Spatial Ecology of Bacteria at the Microscale in Soil
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{"title"=>"Spatial ecology of bacteria at the microscale in soil", "type"=>"journal", "authors"=>[{"first_name"=>"Xavier", "last_name"=>"Raynaud", "scopus_author_id"=>"12752610500"}, {"first_name"=>"Naoise", "last_name"=>"Nunan", "scopus_author_id"=>"56017037300"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-84900339353", "sgr"=>"84900339353", "pui"=>"373059242", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "pmid"=>"24489873", "doi"=>"10.1371/journal.pone.0087217"}, "id"=>"037358b0-ed44-3fce-9e6e-68db372cecf4", "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 (10(8) 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.", "link"=>"http://www.mendeley.com/research/spatial-ecology-bacteria-microscale-soil", "reader_count"=>248, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>9, "Researcher"=>52, "Student > Doctoral Student"=>14, "Student > Ph. D. Student"=>102, "Student > Postgraduate"=>8, "Student > Master"=>29, "Other"=>5, "Student > Bachelor"=>15, "Lecturer"=>2, "Professor"=>10}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>9, "Researcher"=>52, "Student > Doctoral Student"=>14, "Student > Ph. D. Student"=>102, "Student > Postgraduate"=>8, "Student > Master"=>29, "Other"=>5, "Student > Bachelor"=>15, "Lecturer"=>2, "Professor"=>10}, "reader_count_by_subject_area"=>{"Unspecified"=>10, "Agricultural and Biological Sciences"=>135, "Veterinary Science and Veterinary Medicine"=>1, "Business, Management and Accounting"=>1, "Chemical Engineering"=>1, "Chemistry"=>5, "Earth and Planetary Sciences"=>13, "Engineering"=>4, "Environmental Science"=>43, "Biochemistry, Genetics and Molecular Biology"=>20, "Mathematics"=>3, "Medicine and Dentistry"=>1, "Neuroscience"=>1, "Physics and Astronomy"=>1, "Social Sciences"=>1, "Immunology and Microbiology"=>8}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Social Sciences"=>{"Social Sciences"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Mathematics"=>{"Mathematics"=>3}, "Unspecified"=>{"Unspecified"=>10}, "Environmental Science"=>{"Environmental Science"=>43}, "Chemical Engineering"=>{"Chemical Engineering"=>1}, "Engineering"=>{"Engineering"=>4}, "Chemistry"=>{"Chemistry"=>5}, "Neuroscience"=>{"Neuroscience"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>13}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>8}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>135}, "Business, Management and Accounting"=>{"Business, Management and Accounting"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>20}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>1}}, "reader_count_by_country"=>{"Canada"=>1, "Czech Republic"=>1, "United States"=>17, "Denmark"=>1, "Brazil"=>2, "United Kingdom"=>6, "France"=>4, "Australia"=>1, "Switzerland"=>3}, "group_count"=>4}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1365129"], "description"=>"<p>(a) Bright field image of a soil thin section showing various soil features that characterise the soil microbial habitat and (b) bacterial distribution observed in the same thin section. (c) Random probability field generated using parameters estimated from b (μ = −7.64; σ<sup>2</sup> = 2.0 and β = 12.95) and (d) simulated bacterial distribution using c. as random intensity (LGCP model). Colours for the random field were chosen to match those of the thin section image. Darker shades indicate higher probability of bacterial presence. The scale for all panels is identical and is indicated in c. (e) Transformed Ripley functions L(r) - r for the observed bacterial distribution shown in a. (solid line) and envelopes of 99 simulations under CSR and LGCP. The dashed lines indicate the envelope of CSR simulations of the same intensity as a. and the shaded area the envelope of simulations of an LGCP with parameters estimated from the observed point distribution. The dotted line corresponds to the theoretical functions under LGCP and the dashed-dotted line to the theoretical function under CSR. In e., L(r)-r above 0 indicates that the point pattern is more aggregated than a random process.</p>", "links"=>[], "tags"=>["Soil science", "ecology", "biodiversity", "microbial ecology", "Soil ecology", "Spatial and landscape ecology", "microbiology", "bacteriology", "Environmental sciences", "statistics", "Statistical methods", "observed", "simulated"], "article_id"=>917023, "categories"=>["Biological Sciences", "Mathematics", "Medicine"], "users"=>["Xavier Raynaud", "Naoise Nunan"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0087217.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Bacterial_habitat_observed_and_simulated_distribution_of_bacteria_in_a_soil_thin_section_/917023", "title"=>"Bacterial habitat, observed and simulated distribution of bacteria in a soil thin section.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-28 04:13:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/1365130"], "description"=>"<p>(a) 3D representation of bacterial distribution in a 100×100×100 µm<sup>3</sup> cube as simulated by LGCP. The model parameters for the simulation were μ = −7.52, σ<sup>2</sup> = 1.90 and β = 25. (b) Number of neighbours as a function of distance for each bacterium (scatterplot), average number of neighbours (red line) and theoretical number of neighbours for the LGCP (blue line) and (c) Number of neighbouring species assuming a random distribution of species among individuals (line colours are the same as in b). The number of species considered in this simulation was S = 450, corresponding to Fisher's α = 221.86 (estimated from <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0087217#pone.0087217-Torsvik1\" target=\"_blank\">[1]</a>).</p>", "links"=>[], "tags"=>["Soil science", "ecology", "biodiversity", "microbial ecology", "Soil ecology", "Spatial and landscape ecology", "microbiology", "bacteriology", "Environmental sciences", "statistics", "Statistical methods", "simulation", "bacterial"], "article_id"=>917024, "categories"=>["Biological Sciences", "Mathematics", "Medicine"], "users"=>["Xavier Raynaud", "Naoise Nunan"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0087217.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_3D_simulation_of_bacterial_distribution_/917024", "title"=>"3D simulation of bacterial distribution.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-28 04:13:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/1365131"], "description"=>"<p>(a) Mean number of neighbours and (b) neighbouring species around an “average” bacterium as a function of distance from the bacterium and as a function of bacterial density. The mean number of neighbours and neighbouring species are derived from Ripley's K(r) function of LGCP with parameters μ = −10.26, σ<sup>2</sup> = 2.90, β = 20 for the 10<sup>8</sup> cells g<sup>−1</sup> soil density, μ = −7.52, σ<sup>2</sup> = 1.90, β = 25 for the 10<sup>9</sup> cells g<sup>−1</sup> soil density and μ = −4.91, σ<sup>2</sup> = 1.29, β = 25 for the 10<sup>10</sup> cells g<sup>−1</sup> soil density. Grey envelopes surrounding curves represent the maximum and minimum of these numbers calculated from 39 simulations. Note the logarithmic scale on the y axis.</p>", "links"=>[], "tags"=>["Soil science", "ecology", "biodiversity", "microbial ecology", "Soil ecology", "Spatial and landscape ecology", "microbiology", "bacteriology", "Environmental sciences", "statistics", "Statistical methods", "neighbours", "neighbouring"], "article_id"=>917025, "categories"=>["Biological Sciences", "Mathematics", "Medicine"], "users"=>["Xavier Raynaud", "Naoise Nunan"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0087217.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Number_of_neighbours_and_neighbouring_species_/917025", "title"=>"Number of neighbours and neighbouring species.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-28 04:13:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/1365132"], "description"=>"<p>Data for cell numbers, cell densities and average distance to nearest neighbour are given as mean±sd (range). Cell density in g<sub>soil</sub><sup>−1</sup> is calculated assuming a microscope depth of field of 2 µm and a soil density of 1.3 g cm<sup>−3</sup>.</p>", "links"=>[], "tags"=>["Soil science", "ecology", "biodiversity", "microbial ecology", "Soil ecology", "Spatial and landscape ecology", "microbiology", "bacteriology", "Environmental sciences", "statistics", "Statistical methods", "observed", "maps", "depths"], "article_id"=>917026, "categories"=>["Biological Sciences", "Mathematics", "Medicine"], "users"=>["Xavier Raynaud", "Naoise Nunan"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0087217.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_General_properties_of_all_observed_distribution_maps_of_bacteria_at_different_depths_in_soil_/917026", "title"=>"General properties of all observed distribution maps of bacteria at different depths in soil.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-01-28 04:13:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/1365133"], "description"=>"<p>Deviations are calculated based on a goodness of fit test between summary statistics for each observed distribution (Ripley's K or G function) and the corresponding statistics under the null model (CSR of LGCP). Ripley's K is a summary statistics related to the number of points in a point pattern that are within a certain distance to an average point. The nearest neighbour distance distribution G is the distribution function of the distance from an average point to its nearest neighbour.</p>", "links"=>[], "tags"=>["Soil science", "ecology", "biodiversity", "microbial ecology", "Soil ecology", "Spatial and landscape ecology", "microbiology", "bacteriology", "Environmental sciences", "statistics", "Statistical methods", "samples", "deviating", "csr", "lgcp", "depths", "bacterial", "having", "cells"], "article_id"=>917027, "categories"=>["Biological Sciences", "Mathematics", "Medicine"], "users"=>["Xavier Raynaud", "Naoise Nunan"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0087217.t002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Total_number_of_samples_number_proportions_of_samples_deviating_from_CSR_and_number_proportions_of_samples_deviating_from_the_LGCP_model_for_different_soil_depths_for_all_bacterial_distribution_having_more_than_5_bacterial_cells_in_the_field_of_view_/917027", "title"=>"Total number of samples, number (proportions %) of samples deviating from CSR and number (proportions %) of samples deviating from the LGCP model for different soil depths for all bacterial distribution having more than 5 bacterial cells in the field of view.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-01-28 04:13:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/1365134", "https://ndownloader.figshare.com/files/1365135"], "description"=>"<div><p>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 (10<sup>8</sup> cells g<sup>−1</sup> 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.</p></div>", "links"=>[], "tags"=>["Soil science", "ecology", "biodiversity", "microbial ecology", "Soil ecology", "Spatial and landscape ecology", "microbiology", "bacteriology", "Environmental sciences", "statistics", "Statistical methods", "microscale"], "article_id"=>917028, "categories"=>["Biological Sciences", "Mathematics", "Medicine"], "users"=>["Xavier Raynaud", "Naoise Nunan"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0087217.s001", "https://dx.doi.org/10.1371/journal.pone.0087217.s002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Spatial_Ecology_of_Bacteria_at_the_Microscale_in_Soil_/917028", "title"=>"Spatial Ecology of Bacteria at the Microscale in Soil", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-01-28 04:13:13"}

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