Next generation restoration metrics: Using soil eDNA bacterial community data to measure trajectories towards rehabilitation targets
Tài liệu tham khảo
Anderson, 2006, Multivariate dispersion as a measure of beta diversity, Ecol. Lett., 9, 683, 10.1111/j.1461-0248.2006.00926.x
Australian Government, 2016
BenDor, 2015, Estimating the size and impact of the ecological restoration economy, PLoS One, 10, 10.1371/journal.pone.0128339
Bissett, 2016, Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database, GigaScience, 5, 21, 10.1186/s13742-016-0126-5
Breed, 2019, The potential of genomics for restoring ecosystems and biodiversity, Nat. Rev. Genet., 20, 615, 10.1038/s41576-019-0152-0
Brown, 2018, Natural vs anthropogenic streams in Europe: history, ecology and implications for restoration, river-rewilding and riverine ecosystem services, Earth Sci. Rev., 180, 185, 10.1016/j.earscirev.2018.02.001
Bulgarelli, 2013, Structure and functions of the bacterial microbiota of plants, Annu. Rev. Plant Biol., 64, 807, 10.1146/annurev-arplant-050312-120106
de Bruin, 1998, Soil-landscape modelling using fuzzy c-means clustering of attribute data derived from a Digital Elevation Model (DEM), Geoderma, 83, 17, 10.1016/S0016-7061(97)00143-2
Delgado‐Baquerizo, 2018, Ecological drivers of soil microbial diversity and soil biological networks in the Southern Hemisphere, Ecology, 99, 583, 10.1002/ecy.2137
Deyett, 2019, Temporal dynamics of the sap microbiome of grapevine under high pierce's disease pressure, Front. Plant Sci., 10, 10.3389/fpls.2019.01246
Fausto, 2018, Olive orchard microbiome: characterisation of bacterial communities in soil-plant compartments and their comparison between sustainable and conventional soil management systems, Plant Ecol. Divers., 11, 597, 10.1080/17550874.2019.1596172
Fernandez Nuñez, 2021, Potential of high-throughput eDNA sequencing of soil fungi and bacteria for monitoring ecological restoration in ultramafic substrates: the case study of the New Caledonian biodiversity hotspot, Ecol. Eng., 173, 106416, 10.1016/j.ecoleng.2021.106416
Gann, 2019, International principles and standards for the practice of ecological restoration, Restor. Ecol., 27, S1, 10.1111/rec.13035
Gloor, 2017, Microbiome datasets are compositional: and this is not optional, Front. Microbiol., 8, 10.3389/fmicb.2017.02224
Harris, 2009, Soil microbial communities and restoration ecology: facilitators or followers?, Science, 325, 573, 10.1126/science.1172975
2018, The IPBES assessment report on land degradation and restoration, 744
Janzen, 2016, The soil remembers, Soil Sci. Soc. Am. J., 80, 1429, 10.2136/sssaj2016.05.0143
Jiao, 2018, Soil microbiomes with distinct assemblies through vertical soil profiles drive the cycling of multiple nutrients in reforested ecosystems, Microbiome, 6, 146, 10.1186/s40168-018-0526-0
Legendre, 2012, Chapter 7 - ecological resemblance, 265, 10.1016/B978-0-444-53868-0.50007-1
Liddicoat, 2019, Can bacterial indicators of a grassy woodland restoration inform ecosystem assessment and microbiota-mediated human health?, Environ. Int., 129, 105, 10.1016/j.envint.2019.05.011
Lloyd-Price, 2016, The healthy human microbiome, Genome Med., 8, 51, 10.1186/s13073-016-0307-y
Lovell, 2020, Counts: an outstanding challenge for log-ratio analysis of compositional data in the molecular biosciences, NAR Genom. Bioinform., 2
Lozupone, 2007, Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities, Appl. Environ. Microbiol., 73, 1576, 10.1128/AEM.01996-06
Manero, 2021, Mine completion criteria defined by best-practice: a global meta-analysis and Western Australian case studies, J. Environ. Manag., 282, 111912, 10.1016/j.jenvman.2020.111912
Martín-Fernández, 2015, Bayesian-multiplicative treatment of count zeros in compositional data sets, Stat. Model. Int. J., 15, 134, 10.1177/1471082X14535524
McMurdie, 2013, Phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data, PLoS One, 8, 10.1371/journal.pone.0061217
Menz, 2013, Hurdles and opportunities for landscape-scale restoration, Science, 339, 526, 10.1126/science.1228334
Mohr, 2022
Neumann, 2012, The magnitude of hydraulic redistribution by plant roots: a review and synthesis of empirical and modeling studies, New Phytol., 194, 337, 10.1111/j.1469-8137.2012.04088.x
Oksanen, 2020
Orozco-Aceves, 2015, Soil conditioning and plant-soil feedbacks in a modified forest ecosystem are soil-context dependent, Plant Soil, 390, 183, 10.1007/s11104-015-2390-z
Orozco-Aceves, 2017, Correlation between soil development and native plant growth in forest restoration after surface mining, Ecol. Eng., 106, 209, 10.1016/j.ecoleng.2017.06.004
Palarea-Albaladejo, 2015, zCompositions — R package for multivariate imputation of left-censored data under a compositional approach, Chemometr. Intell. Lab. Syst., 143, 85, 10.1016/j.chemolab.2015.02.019
Quinn, 2019, A field guide for the compositional analysis of any-omics data, GigaScience, 8, 10.1093/gigascience/giz107
Quinn, 2017, Propr: an R-package for identifying proportionally abundant features using compositional data analysis, Sci. Rep., 7, 16252, 10.1038/s41598-017-16520-0
R-Core-Team, 2020
Rydgren, 2019, Advancing restoration ecology: a new approach to predict time to recovery, J. Appl. Ecol., 56, 225, 10.1111/1365-2664.13254
Schloss, 2020, Removal of rare amplicon sequence variants from 16S rRNA gene sequence surveys biases the interpretation of community structure data, bioRxiv, 2012, 422279
Schmid, 2020, 52 years of ecological restoration following a major disturbance by opencast lignite mining does not reassemble microbiome structures of the original arable soils, Sci. Total Environ., 745, 140955, 10.1016/j.scitotenv.2020.140955
Tibbett, 2010, Large-scale mine site restoration of Australian eucalypt forests after bauxite mining: soil management and ecosystem development, Ecol. Ind. Pollut., 309
Tibbett, 2015
Turner, 2013, Comparative metatranscriptomics reveals kingdom level changes in the rhizosphere microbiome of plants, ISME J., 7, 2248, 10.1038/ismej.2013.119
van der Heyde, 2020, Changes in soil microbial communities in post mine ecological restoration: implications for monitoring using high throughput DNA sequencing, Sci. Total Environ., 749, 142262, 10.1016/j.scitotenv.2020.142262
Walker, 2010, The use of chronosequences in studies of ecological succession and soil development, J. Ecol., 98, 725, 10.1111/j.1365-2745.2010.01664.x
Watkins, 2020, Microbiome-inspired green infrastructure: a toolkit for multidisciplinary landscape design, Trends Biotechnol., 38, 1305, 10.1016/j.tibtech.2020.04.009
Webster, 2007
Weiss, 2017, Normalization and microbial differential abundance strategies depend upon data characteristics, Microbiome, 5, 27, 10.1186/s40168-017-0237-y
Zhu, 2021, Determination of the direct and indirect effects of bend on the urban river ecological heterogeneity, Environ. Res., 112166
