Trumbore, S., Brando, P. & Hartmann, H. Forest health and global change. Science 349, 814–818 (2015).
Gibbs, H. K. et al. Tropical forests were the primary sources of new agricultural land in the 1980s and 1990s. Proc. Natl. Acad. Sci. 107, 16732–16737 (2010).
Laurance, W. F. Have we overstated the tropical biodiversity crisis?. Trends Ecol. Evol. 22, 65–70 (2007).
Brienen, R. J. W. et al. Long-term decline of the Amazon carbon sink. Nature 519, 344–348 (2015).
Nottingham, A. T. et al. Climate warming and soil carbon in tropical forests: insights from an elevation gradient in the Peruvian Andes. Bioscience 65, 906–921 (2015).
Seymour, F. & Busch, J. Why Forests? Why Now? The Science, Economics and Politics of Tropical Forests and Climate Change 1–450 (Center for Global Development, Washington, 2016).
de Quadros, P. D. et al. Coal mining practices reduce the microbial biomass, richness and diversity of soil. Appl. Soil Ecol. 98, 195–203 (2016).
Beer, C. et al. Terrestrial gross carbon dioxide uptake: global distribution and covariation with climate. Science 329, 834–838 (2010).
Jobbágy, E. G. & Jackson, R. B. The vertical distribution of soil organic carbon and its relation to climate and vegetation. Ecol. Appl. 10, 423–426 (2000).
Chazdon, R. L. et al. Carbon sequestration potential of second-growth forest regeneration in the Latin American tropics. Sci. Adv. 2, e1501639–e1501639 (2016).
Chazdon, R. L. Beyond deforestation: restoring forests and ecosystem services on degraded lands. Science 320, 1458–1460 (2008).
Chazdon, R. L. Tropical forest recovery: legacies of human impact and natural disturbances. Perspect. Plant Ecol. 6, 51–71 (2003).
Arroyo-Rodríguez, V. et al. Multiple successional pathways in human-modified tropical landscapes: new insights from forest succession, forest fragmentation and landscape ecology research. Biol. Rev. 92, 326–340 (2017).
Vashum, K. T., Kasomwoshi, T. & Jayakumar, S. Soil organic carbon sequestration potential of primary and secondary forests in Northeast India. Proc. Int. Acad. Ecol. Environ. Sci. 6, 67 (2016).
Uriarte, M. et al. Natural disturbance and human land use as determinants of tropical forest dynamics: results from a forest simulator. New Phytol. 79, 423–443 (2009).
Calderón, K. et al. Effectiveness of ecological rescue for altered soil microbial communities and functions. ISME J. 11, 272–283 (2017).
Rodrigues, J. L. M. et al. Conversion of the Amazon rainforest to agriculture results in biotic homogenization of soil bacterial communities. Proc. Natl. Acad. Sci. USA 110, 988–993 (2013).
Coyle, D. R. et al. Soil fauna responses to natural disturbances, invasive species, and global climate change: current state of the science and a call to action. Soil Biol. Biochem. 110, 116–133 (2017).
Brussaard, L. Biodiversity and ecosystem functioning in soil. Ambio 26, 563–570 (1997).
Brussaard, L., de Ruiter, P. C. & Brown, G. G. Soil biodiversity for agricultural sustainability. Agric. Ecosyst. Environ. 121, 233–244 (2007).
Lavelle, P. et al. Soil invertebrates and ecosystem services. Eur. J. Soil Biol. 42, S3–S15 (2006).
Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 17, 10–12 (2011).
Eisenhauer, N., Sabais, A. C. W. & Scheu, S. Collembola species composition and diversity effects on ecosystem functioning vary with plant functional group identity. Soil Biol. Biochem. 43, 1697–1704 (2011).
Griffiths, B. S., de Groot, G. A., Laros, I., Stone, D. & Geisen, S. The need for standardisation: exemplified by a description of the diversity, community structure and ecological indices of soil nematodes. Ecol. Indic. 87, 43–46 (2018).
Mulder, C. Driving forces from soil invertebrates to ecosystem functioning: the allometric perspective. Naturwissenschaften 93, 467–479 (2006).
Menta, C. Soil fauna diversity. In Biodiversity Conservation and Utilization in a Diverse World (ed. Lameed, G. A.) (InTech, London, 2012). https://doi.org/10.5772/51091.
Errington, I. et al. The influence of vegetation and soil properties on springtail communities in a diesel-contaminated soil. Sci. Total Environ. 619–620, 1098–1104 (2018).
Korboulewsky, N., Perez, G. & Chauvat, M. How tree diversity affects soil fauna diversity: a review. Soil Biol. Biochem. 94, 94–106 (2016).
Beng, K. C. et al. The utility of DNA metabarcoding for studying the response of arthropod diversity and composition to land-use change in the tropics. Sci. Rep. 6, 1–13 (2016).
McGee, K. M., Robinson, C. V. & Hajibabaei, M. Gaps in DNA-based biomonitoring across the globe. Front. Ecol. Evolut. 7, 337 (2019).
Ji, Y. et al. Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding. Ecol. Lett. 16, 1245–1257 (2013).
Liu, S. et al. SOAP Barcode: revealing arthropod biodiversity through assembly of Illumina shotgun sequences of PCR amplicons. Methods Ecol. Evol. 4, 1142–1150 (2013).
Bienert, F. et al. Tracking earthworm communities from soil DNA: tracking earthworm communities from soil DNA. Mol. Ecol. 21, 2017–2030 (2012).
Dell’Anno, A., Carugati, L., Corinaldesi, C., Riccioni, G. & Danovaro, R. Unveiling the biodiversity of deep-sea nematodes through metabarcoding: are we ready to bypass the classical taxonomy?. PLoS ONE 10, e0144928 (2015).
Fonseca, V. G. et al. Metagenetic analysis of patterns of distribution and diversity of marine meiobenthic eukaryotes: macroecology of microscopic marine eukaryotes. Glob. Ecol. Biogeogr. 23, 1293–1302 (2014).
Pansu, J. et al. Landscape-scale distribution patterns of earthworms inferred from soil DNA. Soil Biol. Biochem. 83, 100–105 (2015).
Saitoh, S. et al. A quantitative protocol for DNA metabarcoding of springtails (Collembola). Genome 59, 705–723 (2016).
Baird, D. J. & Hajibabaei, M. Biomonitoring 2.0: a new paradigm in ecosystem assessment made possible by next-generation DNA sequencing: news and views: opinion. Mol. Ecol. 21, 2039–2044 (2012).
Edge, T. A. et al. The ecobiomics project: advancing metagenomics assessment of soil health and freshwater quality in Canada. Sci. Total Environ. 710, 135906 (2020).
Porter, T. M. & Hajibabaei, M. Scaling up: a guide to high-throughput genomic approaches for biodiversity analysis. Mol. Ecol. 27, 313–338 (2018).
Porter, T. M. & Hajibabaei, M. Automated high throughput animal CO1 metabarcode classification. Sci. Rep. 8, 1–10 (2018).
Porter, T. M. & Hajibabaei, M. Over 2.5 million COI sequences in GenBank and growing. PLoS ONE 13, e0200177 (2018).
Fernandes, K. et al. DNA metabarcoding-a new approach to fauna monitoring in mine site restoration. Restor. Ecol. 26, 1098–1107 (2018).
Gibson, J. F. et al. Large-scale biomonitoring of remote and threatened ecosystems via high-throughput sequencing. PLoS ONE 10, e0138432-e138515 (2015).
Martin, G. K., Adamowicz, S. J. & Cottenie, K. Taxonomic resolution based on DNA barcoding affects environmental signal in metacommunity structure. Freshw. Sci. 35, 701–711 (2016).
Banerjee, S. et al. Determinants of bacterial communities in Canadian agroforestry systems. Environ. Microbiol. 18, 1805–1816 (2016).
Chikoski, J. M., Ferguson, S. H. & Meyer, L. Effects of water addition on soil arthropods and soil characteristics in a precipitation-limited environment. Acta Oecologica 30, 203–211 (2006).
Wall, D. H. et al. Soil Ecology and Ecosystem Services (Oxford University Press, Oxford, 2012).
Yu, Y. et al. Shifts in microbial community function and structure along the successional gradient of coastal wetlands in Yellow River Estuary. Eur. J. Soil Biol. 49, 12–21 (2012).
Convey, P., Block, W. & Peat, H. J. Soil arthropods as indicators of water stress in Antarctic terrestrial habitats?. Glob. Change Biol. 9, 1718–1730 (2003).
Marra, J. L. & Edmonds, R. L. Soil arthropod responses to different patch types in a mixed-conifer forest of the Sierra Nevada. For. Sci. 51, 255–265 (1998).
McCluney, K. E. & Sabo, J. L. Sensitivity and tolerance of riparian arthropod communities to altered water resources along a drying river. PLoS ONE 9, e109276 (2014).
Villani, M. G. & Wright, R. J. Environmental influences on soil macroarthropod behavior in agricultural systems 35, 249–269 (1990).
Zahran, H. H., Moharram, A. M. & Mohammad, H. A. Some ecological and physiological studies on bacteria isolated from salt-affected soils of Egypt. J. Basic Microbiol. 32, 405–413 (1992).
McGee, K. M., Eaton, W. D., Shokralla, S. & Hajibabaei, M. Determinants of soil bacterial and fungal community composition toward carbon-use efficiency across primary and secondary forests in a costa rican conservation area. Microb. Ecol. 10, 423 (2018).
Oba, Y., Ôhira, H., Murase, Y., Moriyama, A. & Kumazawa, Y. DNA barcoding of Japanese click beetles (Coleoptera, Elateridae). PLoS ONE 10, e0116612 (2015).
Ensafi, P. et al. Soil type mediates the effectiveness of biological control against Limonius californicus (Coleoptera: Elateridae). J. Econ. Entomol. 111, 2053–2058 (2018).
Poggi, S. et al. Relative influence of climate and agroenvironmental factors on wireworm damage risk in maize crops. J. Pest. Sci. 91, 585–599 (2018).
Di, S., Huang, L., Diao, J. & Zhou, Z. Selective bioaccumulation and elimination of hexachlorocyclohexane isomers in Tubifex tubifex (Oligochaeta, Tubificidae). Environ. Sci. Pollut. Res. 23, 6990–6998 (2016).
Pelegrí, S. & Blackburn, T. H. Effects of Tubifex tubifex (Oligochaeta:Tubificidae) on N-mineralization in freshwater sediments, measured with 15-N isotopes. Aquat. Microb. Ecol. 9, 289–294 (1995).
Saaltink, R. M. Respiration and aeration by bioturbating Tubificidae alter biogeochemical processes in aquatic sediment. Aquat. Sci. 81, 1–13 (2019).
Booth, M. S., Stark, J. M. & Rastetter, E. Controls on nitrogen cycling in terrestrial ecosystems: a synthetic analysis of literature data. New Phytol. 75, 139–157 (2005).
Feldpausch, T. R., Rondon, M. A., Fernandes, E. C. M., Riha, S. J. & Wandelli, E. Carbon and nutrient accumulation in secondary forests regenerating on pastures in central Amazonia. Ecol. Appl. 14, 164–176 (2004).
Gehring, C., Vlek, P. L. G., de Souza, L. A. G. & Denich, M. Biological nitrogen fixation in secondary regrowth and mature rainforest of central Amazonia. Agric. Ecosyst. Environ. 111, 237–252 (2005).
Guariguata, M. R. & Ostertag, R. Neotropical secondary forest succession: changes in structural and functional characteristics. For. Ecol. Manag. 148, 185–206 (2001).
Chassot, O. & Monge, G. Connectivity conservation of the great green macaw’s landscape in costa rica and nicaragua (1994–2012). Parks 18, 1–10 (2012).
Hartshorn, G. S. et al. Vegetation Types and Floristic Patterns. La Selva: Ecology and Natural History of a Neotropical Rain Forest (The University of Chicago Press, Chicago, 1994).
van der Gast, C. J., Gosling, P., Tiwari, B. & Bending, G. D. Spatial scaling of arbuscular mycorrhizal fungal diversity is affected by farming practice: spatial scaling of arbuscular mycorrhizal fungi. Environ. Microbiol. 13, 241–249 (2011).
McGee, K. M., Eaton, W. D., Porter, T. M., Shokralla, S. & Hajibabaei, M. Soil microbiomes associated with two dominant Costa Rican tree species, and implications for remediation. A case study from a Costa Rican conservation area. Appl. Soil Ecol. 137, 139–153 (2019).
Eaton, W. D. et al. Differences in the soil microbial community and carbon-use efficiency following development of Vochysia guatemalensis tree plantations in unproductive pastures in Costa Rica. Restor. Ecol. https://doi.org/10.1111/rec.12978 (2019).
Folmer, O., Black, M., Hoeh, W., Lutz, R. & Vrijenhoek, R. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol. Mar. Biol. Biochem. 3, 294–299 (1994).
Hajibabaei, M., Spall, J. L., Shokralla, S. & van Konynenburg, S. Assessing biodiversity of a freshwater benthic macroinvertebrate community through non-destructive environmental barcoding of DNA from preservative ethanol. BMC Ecol. 12, 28 (2012).
Gibson, J. et al. Simultaneous assessment of the macrobiome and microbiome in a bulk sample of tropical arthropods through DNA metasystematics. Proc. Nat. Acad. Sci. 111, 8007–8012 (2014).
St. John, J. SeqPrep. Retrieved https://github.com/jstjohn/SeqPrep (2016).
Edgar, R. C. UNOISE2: improved error-correction for Illumina 16S and ITS amplicon sequencing. bioRxiv. https://doi.org/10.1101/081257 (2016).
Callahan, B. J., McMurdie, P. J. & Holmes, S. P. Exact sequence variants should replace operational taxonomic units in marker-gene data analysis. ISME J. 11, 2639–2643 (2017).
Reeder, J. & Knight, R. The ‘rare biosphere’: a reality check. Nat. Methods 6, 636–637 (2009).
Tedersoo, L. et al. 454 Pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases. New Phytol. 188, 291–301 (2010).
Weiss, S. et al. Normalization and microbial differential abundance strategies depend upon data characteristics. Microbiome 5, 27 (2017).
Anderson, M. J., Gorley, R. N. & Clarke, R. K. PERMANOVA+ for Primer: guide to Software and Statistical Methods (PRIMER-E Ltd., Plymouth, UK, 2008).
Clarke, K. R. Non-parametric multivariate analyses of changes in community structure. Aust. J. Ecol. 18, 117–143 (1993).
Anderson, M. J. & Willis, T. J. Canonical analysis of principal coordinates: a useful method of constrained ordination for ecology. Ecology 84, 511–525 (2003).
DiStefano, J., Fidler, F. & Cumming, G. Effect size estimates and confidence intervals: An alternative focus for the presentation and interpretation of ecological data. In New Trends in Ecology Research. 1st edn. (ed. Burk, A.). (Nova Science Publishers Inc., New York, 2005).
Clarke, K. R., & Gorley, R. N. PRIMER v6: user manual/tutorial (Plymouth routines in multivariate ecological research) (PRIMER-E Ltd., Plymouth, UK, 2006).
Burnham, K. P. & Anderson, D. R. Model selection and multimodel inference: a practical information-theoretic approach. In Model Selection and Multimodel Inference (eds Burnham, K. P. & Anderson, D. R.) 1–515 (Springer, Berlin, 2003).
Legendre, P. & Anderson, M. J. Distance-based redundancy analysis: testing multispecies responses in multifactorial ecological experiments. New Phytol. 69, 1–24 (1999).
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