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Light structures phototroph, bacterial and fungal communities at the soil surface.

Davies LO, Schäfer H, Marshall S, Bramke I, Oliver RG, Bending GD - PLoS ONE (2013)

Bottom Line: Microbial community structure changed with time and structurally similar phototrophic communities were found at the soil surface and in bulk soil in the light exposed microcosms suggesting that light can influence phototroph community structure even in the underlying bulk soil. 454 pyrosequencing showed a significant selection for diazotrophic cyanobacteria such as Nostoc punctiforme and Anabaena spp., in addition to the green alga Scenedesmus obliquus.The soil surface also harboured distinct heterotrophic bacterial and fungal communities in the presence of light, in particular, the selection for the phylum Firmicutes.However, these light driven changes in bacterial community structure did not extend to the underlying soil suggesting a discrete zone of influence, analogous to the rhizosphere.

View Article: PubMed Central - PubMed

Affiliation: School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry, United Kingdom. l.o.davies@warwick.ac.uk

ABSTRACT
The upper few millimeters of soil harbour photosynthetic microbial communities that are structurally distinct from those of underlying bulk soil due to the presence of light. Previous studies in arid zones have demonstrated functional importance of these communities in reducing soil erosion, and enhancing carbon and nitrogen fixation. Despite being widely distributed, comparative understanding of the biodiversity of the soil surface and underlying soil is lacking, particularly in temperate zones. We investigated the establishment of soil surface communities on pasture soil in microcosms exposed to light or dark conditions, focusing on changes in phototroph, bacterial and fungal communities at the soil surface (0-3 mm) and bulk soil (3-12 mm) using ribosomal marker gene analyses. Microbial community structure changed with time and structurally similar phototrophic communities were found at the soil surface and in bulk soil in the light exposed microcosms suggesting that light can influence phototroph community structure even in the underlying bulk soil. 454 pyrosequencing showed a significant selection for diazotrophic cyanobacteria such as Nostoc punctiforme and Anabaena spp., in addition to the green alga Scenedesmus obliquus. The soil surface also harboured distinct heterotrophic bacterial and fungal communities in the presence of light, in particular, the selection for the phylum Firmicutes. However, these light driven changes in bacterial community structure did not extend to the underlying soil suggesting a discrete zone of influence, analogous to the rhizosphere.

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Phototroph community structure at the soil surface under light and dark conditions.The diversity and abundance of phototrophs (23S rRNA genes of plastids) at the soil surface of a pasture soil after 80 days incubation under light or dark conditions. Data is presented in MEGAN as an OTU table created in QIIME at a 97% similarity threshold (uclust). The number of reads that can be assigned to each taxon are shown at the end of each node. Pie charts show the proportion of reads assigned to each sample incubated under light (green) and dark (brown) conditions with replicates displayed as shades of these colours. Taxonomic assignments with only one read were removed. Significant differences in the read abundance of sequences between light and dark samples are highlighted in green when abundance is significantly higher under light conditions and in blue when abundance is significantly higher under dark conditions (p<0.05).
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pone-0069048-g004: Phototroph community structure at the soil surface under light and dark conditions.The diversity and abundance of phototrophs (23S rRNA genes of plastids) at the soil surface of a pasture soil after 80 days incubation under light or dark conditions. Data is presented in MEGAN as an OTU table created in QIIME at a 97% similarity threshold (uclust). The number of reads that can be assigned to each taxon are shown at the end of each node. Pie charts show the proportion of reads assigned to each sample incubated under light (green) and dark (brown) conditions with replicates displayed as shades of these colours. Taxonomic assignments with only one read were removed. Significant differences in the read abundance of sequences between light and dark samples are highlighted in green when abundance is significantly higher under light conditions and in blue when abundance is significantly higher under dark conditions (p<0.05).

Mentions: A wide range of cyanobacteria and eukaryotic phototrophs were detected, including green, red and brown algae, cryptomonads, diatoms, mosses, and angiosperms (Figure 4). Relative composition analysis showed that cyanobacteria, rather than eukaryotic phototrophs, dominated under both treatments, with a relatively greater number of reads assigned to cyanobacteria under light compared to dark conditions (p<0.01) (Table 2). Further, the relative composition of cyanobacteria differed between light treatments e.g. 65.1%±SE 0.96% and 12.6%±SE 2.17% of reads had close homology to N. punctiforme PCC 73102 under light and dark conditions, respectively (p≤0.001), 11.6%±SE 2.02% and 2.4%±SE 0.11% of reads had close homology to Anabaena variabilis ATCC 29413 under light and dark, respectively (p≤0.01), and 2.5%±SE 0.26% and 1.0%±SE 0.29% of reads had close homology to A. cylindrica PCC 7122 under light and dark, respectively (p≤0.05) (Figure 4). There were no clearly dominant taxa under dark conditions, rather, seven taxa had a relative read abundance between 6% and 15%, which ranked as follows: Cyanothece sp.>N. punctiforme>Thermosynechococcus elongatus>Cryptomonas paramecium>Ricinus communis>Gloeobacter violaceus>Scenedesmus obliquus (Figure 4).


Light structures phototroph, bacterial and fungal communities at the soil surface.

Davies LO, Schäfer H, Marshall S, Bramke I, Oliver RG, Bending GD - PLoS ONE (2013)

Phototroph community structure at the soil surface under light and dark conditions.The diversity and abundance of phototrophs (23S rRNA genes of plastids) at the soil surface of a pasture soil after 80 days incubation under light or dark conditions. Data is presented in MEGAN as an OTU table created in QIIME at a 97% similarity threshold (uclust). The number of reads that can be assigned to each taxon are shown at the end of each node. Pie charts show the proportion of reads assigned to each sample incubated under light (green) and dark (brown) conditions with replicates displayed as shades of these colours. Taxonomic assignments with only one read were removed. Significant differences in the read abundance of sequences between light and dark samples are highlighted in green when abundance is significantly higher under light conditions and in blue when abundance is significantly higher under dark conditions (p<0.05).
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3716809&req=5

pone-0069048-g004: Phototroph community structure at the soil surface under light and dark conditions.The diversity and abundance of phototrophs (23S rRNA genes of plastids) at the soil surface of a pasture soil after 80 days incubation under light or dark conditions. Data is presented in MEGAN as an OTU table created in QIIME at a 97% similarity threshold (uclust). The number of reads that can be assigned to each taxon are shown at the end of each node. Pie charts show the proportion of reads assigned to each sample incubated under light (green) and dark (brown) conditions with replicates displayed as shades of these colours. Taxonomic assignments with only one read were removed. Significant differences in the read abundance of sequences between light and dark samples are highlighted in green when abundance is significantly higher under light conditions and in blue when abundance is significantly higher under dark conditions (p<0.05).
Mentions: A wide range of cyanobacteria and eukaryotic phototrophs were detected, including green, red and brown algae, cryptomonads, diatoms, mosses, and angiosperms (Figure 4). Relative composition analysis showed that cyanobacteria, rather than eukaryotic phototrophs, dominated under both treatments, with a relatively greater number of reads assigned to cyanobacteria under light compared to dark conditions (p<0.01) (Table 2). Further, the relative composition of cyanobacteria differed between light treatments e.g. 65.1%±SE 0.96% and 12.6%±SE 2.17% of reads had close homology to N. punctiforme PCC 73102 under light and dark conditions, respectively (p≤0.001), 11.6%±SE 2.02% and 2.4%±SE 0.11% of reads had close homology to Anabaena variabilis ATCC 29413 under light and dark, respectively (p≤0.01), and 2.5%±SE 0.26% and 1.0%±SE 0.29% of reads had close homology to A. cylindrica PCC 7122 under light and dark, respectively (p≤0.05) (Figure 4). There were no clearly dominant taxa under dark conditions, rather, seven taxa had a relative read abundance between 6% and 15%, which ranked as follows: Cyanothece sp.>N. punctiforme>Thermosynechococcus elongatus>Cryptomonas paramecium>Ricinus communis>Gloeobacter violaceus>Scenedesmus obliquus (Figure 4).

Bottom Line: Microbial community structure changed with time and structurally similar phototrophic communities were found at the soil surface and in bulk soil in the light exposed microcosms suggesting that light can influence phototroph community structure even in the underlying bulk soil. 454 pyrosequencing showed a significant selection for diazotrophic cyanobacteria such as Nostoc punctiforme and Anabaena spp., in addition to the green alga Scenedesmus obliquus.The soil surface also harboured distinct heterotrophic bacterial and fungal communities in the presence of light, in particular, the selection for the phylum Firmicutes.However, these light driven changes in bacterial community structure did not extend to the underlying soil suggesting a discrete zone of influence, analogous to the rhizosphere.

View Article: PubMed Central - PubMed

Affiliation: School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry, United Kingdom. l.o.davies@warwick.ac.uk

ABSTRACT
The upper few millimeters of soil harbour photosynthetic microbial communities that are structurally distinct from those of underlying bulk soil due to the presence of light. Previous studies in arid zones have demonstrated functional importance of these communities in reducing soil erosion, and enhancing carbon and nitrogen fixation. Despite being widely distributed, comparative understanding of the biodiversity of the soil surface and underlying soil is lacking, particularly in temperate zones. We investigated the establishment of soil surface communities on pasture soil in microcosms exposed to light or dark conditions, focusing on changes in phototroph, bacterial and fungal communities at the soil surface (0-3 mm) and bulk soil (3-12 mm) using ribosomal marker gene analyses. Microbial community structure changed with time and structurally similar phototrophic communities were found at the soil surface and in bulk soil in the light exposed microcosms suggesting that light can influence phototroph community structure even in the underlying bulk soil. 454 pyrosequencing showed a significant selection for diazotrophic cyanobacteria such as Nostoc punctiforme and Anabaena spp., in addition to the green alga Scenedesmus obliquus. The soil surface also harboured distinct heterotrophic bacterial and fungal communities in the presence of light, in particular, the selection for the phylum Firmicutes. However, these light driven changes in bacterial community structure did not extend to the underlying soil suggesting a discrete zone of influence, analogous to the rhizosphere.

Show MeSH
Related in: MedlinePlus