Combination of techniques to quantify the distribution of bacteria in their soil microhabitats at different spatial scales
Tài liệu tham khảo
Dechesne, 2003, A novel method for characterizing the microscale 3D spatial distribution of bacteria in soil, Soil Biol. Biochem., 35, 1537, 10.1016/S0038-0717(03)00243-8
Dechesne, 2005, Impact of the microscale distribution of a Pseudomonas strain introduced into soil on potential contacts with indigenous bacteria, Appl. Environ. Microbiol., 71, 8123, 10.1128/AEM.71.12.8123-8131.2005
Eickhorst, 2008, Detection of microorganisms in undisturbed soil by combining fluorescence in situ hybridization (FISH) and micropedological methods, Soil Biol. Biochem., 40, 1284, 10.1016/j.soilbio.2007.06.019
Falconer, 2015, Microscale heterogeneity explains experimental variability and non-linearity in soil organic matter mineralisation, PLoS One, 10, 10.1371/journal.pone.0123774
Franklin, 2007, 1
Grundmann, 2004, Spatial scales of soil bacterial diversity–the size of a clone, FEMS Microbiol. Ecol., 48, 119, 10.1016/j.femsec.2004.01.010
Hapca, 2011, Automated statistical method to align 2D chemical maps with 3D X-ray computed micro-tomographic images of soils, Geoderma, 164, 146, 10.1016/j.geoderma.2011.05.018
Hapca, 2015, Three-dimensional mapping of soil chemical characteristics at micrometric scale by combining 2D SEM-EDX data and 3D X-ray CT images, PLoS One, 10, 10.1371/journal.pone.0137205
Houston, 2013, Adaptive-window indicator kriging: a thresholding method for computed tomography images of porous media, Comput. Geosci., 54, 239, 10.1016/j.cageo.2012.11.016
Houston, 2013, Effect of scanning and image reconstruction settings in X-ray computed microtomography on quality and segmentation of 3D soil images, Geoderma, 207, 154, 10.1016/j.geoderma.2013.05.017
Juarez, 2013, Effects of different soil structures on the decomposition of native and added organic carbon, Eur. J. Soil Biol., 58, 81, 10.1016/j.ejsobi.2013.06.005
Juyal, 2018, Control of pore geometry in soil microcosms and its effect on the growth and spread of Pseudomonas and Bacillus sp, Front. Environ. Sci., 6, 73, 10.3389/fenvs.2018.00073
Kizungu, 2001, Spatial modeling of nitrifier microhabitats in soil, Soil Sci. Soc. Am. J., 1709, 1709
Kravchenko, 2013, Relationships between intra-aggregate pore structures and distributions of Escherichia coli within soil macro-aggregates, Appl. Soil Ecol., 63, 134, 10.1016/j.apsoil.2012.10.001
Kravchenko, 2014, Intra-aggregate pore structure influences phylogenetic composition of bacterial community in macroaggregates, Soil Sci. Soc. Am. J., 78, 1924, 10.2136/sssaj2014.07.0308
Kuzyakov, 2015, Microbial hotspots and hot moments in soil: concept & review, Soil Biol. Biochem., 83, 184, 10.1016/j.soilbio.2015.01.025
Li, 2003, Evaluation of fluorochromes for imaging bacteria in soil, Soil Biol. Biochem., 35, 737, 10.1016/S0038-0717(02)00196-7
Li, 2004, Fluorescence microscopy for visualization of soil microorganisms: a review, Biol. Fertil. Soils, 39, 301, 10.1007/s00374-004-0722-x
Negassa, 2015, Properties of soil pore space regulate pathways of plant residue decomposition and community structure of associated bacteria, PLoS One, 10, e0123999, 10.1371/journal.pone.0123999
Nunan, 2001, Quantification of the in situ distribution of soil bacteria by large-scale imaging of thin sections of undisturbed soil, FEMS Microbiol. Ecol., 36, 67, 10.1111/j.1574-6941.2001.tb00854.x
Nunan, 2002, In situ spatial patterns of soil bacterial populations, mapped at multiple scales, in an arable soil, Microb. Ecol., 44, 296, 10.1007/s00248-002-2021-0
Nunan, 2003, Spatial distribution of bacterial communities and their relationships with the micro-architecture of soil, FEMS Microbiol. Ecol., 44, 203, 10.1016/S0168-6496(03)00027-8
O'Donnell, 2007, Visualization, modelling and prediction in soil microbiology, Nat. Rev. Microbiol., 5, 689, 10.1038/nrmicro1714
Or, 2007, Physical constraints affecting bacterial habitats and activity in unsaturated porous media–a review, Adv. Water Resour., 30, 1505, 10.1016/j.advwatres.2006.05.025
Pallud, 2004, Modification of spatial distribution of 2,4-dichlorophenoxyacetic acid degrader microhabitats during growth in soil columns, Appl. Environ. Microbiol., 70, 2709, 10.1128/AEM.70.5.2709-2716.2004
Portell, 2018, Microscale heterogeneity of the spatial distribution of organic matter can promote bacterial biodiversity in soils: insights from computer simulations, Front. Microbiol., 9, 1583, 10.3389/fmicb.2018.01583
Ranjard, 2001, Quantitative and qualitative microscale distribution of bacteria in soil, Res. Microbiol., 152, 707, 10.1016/S0923-2508(01)01251-7
Raynaud, 2014, Spatial ecology of bacteria at the microscale in soil, PLoS One, 9, 87217, 10.1371/journal.pone.0087217
Ruamps, 2011, Microbial biogeography at the soil pore scale, Soil Biol. Biochem., 43, 280, 10.1016/j.soilbio.2010.10.010
Ruamps, 2013, Regulation of soil organic C mineralisation at the pore scale, FEMS Microbiol. Ecol., 86, 26, 10.1111/1574-6941.12078
Sessitsch, 2001, Microbial population structures in soil particle size fractions of a long-term fertilizer field experiment, Appl. Environ. Microbiol., 67, 4215, 10.1128/AEM.67.9.4215-4224.2001
Vandevivere, 1992, Saturated hydraulic conductivity reduction caused by aerobic bacteria in sand columns, Soil Sci. Soc. Am. J., 56, 1, 10.2136/sssaj1992.03615995005600010001x
Vieublé Gonod, 2006, Spatial distribution of microbial 2, 4-dichlorophenoxy acetic acid mineralization from field to microhabitat scales, Soil Sci. Soc. Am. J., 70, 64, 10.2136/sssaj2004.0034
Vos, 2013, Micro-scale determinants of bacterial diversity in soil, FEMS Microbiol. Rev., 37, 936, 10.1111/1574-6976.12023
Wang, 2013, Transport and fate of microorganisms in soils with preferential flow under different solution chemistry conditions, Water Resour. Res., 49, 2424, 10.1002/wrcr.20174
White, 1994, Use of stained bacterial inocula to assess spatial distribution after introduction into soil, Geoderma, 63, 245, 10.1016/0016-7061(94)90066-3
Young, 2008, Microbial distribution in soils: physics and scaling, Adv. Agron., 100, 81, 10.1016/S0065-2113(08)00604-4