Bardgett RD, van der Putten WH. Belowground biodiversity and ecosystem functioning. Nature. 2014;515:505–11.
Article
CAS
PubMed
Google Scholar
Dini-Andreote F, Stegen JC, van Elsas JD, Salles JF. Disentangling mechanisms that mediate the balance between stochastic and deterministic processes in microbial succession. Pro Natl Acad Sci. 2015;112:E1326–32.
Article
CAS
Google Scholar
Hanson CA, Fuhrman JA, Horner-Devine MC, Martiny JBH. Beyond biogeographic patterns: Processes shaping the microbial landscape. Nat Rev Micro. 2012;10:497–506.
CAS
Google Scholar
Bell T, Newman JA, Silverman BW, Turner SL, Lilley AK. The contribution of species richness and composition to bacterial services. Nature. 2005;436:1157–60.
Article
CAS
PubMed
Google Scholar
Wittebolle L, Marzorati M, Clement L, Balloi A, Daffonchio D, Heylen K, De Vos P, Verstraete W, Boon N. Initial community evenness favours functionality under selective stress. Nature. 2009;458:623–6.
Article
CAS
PubMed
Google Scholar
Davidson EA, Janssens IA. Temperature sensitivity of soil carbon decomposition and feedbacks to climate change. Nature. 2006;440:165–73.
Article
CAS
PubMed
Google Scholar
Jones CM, Spor A, Brennan FP, Breuil M-C, Bru D, Lemanceau P, Griffiths B, Hallin S, Philippot L. Recently identified microbial guild mediates soil n2o sink capacity. Nature Clim Change. 2014;4:801–5.
Article
CAS
Google Scholar
Powell JR, Welsh A, Hallin S. Microbial functional diversity enhances predictive models linking environmental parameters to ecosystem properties. Ecology. 2015;96:1985–93.
Article
PubMed
Google Scholar
Wieder WR, Bonan GB, Allison SD. Global soil carbon projections are improved by modelling microbial processes. Nature Clim Change. 2013;3:909–12.
Article
CAS
Google Scholar
Skinner FA, Jones PCT, Mollison JE. A comparison of a cirect- and a plate-counting technique for the quantitative estimation of soil micro-organisms. Microbiology. 1952;6:261–71.
CAS
Google Scholar
Hugenholtz P, Goebel BM, Pace NR. Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol. 1998;180:4765–74.
CAS
PubMed
PubMed Central
Google Scholar
Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS, Banfield JF. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature. 2004;428:37–43.
Article
CAS
PubMed
Google Scholar
Andersen A, Beringer J, Bull CM, Byrne M, Cleugh H, Christensen R, French K, Harch B, Hoffmann A, Lowe AJ, et al. Foundations for the future: A long-term plan for australian ecosystem science. Austral Ecol. 2014;39:739–48.
Article
Google Scholar
Odgers NP, Holmes KW, Griffin T, Liddicoat C. Derivation of soil-attribute estimations from legacy soil maps. Soil Res. 2015;53:881–94.
Google Scholar
Terrain NCoSa. Australian soil and land survey field handbook. 3rd ed. Melbourne: CSIRO Publishing; 2009.
Google Scholar
White A, Sparrow B, Leitch E, Foulkes J, Flitton R, Lowe AJ, Caddy-Retalic S. Ausplots rangelands - survey protocols manual. Adelaide: University of Adelaide Press; 2012.
Google Scholar
Rayment GE, Higginson FR. Australian laboratory handbook of soil and water chemical methods. Melbourne: Inkata Press; 1992.
Google Scholar
QuikChem Systems. 1992. QuikChem method No. 12-107-04-1-B.QuikChem Systems, division of Lachat Chemicals Inc., Mequon, WI.
Searle PL. The bertholet or indophenol reaction and its use in the analytical chemistry of nitrogen. Analyst. 1984;109:549–68.
Article
CAS
Google Scholar
Blair G, Chinoim N, Lefroy R, Anderson G, Crocker G. A soil sulfur test for pastures and crops. Soil Res. 1991;29:619–26.
Article
CAS
Google Scholar
Walkley A, Black IA. An examination of the degtjareff method for determining organic carbon in soils: Effect of variations in digestion conditions and of inorganic soil constituents. Soil Sci. 1934;63:251–63.
Article
Google Scholar
Bromfield SM. Simple tests for the assessment of aluminium and manganese levels in acid soils. Aust J Agri. 1987;27:399–404.
Article
CAS
Google Scholar
Indorante SJ, Follmer LR, Hammer RD, Koenig PG. Particle-size analysis by a modified pipette procedure. Soil Sci Soc Am J. 1990;54:560–3.
Article
Google Scholar
Lane DJ. 16s/23s rrna sequencing. In: Stackbrandt E, Goodfellow M, editors. Nucleic acid techniques in bacterial systematics. New York: John Wiley and Sons; 1991. p. 115–75.
Google Scholar
Lane DJ, Pace B, Olsen GJ, Stahl DA, Sogin ML, Pace NR. Rapid determination of 16 s ribosomal rna sequences for phylogenetic analyses. Pro Natl Acad Sci. 1985;82:6955–9.
Article
CAS
Google Scholar
DeLong EF. Archaea in coastal marine environments. Pro Natl Acad Sci. 1992;89:5685–9.
Article
CAS
Google Scholar
Gardes M, Bruns TD. Its primers with enhanced specificity for basidiomycetes--application to the identification of mycorrhizae and rusts. Mol Ecol. 1993;2:113–8.
Article
CAS
PubMed
Google Scholar
White T, Bruns T, Lee S, Taylor J, Innis M, Gelfand D, Shinsky J. Amplification and direct sequencing of fungal ribosomal rna genes for phylogenetics. In. Pcr protocols: A guide to methods and applications. New York, NY: Academic Press; 1990:315-322
Andrews S. Fastqc a quality control tool for high throughput sequence data. http://www.bioinformatics.babraham.ac.uk/projects/fastqc/.
Magoč T, Salzberg SL. Flash: Fast length adjustment of short reads to improve genome assemblies. Bioinformatics. 2011;27(21):2957-63. doi:10.1093/bioinformatics/btr507.
Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, et al. Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol. 2009;75:7537–41.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bengtsson-Palme J, Ryberg M, Hartmann M, Branco S, Wang Z, Godhe A, De Wit P, Sánchez-García M, Ebersberger I, de Sousa F, et al. Improved software detection and extraction of its1 and its2 from ribosomal its sequences of fungi and other eukaryotes for analysis of environmental sequencing data. Methods Ecol Evol. 2013;4:914–9.
Google Scholar
Rideout JR, He Y, Navas-Molina JA, Walters WA, Ursell LK, Gibbons SM, Chase J, McDonald D, Gonzalez A, Robbins-Pianka A, et al. Subsampled open-reference clustering creates consistent, comprehensive otu definitions and scales to billions of sequences. Peer J. 2014;2:e545.
Article
PubMed
PubMed Central
Google Scholar
Edgar RC. Uparse: Highly accurate otu sequences from microbial amplicon reads. Nat Meth. 2013;10:996–8.
Article
CAS
Google Scholar
Edgar RC. Search and clustering orders of magnitude faster than blast. Bioinformatics. 2010;26:2460–1.
Article
CAS
PubMed
Google Scholar
Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive bayesian classifier for rapid assignment of rrna sequences into the new bacterial taxonomy. Appl Environ Microbiol. 2007;73:5261–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
BASE. Biomes of australian soil environments (base). 2015. doi:10.4227/71/561c9bc670099.
Google Scholar
Martin-Laurent F, Philippot L, Hallet S, Chaussod R, Germon JC, Soulas G, Catroux G. DNA extraction from soils: Old bias for new microbial diversity analysis methods. Appl Environ Microbiol. 2001;67:2354–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Fredriksson NJ, Hermansson M, Wilén B-M. The choice of pcr primers has great impact on assessments of bacterial community diversity and dynamics in a wastewater treatment plant. PLoS ONE. 2013;8:e76431.
Article
CAS
PubMed
PubMed Central
Google Scholar
Parada A, Needham DM, Fuhrman JA. Every base matters. Assessing small subunit rRNA primers for marine microbiomes with mock communities, time-series and global field samples: Environ. Microbiol. 2016;18:1403–1414. doi:10.1111/1462-2920.13023.
Nadkarni MA, Martin FE, Jacques NA, Hunter N. Determination of bacterial load by real-time pcr using a broad-range (universal) probe and primers set. Microbiology-Sgm. 2002;148:257–66.
Article
CAS
Google Scholar
Gilbert JA, Jansson JK, Knight R. The earth microbiome project: Successes and aspirations. BMC Biol. 2014;12:69.
Article
PubMed
PubMed Central
Google Scholar
Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, Fierer N, Knight R. Global patterns of 16 s rrna diversity at a depth of millions of sequences per sample. Pro Natl Acad Sci. 2011;108:4516–22.
Article
CAS
Google Scholar
Belbin L, Williams KJ. Towards a national bio-environmental data facility: Experiences from the atlas of living australia. Int J Geogr Inf Sci. 2016;30:108–25.
Article
Google Scholar
Robinson N, Brackin R, Vinall K, Soper F, Holst J, Gamage H, Paungfoo-Lonhienne C, Rennenberg H, Lakshmanan P, Schmidt S. Nitrate paradigm does not hold up for sugarcane. PLoS ONE. 2011;6:e19045.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yeoh YK, Paungfoo-Lonhienne C, Dennis PG, Robinson N, Ragan MA, Schmidt S, Hugenholtz P: The core root microbiome of sugarcanes cultivated under varying nitrogen fertilizer application. Environ Microbiol. Environ Microbiol. 2016;18(5):1338-51. doi: 10.1111/1462-2920.12925..
Paungfoo-Lonhienne C, Yeoh YK, Kasinadhuni NRP, Lonhienne TGA, Robinson N, Hugenholtz P, Ragan MA, Schmidt S. Nitrogen fertilizer dose alters fungal communities in sugarcane soil and rhizosphere. Sci Rep. 2015;5:8678.
Article
CAS
PubMed
Google Scholar
Paungfoo-Lonhienne C, Lonhienne TGA, Yeoh YK, Webb RI, Lakshmanan P, Chan CX, Lim P-E, Ragan MA, Schmidt S, Hugenholtz P. A new species of burkholderia isolated from sugarcane roots promotes plant growth. Microb Biotechnol. 2014;7:142–54.
Article
CAS
PubMed
PubMed Central
Google Scholar
Faith DP, Walker PA. Environmental diversity: On the best-possible use of surrogate data for assessing the relative biodiversity of sets of areas. Biodivers Conserv. 1996;5:399–415.
Funk VA, Richardson KS, Ferrier S. Survey-gap analysis in expeditionary research: Where do we go from here? Biol J Linn Soc. 2005;85:549–67.
Article
Google Scholar
Ferrier S. Mapping spatial pattern in biodiversity for regional conservation planning: Where to from here? Syst Biol. 2002;51:331–63.
Article
PubMed
Google Scholar
Ferrier S, Manion G, Elith J, Richardson K. Using generalized dissimilarity modelling to analyse and predict patterns of beta diversity in regional biodiversity assessment. Divers Distrib. 2007;13:252–64.
Article
Google Scholar
Jolley-Rogers G, Varghese T, Harvey P, dos Remedios N, Miller JT. Phylojive: Integrating biodiversity data with the tree of life. Bioinformatics. 2014;30(9):1308-9. doi: 10.1093/bioinformatics/btu024.