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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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Related in: MedlinePlus

Phototroph diversity at the soil surface under light and dark conditions.α diversity estimates Chao1 (a) and Observed Species (b) and non-metric multidimensional scaling of community structure similarity (c) for phototrophs (23S rRNA genes of plastids) at the soil surface of a pasture soil after 80 days incubation under light (open symbols) or dark (closed symbols) conditions. OTU clustering was performed at the 97% similarity threshold using UCLUST. Error bars are ±1 S.E. Non-metric multidimensional scaling shows clustering based on the similarity of microbial community structure between treatments: 20% (red cluster), 25% (black cluster) and 80% (blue cluster).
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pone-0069048-g003: Phototroph diversity at the soil surface under light and dark conditions.α diversity estimates Chao1 (a) and Observed Species (b) and non-metric multidimensional scaling of community structure similarity (c) for phototrophs (23S rRNA genes of plastids) at the soil surface of a pasture soil after 80 days incubation under light (open symbols) or dark (closed symbols) conditions. OTU clustering was performed at the 97% similarity threshold using UCLUST. Error bars are ±1 S.E. Non-metric multidimensional scaling shows clustering based on the similarity of microbial community structure between treatments: 20% (red cluster), 25% (black cluster) and 80% (blue cluster).

Mentions: Pyrosequencing revealed a total of 533 phototrophic OTUs across all samples with an average length of 351 bp, and an average of 71.7 reads assigned to each OTU, out of a total of 38203 processed reads. Chao1 index and Observed Species were both significantly higher at the soil surface incubated in the dark compared to light conditions (p≤0.001) (Figures 3a & 3b). Moreover, there were an estimated 246 unique phototroph OTUs under dark conditions compared to only 80 under light conditions (Figure 3b). Figures 3a and 3b both show that diversity plateaus under light as sampling depth increased, however, under dark conditions a plateau was not observed. NMDS analysis of phototroph community structure showed a closer clustering of samples under light compared to dark conditions, which suggests that phototroph community structure was less variable under light conditions (Figure 3c).


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 diversity at the soil surface under light and dark conditions.α diversity estimates Chao1 (a) and Observed Species (b) and non-metric multidimensional scaling of community structure similarity (c) for phototrophs (23S rRNA genes of plastids) at the soil surface of a pasture soil after 80 days incubation under light (open symbols) or dark (closed symbols) conditions. OTU clustering was performed at the 97% similarity threshold using UCLUST. Error bars are ±1 S.E. Non-metric multidimensional scaling shows clustering based on the similarity of microbial community structure between treatments: 20% (red cluster), 25% (black cluster) and 80% (blue cluster).
© Copyright Policy
Related In: Results  -  Collection

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

pone-0069048-g003: Phototroph diversity at the soil surface under light and dark conditions.α diversity estimates Chao1 (a) and Observed Species (b) and non-metric multidimensional scaling of community structure similarity (c) for phototrophs (23S rRNA genes of plastids) at the soil surface of a pasture soil after 80 days incubation under light (open symbols) or dark (closed symbols) conditions. OTU clustering was performed at the 97% similarity threshold using UCLUST. Error bars are ±1 S.E. Non-metric multidimensional scaling shows clustering based on the similarity of microbial community structure between treatments: 20% (red cluster), 25% (black cluster) and 80% (blue cluster).
Mentions: Pyrosequencing revealed a total of 533 phototrophic OTUs across all samples with an average length of 351 bp, and an average of 71.7 reads assigned to each OTU, out of a total of 38203 processed reads. Chao1 index and Observed Species were both significantly higher at the soil surface incubated in the dark compared to light conditions (p≤0.001) (Figures 3a & 3b). Moreover, there were an estimated 246 unique phototroph OTUs under dark conditions compared to only 80 under light conditions (Figure 3b). Figures 3a and 3b both show that diversity plateaus under light as sampling depth increased, however, under dark conditions a plateau was not observed. NMDS analysis of phototroph community structure showed a closer clustering of samples under light compared to dark conditions, which suggests that phototroph community structure was less variable under light conditions (Figure 3c).

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