Changes in microbial community structure and physiological profile in a kaolinitic tropical soil under different conservation agricultural practices

Aboim, 2008, Soil bacterial community structure and soil quality in a slash-and-burn cultivation system in Southeastern Brazil, Appl. Soil Ecol., 38, 100, 10.1016/j.apsoil.2007.09.004 Allison, 2008, Resistance, resilience, and redundancy in microbial communities, Proceedings of the National Academy of Sciences USA, 105, 11512, 10.1073/pnas.0801925105 Anderson, 1993, The metabolic quotient for CO2 (qCO2) as a specific activity parameter to assess the effects of environmental conditions, such as pH, on the microbial biomass of forest soils, Soil Biol. Biochem., 25, 393, 10.1016/0038-0717(93)90140-7 Bartlett, 1988, Colorimetric determination of oxidizable carbon in acid soil solutions, Soil Science Society American Journal, 52, 1191, 10.2136/sssaj1988.03615995005200040055x Berg, 2009, Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere, FEMS Microbiol. Ecol., 68, 1, 10.1111/j.1574-6941.2009.00654.x Bossio, 2005, Soil microbial community response to land use change in an agricultural landscape of Western Kenya, Microb. Ecol., 49, 50, 10.1007/s00248-003-0209-6 Bossuyt, 2001, Influence of microbial populations and residue quality on aggregate stability, Appl. Soil Ecol., 16, 195, 10.1016/S0929-1393(00)00116-5 Brooker, 2015, Improving intercropping: a synthesis of research in agronomy, plant physiology and ecology, New Phytol., 206, 107, 10.1111/nph.13132 Butler, 2003, Microbial community dynamics associated with rhizosphere carbon flow, Appl. Environ. Microbiol., 69, 6793, 10.1128/AEM.69.11.6793-6800.2003 Cesarano, 2017, Organic amendment type and application frequency affect crop yields, soil fertility and microbiome composition, Appl. Soil Ecol., 120, 254, 10.1016/j.apsoil.2017.08.017 Chaer, 2009, Shifts in microbial community composition and physiological profiles across a gradient of induced soil degradation, Soil Science Society of American Journal, 73, 1327, 10.2136/sssaj2008.0276 Chazarenc, 2010, Seasonal and spatial changes of microorganisms communities in constructed wetlands: a community level physiological profiling analysis, Int. J. Chem. Eng., 2010, 1 Curaqueo, 2011, Effects of different tillage systems on arbuscular mycorrhizal fungal propagules and physical properties in a Mediterranean agroecosystem in Central Chile, Soil Tillage Res., 113, 11, 10.1016/j.still.2011.02.004 Daigh, 2018, Yields and yield stability of no-till and chisel-plow fields in the Midwestern US Corn Belt, Field Crop Res., 218, 243, 10.1016/j.fcr.2017.04.002 DeAngelis, 2009, Selective progressive response of soil microbial community to wild oat roots, The ISME Journal, 3, 168, 10.1038/ismej.2008.103 De’ath, 2002, Multivariate regression trees: a new technique for modeling species-environment relationships, Ecology, 83, 1105 1997 Fernandes, 2010, Impact of tillage and maize cropping system on the physical properties of a kaolinitic soil in the Brazilian coastal tablelands Fernandes, 2011, Short-term response of physical and chemical aspects of soil quality of a kaolinitic Kandiudalfs to agricultural practices and its association with microbiological variables, Agric. Ecosyst. Environ., 142, 419, 10.1016/j.agee.2011.07.002 Fernández-Gómez, 2019, Bacterial communities associated to Chilean altiplanic native plants from the Andean grassland soils, Sci. Rep., 9, 1042, 10.1038/s41598-018-37776-0 Fierer, 2006, The diversity and biogeography of soil bacterial communities, Proceedings of the National Academy of Science USA, 103, 626, 10.1073/pnas.0507535103 Fierer, 2007, Toward an ecological classification of soil bacteria, Ecology, 88, 1354, 10.1890/05-1839 Fierer, 2012, Cross-biome metagenomics analyses of soil microbial communities and their functional attributes, Proceedings of the National Academy of Sciences USA, 109, 21390, 10.1073/pnas.1215210110 Fustec, 2010, Nitrogen rhizodeposition by legumes. A review, Agron. Sustain. Dev., 30, 57, 10.1051/agro/2009003 Garland, 1991, Classification and characterization of heterotrophic microbial communities on the basis of patterns of community-level-sole-carbon-source utilization, Appl. Environ. Microbiol., 57, 2351, 10.1128/AEM.57.8.2351-2359.1991 Girvan, 2003, Soil type is the primary determinant of the composition of the total and active bacterial communities in arable soils, Appl. Environ. Microbiol., 69, 1800, 10.1128/AEM.69.3.1800-1809.2003 Grant, 2005, Soil and fertilizer phosphorus: effects on plant P supply and mycorrhizal development, Can. J. Plant Sci., 85, 3, 10.4141/P03-182 Grosso, 2016, Bacterial and fungal growth on different plant litter in Mediterranean soils: effects of C/N ratio and soil pH, Appl. Soil Ecol., 108, 1, 10.1016/j.apsoil.2016.07.020 Guckert, 1986, Phospholipid ester-linked fatty acid profile changes during nutrient deprivation of Vibrio cholerae: increases in the trans/cis ratio and proportions of cyclopropyl fatty acids, Appl. Environ. Microbiol., 52, 794, 10.1128/AEM.52.4.794-801.1986 Hatakka, 2001, Biodegradation of lignin, 129 Jansa, 2003, Soil tillage affects the community structure of mycorrhizal fungi in maize roots, Ecol. Appl., 13, 1164, 10.1890/1051-0761(2003)13[1164:STATCS]2.0.CO;2 Jenkinson, 1976, The effects of biocidal treatments on metabolism in soil. A method for measuring soil biomass, Soil Biol. Biochem., 8, 209, 10.1016/0038-0717(76)90005-5 Kaiser, 2010, Negligible contribution from roots to soil-borne phospholipids fatty acid fungal biomarkers 18:2ω6,9 and 18:1ω9, Soil Biol. Biochem., 42, 1650, 10.1016/j.soilbio.2010.05.019 Kavamura, 2013, Water regime influences bulk soil and rhizosphere of Cereus Jamacaru bacterial communities in the Brazilian Caatinga biome, PLoS One, 8, e73606, 10.1371/journal.pone.0073606 Krause, 2019, Initial microaggregate formation: association of microorganisms to montmorillonite-goethite aggregates under wetting and drying cycles, Geoderma, 351, 250, 10.1016/j.geoderma.2019.05.001 Lehmann, 2017, Soil biota contributions to soil aggregation, Nature Ecology and Evolution, 1, 1828, 10.1038/s41559-017-0344-y Lopes, 2016, Bacterial abilities and adaptation toward the rhizosphere colonization, Front. Microbiol., 7, 1341, 10.3389/fmicb.2016.01341 Lovelock, 2004, Using glomalin as an indicator for arbuscular mycorrhizal hyphal growth: an example from a tropical rain forest soil, Soil Biol. Biochem., 36, 1009, 10.1016/j.soilbio.2004.02.010 Mantel, 1967, The detection of disease clustering and a generalized regression approach, Cancer Res., 27, 209 McCune, 2011 Mendes, 2015, Soil-borne microbiome: linking diversity to function, Microb. Ecol., 70, 255, 10.1007/s00248-014-0559-2 Mielke, 2000 Peiffer, 2013, Diversity and heritability of the maize rhizosphere microbiome under field conditions, Proceedings of the National Academy of Sciences USA, 110, 6548, 10.1073/pnas.1302837110 Philippot, 2013, Going back to the roots: the microbial ecology of the rhizosphere, Nat. Rev. Microbiol., 11, 789, 10.1038/nrmicro3109 Pontes, 2017, Diversity of arbuscular mycorrhizal fungi in the Brazilian’s Cerrado and in soybean under conservation and conventional tillage, Appl. Soil Ecol., 117–118, 178, 10.1016/j.apsoil.2017.04.023 Preston-Mafham, 2002, Analysis of microbial community functional diversity using sole-carbon source utilization profiles: a critique, FEMS Microbiol. Ecol., 42, 1 Prober, 2015, Plant diversity predicts beta but not alpha diversity of soil microbes across grasslands worldwide, Ecol. Lett., 18, 85, 10.1111/ele.12381 Robertson, 2014, Nitrogen transformations, 421 Roes-Hill, 2011, Actinobacterial peroxidases: an unexplored resource for biocatalysis, Appl. Biochem. Biotechnol., 164, 681, 10.1007/s12010-011-9167-5 Rossi, 2018, Interactive effects of pesticides and nutrients on microbial communities responsible of litter decomposition in streams, Front. Microbiol., 9, 2437, 10.3389/fmicb.2018.02437 Rousk, 2010, Soil bacterial and fungal communities across a pH gradient in an arable soil, The ISME Journal, 4, 1340, 10.1038/ismej.2010.58 Säle, 2015, Impact of conservation tillage and organic farming on the diversity of arbuscular mycorrhizal fungi, Soil Biol. Biochem., 84, 38, 10.1016/j.soilbio.2015.02.005 Schimel, 2007, Microbial stress-response physiology and its implications for ecosystem function, Ecology, 88, 1386, 10.1890/06-0219 Sokal, 1979, Testing statistical significance of geographic variation patterns, Systematics Zoology, 28, 627 Souza, 2015, Metagenomic analysis reveals microbial functional redundancies and specificities in a soil under different tillage and crop-management regimes, Appl. Soil Ecol., 86, 106, 10.1016/j.apsoil.2014.10.010 Strickland, 2009, Testing the functional significance of microbial community composition, Ecology, 90, 441, 10.1890/08-0296.1 Tewari, 2020, Next generation bioformulation prepared by amalgamating Bradyrhizobium, cell free culture supernatant, and exopolysaccharides enhances the indigenous rhizospheric rhizobial population, nodulation, and productivity of pigeon pea, Appl. Soil Ecol., 147, 103363, 10.1016/j.apsoil.2019.103363 Tisdall, 1982, Organic matter and water-stable aggregates in soils, J. Soil Sci., 33, 141, 10.1111/j.1365-2389.1982.tb01755.x Uroz, 2010, Pyrosequencing reveals a contrasted bacterial diversity between oak rhizosphere and surrounding soil, Environ. Microbiol. Rep., 2, 281, 10.1111/j.1758-2229.2009.00117.x Van Aarle, 2002, Arbuscular mycorrhizal fungi respond to the substrate pH of their extraradical mycelium by altered growth and root colonization, New Phytol., 155, 173, 10.1046/j.1469-8137.2002.00439.x Vance, 1987, An extraction method for measuring soil microbial biomass-C, Soil Biol. Biochem., 19, 703, 10.1016/0038-0717(87)90052-6 Waldrop, 2000, Linking microbial community composition to function in a tropical soil, Soil Biol. Biochem., 32, 1837, 10.1016/S0038-0717(00)00157-7 White, 1998, Signature lipid biomarker analysis, 255 Wilhelm, 2019, Bacterial contributions to delignification and lignocellulose degradation in forest soils with metagenomic and quantitative stable isotope probing, ISME J., 13, 413, 10.1038/s41396-018-0279-6 Wright, 1996, Extraction of an abundant and unusual protein from soil and comparison with hyphal protein of arbuscular mycorrhizal fungi, Soil Sci., 161, 575, 10.1097/00010694-199609000-00003 Zelles, 1999, Fatty acid patterns of phospholipids and lipopolisaccharides in the characterization of microbial communities in soil: a review, Biol. Fertil. Soils, 29, 111, 10.1007/s003740050533