2011] [Accepted: 03/16/2011] [Indexed: 12/01/2022]
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17
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Bertrand EM, Saito MA, Jeon YJ, Neilan BA. Vitamin B₁₂ biosynthesis gene diversity in the Ross Sea: the identification of a new group of putative polar B₁₂ biosynthesizers. Environ Microbiol 2011; 13:1285-98. [PMID: 21410623 DOI: 10.1111/j.1462-2920.2011.02428.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Vitamin B₁₂, a cobalt-containing micronutrient, has been shown to limit phytoplankton growth in the Ross Sea of the Southern Ocean. However, B₁₂ biosynthesis potential in this environment remains uncharacterized. Select bacteria and archaea synthesize B₁₂ while many phytoplankton require it for growth. Low ratios of bacterial biomass production to primary productivity and high concentrations of labile cobalt in Antarctic surface water suggest that factors controlling bacterial growth rather than cobalt availability may determine vitamin production rates here. In order to assess B₁₂ biosynthesis potential, degenerate polymerase chain reaction primers were designed to target the genetic locus cbiA/cobB, encoding cobyrinic acid a,c-diamide synthase, a B₁₂ biosynthesis protein. Sequencing the DNA compliment of Ross Sea 16S rRNA (see Supporting information) allowed targeting of cbiA/cobB probes to dominant bacterial groups. CbiA/cobB DNA sequences were successfully identified in clone libraries from the Ross Sea. To our knowledge, this study represents the first targeted molecular characterization of environmental B₁₂ biosynthesis potential. A newly identified group of cbiA/cobB sequences dominated the diversity of the sequences retrieved; their expression was confirmed via mass spectrometry-based peptide detection. These sequences seem to have originated from a previously undescribed group of bacteria that could dominate the B₁₂ biosynthesizing community in polar systems.
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Affiliation(s)
- Erin M Bertrand
- MIT/WHOI Joint Program in Chemical Oceanography, Woods Hole, MA 02543, USA.
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18
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He Z, Van Nostrand JD, Deng Y, Zhou J. Development and applications of functional gene microarrays in the analysis of the functional diversity, composition, and structure of microbial communities. ACTA ACUST UNITED AC 2011. [DOI: 10.1007/s11783-011-0301-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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19
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Zehr JP, Kudela RM. Nitrogen cycle of the open ocean: from genes to ecosystems. ANNUAL REVIEW OF MARINE SCIENCE 2011; 3:197-225. [PMID: 21329204 DOI: 10.1146/annurev-marine-120709-142819] [Citation(s) in RCA: 167] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The marine nitrogen (N) cycle controls the productivity of the oceans. This cycle is driven by complex biogeochemical transformations, including nitrogen fixation, denitrification, and assimilation and anaerobic ammonia oxidation, mediated by microorganisms. New processes and organisms continue to be discovered, complicating the already complex picture of oceanic N cycling. Genomics research has uncovered the diversity of nitrogen metabolism strategies in phytoplankton and bacterioplankton. The elemental ratios of nutrients in biological material are more flexible than previously believed, with implications for vertical export of carbon and associated nutrients to the deep ocean. Estimates of nitrogen fixation and denitrification continue to be modified, and anaerobic ammonia oxidation has been identified as a new process involved in denitrification in oxygen minimum zones. The nitrogen cycle in the oceans is an integral feature of the function of ocean ecosystems and will be a central player in how oceans respond during global environmental change.
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Affiliation(s)
- Jonathan P Zehr
- Ocean Sciences Department, University of California, Santa Cruz, California 95064, USA.
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20
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Diversity of endophytic bacteria in ginseng and their potential for plant growth promotion. J Microbiol 2010; 48:559-65. [DOI: 10.1007/s12275-010-0082-1] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2010] [Accepted: 05/31/2010] [Indexed: 10/18/2022]
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21
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He Z, Deng Y, Van Nostrand JD, Tu Q, Xu M, Hemme CL, Li X, Wu L, Gentry TJ, Yin Y, Liebich J, Hazen TC, Zhou J. GeoChip 3.0 as a high-throughput tool for analyzing microbial community composition, structure and functional activity. ISME JOURNAL 2010; 4:1167-79. [PMID: 20428223 DOI: 10.1038/ismej.2010.46] [Citation(s) in RCA: 179] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A new generation of functional gene arrays (FGAs; GeoChip 3.0) has been developed, with approximately 28 000 probes covering approximately 57 000 gene variants from 292 functional gene families involved in carbon, nitrogen, phosphorus and sulfur cycles, energy metabolism, antibiotic resistance, metal resistance and organic contaminant degradation. GeoChip 3.0 also has several other distinct features, such as a common oligo reference standard (CORS) for data normalization and comparison, a software package for data management and future updating and the gyrB gene for phylogenetic analysis. Computational evaluation of probe specificity indicated that all designed probes would have a high specificity to their corresponding targets. Experimental analysis with synthesized oligonucleotides and genomic DNAs showed that only 0.0036-0.025% false-positive rates were observed, suggesting that the designed probes are highly specific under the experimental conditions examined. In addition, GeoChip 3.0 was applied to analyze soil microbial communities in a multifactor grassland ecosystem in Minnesota, USA, which showed that the structure, composition and potential activity of soil microbial communities significantly changed with the plant species diversity. As expected, GeoChip 3.0 is a high-throughput powerful tool for studying microbial community functional structure, and linking microbial communities to ecosystem processes and functioning.
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Affiliation(s)
- Zhili He
- Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, 101 David L. Boren Boulevard, Norman, OK 73019, USA
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22
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Leski TA, Malanoski AP, Stenger DA, Lin B. Target amplification for broad spectrum microbial diagnostics and detection. Future Microbiol 2010; 5:191-203. [DOI: 10.2217/fmb.09.126] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Microarrays are massively parallel detection platforms that were first used extensively for gene expression studies, but have also been successfully applied to microbial detection in a number of diverse fields requiring broad-range microbial identification. This technology has enabled researchers to gain an insight into the microbial diversity of environmental samples, facilitated discovery of a number of new pathogens and enabled studies of multipathogen infections. In contrast to gene expression studies, the concentrations of targets in analyzed samples for microbial detection are usually much lower, and require the use of nucleic acid amplification techniques. The rapid advancement of manufacturing technologies has increased the content of the microarrays; thus, the required amplification is a challenging problem. The constant parallel improvements in both microarray and sample amplification techniques in the near future may lead to a radical progression in medical diagnostics and systems for efficient detection of microorganisms in the environment.
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Affiliation(s)
- Tomasz A Leski
- Center for Bio/Molecular Science & Engineering, Code 6900, Naval Research Laboratory, Washington, DC, USA and Nova Research Inc., 1900 Elkin Street, Suite 230, Alexandria, VA, USA
| | - Anthony P Malanoski
- Center for Bio/Molecular Science & Engineering, Code 6900, Naval Research Laboratory, Washington, DC, USA
| | - David A Stenger
- Center for Bio/Molecular Science & Engineering, Code 6900, Naval Research Laboratory, Washington, DC, USA
| | - Baochuan Lin
- Center for Bio/Molecular Science & Engineering, Code 6900, Naval Research Laboratory, Washington, DC, USA
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23
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Taş N, van Eekert MHA, de Vos WM, Smidt H. The little bacteria that can - diversity, genomics and ecophysiology of 'Dehalococcoides' spp. in contaminated environments. Microb Biotechnol 2009; 3:389-402. [PMID: 21255338 PMCID: PMC3815806 DOI: 10.1111/j.1751-7915.2009.00147.x] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The fate and persistence of chlorinated organics in the environment have been a concern for the past 50 years. Industrialization and extensive agricultural activities have led to the accumulation of these pollutants in the environment, while their adverse impact on various ecosystems and human health also became evident. This review provides an update on the current knowledge of specialized anaerobic bacteria, namely ‘Dehalococcoides’ spp., which are dedicated to the transformation of various chlorinated organic compounds via reductive dechlorination. Advances in microbiology and molecular techniques shed light into the diversity and functioning of Dehalococcoides spp. in several different locations. Recent genome sequencing projects revealed a large number of genes that are potentially involved in reductive dechlorination. Molecular approaches towards analysis of diversity and expression especially of reductive dehalogenase‐encoding genes are providing a growing body of knowledge on biodegradative pathways active in defined pure and mixed cultures as well as directly in the environment. Moreover, several successful field cases of bioremediation strengthen the notion of dedicated degraders such as Dehalococcoides spp. as key players in the restoration of contaminated environments.
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Affiliation(s)
- Neslihan Taş
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, the Netherlands
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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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25
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Noar JD, Buckley DH. Ideonella azotifigens sp. nov., an aerobic diazotroph of the Betaproteobacteria isolated from grass rhizosphere soil, and emended description of the genus Ideonella. Int J Syst Evol Microbiol 2009; 59:1941-6. [DOI: 10.1099/ijs.0.003368-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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26
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Pilhofer M, Pavlekovic M, Lee NM, Ludwig W, Schleifer KH. Fluorescence in situ hybridization for intracellular localization of nifH mRNA. Syst Appl Microbiol 2009; 32:186-92. [PMID: 19217232 DOI: 10.1016/j.syapm.2008.12.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2008] [Revised: 12/01/2008] [Accepted: 12/09/2008] [Indexed: 11/18/2022]
Abstract
Few reports on in situ mRNA detection in bacteria have been published, even though a major aim in environmental microbiology is to link function/activity to the identity of the organisms. This study reports a reliable approach for the in situ detection of nifH mRNA using fluorescence hybridization based on a previously described protocol for pmoA. nifH codes for a dinitrogenase reductase, a key enzyme in dinitrogen fixation. nifH mRNA was hybridized with a digoxigenin-labelled polynucleotide probe. The hybrid was detected with an anti-DIG-antibody labelled with horseradish peroxidase. Subsequently, the signal was amplified by catalyzed reporter deposition (CARD) with fluorochrome-labelled tyramides. Furthermore, the imaged organisms were identified using standard fluorescence in situ hybridization of rRNA. Thus, the approach enabled us specifically to link in situ the information from the dinitrogen fixation activity of an organism to its identity. Unexpectedly, the signals derived from nifH mRNA hybridization showed a distinct uneven pattern within the cells. This indicated that the method used could even give insights about the localization of the detected mRNA within the cell, which is a potential use of mRNA fluorescence in situ hybridization (FISH) that has not been reported up to now for bacterial cells.
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Affiliation(s)
- Martin Pilhofer
- Technische Universität München, Lehrstuhl für Mikrobiologie, Am Hochanger 4, 85350 Freising, Germany.
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27
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Mulholland MR, Capone DG. Dinitrogen fixation in the Indian Ocean. ACTA ACUST UNITED AC 2009. [DOI: 10.1029/2009gm000850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
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28
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Evidence for the functional significance of diazotroph community structure in soil. ISME JOURNAL 2008; 3:124-36. [PMID: 18769458 DOI: 10.1038/ismej.2008.82] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Microbial ecologists continue to seek a greater understanding of the factors that govern the ecological significance of microbial community structure. Changes in community structure have been shown to have functional significance for processes that are mediated by a narrow spectrum of organisms, such as nitrification and denitrification, but in some cases, functional redundancy in the community seems to buffer microbial ecosystem processes. The functional significance of microbial community structure is frequently obscured by environmental variation and is hard to detect in short-term experiments. We examine the functional significance of free-living diazotrophs in a replicated long-term tillage experiment in which extraneous variation is minimized and N-fixation rates can be related to soil characteristics and diazotroph community structure. Soil characteristics were found to be primarily impacted by tillage management, whereas N-fixation rates and diazotroph community structure were impacted by both biomass management practices and interactions between tillage and biomass management. The data suggest that the variation in diazotroph community structure has a greater impact on N-fixation rates than do soil characteristics at the site. N-fixation rates displayed a saturating response to increases in diazotroph community diversity. These results show that the changes in the community structure of free-living diazotrophs in soils can have ecological significance and suggest that this response is related to a change in community diversity.
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29
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Piskonen R, Nyyssönen M, Itävaara M. Evaluating the biodegradation of aromatic hydrocarbons by monitoring of several functional genes. Biodegradation 2008; 19:883-95. [PMID: 18425625 DOI: 10.1007/s10532-008-9190-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2007] [Accepted: 04/01/2008] [Indexed: 10/22/2022]
Abstract
Various microbial activities determine the effectiveness of bioremediation processes. In this work, we evaluated the feasibility of gene array hybridization for monitoring the efficiency of biodegradation processes. Biodegradation of 14C-labelled naphthalene and toluene by the aromatic hydrocarbon-degrading Pseudomonas putida F1, P. putida mt-2 and P. putida G7 was followed in mixed liquid culture microcosm by a preliminary, nylon membrane-based gene array. In the beginning of the study, toluene was degraded rapidly and increased amount of toluene degradation genes was detected by the preliminary gene array developed for the study. After toluene was degraded, naphthalene mineralization started and the amount of naphthalene degradation genes increased as biodegradation proceeded. The amount of toluene degradation genes decreased towards the end of the study. The hybridization signal intensities determined by preliminary gene array were in good agreement with mineralization of naphthalene and toluene and with the amount of naphthalene dioxygenase and toluene dioxygenase genes quantified by dot blot hybridization. The clear correlation between the results obtained by the preliminary array and the biodegradation process suggests that gene array methods can be considered as a promising tool for monitoring the efficiency of biodegradation processes.
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Affiliation(s)
- Reetta Piskonen
- VTT Technical Research Centre of Finland, Tietotie 2, P. O. Box 1000, 02044 VTT, Espoo, Finland.
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30
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Moisander PH, Morrison AE, Ward BB, Jenkins BD, Zehr JP. Spatial-temporal variability in diazotroph assemblages in Chesapeake Bay using an oligonucleotide nifH microarray. Environ Microbiol 2008; 9:1823-35. [PMID: 17564615 DOI: 10.1111/j.1462-2920.2007.01304.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The distribution of nitrogen-fixing microorganisms in the Chesapeake Bay was investigated using fingerprints from a nifH microarray comprised of 706 60-mer oligonucleotide nifH probes representing cultivated organisms and environmental clones from different nifH clusters. Diverse nifH targets, amplified from samples using degenerate nifH primers, were detected in water column and sediment samples collected in April and October, 2001-2002. Total nifH richness and diversity (Simpson's and Shannon indices) were highest at the most riverine, oligohaline North Bay station. In most samples, the highest diversity was in nifH Cluster 3, which includes many anaerobes, while Cluster 1 (alpha-, beta- gamma- Proteobacteria, Cyanobacteria) targets had the greatest microarray signal intensities. In a multidimensional scaling analysis, deep water communities from April and October were similar within each of the sampling sites, while the surface communities had more variability. Diazotroph communities in the water column in the North Bay were distinct from the Mid- and South Bay communities, and there was a gradual change in sediment diazotroph assemblages from the North to the South Bay. Diazotrophic assemblages from the majority of the water column samples from the Mid- and South Bay clustered with the sediment assemblage in Mid-Bay. Dissolved inorganic nitrogen, salinity, dissolved organic carbon and dissolved organic phosphorus had a significant relationship with the diazotrophic bacterioplankton community. Higher diversity in the freshwater end of the system may reflect variability in disturbance rates and environmental conditions such as forms and concentrations of organic matter, nutrients and oxygen.
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Affiliation(s)
- Pia H Moisander
- Ocean Sciences Department, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
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31
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Lovell CR, Decker PV, Bagwell CE, Thompson S, Matsui GY. Analysis of a diverse assemblage of diazotrophic bacteria from Spartina alterniflora using DGGE and clone library screening. J Microbiol Methods 2008; 73:160-71. [PMID: 18400320 DOI: 10.1016/j.mimet.2008.02.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2007] [Revised: 02/01/2008] [Accepted: 02/14/2008] [Indexed: 11/30/2022]
Abstract
Methods to assess the diversity of the diazotroph assemblage in the rhizosphere of the salt marsh cordgrass, Spartina alterniflora were examined. The effectiveness of nifH PCR-denaturing gradient gel electrophoresis (DGGE) was compared to that of nifH clone library analysis. Seventeen DGGE gel bands were sequenced and yielded 58 nonidentical nifH sequences from a total of 67 sequences determined. A clone library constructed using the GC-clamp nifH primers that were employed in the PCR-DGGE (designated the GC-Library) yielded 83 nonidentical sequences from a total of 257 nifH sequences. A second library constructed using an alternate set of nifH primers (N-Library) yielded 83 nonidentical sequences from a total of 138 nifH sequences. Rarefaction curves for the libraries did not reach saturation, although the GC-Library curve was substantially dampened and appeared to be closer to saturation than the N-Library curve. Phylogenetic analyses showed that DGGE gel band sequencing recovered nifH sequences that were frequently sampled in the GC-Library, as well as sequences that were infrequently sampled, and provided a species composition assessment that was robust, efficient, and relatively inexpensive to obtain. Further, the DGGE method permits a large number of samples to be examined for differences in banding patterns, after which bands of interest can be sampled for sequence determination.
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Affiliation(s)
- Charles R Lovell
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, United States.
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32
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Malik S, Beer M, Megharaj M, Naidu R. The use of molecular techniques to characterize the microbial communities in contaminated soil and water. ENVIRONMENT INTERNATIONAL 2008; 34:265-276. [PMID: 18083233 DOI: 10.1016/j.envint.2007.09.001] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2007] [Revised: 08/16/2007] [Accepted: 09/02/2007] [Indexed: 05/25/2023]
Abstract
Traditionally, the identification and characterization of microbial communities in contaminated soil and water has previously been limited to those microorganisms that are culturable. The application of molecular techniques to study microbial populations at contaminated sites without the need for culturing has led to the discovery of unique and previously unrecognized microorganisms as well as complex microbial diversity in contaminated soil and water which shows an exciting opportunity for bioremediation strategies. Nucleic acid extraction from contaminated sites and their subsequent amplification by polymerase chain reaction (PCR) has proved extremely useful in assessing the changes in microbial community structure by several microbial community profiling techniques. This review examines the current application of molecular techniques for the characterization of microbial communities in contaminated soil and water. Techniques that identify and quantify microbial population and catabolic genes involved in biodegradation are examined. In addition, methods that directly link microbial phylogeny to its ecological function at contaminated sites as well as high throughput methods for complex microbial community studies are discussed.
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Affiliation(s)
- Seidu Malik
- Centre for Environmental Risk Assessment and Remediation (CERAR), University of South Australia, Mawson Lakes Boulevard, Mawson Lakes, South Australia 5095, Australia
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33
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Hewson I, Moisander PH, Morrison AE, Zehr JP. Diazotrophic bacterioplankton in a coral reef lagoon: phylogeny, diel nitrogenase expression and response to phosphate enrichment. ISME JOURNAL 2008; 1:78-91. [PMID: 18043616 DOI: 10.1038/ismej.2007.5] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
We investigated diazotrophic bacterioplankton assemblage composition in the Heron Reef lagoon (Great Barrier Reef, Australia) using culture-independent techniques targeting the nifH fragment of the nitrogenase gene. Seawater was collected at 3 h intervals over a period of 72 h (i.e. over diel as well as tidal cycles). An incubation experiment was also conducted to assess the impact of phosphate (PO(4)3*) availability on nifH expression patterns. DNA-based nifH libraries contained primarily sequences that were most similar to nifH from sediment, microbial mat and surface-associated microorganisms, with a few sequences that clustered with typical open ocean phylotypes. In contrast to genomic DNA sequences, libraries prepared from gene transcripts (mRNA amplified by reverse transcription-polymerase chain reaction) were entirely cyanobacterial and contained phylotypes similar to those observed in open ocean plankton. The abundance of Trichodesmium and two uncultured cyanobacterial phylotypes from previous studies (group A and group B) were studied by quantitative-polymerase chain reaction in the lagoon samples. These were detected as transcripts, but were not detected in genomic DNA. The gene transcript abundance of these phylotypes demonstrated variability over several diel cycles. The PO(4)3* enrichment experiment had a clearer pattern of gene expression over diel cycles than the lagoon sampling, however PO(4)3* additions did not result in enhanced transcript abundance relative to control incubations. The results suggest that a number of diazotrophs in bacterioplankton of the reef lagoon may originate from sediment, coral or beachrock surfaces, sloughing into plankton with the flooding tide. The presence of typical open ocean phylotype transcripts in lagoon bacterioplankton may indicate that they are an important component of the N cycle of the coral reef.
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Affiliation(s)
- Ian Hewson
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
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He Z, Gentry TJ, Schadt CW, Wu L, Liebich J, Chong SC, Huang Z, Wu W, Gu B, Jardine P, Criddle C, Zhou J. GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes. ISME JOURNAL 2008; 1:67-77. [PMID: 18043615 DOI: 10.1038/ismej.2007.2] [Citation(s) in RCA: 312] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Owing to their vast diversity and as-yet uncultivated status, detection, characterization and quantification of microorganisms in natural settings are very challenging, and linking microbial diversity to ecosystem processes and functions is even more difficult. Microarray-based genomic technology for detecting functional genes and processes has a great promise of overcoming such obstacles. Here, a novel comprehensive microarray, termed GeoChip, has been developed, containing 24,243 oligonucleotide (50 mer) probes and covering >10,000 genes in >150 functional groups involved in nitrogen, carbon, sulfur and phosphorus cycling, metal reduction and resistance, and organic contaminant degradation. The developed GeoChip was successfully used for tracking the dynamics of metal-reducing bacteria and associated communities for an in situ bioremediation study. This is the first comprehensive microarray currently available for studying biogeochemical processes and functional activities of microbial communities important to human health, agriculture, energy, global climate change, ecosystem management, and environmental cleanup and restoration. It is particularly useful for providing direct linkages of microbial genes/populations to ecosystem processes and functions.
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Affiliation(s)
- Zhili He
- Department of Botany and Microbiology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK 73019, USA
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35
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Christen R. Global Sequencing: A Review of Current Molecular Data and New Methods Available to Assess Microbial Diversity. Microbes Environ 2008; 23:253-68. [DOI: 10.1264/jsme2.me08525] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Richard Christen
- Université de Nice et CNRS UMR 6543, Laboratoire de Biologie Virtuelle, Cente de Biochimie, Parc Valrose, Faculté des Sciences
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Moustafa K, Lefebvre-De Vos D, Leprince AS, Savouré A, Laurière C. Analysis of the Arabidopsis Mitogen-Activated Protein Kinase Families: Organ Specificity and Transcriptional Regulation upon Water Stresses. ACTA ACUST UNITED AC 2008. [DOI: 10.3814/2008/143656] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Yamada A, Inoue T, Noda S, Hongoh Y, Ohkuma M. Evolutionary trend of phylogenetic diversity of nitrogen fixation genes in the gut community of wood-feeding termites. Mol Ecol 2007; 16:3768-77. [PMID: 17850544 DOI: 10.1111/j.1365-294x.2007.03326.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nitrogen fixation by gut microorganisms is one of the crucial aspects of symbiosis in wood-feeding termites since these termites thrive on a nitrogen-poor diet. In order to understand the evolution of this symbiosis, we analysed the nitrogenase structural gene nifH in the gut microbial communities. In conjunction with the published sequences, we compared approximately 320 putatively functional NifH protein sequences obtained from a total of 19 termite samples that represent all the major branches of their currently proposed phylogeny, and from one species of the cockroach Cryptocercus that shares a common ancestor with termites. Using multivariate techniques for clustering and ordination, a phylogeny of NifH protein sequences was created and plotted variously with host termite families, genera, and species. Close concordance was observed between NifH communities and the host termites at genus level, but family level relationships were not always congruent with accepted termite clade structure. Host groups examined included basal families (Mastotermitidae, Termopsidae, Kalotermitidae, as well as Cryptocercus), the most derived lower termite family Rhinotermitidae, and subfamilies representing the advanced and highly diverse apical family Termitidae (Macrotermitinae, Termitinae, and Nasutitermitinae). This selection encompassed the major nesting and feeding styles recognized in termites, and it was evident that NifH phylogenetic divergence, as well as the occurrence of alternative nitrogenase-type NifH, was to some extent dependent on host lifestyle as well as phylogenetic position.
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Affiliation(s)
- A Yamada
- Environmental Molecular Biology Laboratory, RIKEN, Hirosawa 2-1, Wako, Saitama 351-0198, Japan
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38
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Man-Aharonovich D, Kress N, Zeev EB, Berman-Frank I, Béjà O. Molecular ecology of nifH genes and transcripts in the eastern Mediterranean Sea. Environ Microbiol 2007; 9:2354-63. [PMID: 17686031 DOI: 10.1111/j.1462-2920.2007.01353.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The eastern Mediterranean Sea is one of the most extreme oligotrophic oceanic regions on earth in terms of nutrient concentrations and primary productivity. Nitrogen fixation has been suggested to contribute to the high N : P molar ratios of approximately 28:1 found in this region. Surprisingly, no molecular biological work has been performed in situ to assess whether N(2) fixation genes actually occur in the eastern Mediterranean Sea, or to determine which organisms are responsible for this process. In this study, we examined the presence and expression of nitrogenase genes (nifH) in the upper water layer of the eastern Mediterranean. Clone libraries constructed from both DNA and reverse-transcribed PCR-amplified mRNA were examined and compared. We observed different nifH genes from diverse microbial groups, such as Cyanobacteria, Proteobacteria and methanogenic Archaea. Interestingly, numerous phylotypes were observed in coastal stations at the DNA level but none were active. However, in far offshore stations, the phylotypes observed at the DNA level were the ones that were actually active. Our preliminary study revealed diverse diazotrophs that possess and express nifH genes, which may support N(2) fixation in the eastern Mediterranean Sea.
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Ward BB, Eveillard D, Kirshtein JD, Nelson JD, Voytek MA, Jackson GA. Ammonia-oxidizing bacterial community composition in estuarine and oceanic environments assessed using a functional gene microarray. Environ Microbiol 2007; 9:2522-38. [PMID: 17803777 DOI: 10.1111/j.1462-2920.2007.01371.x] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The relationship between environmental factors and functional gene diversity of ammonia-oxidizing bacteria (AOB) was investigated across a transect from the freshwater portions of the Chesapeake Bay and Choptank River out into the Sargasso Sea. Oligonucleotide probes (70-bp) designed to represent the diversity of ammonia monooxygenase (amoA) genes from Chesapeake Bay clone libraries and cultivated AOB were used to construct a glass slide microarray. Hybridization patterns among the probes in 14 samples along the transect showed clear variations in amoA community composition. Probes representing uncultivated members of the Nitrosospira-like AOB dominated the probe signal, especially in the more marine samples. Of the cultivated species, only Nitrosospira briensis was detected at appreciable levels. Discrimination analysis of hybridization signals detected two guilds. Guild 1 was dominated by the marine Nitrosospira-like probe signal, and Guild 2's largest contribution was from upper bay (freshwater) sediment probes. Principal components analysis showed that Guild 1 was positively correlated with salinity, temperature and chlorophyll a concentration, while Guild 2 was positively correlated with concentrations of oxygen, dissolved organic carbon, and particulate nitrogen and carbon, suggesting that different amoA sequences represent organisms that occupy different ecological niches within the estuarine/marine environment. The trend from most diversity of AOB in the upper estuary towards dominance of a single type in the polyhaline region of the Bay is consistent with the declining importance of AOB with increasing salinity, and with the idea that AO-Archaea are the more important ammonia oxidizers in the ocean.
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Affiliation(s)
- Bess B Ward
- Department of Geosciences, Guyot Hall, Princeton University, Princeton, NJ, USA.
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Abstract
Like many estuaries, the Chesapeake Bay has pronounced gradients in salinity and nutrients. Previous studies have shown that there is a high diversity of nitrogenase (nifH) genes in the estuary, and that there are specific distributions of individual nifH phylotypes. In contrast to previous work that revealed the remarkable diversity of nifH phylotypes in the Chesapeake estuary, in this study of nifH expression we only detected two phylotypes, and both were phylogenetically related to cyanobacterial nifH genes. One of the phylotypes was closely related to a nifH sequence from the filamentous, heterocystous cyanobacterium Anabaena cylindrica, and was found at the head of the estuary. The other phylotype was found in a sample collected near the mouth of the estuary and was closely related to nifH sequences from Group A unicellular cyanobacteria, which has previously been reported in oceanic waters only. These nifH phylotypes had distinct patterns of expression that were restricted to different regions of the Chesapeake Bay. This study provides the first evidence of nifH expression in the Chesapeake Bay, and suggests that diazotrophic unicellular cyanobacteria have a broader distribution and activity than previously recognized.
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Affiliation(s)
- Steven M Short
- Department of Biological Sciences, University of Denver, Denver, CO 80208, USA.
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Zhang L, Hurek T, Reinhold-Hurek B. A nifH-based oligonucleotide microarray for functional diagnostics of nitrogen-fixing microorganisms. MICROBIAL ECOLOGY 2007; 53:456-70. [PMID: 17186154 DOI: 10.1007/s00248-006-9126-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2006] [Accepted: 06/12/2006] [Indexed: 05/13/2023]
Abstract
Nitrogen fixation is an important process in biogeochemical cycles exclusively carried out by prokaryotes, mostly by an evolutionarily conserved nitrogenase protein complex, of which one of the structural genes (nifH) is highly valuable for phylogenetic and diversity analyses. We developed a nifH-based short oligonucleotide microarray (nifH diagnostic microarray) as a rapid tool to effectively monitor nitrogen-fixing diazotrophic populations in a wide range of environments. Taking account of the overwhelming predominance of environmental nifH fragments from uncultivated microorganisms in public databases, our nifH microarray is mainly based on nifH sequences from as yet unidentified prokaryotes. Standard conditions for microarray performance were determined, and criteria for the design of specific oligonucleotides were defined. A primary set of 56 oligonucleotides was validated with fluorescence-labeled single-stranded nifH targets from five reference strains, 26 environmental clones, and artificial mixtures of reference strains. The nifH microarray was applied to analyze the diversity (based on DNA) and activity (based on mRNA) of diazotrophs in roots of wild rice samples from Namibia. Results demonstrated that only a small subset of diazotrophs being present in the sample were actually fixing nitrogen actively. Our data suggest that the developed nifH microarray is a highly reproducible and semiquantitative method for mapping the variability of diazotrophic diversity, allowing rapid comparisons of the relative abundance and activity of diazotrophic prokaryotes in the environment. A further refined nifH microarray comprising of 194 oligonucleotide probes now covers more than 90% of sequences in our nifH database.
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Affiliation(s)
- Lei Zhang
- Laboratory of General Microbiology, Center of Applied Gene Sensoric, University of Bremen, P.O. Box 33 04 40, D-28334, Bremen, Germany
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Feng S, Tillier ERM. A fast and flexible approach to oligonucleotide probe design for genomes and gene families. Bioinformatics 2007; 23:1195-202. [PMID: 17392329 DOI: 10.1093/bioinformatics/btm114] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION With hundreds of completely sequenced microbial genomes available, and advancements in DNA microarray technology, the detection of genes in microbial communities consisting of hundreds of thousands of sequences may be possible. The existing strategies developed for DNA probe design, geared toward identifying specific sequences, are not suitable due to the lack of coverage, flexibility and efficiency necessary for applications in metagenomics. METHODS ProDesign is a tool developed for the selection of oligonucleotide probes to detect members of gene families present in environmental samples. Gene family-specific probe sequences are generated based on specific and shared words, which are found with the spaced seed hashing algorithm. To detect more sequences, those sharing some common words are re-clustered into new families, then probes specific for the new families are generated. RESULTS The program is very flexible in that it can be used for designing probes for detecting many genes families simultaneously and specifically in one or more genomes. Neither the length nor the melting temperature of the probes needs to be predefined. We have found that ProDesign provides more flexibility, coverage and speed than other software programs used in the selection of probes for genomic and gene family arrays. AVAILABILITY ProDesign is licensed free of charge to academic users. ProDesign and Supplementary Material can be obtained by contacting the authors. A web server for ProDesign is available at http://www.uhnresearch.ca/labs/tillier/ProDesign/ProDesign.html. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Shengzhong Feng
- Institute of Computing Technology, Chinese Academy of Sciences, China
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Buckley DH, Huangyutitham V, Hsu SF, Nelson TA. Stable isotope probing with 15N2 reveals novel noncultivated diazotrophs in soil. Appl Environ Microbiol 2007; 73:3196-204. [PMID: 17369332 PMCID: PMC1907113 DOI: 10.1128/aem.02610-06] [Citation(s) in RCA: 124] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Biological nitrogen fixation is a fundamental component of the nitrogen cycle and is the dominant natural process through which fixed nitrogen is made available to the biosphere. While the process of nitrogen fixation has been studied extensively with a limited set of cultivated isolates, examinations of nifH gene diversity in natural systems reveal the existence of a wide range of noncultivated diazotrophs. These noncultivated diazotrophs remain uncharacterized, as do their contributions to nitrogen fixation in natural systems. We have employed a novel 15N2-DNA stable isotope probing (5N2-DNA-SIP) method to identify free-living diazotrophs in soil that are responsible for nitrogen fixation in situ. Analyses of 16S rRNA genes from 15N-labeled DNA provide evidence for nitrogen fixation by three microbial groups, one of which belongs to the Rhizobiales while the other two represent deeply divergent lineages of noncultivated bacteria within the Betaproteobacteria and Actinobacteria, respectively. Analysis of nifH genes from 15N-labeled DNA also revealed three microbial groups, one of which was associated with Alphaproteobacteria while the others were associated with two noncultivated groups that are deeply divergent within nifH cluster I. These results reveal that noncultivated free-living diazotrophs can mediate nitrogen fixation in soils and that 15N2-DNA-SIP can be used to gain access to DNA from these organisms. In addition, this research provides the first evidence for nitrogen fixation by Actinobacteria outside of the order Actinomycetales.
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MESH Headings
- Actinobacteria/classification
- Actinobacteria/genetics
- Actinobacteria/isolation & purification
- Alphaproteobacteria/classification
- Alphaproteobacteria/genetics
- Alphaproteobacteria/isolation & purification
- Bacteria/classification
- Bacteria/genetics
- Bacteria/isolation & purification
- Base Sequence
- Betaproteobacteria/classification
- Betaproteobacteria/genetics
- Betaproteobacteria/isolation & purification
- DNA, Bacterial/analysis
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Bacterial/isolation & purification
- DNA, Bacterial/metabolism
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- DNA, Ribosomal/isolation & purification
- Isotope Labeling
- Molecular Sequence Data
- Nitrogen Fixation
- Nitrogen Isotopes
- Oxidoreductases/genetics
- Phylogeny
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Soil Microbiology
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Affiliation(s)
- Daniel H Buckley
- Department of Crop and Soil Sciences, 705 Bradfield Hall, Cornell University, Ithaca, NY 14853, USA.
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Jenkins BD, Zehr JP, Gibson A, Campbell L. Cyanobacterial assimilatory nitrate reductase gene diversity in coastal and oligotrophic marine environments. Environ Microbiol 2006; 8:2083-95. [PMID: 17107550 DOI: 10.1111/j.1462-2920.2006.01084.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Cyanobacteria are important primary producers in many marine ecosystems and their abundances and growth rates depend on their ability to assimilate various nitrogen sources. To examine the diversity of nitrate-utilizing marine cyanobacteria, we developed PCR primers specific for cyanobacterial assimilatory nitrate reductase (narB) genes. We obtained amplification products from diverse strains of cultivated cyanobacteria and from several marine environments. Phylogenetic trees constructed with the narB gene are congruent with those based on ribosomal RNA genes and RNA polymerase genes. Analysis of sequence library data from coastal and oligotrophic marine environments shows distinct groups of Synechococcus sp. in each environment; some of which are represented by sequences from cultivated organisms and others that are unrelated to known sequences and likely represent novel phylogenetic groups. We observed spatial differences in the distribution of sequences between two sites in Monterey Bay and differences in the vertical distribution of sequence types at the Hawai'i Ocean Time-series Station ALOHA, suggesting that nitrogen assimilation in Synechococcus living in different ecological niches can be followed with the nitrate reductase gene.
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Affiliation(s)
- Bethany D Jenkins
- Department of Cell and Molecular Biology and Graduate School of Oceanography, University of Rhode Island, 45 Lower College Road, Kingston, RI 02881, USA.
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Dubey SK, Tripathi AK, Upadhyay SN. Exploration of soil bacterial communities for their potential as bioresource. BIORESOURCE TECHNOLOGY 2006; 97:2217-24. [PMID: 16198103 DOI: 10.1016/j.biortech.2005.06.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2005] [Revised: 05/23/2005] [Accepted: 06/02/2005] [Indexed: 05/04/2023]
Abstract
Soil is a repository of diverse microorganisms, which has frequently been used to isolate and exploit microbes for industrial, environmental and agricultural applications. Knowledge about the structure and dynamics of bacterial communities in soil has been limited as only a small fraction of bacterial diversity is accessible to culture methods. Traditional enrichment techniques and the pure culture approach for microbiological studies have offered only a narrow portal for examining the soil microbial flora due to their limited selectivity. Therefore, the morphological and nutritional criteria used to describe bacterial community failed to provide a natural taxonomic order according to evolutionary relationship. Molecular methods under an emerging discipline of biology "molecular microbial ecology" are now helping in getting these constraints removed to some extent. Nucleic acid extraction from soil is the first crucial step in the application of most of the molecular techniques, which have largely been dominated by diverse variations of PCR. Due to its rapidity, sensitivity and specificity, PCR-based finger printing techniques have proved extremely useful in assessing the changes in microbial community structure. Such techniques can yield complex community profiles and can also provide useful phylogenetic information. Fluorescent in situ hybridization (FISH) can be used to evaluate the distribution and function of bacterial population in situ. DNA microarray techniques have also been developed and being frequently used for the evaluation of ecological role and phylogenetic affiliations of bacterial populations in the soil.
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Moisander PH, Shiue L, Steward GF, Jenkins BD, Bebout BM, Zehr JP. Application of a nifH oligonucleotide microarray for profiling diversity of N2-fixing microorganisms in marine microbial mats. Environ Microbiol 2006; 8:1721-35. [PMID: 16958753 DOI: 10.1111/j.1462-2920.2006.01108.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Diazotrophic community structure in microbial mats from Guerrero Negro (GN), Baja California, Mexico, was studied using polymerase chain reaction amplification of the nifH gene and a newly developed nifH oligonucleotide microarray. Ninety-six oligonucleotide probes designed for nifH sequences from cultivated isolates and the environment were printed on glass microarrays. Phylogenetic analysis showed that the probes represented all of the main nifH clusters. Specificity was tested by (i) evaluation of cross hybridization using individual targets, and (ii) comparison of the observed hybridization signals and those predicted from the sequences cloned from microbial mats. Signal intensity had a positive relationship with target concentration and the percentage identity between probe and target. Under moderate stringency and high target concentration, specificity of the probes varied from 77% to 100% with the individual targets tested. At the end of a 7-month long nutrient manipulation experiment in GN microbial mats, no expression of nitrogen fixation under nitrogen loading was detected, although a diverse community of diazotrophs was detected. The diversity in diazotrophic population present was higher than in the population expressing the nifH gene, and there were taxa specific differences in response to nutrients. The nifH microarray is a powerful tool for diazotroph community analysis in the marine environment.
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Affiliation(s)
- Pia H Moisander
- Department of Ocean Sciences, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
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Gentry TJ, Wickham GS, Schadt CW, He Z, Zhou J. Microarray applications in microbial ecology research. MICROBIAL ECOLOGY 2006; 52:159-75. [PMID: 16897303 DOI: 10.1007/s00248-006-9072-6] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2006] [Accepted: 04/07/2006] [Indexed: 05/11/2023]
Abstract
Microarray technology has the unparalleled potential to simultaneously determine the dynamics and/or activities of most, if not all, of the microbial populations in complex environments such as soils and sediments. Researchers have developed several types of arrays that characterize the microbial populations in these samples based on their phylogenetic relatedness or functional genomic content. Several recent studies have used these microarrays to investigate ecological issues; however, most have only analyzed a limited number of samples with relatively few experiments utilizing the full high-throughput potential of microarray analysis. This is due in part to the unique analytical challenges that these samples present with regard to sensitivity, specificity, quantitation, and data analysis. This review discusses specific applications of microarrays to microbial ecology research along with some of the latest studies addressing the difficulties encountered during analysis of complex microbial communities within environmental samples. With continued development, microarray technology may ultimately achieve its potential for comprehensive, high-throughput characterization of microbial populations in near real time.
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Affiliation(s)
- T J Gentry
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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Gibson AH, Jenkins BD, Wilkerson FP, Short SM, Zehr JP. Characterization of cyanobacterial glnA gene diversity and gene expression in marine environments. FEMS Microbiol Ecol 2006; 55:391-402. [PMID: 16466378 DOI: 10.1111/j.1574-6941.2005.00050.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
PCR primers were designed and used to amplify glnA, the gene that encodes glutamine synthetase, from pure cultures of cyanobacteria and four samples from different marine environments. The glnA phylogeny was similar to that of the 16S rRNA gene, indicating that glnA gene sequences can be used to identify cyanobacteria expressing the glnA gene. Diverse unicellular cyanobacteria glnA genes were recovered from the North Pacific Subtropical Gyre, Monterey Bay, Chesapeake Bay and waters off the New Jersey coast. The majority of sequences were closely related to sequences from Synechococcus strains (78-88% identical DNA sequences). A few sequences that clustered with Prochlorococcus glnA genes were recovered from Monterey Bay and the North Pacific Subtropical Gyre. The expression of glnA was assayed by reverse transcriptase PCR to determine if there was a daily pattern in gene expression of samples collected from New Jersey's Longterm Environmental Observatory site (LEO-15). glnA expression varied over the day, with different glnA sequence types exhibiting different daily cycles. Results showed that the glnA gene can be used to characterize the diversity of natural populations of cyanobacteria, and to characterize gene expression patterns of individual species or strains.
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Affiliation(s)
- Angela H Gibson
- Ocean Sciences, University of California Santa Cruz, Santa Cruz, CA, USA.
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Langlois RJ, LaRoche J, Raab PA. Diazotrophic diversity and distribution in the tropical and subtropical Atlantic Ocean. Appl Environ Microbiol 2006; 71:7910-9. [PMID: 16332767 PMCID: PMC1317331 DOI: 10.1128/aem.71.12.7910-7919.2005] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To understand the structure of marine diazotrophic communities in the tropical and subtropical Atlantic Ocean, the molecular diversity of the nifH gene was studied by nested PCR amplification using degenerate primers, followed by cloning and sequencing. Sequences of nifH genes were amplified from environmental DNA samples collected during three cruises (November-December 2000, March 2002, and October-November 2002) covering an area between 0 to 28.3 degrees N and 56.6 to 18.5 degrees W. A total of 170 unique sequences were recovered from 18 stations and 23 depths. Samples from the November-December 2000 cruise contained both unicellular and filamentous cyanobacterial nifH phylotypes, as well as gamma-proteobacterial and cluster III sequences, so far only reported in the Pacific Ocean. In contrast, samples from the March 2002 cruise contained only phylotypes related to the uncultured group A unicellular cyanobacteria. The October-November 2002 cruise contained both filamentous and unicellular cyanobacterial and gamma-proteobacterial sequences. Several sequences were identical at the nucleotide level to previously described environmental sequences from the Pacific Ocean, including group A sequences. The data suggest a community shift from filamentous cyanobacteria in surface waters to unicellular cyanobacteria and/or heterotrophic bacteria in deeper waters. With one exception, filamentous cyanobacterial nifH sequences were present within temperatures ranging between 26.5 and 30 degrees C and where nitrate was undetectable. In contrast, nonfilamentous nifH sequences were found throughout a broader temperature range, 15 to 30 degrees C, more often in waters with temperature of <26 degrees C, and were sometimes recovered from waters with detectable nitrate concentrations.
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Affiliation(s)
- Rebecca J Langlois
- IFM-GEOMAR, Leibniz-Institut fuer Meereswissenschaften, Duesternbrooker Weg 20, 24105 Kiel, Germany
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Sessitsch A, Hackl E, Wenzl P, Kilian A, Kostic T, Stralis-Pavese N, Sandjong BT, Bodrossy L. Diagnostic microbial microarrays in soil ecology. THE NEW PHYTOLOGIST 2006; 171:719-35. [PMID: 16918544 DOI: 10.1111/j.1469-8137.2006.01824.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Soil microbial communities are responsible for important physiological and metabolic processes. In the last decade soil microorganisms have been frequently analysed by cultivation-independent techniques because only a minority of the natural microbial communities are accessible by cultivation. Cultivation-independent community analyses have revolutionized our understanding of soil microbial diversity and population dynamics. Nevertheless, many methods are still laborious and time-consuming, and high-throughput methods have to be applied in order to understand population shifts at a finer level and to be better able to link microbial diversity with ecosystems functioning. Microbial diagnostic microarrays (MDMs) represent a powerful tool for the parallel, high-throughput identification of many microorganisms. Three categories of MDMs have been defined based on the nature of the probe and target molecules used: phylogenetic oligonucleotide microarrays with short oligonucleotides against a phylogenetic marker gene; functional gene arrays containing probes targeting genes encoding specific functions; and community genome arrays employing whole genomes as probes. In this review, important methodological developments relevant to the application of the different types of diagnostic microarrays in soil ecology will be addressed and new approaches, needs and future directions will be identified, which might lead to a better insight into the functional activities of soil microbial communities.
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Affiliation(s)
- A Sessitsch
- ARC Seibersdorf research GmbH, Department. of Bioresources, A-2444 Seibersdorf, Austria.
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