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Spatial Ecology of Bacteria at the Microscale in Soil

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  • Xavier Raynaud
  • Naoise Nunan

Abstract

Despite an exceptional number of bacterial cells and species in soils, bacterial diversity seems to have little effect on soil processes, such as respiration or nitrification, that can be affected by interactions between bacterial cells. The aim of this study is to understand how bacterial cells are distributed in soil to better understand the scaling between cell-to-cell interactions and what can be measured in a few milligrams, or more, of soil. Based on the analysis of 744 images of observed bacterial distributions in soil thin sections taken at different depths, we found that the inter-cell distance was, on average 12.46 µm and that these inter-cell distances were shorter near the soil surface (10.38 µm) than at depth (>18 µm), due to changes in cell densities. These images were also used to develop a spatial statistical model, based on Log Gaussian Cox Processes, to analyse the 2D distribution of cells and construct realistic 3D bacterial distributions. Our analyses suggest that despite the very high number of cells and species in soil, bacteria only interact with a few other individuals. For example, at bacterial densities commonly found in bulk soil (108 cells g−1 soil), the number of neighbours a single bacterium has within an interaction distance of ca. 20 µm is relatively limited (120 cells on average). Making conservative assumptions about the distribution of species, we show that such neighbourhoods contain less than 100 species. This value did not change appreciably as a function of the overall diversity in soil, suggesting that the diversity of soil bacterial communities may be species-saturated. All in all, this work provides precise data on bacterial distributions, a novel way to model them at the micrometer scale as well as some new insights on the degree of interactions between individual bacterial cells in soils.

Suggested Citation

  • Xavier Raynaud & Naoise Nunan, 2014. "Spatial Ecology of Bacteria at the Microscale in Soil," PLOS ONE, Public Library of Science, vol. 9(1), pages 1-9, January.
  • Handle: RePEc:plo:pone00:0087217
    DOI: 10.1371/journal.pone.0087217
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    Cited by:

    1. Stacy Slobodiuk & Caitlin Niven & Greer Arthur & Siddhartha Thakur & Ayse Ercumen, 2021. "Does Irrigation with Treated and Untreated Wastewater Increase Antimicrobial Resistance in Soil and Water: A Systematic Review," IJERPH, MDPI, vol. 18(21), pages 1-19, October.
    2. Brémond, Ulysse & Bertrandias, Aude & Loisel, Denis & Jimenez, Julie & Steyer, Jean-Philippe & Bernet, Nicolas & Carrere, Hélène, 2020. "Assessment of fungal and thermo-alkaline post-treatments of solid digestate in a recirculation scheme to increase flexibility in feedstocks supply management of biogas plants," Renewable Energy, Elsevier, vol. 149(C), pages 641-651.
    3. Ivan Sazykin & Ludmila Khmelevtsova & Tatiana Azhogina & Marina Sazykina, 2023. "Heavy Metals Influence on the Bacterial Community of Soils: A Review," Agriculture, MDPI, vol. 13(3), pages 1-23, March.
    4. Xiaokan Guo & James Q Boedicker, 2016. "The Contribution of High-Order Metabolic Interactions to the Global Activity of a Four-Species Microbial Community," PLOS Computational Biology, Public Library of Science, vol. 12(9), pages 1-13, September.
    5. Shuting Zhao & Taoran Shi & Akihiko Terada & Shohei Riya, 2022. "Evaluation of Pollution Level, Spatial Distribution, and Ecological Effects of Antimony in Soils of Mining Areas: A Review," IJERPH, MDPI, vol. 20(1), pages 1-25, December.
    6. Senka Čaušević & Manupriyam Dubey & Marian Morales & Guillem Salazar & Vladimir Sentchilo & Nicolas Carraro & Hans-Joachim Ruscheweyh & Shinichi Sunagawa & Jan Roelof van der Meer, 2024. "Niche availability and competitive loss by facilitation control proliferation of bacterial strains intended for soil microbiome interventions," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
    7. Xiaoji (Christine) Liu & Kevin D. Floate & Monika A. Gorzelak & Devin B. Holman & Scott Hrycauk & Hiroshi Kubota & Newton Lupwayi & Jonathan A. D. Neilson & Rodrigo Ortega Polo & Renée M. Petri & Lan , 2023. "Prairie Agroecosystems: Interconnected Microbiomes of Livestock, Soil and Insects," Agriculture, MDPI, vol. 13(2), pages 1-28, January.
    8. Shaista Nosheen & Iqra Ajmal & Yuanda Song, 2021. "Microbes as Biofertilizers, a Potential Approach for Sustainable Crop Production," Sustainability, MDPI, vol. 13(4), pages 1-20, February.

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