Functional diversity of microbial communities in two contrasting maize rhizosphere soils

Ali, 2009, Auxin production by plant associated bacteria: impact on endogenous IAA content and growth of Triticum aestivum L, Lett. Appl. Microbiol., 48, 542, 10.1111/j.1472-765X.2009.02565.x Avrain, 2003, Antimicrobial resistance in Campylobacter from broilers: association with production type and antimicrobial use, Vet. Microbiol., 96, 267, 10.1016/j.vetmic.2003.07.001 Avrain, 2004, Antimicrobial resistance in Campylobacter from pigs in French slaughterhouses, Revue de Médecine Vétérinaire, 155, 156 Ayangbenro, 2018, Metal (loid) bioremediation: strategies employed by microbial polymers, Sustainability, 10, 3028, 10.3390/su10093028 Ayangbenro, 2018, Sulfate-reducing bacteria as an effective tool for sustainable acid mine bioremediation, Front. Microbiol., 9, 1986, 10.3389/fmicb.2018.01986 Badri, 2009, Regulation and function of root exudates, Plant Cell Environ., 32, 666, 10.1111/j.1365-3040.2009.01926.x Bae, 2018, Methanogens are major contributors to nitrogen fixation in soils of the Florida Everglades, Appl. Environ. Microbiol., 84 Baker-Austin, 2006, Co-selection of antibiotic and metal resistance, Trends Microbiol., 14, 176, 10.1016/j.tim.2006.02.006 Berdy, 2005, Bioactive microbial metabolites, J. Antibiot., 58, 1, 10.1038/ja.2005.1 Brader, 2017, Ecology and genomic insights into plant-pathogenic and plant-nonpathogenic endophytes, Annu. Rev. Phytopathol., 55, 61, 10.1146/annurev-phyto-080516-035641 Bray, 1945, Determination of total, organic, and available forms of phosphorus in soils, Soil Sci., 59, 39, 10.1097/00010694-194501000-00006 Buckler, 2009, The genetic architecture of maize flowering time, Science, 325, 714, 10.1126/science.1174276 Cabello, 2018, Assimilation of cyanide and cyano-derivatives by Pseudomonas pseudoalcaligenes CECT5344: from omic approaches to biotechnological applications, FEMS (Fed. Eur. Microbiol. Soc.) Microbiol. Lett., 365, fny032, 10.1093/femsle/fny032 Castañeda, 2017, Metagenomic analysis exploring taxonomic and functional diversity of soil microbial communities in Chilean vineyards and surrounding native forests, PeerJ, 5, 10.7717/peerj.3098 Castiglioni, 2008, Bacterial RNA chaperones confer abiotic stress tolerance in plants and improved grain yield in maize under water-limited conditions, Plant Physiol., 147, 446, 10.1104/pp.108.118828 Chen, 2016, Assessment of bacterial communities and predictive functional profiling in soils subjected to short-term fumigation-incubation, Microb. Ecol., 72, 240, 10.1007/s00248-016-0766-0 Chen, 2018, Continuous‐cropping tobacco caused variance of chemical properties and structure of bacterial network in soils, Land Degrad. Dev., 29, 4106, 10.1002/ldr.3167 Chukwuneme, 2020, Characterization of actinomycetes isolates for plant growth promoting traits and their effects on drought tolerance in maize, J. Plant Interact., 15, 93, 10.1080/17429145.2020.1752833 Clarke, 1988, Statistical design and analysis for a'biological effects' study, Mar. Ecol. Prog. Ser., 213, 10.3354/meps046213 Compant, 2019, A review on the plant microbiome: ecology, functions and emerging trends in microbial application, J. Adv. Res., 19, 29, 10.1016/j.jare.2019.03.004 Dinsdale, 2008, Functional metagenomic profiling of nine biomes, Nature, 452, 629, 10.1038/nature06810 El-Fouly, 2015, Impact of long-term intensive cropping under continuous tillage and unbalanced use of fertilizers on soil nutrient contents in a small holding village, Afr. J. Agric. Res., 10, 4850, 10.5897/AJAR2015.10499 Enagbonma, 2019, Profiling the functional diversity of termite mound soil bacteria as revealed by shotgun sequencing, Genes, 10, 637, 10.3390/genes10090637 Enebe, 2018, The influence of plant growth-promoting rhizobacteria in plant tolerance to abiotic stress: a survival strategy, Appl. Microbiol. Biotechnol., 102, 7821, 10.1007/s00253-018-9214-z Foley, 2005, Global consequences of land use, Science, 309, 570, 10.1126/science.1111772 Gao, 2019, Rhizosphere bacterial community characteristics over different years of sugarcane ratooning in consecutive monoculture, BioMed Research International 2019, 10.1155/2019/4943150 Gianoulis, 2009, Quantifying environmental adaptation of metabolic pathways in metagenomics, Proc. Natl. Acad. Sci. Unit. States Am., 106, 1374, 10.1073/pnas.0808022106 Gómez Expósito, 2017, Current insights into the role of rhizosphere bacteria in disease suppressive soils, Front. Microbiol., 8, 2529, 10.3389/fmicb.2017.02529 Gore, 2009, A first-generation haplotype map of maize, Science, 326, 1115, 10.1126/science.1177837 Griggs, 2005, Incidence and mechanism of ciprofloxacin resistance in Campylobacter spp. isolated from commercial poultry flocks in the United Kingdom before, during, and after fluoroquinolone treatment, Antimicrob. Agents Chemother., 49, 699, 10.1128/AAC.49.2.699-707.2005 Hammer, 2001, PAST: paleontological statistics software package for education and data analysis, Palaeontol. Electron., 4, 9 Hanson, 2012, Beyond biogeographic patterns: processes shaping the microbial landscape, Nat. Rev. Microbiol., 10, 497, 10.1038/nrmicro2795 Hwang, 2014, Systems biology and biotechnology of Streptomyces species for the production of secondary metabolites, Biotechnol. Adv., 32, 255, 10.1016/j.biotechadv.2013.10.008 Innerebner, 2011, Protection of Arabidopsis thaliana against leaf-pathogenic Pseudomonas syringae by Sphingomonas strains in a controlled model system, Appl. Environ. Microbiol., 77, 3202, 10.1128/AEM.00133-11 Jangid, 2011, Land-use history has a stronger impact on soil microbial community composition than aboveground vegetation and soil properties, Soil Biol. Biochem., 43, 2184, 10.1016/j.soilbio.2011.06.022 Jin, 2017, Taxonomic structure and functional association of foxtail millet root microbiome, GigaScience, 6, gix089, 10.1093/gigascience/gix089 Kent, 2002, BLAT—the BLAST-like alignment tool, Genome Res., 12, 656 Khomtchouk, 2017, shinyheatmap: ultra fast low memory heatmap web interface for big data genomics, PloS One, 12, 10.1371/journal.pone.0176334 Klimek, 2016, Functional diversity of soil microbial communities in boreal and temperate Scots pine forests, Eur. J. For. Res., 135, 731, 10.1007/s10342-016-0968-5 Kristiansson, 2011, Pyrosequencing of antibiotic-contaminated river sediments reveals high levels of resistance and gene transfer elements, PloS One, 6, 10.1371/journal.pone.0017038 Kumar Behera, 2009, Changes in fractions of iron, manganese, copper, and zinc in soil under continuous cropping for more than three decades, Commun. Soil Sci. Plant Anal., 40, 1380, 10.1080/00103620902818054 Kummerer, 2004, Resistance in the environment, J. Antimicrob. Chemother., 54, 311, 10.1093/jac/dkh325 Lakshmanan, 2014, Functional soil microbiome: belowground solutions to an aboveground problem, Plant Physiol., 166, 689, 10.1104/pp.114.245811 Li, 2014, Functional potential of soil microbial communities in the maize rhizosphere, PloS One, 9 Lindsay, 2010, The abundance of microbial functional genes in grassy woodlands is influenced more by soil nutrient enrichment than by recent weed invasion or livestock exclusion, Appl. Environ. Microbiol., 76, 5547, 10.1128/AEM.03054-09 Luque-Almagro, 2005, Bacterial degradation of cyanide and its metal complexes under alkaline conditions, Appl. Environ. Microbiol., 71, 940, 10.1128/AEM.71.2.940-947.2005 Mendes, 2014, Taxonomical and functional microbial community selection in soybean rhizosphere, ISME J., 8, 1577, 10.1038/ismej.2014.17 Meyer, 2008, The metagenomics RAST server–a public resource for the automatic phylogenetic and functional analysis of metagenomes, BMC Bioinf., 9, 1, 10.1186/1471-2105-9-386 Mohanram, 2019, Rhizosphere microbiome: revisiting the synergy of plant-microbe interactions, Ann. Microbiol., 69, 307, 10.1007/s13213-019-01448-9 Monier, 2011, Metagenomic exploration of antibiotic resistance in soil, Curr. Opin. Microbiol., 14, 229, 10.1016/j.mib.2011.04.010 Moore, 2006, The epidemiology of antibiotic resistance in Campylobacter, Microb. Infect., 8, 1955, 10.1016/j.micinf.2005.12.030 Muwawa, 2010, Chemical properties associated with guts, soil and nest materials of Odontotermes and Macrotermes species from Kenya, Journal of Biological and Environmental Sciences, 4, 253 Nelson, 1996, Total carbon, organic carbon, and organic matter, Methods of soil analysis: Part 3 Chemical methods, 5, 961 Newman, 2016, Natural products as sources of new drugs from 1981 to 2014, J. Nat. Prod., 79, 629, 10.1021/acs.jnatprod.5b01055 NWPG-RSA O'Connor, 2015, Engineering of secondary metabolism, Annu. Rev. Genet., 49, 71, 10.1146/annurev-genet-120213-092053 Olanrewaju, 2019, Plant health: feedback effect of root exudates-rhizobiome interactions, Appl. Microbiol. Biotechnol., 103, 1155, 10.1007/s00253-018-9556-6 Overbeek, 2005, The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes, Nucleic Acids Res., 33, 5691, 10.1093/nar/gki866 Peiffer, 2013, Diversity and heritability of the maize rhizosphere microbiome under field conditions, Proc. Natl. Acad. Sci. Unit. States Am., 110, 6548, 10.1073/pnas.1302837110 Prabha, 2019, Rhizosphere metagenomics of paspalum scrobiculatum L.(Kodo millet) reveals rhizobiome multifunctionalities, Microorganisms, 7, 608, 10.3390/microorganisms7120608 Ranjan, 2016, Analysis of the microbiome: advantages of whole genome shotgun versus 16S amplicon sequencing, Biochem. Biophys. Res. Commun., 469, 967, 10.1016/j.bbrc.2015.12.083 Rao, 2005, Increased erythromycin resistance in clinical Campylobacter in Northern Ireland—an update, J. Antimicrob. Chemother., 55, 395, 10.1093/jac/dkh552 Richter, 2007 Rout, 2015, Role of iron in plant growth and metabolism, Reviews in Agricultural Science, 3, 1, 10.7831/ras.3.1 Shi, 2011, Differences in soil properties and bacterial communities between the rhizosphere and bulk soil and among different production areas of the medicinal plant Fritillaria thunbergii, Int. J. Mol. Sci., 12, 3770, 10.3390/ijms12063770 Shi, 2013, Metagenomic insights into chlorination effects on microbial antibiotic resistance in drinking water, Water Res., 47, 111, 10.1016/j.watres.2012.09.046 Takagi, 2016, L-Cysteine metabolism and fermentation in microorganisms, 129 Tokala, 2002, Novel plant-microbe rhizosphere interaction involving Streptomyces lydicus WYEC108 and the pea plant (Pisum sativum), Appl. Environ. Microbiol., 68, 2161, 10.1128/AEM.68.5.2161-2171.2002 Trivedi, 2012, Huanglongbing alters the structure and functional diversity of microbial communities associated with citrus rhizosphere, ISME J., 6, 363, 10.1038/ismej.2011.100 Waldenström, 2005, Antimicrobial resistance profiles of Campylobacter jejuni isolates from wild birds in Sweden, Appl. Environ. Microbiol., 71, 2438, 10.1128/AEM.71.5.2438-2441.2005 Walkley, 1934, An examination of the Degtjareff method for determining soil organic matter, and a proposed modification of the chromic acid titration method, Soil Sci., 37, 29, 10.1097/00010694-193401000-00003 Wang, 2013, Metagenomic profiling of antibiotic resistance genes and mobile genetic elements in a tannery wastewater treatment plant, PloS One, 8 Weir, 2010, The role of root exudates in rhizosphere interactions with plants and other organisms: An addendum, Annu. Rev. Plant Biol., 0, 109 Wilke, 2012, The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools, BMC Bioinf., 13, 141, 10.1186/1471-2105-13-141 Wilson, 2017, Natural product discovery from the human microbiome, J. Biol. Chem., 292, 8546, 10.1074/jbc.R116.762906 Wrighton, 2012, Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phyla, Science, 337, 1661, 10.1126/science.1224041 Xu, 2018, The structure and function of the global citrus rhizosphere microbiome, Nat. Commun., 9, 1, 10.1038/s41467-018-07343-2 Yin, 2014, Whole-genome sequencing reveals novel insights into sulfur oxidation in the extremophile Acidithiobacillus thiooxidans, BMC Microbiol., 14, 179, 10.1186/1471-2180-14-179 Zhang, 2008, Soil bacteria confer plant salt tolerance by tissue-specific regulation of the sodium transporter HKT1, Mol. Plant Microbe Interact., 21, 737, 10.1094/MPMI-21-6-0737 Zhang, 2016, Metagenome-scale analysis yields insights into the structure and function of microbial communities in a copper bioleaching heap, BMC Genet., 17, 1, 10.1186/s12863-016-0330-4 Zhang, 2017, Huanglongbing impairs the rhizosphere-to-rhizoplane enrichment process of the citrus root-associated microbiome, Microbiome, 5, 97, 10.1186/s40168-017-0304-4