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Armstrong A, Valverde A, Ramond JB, Makhalanyane TP, Jansson JK, Hopkins DW, Aspray TJ, Seely M, Trindade MI, Cowan DA. Temporal dynamics of hot desert microbial communities reveal structural and functional responses to water input. Sci Rep 2016; 6:34434. [PMID: 27680878 PMCID: PMC5041089 DOI: 10.1038/srep34434] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 09/14/2016] [Indexed: 02/01/2023] Open
Abstract
The temporal dynamics of desert soil microbial communities are poorly understood. Given the implications for ecosystem functioning under a global change scenario, a better understanding of desert microbial community stability is crucial. Here, we sampled soils in the central Namib Desert on sixteen different occasions over a one-year period. Using Illumina-based amplicon sequencing of the 16S rRNA gene, we found that α-diversity (richness) was more variable at a given sampling date (spatial variability) than over the course of one year (temporal variability). Community composition remained essentially unchanged across the first 10 months, indicating that spatial sampling might be more important than temporal sampling when assessing β-diversity patterns in desert soils. However, a major shift in microbial community composition was found following a single precipitation event. This shift in composition was associated with a rapid increase in CO2 respiration and productivity, supporting the view that desert soil microbial communities respond rapidly to re-wetting and that this response may be the result of both taxon-specific selection and changes in the availability or accessibility of organic substrates. Recovery to quasi pre-disturbance community composition was achieved within one month after rainfall.
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Affiliation(s)
- Alacia Armstrong
- Centre for Microbial Ecology and Genomics (CMEG), Genomics Research Institute, Department of Genetics, University of Pretoria, Pretoria 0002, South Africa
| | - Angel Valverde
- Centre for Microbial Ecology and Genomics (CMEG), Genomics Research Institute, Department of Genetics, University of Pretoria, Pretoria 0002, South Africa
| | - Jean-Baptiste Ramond
- Centre for Microbial Ecology and Genomics (CMEG), Genomics Research Institute, Department of Genetics, University of Pretoria, Pretoria 0002, South Africa
| | - Thulani P Makhalanyane
- Centre for Microbial Ecology and Genomics (CMEG), Genomics Research Institute, Department of Genetics, University of Pretoria, Pretoria 0002, South Africa
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - David W Hopkins
- The Royal Agricultural University, Cirencester, Gloucestershire GL7 6JS, UK
| | - Thomas J Aspray
- School of Life Sciences, Heriot-Watt University, Edinburgh, EH14 4AS, UK
| | - Mary Seely
- Gobabeb Training and Research Centre (GTRC), Walvis Bay, Namibia.,Animal, Plant and Environmental Sciences, University of Witwatersrand, Johannesburg, South Africa
| | - Marla I Trindade
- Institute for Microbial Biotechnology and Metagenomics (IMBM). University of the Western Cape, Bellville 7535, South Africa
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics (CMEG), Genomics Research Institute, Department of Genetics, University of Pretoria, Pretoria 0002, South Africa
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Adriaenssens EM, van Zyl LJ, Cowan DA, Trindade MI. Metaviromics of Namib Desert Salt Pans: A Novel Lineage of Haloarchaeal Salterproviruses and a Rich Source of ssDNA Viruses. Viruses 2016; 8:v8010014. [PMID: 26761024 PMCID: PMC4728574 DOI: 10.3390/v8010014] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 11/26/2015] [Accepted: 12/14/2015] [Indexed: 11/26/2022] Open
Abstract
Viral communities of two different salt pans located in the Namib Desert, Hosabes and Eisfeld, were investigated using a combination of multiple displacement amplification of metaviromic DNA and deep sequencing, and provided comprehensive sequence data on both ssDNA and dsDNA viral community structures. Read and contig annotations through online pipelines showed that the salt pans harbored largely unknown viral communities. Through network analysis, we were able to assign a large portion of the unknown reads to a diverse group of ssDNA viruses. Contigs belonging to the subfamily Gokushovirinae were common in both environmental datasets. Analysis of haloarchaeal virus contigs revealed the presence of three contigs distantly related with His1, indicating a possible new lineage of salterproviruses in the Hosabes playa. Based on viral richness and read mapping analyses, the salt pan metaviromes were novel and most closely related to each other while showing a low degree of overlap with other environmental viromes.
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Affiliation(s)
- Evelien M Adriaenssens
- Centre for Microbial Ecology and Genomics, Genomics Research Institute, University of Pretoria, Natural Sciences II, Lynnwood Road, 0002 Pretoria, South Africa.
| | - Leonardo Joaquim van Zyl
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, 7535 Bellville, Cape Town, South Africa.
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, Genomics Research Institute, University of Pretoria, Natural Sciences II, Lynnwood Road, 0002 Pretoria, South Africa.
| | - Marla I Trindade
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, 7535 Bellville, Cape Town, South Africa.
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Abstract
The probiotic organism Bifidobacterium lactis was isolated from a yoghurt starter culture with the aim of analyzing its use of carbohydrates for the development of prebiotics. A sucrose utilization gene cluster of B. lactis was identified by complementation of a gene library in Escherichia coli. Three genes, encoding a sucrose phosphorylase (ScrP), a GalR-LacI-type transcriptional regulator (ScrR), and a sucrose transporter (ScrT), were identified by sequence analysis. The scrP gene was expressed constitutively from its own promoter in E. coli grown in complete medium, and the strain hydrolyzed sucrose in a reaction that was dependent on the presence of phosphates. Primer extension experiments with scrP performed by using RNA isolated from B. lactis identified the transcriptional start site 102 bp upstream of the ATG start codon, immediately adjacent to a palindromic sequence resembling a regulator binding site. In B. lactis, total sucrase activity was induced by the presence of sucrose, raffinose, or oligofructose in the culture medium and was repressed by glucose. RNA analysis of the scrP, scrR, and scrT genes in B. lactis indicated that expression of these genes was influenced by transcriptional regulation and that all three genes were similarly induced by sucrose and raffinose and repressed by glucose. Analysis of the sucrase activities of deletion constructs in heterologous E. coli indicated that ScrR functions as a positive regulator.
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Affiliation(s)
- Marla I Trindade
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch 7701, South Africa
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