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Taleski V, Dimkić I, Boev B, Boev I, Živković S, Stanković S. Bacterial and fungal diversity in the lorandite (TlAsS2) mine 'Allchar' in the Republic of North Macedonia. FEMS Microbiol Ecol 2021; 96:5891424. [PMID: 32785579 DOI: 10.1093/femsec/fiaa155] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 08/10/2020] [Indexed: 01/04/2023] Open
Abstract
The Allchar mineral mine is one of the oldest arsenic-antimony mines in the Republic of North Macedonia. The mine is a well-known reservoir of the worldwide purest source of the thallium-bearing mineral, lorandite (TlAsS2). The current study evaluated the bacterial and fungal diversity of three As- and Tl-contaminated sites in Allchar mineral mine. We used a combination of high-throughput sequencing and bioinformatic analyses. Trace metal content was detected using inductively coupled plasma optical emission spectrometry. Our analysis showed the presence of 25 elements and confirmed a high concentration of As and Tl. Alpha diversity indices suggested a high diversity and evenness of bacterial and fungal communities. Bacterial phyla that dominated the environment were Bacteroidetes, Acidobacteria, Planctomycetes, Actinobacteria and Verrucomicrobia. Looking at the genus level, we found the following groups of bacteria: Chryseolinea, Opitutus, Flavobacterium, Pseudomonas, Terrimonas, Sphingomonas and Reyranella. For the fungi genera, we report Tetracladium sp., Coprinellus micaceus, Coprinus sp. from Ascomycota and Basidiomycota phyla in all sites. We also observed a high abundance of the fungal species Pilidium sp., Dendroclathra lignicola, Rosellinia desmazieri, Hypomyces rosellus and Coprinellus disseminatus. This study is the first to identify specific As- and Tl-tolerant fungal (Pilidium sp., Cladophialophora sp., Neobulgaria sp. and Mycena acicula) and bacterial (Trichococcus, Devosia, Litorilinea and Gimesia) genera from Allchar mine, suggesting bioremediation and industrial potential.
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Affiliation(s)
- Vaso Taleski
- Goce Delčev University of Štip, "Krste Misirkov" 10-A, P.O. box 201, Stip, North Macedonia
| | - Ivica Dimkić
- University of Belgrade, Faculty of Biology, Studentski trg 16, P.O. box 11 000 Belgrade, Serbia
| | - Blazo Boev
- Goce Delčev University of Štip, "Krste Misirkov" 10-A, P.O. box 201, Stip, North Macedonia
| | - Ivan Boev
- Goce Delčev University of Štip, "Krste Misirkov" 10-A, P.O. box 201, Stip, North Macedonia
| | - Sanja Živković
- University of Belgrade, Institute of Nuclear Sciences Vinca, Mike Petrovica Alasa 12-14, P.O. box 11 351, Vinca, Belgrade, Serbia
| | - Slaviša Stanković
- University of Belgrade, Faculty of Biology, Studentski trg 16, P.O. box 11 000 Belgrade, Serbia
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Krauße T, Schütze E, Phieler R, Fürst D, Merten D, Büchel G, Kothe E. Changes in element availability induced by sterilization in heavy metal contaminated substrates: A comprehensive study. JOURNAL OF HAZARDOUS MATERIALS 2019; 370:70-79. [PMID: 29153855 DOI: 10.1016/j.jhazmat.2017.11.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 11/03/2017] [Accepted: 11/04/2017] [Indexed: 06/07/2023]
Abstract
Microbiome analyses of soils and microcosm experiments depend on conditions that include sterilization in order to perform experimental manipulation of microbial communities. Still, they should represent conditions close to nature. When using metal contaminated soils, sterilization methods might alter metal availability. Here, four typical metal contaminated substrates were analyzed, representing different contamination histories and soil types. They included two very poor substrates, as they are often found at metal contaminated sites. The low contents in organic carbon and nitrogen as well as two substrates with slightly higher nutrient availability were used to perform a comprehesive study for element availability changes induced by sterilization. Autoclaving, dry heat or gamma raγ sterilization were applied and compared to a non-treated control. The sterile substrates were analyzed using sequential extraction to account for different associations of the elements. Metals forming specific (hydro)oxide layers were specifically analyzed since they in turn may also impact other metals or ions. In addition, (heavy) metals and (micro)nutrients were analyzed for changes in speciation. The effects of autoclaving (wet heat) was found acceptable, while γ-ray irradiation did show unexpected changes in metal associations, especially for one substrate. Dry heat changed metal availability to the highest degree.
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Affiliation(s)
- Thomas Krauße
- Microbial Communication, Institute of Microbiology, Faculty of Biology and Pharmacy, Friedrich Schiller University Jena, Neugasse 25, 07743 Jena, Germany
| | - Eileen Schütze
- Microbial Communication, Institute of Microbiology, Faculty of Biology and Pharmacy, Friedrich Schiller University Jena, Neugasse 25, 07743 Jena, Germany
| | - René Phieler
- Microbial Communication, Institute of Microbiology, Faculty of Biology and Pharmacy, Friedrich Schiller University Jena, Neugasse 25, 07743 Jena, Germany
| | - David Fürst
- Microbial Communication, Institute of Microbiology, Faculty of Biology and Pharmacy, Friedrich Schiller University Jena, Neugasse 25, 07743 Jena, Germany
| | - Dirk Merten
- Applied Geology, Institute of Geosciences, Faculty of Chemistry and Earth Sciences, Friedrich Schiller University Jena, Burgweg 11, 07749 Jena, Germany
| | - Georg Büchel
- Applied Geology, Institute of Geosciences, Faculty of Chemistry and Earth Sciences, Friedrich Schiller University Jena, Burgweg 11, 07749 Jena, Germany
| | - Erika Kothe
- Microbial Communication, Institute of Microbiology, Faculty of Biology and Pharmacy, Friedrich Schiller University Jena, Neugasse 25, 07743 Jena, Germany.
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Lemmel F, Maunoury-Danger F, Fanesi A, Leyval C, Cébron A. Soil Properties and Multi-Pollution Affect Taxonomic and Functional Bacterial Diversity in a Range of French Soils Displaying an Anthropisation Gradient. MICROBIAL ECOLOGY 2019; 77:993-1013. [PMID: 30467715 DOI: 10.1007/s00248-018-1297-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 11/16/2018] [Indexed: 05/20/2023]
Abstract
The intensive industrial activities of the twentieth century have left behind highly contaminated wasteland soils. It is well known that soil parameters and the presence of pollutants shape microbial communities. But in such industrial waste sites, the soil multi-contamination with organic (polycyclic aromatic hydrocarbons, PAH) and metallic (Zn, Pb, Cd) pollutants and long-term exposure may induce a selection pressure on microbial communities that may modify soil functioning. The aim of our study was to evaluate the impact of long-term multi-contamination and soil characteristics on bacterial taxonomic and functional diversity as related to the carbon cycle. We worked on 10 soils from northeast of France distributed into three groups (low anthropised controls, slag heaps, and settling ponds) based on their physico-chemical properties (texture, C, N) and pollution level. We assessed bacterial taxonomic diversity by 16S rDNA Illumina sequencing, and functional diversity using Biolog® and MicroResp™ microtiter plate tools. Although taxonomic diversity at the phylum level was not different among the soil groups, many operational taxonomic units were influenced by metal or PAH pollution, and by soil texture and total nitrogen content. Functional diversity was not influenced by PAH contamination while metal pollution selected microbial communities with reduced metabolic functional diversity but more tolerant to zinc. Limited microbial utilisation of carbon substrates in metal-polluted soils was mainly due to the nitrogen content. Based on these two observations, we hypothesised that reduced microbial activity and lower carbon cycle-related functional diversity may have contributed to the accumulation of organic matter in the soils that exhibited the highest levels of metal pollution.
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Affiliation(s)
- Florian Lemmel
- Université de Lorraine, CNRS, LIEC, 54000, Nancy, France
| | | | - Andrea Fanesi
- Université de Lorraine, CNRS, LIEC, 54000, Nancy, France
| | - Corinne Leyval
- Université de Lorraine, CNRS, LIEC, 54000, Nancy, France
| | - Aurélie Cébron
- Université de Lorraine, CNRS, LIEC, 54000, Nancy, France.
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Tu C, Guan F, Sun Y, Guo P, Liu Y, Li L, Scheckel KG, Luo Y. Stabilizing Effects on a Cd Polluted Coastal Wetland Soil using Calcium Polysulphide. GEODERMA 2018; 332:190-197. [PMID: 30504969 PMCID: PMC6260968 DOI: 10.1016/j.geoderma.2018.07.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
In this study, different dosages of calcium polysulphide (CaSx) were used as an amendment to investigate effects on the immobilizing of Cd in a wetland soil by pot experiment. In addition to chemical analysis (pH and bioavailable Cd concentration), changes in soil enzyme activities, microbial carbon utilization capacity, metabolic and community diversity were examined to assess dynamic impacts on soil environmental quality and toxicity of Cd resulting from ameliorant dosing. Soil pH increased immediately upon CaSx amendment compared to the unamended control (CK), and then declined slowly to a level lower than CK. Diethylenetriamine pentaacetic acid (DTPA) extractable Cd concentration was determined to characterize the bioavailability of Cd in the soil. The CaSx dose-dependent effect observed that with increasing CaSx dosage, the immobilizing efficiency decreased. Soil urease and catalase activity assays and Biolog EcoPlate assay indicated that early stage addition of CaSx significantly inhibited soil microbial activities. However, mid and late stage time periods showed the inhibition effects were alleviated, and the microbial activities could be recovered in 1% and 2% CaSx treatments. Moreover, with increasing incubation time, microbial community diversity and richness were significantly recovered in 1% and 2% CaSx treatments compared to the CK. No considerable changes were observed in the 5% CaSx treatment. Conclusively, the 1% CaSx amendment was an efficient and safe dosage for the stabilization of Cd contaminated wetland soil. This study contributes to the development of in situ remediation ameliorants and technologies for heavy metal polluted wetland soils.
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Affiliation(s)
- Chen Tu
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Feng Guan
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Yuhuan Sun
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Pengpeng Guo
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Ying Liu
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Lianzhen Li
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Kirk G Scheckel
- National Risk Management Research Laboratory, United States Environmental Protection Agency, Cincinnati 45224, USA
| | - Yongming Luo
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
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Pathak RK, Baunthiyal M, Pandey D, Kumar A. Augmentation of crop productivity through interventions of omics technologies in India: challenges and opportunities. 3 Biotech 2018; 8:454. [PMID: 30370195 PMCID: PMC6195494 DOI: 10.1007/s13205-018-1473-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 10/09/2018] [Indexed: 01/19/2023] Open
Abstract
With the continuous increase in the population of developing countries and decline of natural resources, there is an urgent need to qualitatively and quantitatively augment crop productivity by using new tools and technologies for improvement of agriculturally important traits. The new scientific and technological omics-based approaches have enabled us to deal with several issues and challenges faced by modern agricultural system and provided us novel opportunities for ensuring food and nutritional security. Recent developments in sequencing techniques have made available huge amount of genomic and transcriptomic data on model and cultivated crop plants including Arabidopsis thaliana, Oryza sativa, Triticum aestivum etc. The sequencing data along with other data generated through several omics platforms have significantly influenced the disciplines of crop sciences. Gene discovery and expression profiling-based technologies are offering enormous opportunities to the scientific community which can now apply marker-assisted selection technology to assess and enhance diversity in their collected germplasm, introgress essential traits from new sources and investigate genes that control key traits of crop plants. Utilization of omics science and technologies for crop productivity, protection and management has recently been receiving a lot of attention; the majority of the efforts have been put into signifying the possible applications of various omics technologies in crop plant sciences. This article highlights the background of challenges and opportunities for augmentation of crop productivity through interventions of omics technologies in India.
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Affiliation(s)
- Rajesh Kumar Pathak
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
- Department of Biotechnology, G. B. Pant Institute of Engineering and Technology, Pauri Garhwal, Uttarakhand 246194 India
| | - Mamta Baunthiyal
- Department of Biotechnology, G. B. Pant Institute of Engineering and Technology, Pauri Garhwal, Uttarakhand 246194 India
| | - Dinesh Pandey
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Anil Kumar
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
- Present Address: Rani Lakshmi Bai Central Agricultural University, Jhansi, Uttar Pradesh 284003 India
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Yu H, Si P, Shao W, Qiao X, Yang X, Gao D, Wang Z. Response of enzyme activities and microbial communities to soil amendment with sugar alcohols. Microbiologyopen 2016; 5:604-15. [PMID: 27005019 PMCID: PMC4985594 DOI: 10.1002/mbo3.355] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 02/17/2016] [Accepted: 02/23/2016] [Indexed: 01/15/2023] Open
Abstract
Changes in microbial community structure are widely known to occur after soil amendment with low-molecular-weight organic compounds; however, there is little information on concurrent changes in soil microbial functional diversity and enzyme activities, especially following sorbitol and mannitol amendment. Soil microbial functional diversity and enzyme activities can be impacted by sorbitol and mannitol, which in turn can alter soil fertility and quality. The objective of this study was to investigate the effects of sorbitol and mannitol addition on microbial functional diversity and enzyme activities. The results demonstrated that sorbitol and mannitol addition altered the soil microbial community structure and improved enzyme activities. Specifically, the addition of sorbitol enhanced the community-level physiological profile (CLPP) compared with the control, whereas the CLPP was significantly inhibited by the addition of mannitol. The results of a varimax rotated component matrix demonstrated that carbohydrates, polymers, and carboxylic acids affected the soil microbial functional structure. Additionally, we found that enzyme activities were affected by both the concentration and type of inputs. In the presence of high concentrations of sorbitol, the urease, catalase, alkaline phosphatase, β-glucosidase, and N-acetyl-β-d-glucosaminidase activities were significantly increased, while invertase activity was decreased. Similarly, this increase in invertase, catalase, and alkaline phosphatase and N-acetyl-β-d-glucosaminidase activities was especially evident after mannitol addition, and urease activity was only slightly affected. In contrast, β-glucosidase activity was suppressed at the highest concentration. These results indicate that microbial community diversity and enzyme activities are significantly affected by soil amendment with sorbitol and mannitol.
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Affiliation(s)
- Huili Yu
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouHenan450000China
| | - Peng Si
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouHenan450000China
| | - Wei Shao
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouHenan450000China
| | - Xiansheng Qiao
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouHenan450000China
| | - Xiaojing Yang
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouHenan450000China
| | - Dengtao Gao
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouHenan450000China
| | - Zhiqiang Wang
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouHenan450000China
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Sun B, Jia S, Zhang S, McLaughlin NB, Liang A, Chen X, Liu S, Zhang X. No tillage combined with crop rotation improves soil microbial community composition and metabolic activity. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:6472-82. [PMID: 26631020 DOI: 10.1007/s11356-015-5812-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 11/13/2015] [Indexed: 06/05/2023]
Abstract
Soil microbial community can vary with different agricultural managements, which in turn can affect soil quality. The objective of this work was to evaluate the effects of long-term tillage practice (no tillage (NT) and conventional tillage (CT)) and crop rotation (maize-soybean (MS) rotation and monoculture maize (MM)) on soil microbial community composition and metabolic capacity in different soil layers. Long-term NT increased the soil organic carbon (SOC) and total nitrogen (TN) mainly at the 0-5 cm depth which was accompanied with a greater microbial abundance. The greater fungi-to-bacteria (F/B) ratio was found in NTMS at the 0-5 cm depth. Both tillage and crop rotation had a significant effect on the metabolic activity, with the greatest average well color development (AWCD) value in NTMS soil at all three soil depths. Redundancy analysis (RDA) showed that the shift in microbial community composition was accompanied with the changes in capacity of utilizing different carbon substrates. Therefore, no tillage combined with crop rotation could improve soil biological quality and make agricultural systems more sustainable.
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Affiliation(s)
- Bingjie Sun
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 4888 Shengbei Street, Changchun, Jilin, 130102, China
- University of Chinese Academy of Science, Beijing, 100049, China
| | - Shuxia Jia
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 4888 Shengbei Street, Changchun, Jilin, 130102, China.
| | - Shixiu Zhang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 4888 Shengbei Street, Changchun, Jilin, 130102, China
| | - Neil B McLaughlin
- Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, Ottawa, K1A 0C6, Canada
| | - Aizhen Liang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 4888 Shengbei Street, Changchun, Jilin, 130102, China
| | - Xuewen Chen
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 4888 Shengbei Street, Changchun, Jilin, 130102, China
| | - Siyi Liu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 4888 Shengbei Street, Changchun, Jilin, 130102, China
- University of Chinese Academy of Science, Beijing, 100049, China
| | - Xiaoping Zhang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 4888 Shengbei Street, Changchun, Jilin, 130102, China
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Markowicz A, Woźniak G, Borymski S, Piotrowska-Seget Z, Chmura D. Links in the functional diversity between soil microorganisms and plant communities during natural succession in coal mine spoil heaps. Ecol Res 2015. [DOI: 10.1007/s11284-015-1301-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Guo P, Zhu L, Wang J, Wang J, Liu T. Effects of alkyl-imidazolium ionic liquid [Omim]Cl on the functional diversity of soil microbial communities. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:9059-9066. [PMID: 25572271 DOI: 10.1007/s11356-014-4052-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 12/26/2014] [Indexed: 06/04/2023]
Abstract
As low-temperature molten salts, ionic liquids (ILs) were considered to be "green" solvents and have begun to see large-scale applications in the chemical reactions, in separation processes, in electrochemistry studies, etc. In recent years, the toxicity of ILs has started to draw attention. To evaluate the effects of the ionic liquid [Omim]Cl on indigenous microbial community in soil, Biolog-ECO plate method were used with the addition of four different concentrations of [Omim]Cl after four different incubation periods (7, 14, 21, 28 days). The present results showed that the average well color development (AWCD) was strongly activated when the soil was contaminated with [Omim]Cl in the early stages of the incubation. However, the activation effect disappeared with extended incubation time. Therefore, the toxic effects of the alkyl-imidazolium ionic liquid ([Omim]Cl) on the functional diversity of soil microbial communities may be reversible. In addition, the kinetic characteristics of microorganisms that used different categories of carbon sources indicated that phenolic compounds were the main C source in the sample soil.
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Affiliation(s)
- Pengpeng Guo
- College of Resources and Environment, Key Laboratory of Agriculture Environment in Universities of Shandong, Shandong Agricultural University, 61 Daizong Road, Taian, 271018, People's Republic of China,
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Youssef NH, Couger MB, McCully AL, Criado AEG, Elshahed MS. Assessing the global phylum level diversity within the bacterial domain: A review. J Adv Res 2014; 6:269-82. [PMID: 26257925 PMCID: PMC4522544 DOI: 10.1016/j.jare.2014.10.005] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 10/06/2014] [Accepted: 10/23/2014] [Indexed: 12/11/2022] Open
Abstract
Microbial ecology is the study of microbes in the natural environment and their interactions with each other. Investigating the nature of microorganisms residing within a specific habitat is an extremely important component of microbial ecology. Such microbial diversity surveys aim to determine the identity, physiological preferences, metabolic capabilities, and genomic features of microbial taxa within a specific ecosystem. A comprehensive review of various aspects of microbial diversity (phylogenetic, functional, and genomic diversities) in the microbial (bacterial, archaeal, and microeukaryotic) world is clearly a daunting task that could not be aptly summarized in a single review. Here, we focus on one aspect of diversity (phylogenetic diversity) in one microbial domain (the Bacteria). We restrict our analysis to the highest taxonomic rank (phylum) and attempt to investigate the extent of global phylum level diversity within the Bacteria. We present a brief historical perspective on the subject and highlight how the adaptation of molecular biological and phylogenetic approaches has greatly expanded our view of global bacterial diversity. We also summarize recent progress toward the discovery of novel bacterial phyla, present evidences that the scope of phylum level diversity in nature has hardly been exhausted, and propose novel approaches that could greatly facilitate the discovery process of novel bacterial phyla within various ecosystems.
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Affiliation(s)
- Noha H Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - M B Couger
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Alexandra L McCully
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | | | - Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
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