Philippa Kaur

Royse DJ. A global perspective on the high five: Agaricus, Pleurotus, Lentinula, Auricularia and Flammulina. In: Singh M, editor. Proceedings of the 8th International Conference on Mushroom Biology and Mushroom Products. New Delhi; 2014. p. 1–6.Vos AM, Heijboer A, Boschker HTS, Bonnet B, Lugones LG, Wosten HAB. Microbial biomass in compost during colonization of Agaricus bisporus. AMB Express. 2017; 7:12.Jurak E, Punt AM, Arts W, Kabel MA, Gruppen H. Fate of carbohydrates and lignin during composting and mycelium growth of Agaricus bisporus on wheat straw based compost. PLoS ONE. 2015;10:e0138909.PubMed 
PubMed Central 
Article 

Google Scholar 
Beyer DM. Basic procedures for Agaricus mushroom growing PennState Extension: the Pennsylvania State University. 2003. https://extension.psu.edu/basic-procedures-for-agaricus-mushroom-growing.Wang L, Mao J, Zhao H, Li M, Wei Q, Zhou Y, et al. Comparison of characterization and microbial communities in rice straw- and wheat straw-based compost for Agaricus bisporus production. J Ind Microbiol Biotechnol. 2016;43:1249–60.CAS 
PubMed 
Article 

Google Scholar 
Adams JDW, Frostick LE. Investigating microbial activities in compost using mushroom (Agaricus bisporus) cultivation as an experimental system. Bioresour Technol. 2008;99:1097–102.CAS 
PubMed 
Article 

Google Scholar 
Liu L, Wang S, Guo X, Zhao T, Zhang B. Succession and diversity of microorganisms and their association with physicochemical properties during green waste thermophilic composting. Waste Manage. 2018;73:101–12.CAS 
Article 

Google Scholar 
Reyes-Torres M, Oviedo-Ocana ER, Dominguez I, Komilis D, Sanchez A. A systematic review on the composting of green waste: feedstock quality and optimization strategies. Waste Manage. 2018;77:486–99.CAS 
Article 

Google Scholar 
Pardo‐Giménez A, González JEP, Zied DC. Casing materials and techniques in Agaricus bisporus cultivation. In: Zied DC, Pardo‐Giménez A, editors. Edible and medicinal mushrooms technology and applications. Chichester, UK: Wiley; 2017. p. 149–74.Baars JJP, Scholtmeijer K, Sonnenberg ASM, van Peer A. Critical factors involved in primordia building in Agaricus bisporus: a review. Molecules. 2020;25:2984.Vieira FR, Pecchia JA. Bacterial community patterns in the Agaricus bisporus cultivation system, from compost raw materials to mushroom caps. Microb Ecol. 2021;84:20–32.PubMed 
Article 

Google Scholar 
Kristensen JB, Thygesen LG, Felby C, Jorgensen H, Elder T. Cell-wall structural changes in wheat straw pretreated for bioethanol production. Biotechnol Biofuels. 2008;1:1–9.Article 

Google Scholar 
Jurak E, Patyshakuliyeva A, de Vries RP, Gruppen H, Kabel MA. Compost grown Agaricus bisporus lacks the ability to degrade and consume highly substituted xylan fragments. PLoS ONE. 2015;10:e0134169.PubMed 
PubMed Central 
Article 

Google Scholar 
Ryckeboer J, Mergaert J, Vaes K, Klammer S, De Clercq D, Coosemans J, et al. A survey of bacteria and fungi occurring during composting and self-heating processes. Ann Microbiol. 2003;53:349–410.
Google Scholar 
Kutzner HJ. Microbiology of composting. In: Rehm H-J, Reed G, editors. Biotechnology. 11c. 2nd ed. Verlag: Wiley-VCH; 2000. p. 35–100.Carrasco J, Garcia-Delgado C, Lavega R, Tello ML, De Toro M, Barba-Vicente V, et al. Holistic assessment of the microbiome dynamics in the substrates used for commercial champignon (Agaricus bisporus) cultivation. Microb Biotechnol. 2020;13:1933–47.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Vieira FR, Pecchia JA. Bacterial community patterns in the Agaricus bisporus cultivation system, from compost raw materials to mushroom caps. Microb Ecol. 2021;82. https://doi.org/10.1007/s00248-021-1833-5.Vieira FR, Pecchia JA. An exploration into the bacterial community under different pasteurization conditions during substrate preparation (composting–Phase II) for Agaricus bisporus cultivation. Microb Ecol. 2018;75:318–30.CAS 
PubMed 
Article 

Google Scholar 
Cao GT, Song TT, Shen YY, Jin QL, Feng WL, Fan LJ, et al. Diversity of bacterial and fungal communities in wheat straw compost for Agaricus bisporus cultivation. Hortscience. 2019;54:100–9.CAS 
Article 

Google Scholar 
Wiegant WM. Growth characteristics of the thermophilic fungus Scytalidium thermophilum in relation to production of mushroom compost. Appl Environ Microbiol. 1992;58:1301–7.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Fermor T, Randle P, Smith J. Compost as a substrate and its preparation. In: Flegg PB, Spencer DM, Wood D, editors. The biology and technology of the cultivated mushroom. Chichester, UK: John Wiley & Sons, Ltd; 1985. p. 81–109.Straatsma G, Samson RA, Olijnsma TW, Op den Camp HJM, Gerrits JPG, Griensven LJLDV. Ecology of thermophilic fungi in mushroom compost, with emphasis on Scytalidium thermophilum and growth stimulation of Agaricus bisporus mycelium. Appl Environ Microbiol. 1994;60:454–8.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Ross RC, Harris PJ. An investigation into the selective nature of mushroom compost. Sci Hortic. 1983;19:55–64.Article 

Google Scholar 
Coello-Castillo MM, Sanchez JE, Royse DJ. Production of Agaricus bisporus on substrates pre-colonized by Scytalidium thermophilum and supplemented at casing with protein-rich supplements. Bioresour Technol. 2009;100:4488–92.CAS 
PubMed 
Article 

Google Scholar 
Szekely A, Sipos R, Berta B, Vajna B, Hajdu C, Marialigeti K. DGGE and T-RFLP analysis of bacterial succession during mushroom compost production and sequence-aided T-RFLP profile of mature compost. Microb Ecol. 2009;57:522–33.PubMed 
Article 

Google Scholar 
Kertesz M, Safianowicz K, Bell TL. New insights into the microbial communities and biological activities that define mushroom compost. Sci Cultiv Edible Fungi. 2016;19:161–5.
Google Scholar 
McGee CF, Byrne H, Irvine A, Wilson J. Diversity and dynamics of the DNA and cDNA-derived bacterial compost communities throughout the Agaricus bisporus mushroom cropping process. Ann Microbiol. 2017;67:751–61.CAS 
Article 

Google Scholar 
McGee CF, Byrne H, Irvine A, Wilson J. Diversity and dynamics of the DNA- and cDNA-derived compost fungal communities throughout the commercial cultivation process for Agaricus bisporus. Mycologia. 2017;109:475–84.CAS 
PubMed 
Article 

Google Scholar 
Yeates C, Gillings MR. Rapid purification of DNA from soil for molecular biodiversity analysis. Lett Appl Microbiol. 1998;27:49–53.CAS 
Article 

Google Scholar 
Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer N, et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 2012;6:1621–4.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
White TJ, Bruns T, Lee S, Taylor JW. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ, editors. PCR protocols: a guide to methods and applications. New York: Academic Press; 1990. p. 315–22.
Google Scholar 
Lever MA, Torti A, Eickenbusch P, Michaud AB, Santl-Temkiv T, Jorgensen BB. A modular method for the extraction of DNA and RNA, and the separation of DNA pools from diverse environmental sample types. Front Microbiol. 2015;6:476.Muyzer G, Waal ECD, Uitterlinden AG. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol. 1993;59:695–700.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, et al. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc Natl Acad Sci USA. 2011;108:4516–22.CAS 
PubMed 
Article 

Google Scholar 
R Core Team. R: a language and environment for statistical computing. Vienna, Austria: R Foundation For Statistical Computing; 2019.Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP. DADA2: high-resolution sample inference from Illumina aplicon data. Nat Meth. 2016;13:581–3.CAS 
Article 

Google Scholar 
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucl Acids Res. 2012;41:D590–6.PubMed 
PubMed Central 
Article 

Google Scholar 
Schliep KP. phangorn: phylogenetic analysis in R. Bioinformatics. 2010;27:592–3.PubMed 
PubMed Central 
Article 

Google Scholar 
Wright ES. Using DECIPHER v2.0 to analyze big biological sequence data in R. R J. 2016;8:352–9.Article 

Google Scholar 
McMurdie PJ, Holmes S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE. 2013;8:e61217.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Dixon P. VEGAN, a package of R functions for community ecology. J Veget Sci. 2003;14:927–30.Article 

Google Scholar 
Wickham H. ggplot2: elegant graphics for data analysis. New York: Springer; 2016.Sharma HS, Kilpatrick M. Mushroom (Agaricus bisporus) compost quality factors for predicting potential yield of fruiting bodies. Can J Microbiol. 2000;46:515–9.CAS 
PubMed 
Article 

Google Scholar 
Seaby DA. Mushroom (Agaricus bisporus) yield modelling for the bag method of mushroom production using commercial yields and from micro plots. Sci Cultiv Edible Fungi. 1995;14:409–16.
Google Scholar 
O’Donoghue DC. Relationship between some compost factors and their effects on yield of Agaricus. Mushroom Sci. 1965;6:245–54.
Google Scholar 
Andersen B, Sorensen JL, Nielsen KF, van den Ende BG, de Hoog S. A polyphasic approach to the taxonomy of the Alternaria infectoria species-group. Fungal Genet Biol. 2009;46:642–56.CAS 
PubMed 
Article 

Google Scholar 
van den Brink J, Samson RA, Hagen F, Boekhout T, de Vries RP. Phylogeny of the industrial relevant, thermophilic genera Myceliophthora and Corynascus. Fungal Divers. 2012;52:197–207.Article 

Google Scholar 
Souza TP, Marques SC, Santos D, Dias ES. Analysis of thermophilic fungal populations during phase II of composting for the cultivation of Agaricus subrufescens. World J Microbiol Biotechnol. 2014;30:2419–25.PubMed 
Article 

Google Scholar 
Vajna B, Szili D, Nagy A, Márialigeti K. An improved sequence-aided T-RFLP analysis of bacterial succession during oyster mushroom substrate preparation. Microb Ecol. 2012;64:702–13.CAS 
PubMed 
Article 

Google Scholar 
Du R, Yan J, Li S, Zhang L, Zhang S, Li J, et al. Cellulosic ethanol production by natural bacterial consortia is enhanced by Pseudoxanthomonas taiwanensis. Biotechnol Biofuels. 2015;8:10.Kato S, Haruta S, Cui ZJ, Ishii M, Igarashi Y. Stable coexistence of five bacterial strains as a cellulose-degrading community. Appl Environ Microbiol. 2005;71:7099–106.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Haruta S, Cui Z, Huang Z, Li M, Ishii M, Igarashi Y. Construction of a stable microbial community with high cellulose-degradation ability. Appl Microbiol Biotechnol. 2002;59:529–34.CAS 
PubMed 
Article 

Google Scholar 
Vajna B, Adrienn N, Sajben-Nagy E, Manczinger L, Szijártó N, Kádár Z, et al. Microbial community structure changes during oyster mushroom substrate preparation. Appl Microbiol Biotechnol. 2010;86:367–75.CAS 
PubMed 
Article 

Google Scholar 
Karadag D, Özkaya B, Ölmez E, Nissilä ME, Çakmakçı M, Yıldız Ş, et al. Profiling of bacterial community in a full-scale aerobic composting plant. Int Biodeter Biodeg. 2013;77:85–90.CAS 
Article 

Google Scholar 
Rathinam NK, Gorky, Bibra M, Salem DR, Sani RK. Bioelectrochemical approach for enhancing lignocellulose degradation and biofilm formation in Geobacillus strain WSUCF1. Bioresour Technol. 2020;295:122271.Song TT, Shen YY, Jin QL, Feng WL, Fan LJ, Cao GT, et al. Bacterial community diversity, lignocellulose components, and histological changes in composting using agricultural straws for Agaricus bisporus production. PeerJ. 2021;9:e10452.PubMed 
PubMed Central 
Article 

Google Scholar 
Zhang X, Zhong Y, Yang S, Zhang W, Xu M, Ma A, et al. Diversity and dynamics of the microbial community on decomposing wheat straw during mushroom compost production. Bioresour Technol. 2014;170:183–95.CAS 
PubMed 
Article 

Google Scholar 
Goodfellow M, Maldonado LA, Quintana ET. Reclassification of Nonomuraea flexuosa (Meyer 1989) Zhang et al. 1998 as Thermopolyspora flexuosa gen. nov., comb. nov., nom. rev. Int J Syst Evol Microbiol. 2005;55:1979–83.CAS 
PubMed 
Article 

Google Scholar 
Lin SB, Stutzenberger FJ. Purification and characterization of the major beta-1,4-endoglucanase from Thermomonospora curvata. J Appl Bacteriol. 1995;79:447–53.CAS 
PubMed 
Article 

Google Scholar 
Kukolya J, Nagy I, Láday M, Tóth E, Oravecz O, Márialigeti K, et al. Thermobifida cellulolytica sp. nov., a novel lignocellulose-decomposing actinomycete. Int J Syst Evol Microbiol. 2002;52:1193–9.CAS 
PubMed 

Google Scholar 
Weon H-Y, Lee S-Y, Kim B-Y, Noh H-J, Schumann P, Kim J-S, et al. Ureibacillus composti sp. nov. and Ureibacillus thermophilus sp. nov., isolated from livestock-manure composts. Int J Syst Evol Microbiol. 2007;57:2908–11.CAS 
PubMed 
Article 

Google Scholar 
Poli A, Laezza G, Gul-Guven R, Orlando P, Nicolaus B. Geobacillus galactosidasius sp. nov., a new thermophilic galactosidase-producing bacterium isolated from compost. Syst Appl Microbiol. 2011;34:419–23.CAS 
PubMed 
Article 

Google Scholar 
Gavande PV, Basak A, Sen S, Lepcha K, Murmu N, Rai V, et al. Functional characterization of thermotolerant microbial consortium for lignocellulolytic enzymes with central role of Firmicutes in rice straw depolymerization. Sci Rep. 2021;11:3032.Xu JQ, Lu YY, Shan GC, He XS, Huang JH, Li QL. Inoculation with compost-born thermophilic complex microbial consortium induced organic matters degradation while reduced nitrogen loss during co-composting of dairy manure and sugarcane leaves. Waste Biomass Valor. 2019;10:2467–77.CAS 
Article 

Google Scholar 
Yoon JH, Kang SJ, Im WT, Lee ST, Oh TK. Chelatococcus daeguensis sp nov., isolated from wastewater of a textile dye works, and emended description of the genus Chelatococcus. Int J Syst Evol Microbiol. 2008;58:2224–8.CAS 
PubMed 
Article 

Google Scholar 
Zhou C, Liu Z, Huang Z-L, Dong M, Yu X-L, Ning P. A new strategy for co-composting dairy manure with rice straw: addition of different inocula at three stages of composting. Waste Manage. 2015;40:38–43.CAS 
Article 

Google Scholar 
Gómez A. New technology in Agaricus bisporus cultivation. In: Zied DC, Pardo-Giménez A, editors. Edible and medicinal mushrooms. Chichester, UK: John Wiley & Sons; 2017. p. 211–20.von Minnigerode HF, editor. Method for controlling and regulating the composting process. Proceedings of the Eleventh International Scientific Congress on the Cultivation of Edible Fungi. Sydney, Australia: The International Society for Mushroom Science; 1981.Jurak E, Gruppen H, Kabel MA, Eggink G, Meyer AS, van der Maarel MJEC, et al. How mushrooms feed on compost: conversion of carbohydrates and lignin in industrial wheat straw based compost enabling the growth of Agaricus bisporus. Wageningen University—Graduate School VLAG; 2015.Miller FC, Macauley BJ, Harper ER. Investigation of various gases, pH and redox potential in mushroom composting Phase-I stacks. Aust J Exper Agric. 1991;31:415–25.Article 

Google Scholar 
Miller FC, Harper ER, Macauley BJ, Gulliver A. Composting based on moderately thermophilic and aerobic conditions for the production of commercial growing compost. Aust J Exper Agric. 1990;30:287–96.Article 

Google Scholar 
Carrasco J, Preston GM. Growing edible mushrooms: a conversation between bacteria and fungi. Environ Microbiol. 2020;22:858–72.PubMed 
Article 

Google Scholar  More

Yuan, F. & Miyamoto, S. Dominant processes controlling water chemistry of the Pecos River in American Southwest. Geophys. Res. Lett. 32(17), L17406. https://doi.org/10.1029/2005GL023359 (2005).ADS 
CAS 
Article 

Google Scholar 
Yuan, F., Miyamoto, S. & Anand, S. Changes in major element hydrochemistry of the Pecos River in the American Southwest since 1935. Appl. Geochem. 22(8), 1798–1813. https://doi.org/10.1016/j.apgeochem.2007.03.036 (2007).ADS 
CAS 
Article 

Google Scholar 
Harley, G. L. & Maxwell, J. T. Current declines of Pecos River (New Mexico, USA) streamflow in a 700-year context. Holocene 28(5), 766–777. https://doi.org/10.1177/0959683617744263 (2018).ADS 
Article 

Google Scholar 
Jensen, R., Hatler, W., Mecke, M. & Hart, C. The Influences of Human Activities on the Water of the Pecos River Basin of Texas: A Brief Overview. Technical Report. SR-2006-03. Texas Water Resources Institute (2006).Hoagstrom, C. W. Causes and impacts of salinization in the lower Pecos River. Gt. Plains Res. 19(1), 27–44 (2009).
Google Scholar 
Williams, A. P., Cook, B. I. & Smerdon, J. E. Rapid intensification of the emerging North American megadrought in 2020–2021. Nat. Clim. Change 12(3), 232–234. https://doi.org/10.1038/s41558-022-01290-z (2022).ADS 
Article 

Google Scholar 
Cheek, C. A. & Taylor, C. M. Salinity and geomorphology drive long-term changes to local and regional fish assemblage attributes in the lower Pecos River, Texas. Ecol. Freshw. Fish 25(3), 340–351. https://doi.org/10.1111/eff.12214 (2015).Article 

Google Scholar 
Pease, A. A. & Delaune, K. D. Dried and salted: cumulative impacts of diminished flows and salinization on the lower Pecos River food webs. In Proceedings of the Desert Fishes Council Special Publication. Vol. 2021, 2–19. https://doi.org/10.26153/tsw/12364 (2021)Linam, G. W. & Kleinsasser, L. J. Relationships Between Fishes and Water Quality in the Pecos River, Texas. River Studies Report. No. 9. Texas Parks and Wildlife Department (1996).Hoagstrom, C. W., Zymonas, N. D., Davenport, S. R., Propst, D. L. & Brooks, J. E. Rapid species replacements between fishes of the North American plains: A case history from the Pecos River. Aquat. Invasions 5(2), 141–153. https://doi.org/10.3391/ai.2010.5.2.03 (2010).Article 

Google Scholar 
Randklev, C. R. et al. A semi-arid river in distress: Contributing factors and recovery solutions for three imperiled freshwater mussels (Family Unionidae) endemic to the Rio Grande Basin in North America. Sci. Total Environ. 631–632, 733–744. https://doi.org/10.1016/j.scitotenv.2018.03.032 (2018).ADS 
CAS 
Article 
PubMed 

Google Scholar 
Kimmons, J. B. & Moll, D. Seed dispersal by Red-eared sliders (Trachemys scripta elegans) and Common snapping turtles (Chelydra serpentina). Chelonian Conserv. Biol. 9(2), 289–294. https://doi.org/10.2744/CCB-0797.1 (2010).Article 

Google Scholar 
Lazar, B. et al. Loggerhead sea turtles (Caretta caretta) as bioturbators in neritic habitats: An insight through the analysis of benthic molluscs in the diet. Mar. Ecol. 32(1), 65–74. https://doi.org/10.1111/j.1439-0485.2010.00402.x (2011).ADS 
Article 

Google Scholar 
Lovich, J. E., Ennen, J. R., Agha, M. & Gibbons, J. W. Where have all the turtles gone, and why does it matter?. Bioscience 68(10), 771–781. https://doi.org/10.1093/biosci/biy095 (2018).Article 

Google Scholar 
de Solla, S. R., Fernie, K. J. & Ashpole, S. Snapping turtles (Chelydra serpentina) as bioindicators in Canadian areas of concern in the Great Lakes Basin. II. Changes in hatching success and hatchling deformities in relation to persistent organic pollutants. Environ. Pollut. 153(3), 529–536. https://doi.org/10.1016/j.envpol.2007.09.017 (2008).CAS 
Article 
PubMed 

Google Scholar 
Adams, C. I. M., Baker, J. E. & Kjellerup, B. V. Toxicological effects of polychlorinated biphenyls (PCBs) on freshwater turtles in the United States. Chemosphere 154, 148–154. https://doi.org/10.1016/j.chemosphere.2016.03.102 (2016).ADS 
CAS 
Article 

Google Scholar 
Beau, F., Bustamante, P., Michaud, B. & Brischoux, F. Environmental causes and reproductive correlates of mercury contamination in European pond turtles (Emys orbicularis). Environ. Res. 172(4), 338–344. https://doi.org/10.1016/j.envres.2019.01.043 (2019).CAS 
Article 
PubMed 

Google Scholar 
van Dijk, P. P. Pseudemys gorzugi (errata version published in 2016). The IUCN Red List of Threatened Species Vol. 2011, e.T18459A97. (2011).NMDGF [New Mexico Department of Game and Fish]. Threatened and Endangered Species of New Mexico, 2020 Biennial Review. Management and Fisheries Management Divisions (2020).SEMARNAT [Secretaríade Medio Ambiente y Recursos Naturales]. NORMA Oficial Mexicana NOM-059-SEMARNAT-2010, Protección ambiental–Especies nativas de México de flora y fauna silvestres–Categorías de riesgo y especificaciones para su inclusión, exclusión o cambio–Lista de especies en riesgo. Diario Oficial de la Federación Vol. 2 (2010).TPWD [Texas Parks & Wildlife Department]. Species Account: the Rio Grande River Cooter (Pseudemys gorzugi). In Texas Comprehensive Wildlife Conservation Strategy 2005–2010 (eds Bender, S., Shelton, S., Bender, K. & Kalmbach, A.). Nongame Division, 1075–7076 (2012).Pierce, L. J. S., Stuart, J. N., Ward, J. P. & Painter, C. W. Pseudemys gorzugi Ward 1984–Rio Grande Cooter, Western River Cooter, Tortuga de Oreja Amarilla, Jicotéa del Rio Bravo In Conservation Biology of Freshwater Turtles and Tortoises: A Compilation Project of the IUCN/SSC Tortoise and Freshwater Turtle Specialist Group (eds. Rhodin, A. G. J. et al.). Chelonian Res. Monog. Vol. 5, No. 9, 100.1–100.12. https://doi.org/10.3854/crm.5.100.gorzugi.v1.2016 (2016).Endangered and Threatened Wildlife and Plants. Endangered and Threatened Wildlife and Plants; three species not warranted for listing as endangered or threatened species. Fed. Reg. 87(49), 14227–14228 (2022).
Google Scholar 
Bailey, L. A., Forstner, M. R. J., Dixon, J. R. & Hudson, R. Contemporary status of the Rio Grande Cooter (Testudines: Emydidae: Pseudemys gorzugi) in Texas: phylogenetic, ecological and conservation consideration. In Proceedings of the Sixth Symposium on the Natural Resources of the Chihuahuan Desert Region (eds. Hoyt, C. A. & Karges, J.) 320–324. (Chihuahuan Desert Research Institute, 2014).Suriyamongkol, T., Waldon, K. J. & Mali, I. Trachemys scripta (Red-eared Slider) and Pseudemys gorzugi (Rio Grande Cooter). Fish hook ingestion and shooting. Herpetol. Rev. 50(4), 776–777 (2019).
Google Scholar 
Degenhardt, W. G., Painter, C. W. & Price, A. H. Amphibians and Reptiles of New Mexico (University of New Mexico Press, 1996).
Google Scholar 
Ernst, C. H. Turtles of the United States and Canada 2nd edn. (Johns Hopkins University Press, 2009).
Google Scholar 
Dixon, J. R. Amphibians and Reptiles of Texas: With Keys, Taxonomic Synopses, Bibliography, and Distribution Maps 3rd edn. (Texas A&M University Press, 2013).
Google Scholar 
Suriyamongkol, T. et al. Geographic distribution. Pseudemys gorzugi (Rio Grande Cooter). Herpetol. Rev. 51(3), 536–537 (2020).
Google Scholar 
Christman, B. L. & Kamees, L. K. Current Distribution of the Blotched Watersnake (Nerodia erythrogaster) and the Rio Grande Cooter (Pseudemys gorzugi) in the Lower Pecos River System Eddy County, New Mexico 2006–2007. Final Report. New Mexico Department of Game and Fish (2007).Bogolin, A. P., Davis, D. R., Ruppert, K. M., Kline, R. J. & Rahmann, A. F. Geographic distribution. Pseudemys gorzugi (Rio Grande Cooter). Herpetol. Rev. 50(4), 745 (2019).
Google Scholar 
Congdon, J. D., Dunham, A. E. & Van Loben Sels, R. C. Demographics of common snapping turtles (Chelydra serpentina): Implications for conservation and management of long-lived organisms. Am. Zool. 34, 397–408. https://doi.org/10.1093/icb/34.3.397 (1994).Article 

Google Scholar 
Brooks, R. J., Brown, G. P. & Galbraith, D. A. Effects of a sudden increase in natural mortality of adults on a population of the common snapping turtle (Chelydra serpentina). Can. J. Zool. 69, 1314–1320. https://doi.org/10.1139/z91-185 (1991).Article 

Google Scholar 
Congdon, J. D., Dunham, A. E. & Van Loben Sels, R. C. Delayed sexual maturity and demographics of Blanding’s turtles (Emydoidea blandingii): Implications for conservation and management of long-lived organisms. Conserv. Biol. 7(4), 826–833. https://doi.org/10.1046/j.1523-1739.1993.740826.x (1993).Article 

Google Scholar 
Suriyamongkol, M. & Mali, I. Aspects of the reproductive biology of the Rio Grande Cooter (Pseudemys gorzugi) on the Black River, New Mexico. Chelonian Conserv. Biol. https://doi.org/10.2744/CCB-1385.1 (2019).Article 

Google Scholar 
Bailey, L. A., Dixon, J. R., Hudson, R. & Forstner, M. R. J. Minimal genetic structure of the Rio Grande Cooter (Pseudemys gorzugi). Southwest. Nat. 53(3), 406–411. https://doi.org/10.1894/GC-179.1 (2008).Article 

Google Scholar 
Mali, I., Duarte, A. & Forstner, M. R. J. Comparison of hoop-net trapping and visual surveys to monitor abundance of the Rio Grande Cooter (Pseudemys gorzugi). PeerJ 6, e4677:1-16. https://doi.org/10.7717/peerj.4677 (2018).Article 

Google Scholar 
Hart, C. R., McDonald, A. & Hatler, W. Pecos River Ecosystem Monitoring Project. Technical Report. Texas Cooperative Extension: The Texas A&M University System. (2005).Hong, M., Zhang, K., Shu, C., Xie, D. & Shi, H. Effect of salinity on the survival, ions, and urea modulation in Red-eared Slider (Trachemys scripta elegans). Asian Herpetol. Res. 5(2), 128–136. https://doi.org/10.3724/SP.J.1245.2014.00128 (2014).Article 

Google Scholar 
Hintz, W. D. et al. Salinization triggers a trophic cascade in experimental freshwater communities with varying food-chain length. Ecol. Appl. 27(3), 833–844. https://doi.org/10.1002/eap.1487 (2017).Article 
PubMed 

Google Scholar 
Letter, A. W., Waldon, K. J., Pollock, D. A. & Mali, I. Dietary habits of Rio Grande Cooters (Pseudemys gorzugi) from two sites within the Black River, Eddy County, New Mexico, USA. J. Herpetol. 53(3), 204–208. https://doi.org/10.1670/18-057 (2019).Article 

Google Scholar 
Suriyamongkol, T., Ortega-Berno, V., Mahan, L. B. & Mali, I. Using stable isotopes to study resource partitioning between Red-eared Slider and Rio Grande Cooter in the Pecos River watershed. Ichthyol. Herpetol. 110(1), 96–105. https://doi.org/10.1643/h2021023 (2022).Article 

Google Scholar 
Bassett, L. G., Mali, I., Nowlin, W. H., Foley, D. H. & Forstner, M. R. J. Diet and isotopic niche of the Rio Grande Cooter (Pseudemys gorzugi) and syntopic Red-eared Slider (Trachemys scripta elegans) in San Felipe Creek, Texas, USA. Chelonian Conserv. Biol. (in Press).Bárcenas-García, A. et al. Impacts of dams on freshwater turtles: A global review to identify conservation solutions. Trop. Conserv. Sci. 15(4), 1–21. https://doi.org/10.1177/194008292211037098 (2021).Article 

Google Scholar 
Smith, M. J. et al. Association between anuran tadpoles and salinity in a landscape mosaic of wetlands impacted by secondary salinisation. Freshw. Biol. 52(1), 75–84. https://doi.org/10.1111/j.1365-2427.2006.01672.x (2007).Article 

Google Scholar 
Wohner, P. J. et al. Integrating monitoring and optimization modeling to inform flow decisions for Chinook salmon smolts. Ecol. Model. 471(2022), 110058. https://doi.org/10.1016/j.ecolmodel.2022.110058 (2022).Article 

Google Scholar 
Suriyamongkol, T., Tian, W. & Mali, I. Monitoring the basking behavior of Rio Grande Cooter (Pseudemys gorzugi) through game camerias in southeastern New Mexico, USA. West. N. Am. Nat. 81(3), 361–371. https://doi.org/10.3398/064.081.0305 (2021).Article 

Google Scholar 
Painter, C. W. Preliminary Investigations of the Distribution and Natural History of the Rio Grande River Cooter (Pseudemys gorzugi) in New Mexico. Preliminary Report. (United States Department of the Interior–Bureau of Land Management, 1993).Hak, J. C. & Comer, P. J. Modeling landscape condition for biodiversity assessment—Application in temperate North America. Ecol. Indic. 82, 206–216. https://doi.org/10.1016/j.ecolind.2017.06.049 (2017).Article 

Google Scholar 
ESRI. ArcGIS Desktop. Ver. 10.8 (Environmental System Research Institute, 2020).MacKenzie, D. I. et al. Estimating site occupancy rates when detection probabilities are less than one. Ecology 83(8), 2248–2255. https://doi.org/10.1890/0012-9658(2002)083[2248:ESORWD]2.0.CO;2 (2002).Article 

Google Scholar 
Tyre, A. J. et al. Improving precision and reducing bias in biological surveys: Estimating false-negative error rates. Ecol. Appl. 13(6), 1790–1801. https://doi.org/10.1890/02-5078 (2003).Article 

Google Scholar 
Mackenzie, D. I. et al. Occupancy Estimation and Modeling: Inferring Dynamics of Species Occurrence 2nd edn. (Elsevier, 2017).
Google Scholar 
Duarte, A., Whitlock, S. L. & Peterson, J. T. Species distribution modeling. In Encyclopedia of Ecology 2nd edn (ed. Fath, B. D.) (Elsevier, 2019).
Google Scholar 
MacLaren, A. R., Foley, D. H., Sirsi, S. & Forstner, M. R. J. Updating methods of satellite transmitter attachment for long-term monitoring of the Rio Grande Cooter (Pseudemys gorzugi). Herpetol. Rev. 48(1), 48–52 (2017).
Google Scholar 
MacLaren, A. R., Sirsi, S., Foley, D. H. & Forstner, M. R. J. Pseudemys gorzugi (Rio Grande Cooter). Long distance dispersal. Herpetol. Rev. 48(1), 180–181 (2017).
Google Scholar 
Fiske, I. & Chandler, R. unmarked: An R package for fitting hierarchical models of wildlife occurrence and abundance. J. Stat. Softw. 43(10), 1–23. https://doi.org/10.18637/jss.v043.i10 (2011).Article 

Google Scholar 
R Core Team. R: A Language and Environment for Statistical Computing (Foundation For Statistical Computing, 2021).
Google Scholar 
Morin, D. J. et al. Is your ad hoc model selection strategy affecting your multimodel inference?. Ecosphere 11(1), e02997. https://doi.org/10.1002/ecs2.2997 (2020).Article 

Google Scholar 
Burnham, K. P. & Anderson, D. R. Model Selection and Inference: A Practical Information-Theoretic Approach 1st edn. (Springer, XXX, 1998).Book 

Google Scholar 
Hosmer, D. W., Lemeshow, S. & Sturdivant, R. X. Applied Logistic Regression 3rd edn. (Wiley, 2013).Book 

Google Scholar 
Gasparrini, A., Armstrong, B. & Kenward, M. G. Multivariate meta-analysis for non-linear and other multi-parameter associations. Stat. Med. 31(29), 3821–3839. https://doi.org/10.1002/sim.5471 (2012).MathSciNet 
CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Jackson, D., White, I. R. & Riley, R. D. A matrix-based method of moments for fitting the multivariate random effects model for meta-analysis and meta-regression. Biom. J. 55(2), 231–245. https://doi.org/10.1002/bimj.201200152 (2013).MathSciNet 
Article 
PubMed 
PubMed Central 
MATH 

Google Scholar  More

Bonan, G. B. Forests and climate change: Forcings, feedbacks, and the climate benefits of forests. Science 320, 1444–1449. https://doi.org/10.1126/science.1155121 (2008).ADS 
CAS 
Article 
PubMed 

Google Scholar 
Le Quere, C. et al. Global carbon budget 2016. Earth Syst. Sci. Data 8, 605–649. https://doi.org/10.5194/essd-8-605-2016 (2016).ADS 
Article 

Google Scholar 
DavidMorales-Hidalgo, D., Oswalt, S. N. & Somanathan, E. Status and trends in global primary forest, protected areas, and areas designated for conservation of biodiversity from the Global Forest Resources Assessment 2015. Forest Ecol. Manag. 352, 68–77. https://doi.org/10.1016/j.foreco.2015.06.011 (2015).Article 

Google Scholar 
Kauppi, P. E., Sandstrom, V. & Lipponen, A. Forest resources of nations in relation to human well-being. PLoS One 13, e0196248. https://doi.org/10.1371/journal.pone.0196248 (2018).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Anderegg, W. R. L. et al. Climate-driven risks to the climate mitigation potential of forests. Science 368, 1327. https://doi.org/10.1126/science.aaz7005 (2020).CAS 
Article 

Google Scholar 
Wilson, M. C. et al. Habitat fragmentation and biodiversity conservation: Key findings and future challenges. Landsc. Ecol. 31, 219–227. https://doi.org/10.1007/s10980-015-0312-3 (2016).Article 

Google Scholar 
Haddad, N. M. et al. Habitat fragmentation and its lasting impact on earth’s ecosystems. Sci. Adv. 1, e1500052. https://doi.org/10.1126/sciadv.1500052 (2015).ADS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Holl, K. D. Restoring tropical forests from the bottom up. Science 355, 455–456. https://doi.org/10.1126/science.aam5432 (2017).ADS 
CAS 
Article 
PubMed 

Google Scholar 
Audino, L. D., Murphy, S. J., Zambaldi, L., Louzada, J. & Comita, L. S. Drivers of community assembly in tropical forest restoration sites: Role of local environment, landscape, and space. Ecol. Appl. 27, 1731–1745. https://doi.org/10.1002/eap.1562 (2017).Article 
PubMed 

Google Scholar 
Temperton, V. M., Hobbs, R. J., Nuttle, T. & Halle, S. in Assembly Rules and Restoration Ecology: Bridging the Gap Between Theory and Practice [Science and Practice of Ecological Restoration]. i–xv, 1–439 (2004).Young, T. P., Chase, J. M. & Huddleston, R. T. Community succession and assembly: Comparing, contrasting and combining paradigms in the context of ecological restoration. Ecol. Restor. 19, 5–18 (2001).Article 

Google Scholar 
Vellend, M. The Theory of Ecological Communities (Princeton University Press, 2016).
Google Scholar 
HilleRisLambers, J., Adler, P. B., Harpole, W. S., Levine, J. M. & Mayfield, M. M. Rethinking community assembly through the lens of coexistence theory. Annu. Rev. Ecol. Evol. Syst. 43(43), 227–248. https://doi.org/10.1146/annurev-ecolsys-110411-160411 (2012).Article 

Google Scholar 
Connell, J. H. On the role of natural enemies in preventing competitive exclusion in some marine animals and in rain forest trees. In Dynamics of Populations (eds Den Boer, P. J. & Gradwell, G. R.) (Centre for Agricultural Publishing and Documentation, 1971).
Google Scholar 
Janzen, D. H. Herbivores and the number of tree species in tropical forests. Am. Nat. 104, 501. https://doi.org/10.1086/282687 (1970).Article 

Google Scholar 
Schmid, J. S., Taubert, F., Wiegand, T., Sun, I. F. & Huth, A. Network science applied to forest megaplots: Tropical tree species coexist in small-world networks. Sci. Rep. https://doi.org/10.1038/s41598-020-70052-8 (2020).Article 
PubMed 
PubMed Central 

Google Scholar 
Wang, H. X. et al. Prevalence of inter-tree competition and its role in shaping the community structure of a natural Mongolian scots pine (Pinus sylvestris var. mongolica) forest. Forests https://doi.org/10.3390/f8030084 (2017).Article 

Google Scholar 
Hubbell, S. P. et al. Light-gap disturbances, recruitment limitation, and tree diversity in a neotropical forest. Science 283, 554–557. https://doi.org/10.1126/science.283.5401.554 (1999).ADS 
CAS 
Article 
PubMed 

Google Scholar 
Janik, D. et al. Breaking through beech: A three-decade rise of sycamore in old-growth European forest. Forest Ecol. Manag. 366, 106–117. https://doi.org/10.1016/j.foreco.2016.02.003 (2016).Article 

Google Scholar 
Svatek, M., Rejzek, M., Kvasnica, J., Repka, R. & Matula, R. Frequent fires control tree spatial pattern, mortality and regeneration in argentine open woodlands. Forest Ecol. Manag. 408, 129–136. https://doi.org/10.1016/j.foreco.2017.10.048 (2018).Article 

Google Scholar 
Giammarchi, F. et al. Effects of the lack of forest management on spatiotemporal dynamics of a subalpine Pinus cembra forest. Scand. J. Forest Res. 32, 142–153. https://doi.org/10.1080/02827581.2016.1207802 (2017).Article 

Google Scholar 
Janik, D. et al. Patterns of Fraxinus angustifolia in an alluvial old-growth forest after declines in flooding events. Eur. J. Forest Res. 135, 215–228. https://doi.org/10.1007/s10342-015-0925-8 (2016).Article 

Google Scholar 
Bagchi, R. et al. Defaunation increases the spatial clustering of lowland western amazonian tree communities. J. Ecol. 106, 1470–1482. https://doi.org/10.1111/1365-2745.12929 (2018).Article 

Google Scholar 
Zhang, L. Y., Dong, L. B., Liu, Q. & Liu, Z. G. Spatial patterns and interspecific associations during natural regeneration in three types of secondary forest in the central part of the greater Khingan mountains, Heilongjiang province, China. Forests https://doi.org/10.3390/f11020152 (2020).Article 

Google Scholar 
Obiang, N. L. E. et al. Determinants of spatial patterns of canopy tree species in a tropical evergreen forest in Gabon. J. Veg. Sci. 30, 929–939. https://doi.org/10.1111/jvs.12778 (2019).Article 

Google Scholar 
Wiegand, T. et al. Spatially explicit metrics of species diversity, functional diversity, and phylogenetic diversity: Insights into plant community assembly processes. Annu. Rev. Ecol. Evol. Syst. 48(48), 329–351. https://doi.org/10.1146/annurev-ecolsys-110316-022936 (2017).Article 

Google Scholar 
Gabriel, E. Spatial point patterns: Methodology and applications with R. Math. Geosci. 49, 815–817. https://doi.org/10.1007/s11004-016-9670-x (2017).CAS 
Article 
MATH 

Google Scholar 
Baddeley, A., Rubak, R. & Turner, R. Spatial Point Patterns, Methodology and Applications with R (CRC Press, 2016).MATH 

Google Scholar 
Wiegand, T. & Moloney, K. A. Rings, circles, and null-models for point pattern analysis in ecology. Oikos 104, 209–229. https://doi.org/10.1111/j.0030-1299.2004.12497.x (2004).Article 

Google Scholar 
Plotkin, J. B., Chave, J. M. & Ashton, P. S. Cluster analysis of spatial patterns in Malaysian tree species. Am. Nat. 160, 629–644. https://doi.org/10.1086/342823 (2002).Article 
PubMed 

Google Scholar 
Ripley, B. D. Modeling spatial patterns. J. R. Stat. Soc. B 39, 172–212 (1977).
Google Scholar 
He, F. L. & Gaston, K. J. Estimating species abundance from occurrence. Am. Nat. 156, 553–559. https://doi.org/10.1086/303403 (2000).Article 
PubMed 

Google Scholar 
Diggle, P. Statistical Analysis of Spatial Point Patterns (Academic Press, 1983).MATH 

Google Scholar 
Pielou, E. C. The use of point-to-plant distances in the study of the pattern of plant-populations. J. Ecol. 47, 607–613. https://doi.org/10.2307/2257293 (1959).Article 

Google Scholar 
Losapio, G., Montesinos-Navarro, A. & Saiz, H. Perspectives for ecological networks in plant ecology. Plant Ecol. Divers. 12, 87–102. https://doi.org/10.1080/17550874.2019.1626509 (2019).Article 

Google Scholar 
Fuller, M. M., Wagner, A. & Enquist, B. J. Using network analysis to characterize forest structure. Nat. Resour. Model. 21, 225–247. https://doi.org/10.1111/j.1939-7445.2008.00004.x (2008).MathSciNet 
Article 

Google Scholar 
Montoya, J. M., Pimm, S. L. & Sole, R. V. Ecological networks and their fragility. Nature 442, 259–264. https://doi.org/10.1038/nature04927 (2006).ADS 
CAS 
Article 
PubMed 

Google Scholar 
Proulx, S. R., Promislow, D. E. L. & Phillips, P. C. Network thinking in ecology and evolution. Trends Ecol. Evol. 20, 345–353. https://doi.org/10.1016/j.tree.2005.04.004 (2005).Article 
PubMed 

Google Scholar 
Nakagawa, Y., Yokozaw, M. & Hara, T. Complex network analysis reveals novel essential properties of competition among individuals in an even-aged plant population. Ecol. Complex 26, 95–116. https://doi.org/10.1016/j.ecocom.2016.03.005 (2016).Article 

Google Scholar 
Wiegand, T. & Moloney, K. A. Handbook of Spatial Point Pattern Analysis in Ecology (CRC Press, 2013).Book 

Google Scholar 
Barthelemy, M. Spatial networks. Phys. Rep. Rev. Sect. Phys. Lett. 499, 1–101. https://doi.org/10.1016/j.physrep.2010.11.002 (2011).MathSciNet 
CAS 
Article 

Google Scholar 
Keren, S. Modeling tree species count data in the understory and canopy layer of two mixed old-growth forests in the Dinaric region. Forests https://doi.org/10.3390/f11050531 (2020).Article 

Google Scholar 
Podlaski, R. Models of the fine-scale spatial distributions of trees in managed and unmanaged forest patches with Abies alba Mill. and Fagus sylvatica L. Forest Ecol. Manag. 439, 1–8 (2019).Article 

Google Scholar 
Levin, S. A. Theoretical ecology—Principles and applications, 3rd edition. Science 316, 1699–1700. https://doi.org/10.1126/science.1141870 (2007).CAS 
Article 

Google Scholar 
Martinez-Lopez, V., Garcia, C., Zapata, V., Robledano, F. & De la Rua, P. Intercontinental long-distance seed dispersal across the Mediterranean basin explains population genetic structure of a bird-dispersed shrub. Mol. Ecol. 29, 1408–1420. https://doi.org/10.1111/mec.15413 (2020).Article 
PubMed 

Google Scholar 
Dale, M. R. T. & Fortin, M. J. From graphs to spatial graphs. Annu. Rev. Ecol. Evol. Syst. 41, 21–38. https://doi.org/10.1146/annurev-ecolsys-102209-144718 (2010).Article 

Google Scholar 
Silva, C. A. et al. Treetop: A shiny-based application and R package for extracting forest information from LiDAR data for ecologists and conservationists. Methods Ecol. Evol. 13, 1164–1176. https://doi.org/10.1111/2041-210x.13830 (2022).Article 

Google Scholar 
Tatsumi, S., Yamaguchi, K. & Furuya, N. Forestscanner: A mobile application for measuring and mapping trees with LiDAR-equipped iPhone and iPad. Methods Ecol. Evol. https://doi.org/10.1111/2041-210x.13900 (2022).Article 

Google Scholar 
Ferraz, A., Saatchi, S. S., Longo, M. & Clark, D. B. Tropical tree size-frequency distributions from airborne LiDAR. Ecol. Appl. 30, e02154. https://doi.org/10.1002/eap.2154 (2020).Article 
PubMed 

Google Scholar 
Bianchi, E., Bugmann, H., Hobi, M. L. & Bigler, C. Spatial patterns of living and dead small trees in subalpine Norway spruce forest reserves in Switzerland. Forest Ecol. Manag. 494, 119315. https://doi.org/10.1016/j.foreco.2021.119315 (2021).Article 

Google Scholar 
Tatsumi, S., Owari, T., Yin, M. F. & Ning, L. Z. Neighborhood analysis of underplanted Korean pine demography in larch plantations: Implications for uneven-aged management in northeast china. Forest Ecol. Manag. 322, 10–18. https://doi.org/10.1016/j.foreco.2014.03.022 (2014).Article 

Google Scholar 
Cornett, M. W., Reich, P. B. & Puettmann, K. J. Canopy feedbacks and microtopography regulate conifer seedling distribution in two Minnesota conifer-deciduous forests. Ecoscience 4, 353–364. https://doi.org/10.1080/11956860.1997.11682414 (1997).Article 

Google Scholar 
Wang, X. F., Zheng, G., Yun, Z. X. & Moskal, L. M. Characterizing tree spatial distribution patterns using discrete aerial LiDAR data. Remote Sens. Basel 12, 712. https://doi.org/10.3390/rs12040712 (2020).ADS 
Article 

Google Scholar 
Matérn, B. Spatial variation: Stochastic models and their application to some problems in forest surveys and other sampling investigations. Meddelanden från Statens Skogsforskningsinstitut 49, 1–144 (1960).MathSciNet 

Google Scholar 
Matérn, B. Spatial Variation. Lecture Notes in Statistics Vol. 36 (Springer, 1986).Book 

Google Scholar 
Thomas, M. A generalisation of Poisson’s binomial limit for use in ecology. Biometrika 36, 18–25 (1949).MathSciNet 
CAS 
Article 

Google Scholar 
Lotwick, H. W. Simulation of some spatial hard core models, and the complete packing problem. J. Stat. Comput. Simul. 15, 295–314 (1982).MathSciNet 
Article 

Google Scholar 
Strauss, D. J. A model for clustering. Biometrika 62, 467–475 (1975).MathSciNet 
Article 

Google Scholar 
Cressie Noel, A. C. Statistics for Spatial Data (Wiley-Interscience, 1993).Book 

Google Scholar 
Besag, J. E. Contribution to the discussion of the paper by Ripley. J. R. Stat. Soc. 39, 193–195 (1977).MathSciNet 

Google Scholar  More

Little, C. M., Chapman, T. W. & Hillier, N. K. Plasticity is key to success of Drosophila suzukii (Diptera: Drosophilidae) invasion. J. Insect Sci. 20, 5. https://doi.org/10.1093/jisesa/ieaa034 (2020).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Tait, G. et al. Drosophila suzukii (Diptera: Drosophilidae): A decade of research towards a sustainable integrated pest management program. J. Economic Entomol. 114, 1950–1974. https://doi.org/10.1093/jee/toab158 (2021).Article 

Google Scholar 
Walsh, D. B. et al. Drosophila suzukii (Diptera: Drosophilidae): Invasive pest of ripening soft fruit expanding its geographic range and damage potential. J. Integ. Pest Manag. 2, G1–G7. https://doi.org/10.1603/IPM10010 (2011).Article 

Google Scholar 
Hamby, K. A. et al. Biotic and abiotic factors impacting development, behavior, phenology, and reproductive biology of Drosophila suzukii. J. Pest Sci. 89, 605–619. https://doi.org/10.1007/s10340-016-0756-5 (2016).Article 

Google Scholar 
Stewart, T. J., Wang, X. G., Molinar, A. & Daane, K. M. Factors limiting peach as a potential host for Drosophila suzukii (Diptera: Drosophilidae). J. Economic Entomol. 107, 1771–1779. https://doi.org/10.1603/EC14197 (2014).Article 

Google Scholar 
Keesey, I. W., Knaden, M. & Hansson, B. S. Olfactory specialization in Drosophila suzukii supports an ecological shift in host preference from rotten to fresh fruit. J. Chem. Ecol. 41, 121–128. https://doi.org/10.1007/s10886-015-0544-3 (2015).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Poyet, M. et al. The wide potential trophic niche of the Asiatic fruit fly Drosophila suzukii: The key of its invasion success in temperate Europe?. PLoS ONE 10, e0152785. https://doi.org/10.1371/journal.pone.0142785 (2015).CAS 
Article 

Google Scholar 
Lee, J. C. et al. Characterization and manipulation of fruit susceptibility to Drosophila suzukii. J. Pest Sci. 89, 771–780. https://doi.org/10.1007/s10340-015-0692-9 (2016).Article 

Google Scholar 
Entling, W., Anslinger, S., Jarausch, B., Michl, G. & Hoffmann, C. Berry skin resistance explains oviposition preferences of Drosophila suzukii at the level of grape cultivars and single berries. J. Pest Sci. 92, 477–484. https://doi.org/10.1007/s10340-018-1040-7 (2019).Article 

Google Scholar 
Guo, L. et al. Identification of potential mechanosensitive ion channels involved in texture discrimination during Drosophila suzukii egg-laying behavior. Insect Mol. Biol. 29, 444–451. https://doi.org/10.1111/imb.12654 (2020).CAS 
Article 
PubMed 

Google Scholar 
Kidera, H. & Takahashi, K. H. Chemical cues from competitors change the oviposition preference of Drosophila suzukii. Entomol. Exp. Appl. 168, 304–310. https://doi.org/10.1111/eea.12889 (2020).CAS 
Article 

Google Scholar 
Little, C. M., Dixon, P. L., Chapman, T. W. & Hillier, N. K. Role of fruit characters and colour on host selection of boreal fruits and berries by Drosophila suzukii (Diptera: Drosophilidae). Can. Entomol. 152, 546–562. https://doi.org/10.4039/tce.2020.1 (2020).Article 

Google Scholar 
Tait, G. et al. Reproductive site selection: evidence of an oviposition cue in a highly adaptive Dipteran, Drosophila suzukii (Diptera: Drosophilidae). Environ. Entomol. 49, 355–363. https://doi.org/10.1093/ee/nvaa005 (2020).CAS 
Article 
PubMed 

Google Scholar 
Tonina, L. et al. Texture features explain the susceptibility of grapevine cultivars to Drosophila suzukii (Diptera: Drosophilidae) infestation in ripening and drying grapes. Sci. rep. 10, 10245. https://doi.org/10.1038/s41598-020-66567-9 (2020).ADS 
CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Wernicke, M., Lethmayer, C. & Bluemel, S. Laboratory trials to investigate potential repellent/oviposition deterrent effects of selected substances on Drosophila suzukii adults. Bull. Insectol 73, 249–255 (2020).
Google Scholar 
Durkin, S. M. et al. Behavioral and genomic sensory adaptation underlying the pest activity of Drosophila suzukii. Mol. Biol. Evol. 38, 2532–2546. https://doi.org/10.1093/molbev/msab048 (2021).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Dweck, H. K. M., Talross, G. J. S., Wang, W. & Carlson, J. R. Evolutionary shifts in taste coding in the fruit pest Drosophila suzukii. Elife 10, e64317. https://doi.org/10.7554/eLife.64317 (2021).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Elsensohn, J. E., Aly, M. F. K., Schal, C. & Burrack, H. J. Social signals mediate oviposition site selection in Drosophila suzukii. Sci. Rep. 11, 3796. https://doi.org/10.1038/s41598-021-83354-2 (2021).ADS 
CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Kienzle, R. & Rohlfs, M. Mind the wound!—fruit injury ranks higher than, and interacts with, heterospecific cues for Drosophila suzukii oviposition. Insects 12, 424. https://doi.org/10.3390/insects12050424 (2021).Article 
PubMed 
PubMed Central 

Google Scholar 
Sato, A., Tanaka, K. M., Yew, J. Y. & Takahashi, A. Drosophila suzukii avoidance of microbes in oviposition choice. R. Soc. Open Sci. 8, 201601. https://doi.org/10.1098/rsos.201601 (2021).ADS 
CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Stockton, D. G., Cha, D. H. & Loeb, G. M. Does habituation affect the efficacy of semiochemical oviposition repellents developed against Drosophila suzukii?. Environ. Entomol. 50, 1322–1331. https://doi.org/10.1093/ee/nvab099 (2021).CAS 
Article 
PubMed 

Google Scholar 
Wöhner, T. et al. Insights into the susceptibility of raspberries to Drosophila suzukii oviposition. J. Appl Entomol. 145, 182–190. https://doi.org/10.1111/jen.12839 (2021).CAS 
Article 

Google Scholar 
Baena, R. et al. Ripening stages and volatile compounds present in strawberry fruits are involved in the oviposition choice of Drosophila suzukii (Diptera: Drosophilidae). Crop Prot. 153, 105883. https://doi.org/10.1016/j.cropro.2021.105883 (2022).CAS 
Article 

Google Scholar 
R Core Team R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org/ (2022).Broström, G. & Holmberg, H. Generalized linear models with clustered data: Fixed and random effects models. Comput. Stat. Data Anal. 55, 3123–3134. https://doi.org/10.1016/j.csda.2011.06.011 (2011).MathSciNet 
Article 
MATH 

Google Scholar 
Asplen, M. K. et al. Invasion biology of spotted wing Drosophila (Drosophila suzukii): A global perspective and future priorities. J. Pest Sci. 88, 469–494. https://doi.org/10.1007/s10340-015-0681-z (2015).Article 

Google Scholar 
Knapp, L., Mazzi, D. & Finger, R. The economic impact of Drosophila suzukii: Perceived costs and revenue losses of Swiss cherry, plum and grape growers. Pest Management Sci. 77, 978–1000. https://doi.org/10.1002/ps.6110 (2020).CAS 
Article 

Google Scholar 
Ishii, S. Studies on the host preference of the cowpea weevil (Callosobruchus chinensis L.). Bull. Natl. Inst. Agric. Sci. Ser. C 1, 185–156 (1952).
Google Scholar 
Katsoyannos, B. I. & Pittara, I. S. Effect of size of artificial oviposition substrates and presence of natural host fruits on the selection of oviposition site by Dacus oleae. Entmol. Exp. Appl. 34, 326–332 (1983).Article 

Google Scholar 
McDonald, P. T. & McInnis, D. O. Ceratitis capitata: Effect of host fruit size on the number of eggs per clutch. Entomol. Exp. Appl. 37, 207–211 (1985).Article 

Google Scholar 
Pittara, I. S. & Katsoyannos, B. I. Effect of shape, size and color on selection of oviposition sites by Chaetorellia australis. Entomol. Exp. Appl. 63, 105–113 (1992).Article 

Google Scholar 
Greenberg, S. M., Sappington, T. W., Sétamou, M. & Coleman, R. J. Influence of different cotton fruit sizes on boll weevil (Coleoptera: Curculionidae) oviposition and survival to adulthood. Environ. Entomol. 33, 443–449. https://doi.org/10.1603/0046-225X-33.2.443 (2004).Article 

Google Scholar 
Showler, A. T. Relationship of different cotton square sizes to boll weevil (Coleoptera: Curculionidae) feeding and oviposition in field conditions. J. Econ. Entomol. 98, 1572–1579. https://doi.org/10.1603/0022-0493-98.5.1572 (2005).Article 
PubMed 

Google Scholar 
Charnov, E. L., Los-den Hartogh, R. L., Jones, W. T. & van den Assem, J. Sex ratio evolution in a variable environment. Nature 289, 27–33 (1981).ADS 
CAS 
Article 

Google Scholar 
Avidov, Z., Berlinger, M. J. & Applebaum, S. W. Physiological aspects of host specificity in the Bruchidae: III. Effect of curvature and surface area on oviposition of Callosobruchus chinensis L.. Anim. Behav. 13, 178–180 (1965).Article 

Google Scholar 
Sambaraju, K. R. & Phillips, T. W. Effects of physical and chemical factors on oviposition by Plodia interpunctella (Lepidoptera: Pyralidae). Ann. Entomol. Soc. Am. 101, 955–963 (2008).Article 

Google Scholar 
Schmidt, J. M. & Smith, J. J. B. Correlations between body angles and substrate curvature in the parasitoid wasp Trichogramma minutum: A possible mechanism of host radius measurement. J. Exp. Biol. 125, 271–285 (1986).Article 

Google Scholar 
Jois, S. et al. Sexually dimorphic peripheral sensory neurons regulate copulation duration and persistence in male Drosophila. Sci. Rep. 12, 1–12. https://doi.org/10.1038/s41598-022-10247-3 (2022).CAS 
Article 

Google Scholar 
Crava, C. M. et al. Structural and transcriptional evidence of mechanotransduction in the Drosophila suzukii ovipositor. J. Insect Physiol. 125, 104088. https://doi.org/10.1016/j.jinsphys.2020.104088 (2020).CAS 
Article 
PubMed 

Google Scholar 
Sampson, B. J. et al. Novel aspects of Drosophila suzukii (Diptera: Drosophilidae) biology and an improved method for culturing this invasive species with a modified D. melanogaster diet. Florida Entomol. 99, 774–780. https://doi.org/10.1653/024.099.0433 (2016).Article 

Google Scholar  More

Klein, A. M. et al. Importance of pollinators in changing landscapes for world crops. P. R. Soc. B 274, 303–313 (2007).
Google Scholar 
Potts, S. G. et al. Global pollinator declines: trends, impacts and drivers. Trends Ecol. Evol. 25, 345–353 (2010).PubMed 

Google Scholar 
Gallai, N., Salles, J. M., Settele, J. & Vaissiere, B. E. Economic valuation of the vulnerability of world agriculture confronted with pollinator decline. Ecol. Econ. 68, 810–821 (2009).
Google Scholar 
Ollerton, J. Pollinator diversity: Distribution, ecological function, and conservation. Annu. Rev. Ecol. Evol. Syst. 48, 353–376 (2017).
Google Scholar 
Biesmeijer, J. C. et al. Parallel declines in pollinators and insect-pollinated plants in Britain and the Netherlands. Science 313, 351–354 (2006).ADS 
CAS 
PubMed 

Google Scholar 
Kosior, A. et al. The decline of the bumble bees and cuckoo bees (Hymenoptera : Apidae : Bombini) of Western and Central Europe. Oryx 41, 79–88 (2007).
Google Scholar 
Cameron, S. A. et al. Patterns of widespread decline in North American bumble bees. Proc. Natl. Acad. Sci. U. S. A. 108, 662–667 (2011).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Cameron, S. A., Lim, H. C., Lozier, J. D., Duennes, M. A. & Thorp, R. Test of the invasive pathogen hypothesis of bumble bee decline in North America. Proc. Natl. Acad. Sci. U. S. A. 113, 4386–4391 (2016).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Gill, R. J., Ramos-Rodriguez, O. & Raine, N. E. Combined pesticide exposure severely affects individual- and colony-level traits in bees. Nature 491, 105–108 (2012).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Whitehorn, P. R., O’Connor, S., Wackers, F. L. & Goulson, D. Neonicotinoid pesticide reduces bumble bee colony growth and queen production. Science 336, 351–352 (2012).ADS 
CAS 
PubMed 

Google Scholar 
Stanley, D. A. et al. Neonicotinoid pesticide exposure impairs crop pollination services provided by bumblebees. Nature 528, 548–550 (2015).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Baron, G. L., Raine, N. E. & Brown, M. J. F. General and species-specific impacts of a neonicotinoid insecticide on the ovary development and feeding of wild bumblebee queens. P. R. Soc. B 284, 20170123 (2017).
Google Scholar 
Siviter, H., Folly, A. J., Brown, M. J. F. & Leadbeater, E. Individual and combined impacts of sulfoxaflor and Nosema bombi on bumblebee (Bombus terrestris) larval growth. Proc. Biol. Sci. 287, 20200935 (2020).CAS 
PubMed 
PubMed Central 

Google Scholar 
Blacquière, T., Smagghe, G., van Gestel, C. A. M. & Mommaerts, V. Neonicotinoids in bees: a review on concentrations, side-effects and risk assessment. Ecotoxicology 21, 973–992 (2012).PubMed 
PubMed Central 

Google Scholar 
Richardson, L. L. et al. Secondary metabolites in floral nectar reduce parasite infections in bumblebees. Proc. Biol. Sci. 282, 20142471 (2015).PubMed 
PubMed Central 

Google Scholar 
McAulay, M. K. & Forrest, J. R. K. How do sunflower pollen mixtures affect survival of queenless microcolonies of bumblebees (Bombus impatiens)?. Arthropod Plant Interact. 13, 517–529 (2019).
Google Scholar 
European Food Safety Authority. Guidance on the risk assessment of plant protection products on bees (Apis mellifera, Bombus spp. and solitary bees). EFSA J. 11, 3295 (2013).Besard, L. et al. Compatibility of traditional and novel acaricides with bumblebees (Bombus terrestris): a first laboratory assessment of toxicity and sublethal effects. Pest Manag. Sci. 66, 786–793 (2010).CAS 
PubMed 

Google Scholar 
Elston, C., Thompson, H. M. & Walters, K. F. A. Sub-lethal effects of thiamethoxam, a neonicotinoid pesticide, and propiconazole, a DMI fungicide, on colony initiation in bumblebee (Bombus terrestris) micro-colonies. Apidologie 44, 563–574 (2013).CAS 

Google Scholar 
Barbosa, W. F., De Meyer, L., Guedes, R. N. C. & Smagghe, G. Lethal and sublethal effects of azadirachtin on the bumblebee Bombus terrestris (Hymenoptera: Apidae). Ecotoxicology 24, 130–142 (2015).CAS 
PubMed 

Google Scholar 
Dance, C., Botías, C. & Goulson, D. The combined effects of a monotonous diet and exposure to thiamethoxam on the performance of bumblebee micro-colonies. Ecotoxicol. Environ. Saf. 139, 194–201 (2017).CAS 
PubMed 

Google Scholar 
Schmehl, D. R., Tome, H. V. V., Mortensen, A. N., Martins, G. F. & Ellis, J. D. Protocol for the in vitro rearing of honey bee (Apis mellifera L.) workers. J. Apic. Res. 55, 113–129 (2016).Pereboom, J. J. M., Velthuis, H. H. W. & Duchateau, M. J. The organisation of larval feeding in bumblebees (Hymenoptera, Apidae) and its significance to caste differentiation. Insectes Soc. 50, 127–133 (2003).
Google Scholar 
Dorigo, A. S., Rosa-Fontana, A. D., Soares-Lima, H. M., Galaschi-Teixeira, J. S., Nocelli, R. C. F. & Malaspina, O. In Vitro larval rearing protocol for the stingless bee species Melipona scutellaris for toxicological studies. PLoS One 14. https://doi.org/10.1371/journal.pone.0213109 (2019).Botina, L. L. et al. Toxicological assessments of agrochemical effects on stingless bees (Apidae, Meliponini). MethodsX 7, 100906 (2020).PubMed 
PubMed Central 

Google Scholar 
Black, B. C., Hollingworth, R. M., Ahammadsahib, K. I., Kukel, C. D. & Donovan, S. Insecticidal Action and Mitochondrial Uncoupling Activity of AC-303,630 and Related Halogenated Pyrroles. Pestic. Biochem. Physiol. 50, 115–128 (1994).CAS 

Google Scholar 
Wakita, T. et al. The discovery of dinotefuran: a novel neonicotinoid. Pest Manag. Sci. 59, 1016–1022 (2003).CAS 
PubMed 

Google Scholar 
Shafiei, M., Moczek, A. P. & Nijhout, H. F. Food availability controls the onset of metamorphosis in the dung beetle Onthophagus taurus (Coleoptera: Scarabaeidae). Physiol. Entomol. 26, 173–180 (2001).
Google Scholar 
Stieper, B. C., Kupershtok, M., Driscoll, M. V. & Shingleton, A. W. Imaginal discs regulate developmental timing in Drosophila melanogaster. Dev. Biol. 321, 18–26 (2008).CAS 
PubMed 

Google Scholar 
Nijhout, H. F. & Williams, C. Control of moulting and metamorphosis in the tobacco hornworm, Manduca sexta (L.): growth of the last-instar larva and the decision to pupate. J. Exp. Biol. 61, 481–491 (1974).Cnaani, J., Robinson, G. E. & Hefetz, A. The critical period for caste determination in Bombus terrestris and its juvenile hormone correlates. J. Comp. Physiol. A 186, 1089–1094 (2000).CAS 
PubMed 

Google Scholar 
Goulson, D. et al. Can alloethism in workers of the bumblebee, Bombus terrestris, be explained in terms of foraging efficiency?. Anim. Behav. 64, 123–130 (2002).
Google Scholar 
Syromyatnikov, M., Nesterova, E., Smirnova, T. & Popov, V. Methylene blue can act as an antidote to pesticide poisoning of bumble bee mitochondria. Sci. Rep. 11, 14710 (2021).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Raghavendra, K. et al. Chlorfenapyr: a new insecticide with novel mode of action can control pyrethroid resistant malaria vectors. Malar. J. 10, 16 (2011).PubMed 
PubMed Central 

Google Scholar 
Cao, Y. et al. HPLC/UV analysis of chlorfenapyr residues in cabbage and soil to study the dynamics of different formulations. Sci. Total Environ. 350, 38–46 (2005).ADS 
CAS 
PubMed 

Google Scholar 
Costa, E. M. et al. Toxicity of insecticides used in the Brazilian melon crop to the honey bee Apis mellifera under laboratory conditions. Apidologie 45, 34–44 (2014).CAS 

Google Scholar 
Cresswell, J. E., Robert, F.-X.L., Florance, H. & Smirnoff, N. Clearance of ingested neonicotinoid pesticide (imidacloprid) in honey bees (Apis mellifera) and bumblebees (Bombus terrestris). Pest Manag. Sci. 70, 332–337 (2014).CAS 
PubMed 

Google Scholar 
Czerwinski, M. A. & Sadd, B. M. Detrimental interactions of neonicotinoid pesticide exposure and bumblebee immunity. J Exp Zool A Ecol Integr Physiol 327, 273–283 (2017).CAS 
PubMed 

Google Scholar 
Mobley, M. W. & Gegear, R. J. One size does not fit all: Caste and sex differences in the response of bumblebees (Bombus impatiens) to chronic oral neonicotinoid exposure. PLoS ONE 13, e0200041 (2018).PubMed 
PubMed Central 

Google Scholar 
Simmons, W. R. & Angelini, D. R. Chronic exposure to a neonicotinoid increases expression of antimicrobial peptide genes in the bumblebee Bombus impatiens. Sci. Rep. 7, 44773 (2017).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Doublet, V., Labarussias, M., de Miranda, J. R., Moritz, R. F. A. & Paxton, R. J. Bees under stress: sublethal doses of a neonicotinoid pesticide and pathogens interact to elevate honey bee mortality across the life cycle. Environ. Microbiol. 17, 969–983 (2015).CAS 
PubMed 

Google Scholar 
Eiri, D. M., Suwannapong, G., Endler, M. & Nieh, J. C. Nosema ceranae can infect honey bee larvae and reduces subsequent adult longevity. PLoS One 10, (2015).Dai, P., Jack, C. J., Mortensen, A. N. & Ellis, J. D. Acute toxicity of five pesticides to Apis mellifera larvae reared in vitro. Pest Manag. Sci. 73, 2282–2286 (2017).CAS 
PubMed 

Google Scholar 
du Rand, E. E. et al. Proteomic and metabolomic analysis reveals rapid and extensive nicotine detoxification ability in honey bee larvae. Insect Biochem. Mol. Biol. 82, 41–51 (2017).PubMed 

Google Scholar 
R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria (2021). R Core Team (2021). URL https://www.R-project.org/. More

Long-term acoustic data collectionPassive acoustic monitoring was conducted from November 19, 2018 to October 3, 2020, with 683 days of recording effort overall (Supplementary Table 2), using a High-frequency Acoustic Recording Package (HARP)37. The HARP was deployed in Bahía Norte, Guadalupe Island, located approximately 150 miles offshore of México’s Baja California Peninsula (Fig. 1). The HARP was bottom-mounted and deployed to a depth of approximately 1100 m, with a calibrated hydrophone suspended ~30 m above the seafloor. The same hydrophone was used for both deployments to facilitate data comparison. The omnidirectional hydrophone sensor (ITC-1042, International Transducer Corporation, Santa Barbara, CA) had an approximately flat (±3 dB) hydrophone sensitivity from 10 Hz to 100 kHz of −200 dB re V/μPa. The sensor was connected to a custom-built preamplifier board and bandpass filter. The calibrated system response was corrected for during analysis. Data were sampled continuously at a 200 kHz sampling rate with 16-bit quantization, effectively monitoring a frequency range of 10 Hz–100 kHz.Automatic detection and manual classification of beaked whale echolocation clicksBeaked whales can be acoustically identified by their echolocation clicks38. These signals are frequency-modulated (FM) upswept pulses, which appear to be species-specific and are distinguishable by their spectral and temporal features. Cuvier’s beaked whale echolocation signals are well differentiated from the acoustic signals of other beaked whale species. They are polycyclic with a characteristic FM pulse upsweep, peak frequency around 40 kHz, and uniform inter-pulse interval of about 0.4–0.5 s39,40. Additionally, Cuvier’s beaked whale FM pulses have characteristic spectral peaks at approximately 17 and 23 kHz.Beaked whale FM pulses were detected in the HARP data with an automated method using the MATLAB-based (Mathworks, Natick, MA) custom software program Triton (https://github.com/MarineBioAcousticsRC/Triton) and other MATLAB custom routines. After all potential echolocation signals were identified with a Teager–Kaiser energy detector41,42, an expert system discriminated between delphinid clicks and beaked whale FM pulses. A decision about presence or absence of beaked whale signals was based on detections within a 75 s segment. Only segments with more than seven detections were used in further analysis. All echolocation signals with a peak and center frequency below 32 and 25 kHz, respectively, a duration less than 355 μs, and a sweep rate of More

Stigall, A. L., Edwards, C. T., Freeman, R. L. & Rasmussen, C. M. Ø. Coordinated biotic and abiotic change during the Great Ordovician Biodiversification Event: Darriwilian assembly of early Paleozoic building blocks. Palaeogeogr. Palaeoclimatol. Palaeoecol. 530, 249–270 (2019).
Google Scholar 
Alroy, J. Colloquium paper: dynamics of origination and extinction in the marine fossil record. Proc. Natl. Acad. Sci. USA 105, 11536–11542 (2008). Suppl 1.CAS 

Google Scholar 
Servais, T., Cascales-Miñana, B. & Harper, D. A. T. The Great Ordovician Biodiversification Event (GOBE) is not a single event. Paleontological Res. 25, 315–328 (2021).Miller, A. I. & Foote, M. Calibrating the Ordovician Radiation of marine life: implications for Phanerozoic diversity trends. Paleobiology 22, 304–309 (1996).CAS 

Google Scholar 
Sepkoski, J. J. A compendium of marine fossil genera. vol. 2002 (Paleontological Research Institution, 2002).Zhan, R. & Harper, D. A. T. Biotic diachroneity during the Ordovician Radiation: evidence from South China. Lethaia 39, 211–226 (2006).
Google Scholar 
Fan, J. et al. A high-resolution summary of Cambrian to Early Triassic marine invertebrate biodiversity. Science 367, 272–277 (2020).CAS 

Google Scholar 
Deng, Y. et al. Timing and patterns of the Great Ordovician Biodiversification Event and Late Ordovician mass extinction: Perspectives from South China. Earth-Sci. Rev. 220, 103743 (2021).
Google Scholar 
Kröger, B., Franeck, F. & Rasmussen, C. M. Ø. The evolutionary dynamics of the early Palaeozoic marine biodiversity accumulation. Proc. R. Soc. B: Biol. Sci. 286, 3–8 (2019).
Google Scholar 
Rasmussen, C. M. Ø., Kröger, B., Nielsen, M. L. & Colmenar, J. Cascading trend of Early Paleozoic marine radiations paused by Late Ordovician extinctions. Proc. Natl. Acad. Sci. USA 116, 7207–7213 (2019).CAS 

Google Scholar 
Sepkoski, J. J. A factor analytic description of the phanerozoic marine fossil record. Paleobiology 7, 36–53 (1981).
Google Scholar 
Sepkoski, J. J. & Sheehan, P. M. Diversification, Faunal Change, and Community Replacement during the Ordovician Radiations. in Biotic interactions in recent and fossil benthic communities (eds. Tevesz, M. J. S. & McCall, P. L.) 673–717 (Plenum Press, 1983).Harper, D. A. T. The Ordovician biodiversification: Setting an agenda for marine life. Palaeogeogr. Palaeoclimatol. Palaeoecol. 232, 148–166 (2006).
Google Scholar 
Stigall, A. L., Bauer, J. E., Lam, A. R. & Wright, D. F. Biotic immigration events, speciation, and the accumulation of biodiversity in the fossil record. Global Planet. Change 148, 242–257 (2017).
Google Scholar 
Copper, P. Coral Reefs Reports Ancient reef ecosystem expansion and collapse. Coral Reefs 13, 3–11 (1994).
Google Scholar 
Trotter, J. A., Williams, I. S., Barnes, C. R., Lécuyer, C. & Nicoll, R. S. Did Cooling Oceans Trigger Ordovician Biodiversification? Evidence from Conodont Thermometry. Science 321, 550–554 (2008).CAS 

Google Scholar 
Lindström, M. The Ordovician climate based on the study of carbonate rocks. in Aspects of the Ordovician System, Paleontological Contribution of the University of Oslo (ed. Bruton, D. L.) vol. 295 81–88 (Universitetsforlaget, 1984).Rasmussen, C. M. Ø., Nielsen, A. T. & Harper, D. A. T. Ecostratigraphical interpretation of lower Middle Ordovician East Baltic sections based on brachiopods. Geological Mag. 146, 717–731 (2009).
Google Scholar 
Dabard, M. P. et al. Sea-level curve for the Middle to early Late Ordovician in the Armorican Massif (western France): Icehouse third-order glacio-eustatic cycles. Palaeogeogr. Palaeoclimatol. Palaeoecol. 436, 96–111 (2015).
Google Scholar 
Rasmussen, C. M. Ø. et al. Onset of main Phanerozoic marine radiation sparked by emerging Mid Ordovician icehouse. Sci. Rep. 6, 1–9 (2016).
Google Scholar 
Deutsch, C., Ferrel, A., Seibel, B., Pörtner, H.-O. & Huey, R. B. Climate change tightens a metabolic constraint on marine habitats. Science 348, 1132–1135 (2015).CAS 

Google Scholar 
Penn, J. L., Deutsch, C., Payne, J. L. & Sperling, E. A. Temperature-dependent hypoxia explains biogeography and severity of end-Permian marine mass extinction. Science 362, eaat1327 (2018).
Google Scholar 
Saltzman, M. R., Edwards, C. T., Adrain, J. M. & Westrop, S. R. Persistent oceanic anoxia and elevated extinction rates separate the Cambrian and Ordovician radiations. Geology 43, 807–811 (2015).CAS 

Google Scholar 
Edwards, C. T., Saltzman, M. R., Royer, D. L. & Fike, D. A. Oxygenation as a driver of the Great Ordovician Biodiversification Event. Nature Geoscience 10, 925–929 (2017).CAS 

Google Scholar 
Sperling, E. A., Knoll, A. H. & Girguis, P. R. The ecological physiology of earth’s second oxygen revolution. Ann. Rev. Ecol. Evolut. Syst. 46, 215–235 (2015).
Google Scholar 
Dahl, T. W. et al. Reorganisation of Earth’s biogeochemical cycles briefly oxygenated the oceans 520 Myr ago. Geochem. Perspect. Lett. 210–220 (2017).Dahl, T. W. et al. Atmosphere-ocean oxygen and productivity dynamics during early animal radiations. Proc. Natl. Acad. Sci. 116, 19352–19361 (2019).CAS 

Google Scholar 
Nursall, J. R. Oxygen as a prerequisite to the origin of the metazoa. Nature 183, 1170–1172 (1959).Knoll, A. H. Biological and Biogeochemical Preludes to the Ediacaran Radiation. In Origin and Early Evolution of the Metazoa (eds. Lipps, J. H. & Signor, P. W.) 53–84 (Springer US, 1992).Brennecka, G. A., Herrmann, A. D., Algeo, T. J. & Anbar, A. D. Rapid expansion of oceanic anoxia immediately before the end-Permian mass extinction. Proc. Natl. Acad. Sci. 108, 17631–17634 (2011).CAS 

Google Scholar 
Lau, K. V. et al. Marine anoxia and delayed Earth system recovery after the end-Permian extinction. Proc. Natl. Acad. Sci. USA 113, 2360–2365 (2016).CAS 

Google Scholar 
Zhang, F. et al. Congruent Permian-Triassic δ238U records at Panthalassic and Tethyan sites: Confirmation of global-oceanic anoxia and validation of the U-isotope paleoredox proxy. Geology 46, 327–330 (2018).CAS 

Google Scholar 
Andersen, M. B., Stirling, C. H. & Weyer, S. Uranium isotope fractionation. Rev. Mineral. Geochem. 82, 799–850 (2017).CAS 

Google Scholar 
Chen, X. et al. Diagenetic effects on uranium isotope fractionation in carbonate sediments from the Bahamas. Geochimica et Cosmochimica Acta 237, 294–311 (2018).CAS 

Google Scholar 
Zhang, F. et al. Uranium isotopes in marine carbonates as a global ocean paleoredox proxy: A critical review. Geochimica et Cosmochimica Acta 287, 27–49 (2020).CAS 

Google Scholar 
Stylo, M. et al. Uranium isotopes fingerprint biotic reduction. Proc. Natl. Acad. Sci. 112, 5619–5624 (2015).CAS 

Google Scholar 
Basu, A. et al. Microbial U isotope fractionation depends on the U(VI) reduction rate. Environ. Sci. Technol. 54, 2295–2303 (2020).CAS 

Google Scholar 
Dunk, R. M., Mills, R. A. & Jenkins, W. J. A reevaluation of the oceanic uranium budget for the Holocene. Chem. Geol. 190, 45–67 (2002).CAS 

Google Scholar 
Dahl, T. W. et al. Uranium isotopes distinguish two geochemically distinct stages during the later Cambrian SPICE event. Earth Planet. Sci. Lett. 401, 313–326 (2014).CAS 

Google Scholar 
Tissot, F. L. H. & Dauphas, N. Uranium isotopic compositions of the crust and ocean: Age corrections, U budget and global extent of modern anoxia. Geochimica et Cosmochimica Acta 167, 113–143 (2015).CAS 

Google Scholar 
Romaniello, S. J., Herrmann, A. D. & Anbar, A. D. Uranium concentrations and 238U/235U isotope ratios in modern carbonates from the Bahamas: Assessing a novel paleoredox proxy. Chem. Geology 362, 305–316 (2013).CAS 

Google Scholar 
Chen, X., Romaniello, S. J., Herrmann, A. D., Samankassou, E. & Anbar, A. D. Biological effects on uranium isotope fractionation (238U/235U) in primary biogenic carbonates. Geochimica et Cosmochimica Acta 240, 1–10 (2018).CAS 

Google Scholar 
Tissot, F. L. H. et al. Controls of eustasy and diagenesis on the 238U/235U of carbonates and evolution of the seawater (234U/238U) during the last 1.4 Myr. Geochimica et Cosmochimica Acta 242, 233–265 (2018).CAS 

Google Scholar 
Lindskog, A. & Eriksson, M. E. Megascopic processes reflected in the microscopic realm: sedimentary and biotic dynamics of the Middle Ordovician “orthoceratite limestone” at Kinnekulle, Sweden. Gff 139, 163–183 (2017).
Google Scholar 
Jaanusson, V. Aspects of carbonate sedimentation in the Ordovician of Baltoscandia. Lethaia 6, 11–34 (1973).
Google Scholar 
Bergström, S. M., Chen, X., Gutiérrez-marco, J. C. & Dronov, A. The new chronostratigraphic classification of the Ordovician System and its relations to major regional series and stages and to δ13C chemostratigraphy. Lethaia 42, 97–107 (2008).
Google Scholar 
Lindskog, A., Lindskog, A. M., Johansson, J. V., Ahlberg, P. & Eriksson, M. E. The Cambrian–Ordovician succession at Lanna, Sweden: stratigraphy and depositional environments. Estonian J. Earth Sci 67, 133 (2018).
Google Scholar 
Bábek, O. et al. Redox geochemistry of the red ‘orthoceratite limestone’ of Baltoscandia: Possible linkage to mid-Ordovician palaeoceanographic changes. Sedimentary Geology 420, 105934 (2021).
Google Scholar 
Azmy, K. et al. Carbon-isotope stratigraphy of the Lower Ordovician succession in Northeast Greenland: Implications for correlations with St. George Group in western Newfoundland (Canada) and beyond. Sedimentary Geology 225, 67–81 (2010).CAS 

Google Scholar 
Bartlett, R. et al. Abrupt global-ocean anoxia during the Late Ordovician–early Silurian detected using uranium isotopes of marine carbonates. Proc Natl Acad Sci USA 115, 5896–5901 (2018).CAS 

Google Scholar 
Dahl, T. W., Hammarlund, E. U., Rasmussen, C. M. Ø., Bond, D. P. G. & Canfield, D. E. Sulfidic anoxia in the oceans during the Late Ordovician mass extinctions – insights from molybdenum and uranium isotopic global redox proxies. Earth-Sci. Rev. 220, 103748 (2021).CAS 

Google Scholar 
Del Rey, Á., Havsteen, J., Bizzarro, M., Connelly, J. & Dahl, T. W. Untangling the diagenetic history of Uranium isotopes in marine carbonates: a case study tracing d238U of late Silurian oceans using calcitic brachiopod shells. Geochimica et Cosmochimica Acta 2020, 93–110.Rasmussen, J. A., Thibault, N. & Mac Ørum Rasmussen, C. Middle Ordovician astrochronology decouples asteroid breakup from glacially-induced biotic radiations.Nat Commun12, 6430 (2021).CAS 

Google Scholar 
Ainsaar, L. et al. Middle and Upper Ordovician carbon isotope chemostratigraphy in Baltoscandia: A correlation standard and clues to environmental history. Palaeogeogr. Palaeoclimatol. Palaeoecol. 294, 189–201 (2010).
Google Scholar 
Wu, R., Calner, M. & Lehnert, O. Integrated conodont biostratigraphy and carbon isotope chemostratigraphy in the Lower-Middle Ordovician of southern Sweden reveals a complete record of the MDICE. Geological Mag. 154, 334–353 (2017).CAS 

Google Scholar 
Lindskog, A., Eriksson, M. E., Bergström, S. M. & Young, S. A. Lower–Middle Ordovician carbon and oxygen isotope chemostratigraphy at Hällekis, Sweden: implications for regional to global correlation and palaeoenvironmental development. Lethaia 52, 204–219 (2019).
Google Scholar 
Rasmussen, C. M. Ø., Hansen, J. & Harper, D. A. T. Baltica: A mid Ordovivian diversity hotspot. Historical Biology 19, 255–261 (2007).
Google Scholar 
Zhang, J. Lithofacies and stratigraphy of the Ordovician Guniutan Formation in its type area, China. Geol. J. 31, 201–215 (1996).
Google Scholar 
Eriksson, M. E. et al. Biotic dynamics and carbonate microfacies of the conspicuous Darriwilian (Middle Ordovician) ‘Täljsten’ interval, south-central Sweden. Palaeogeogr. Palaeoclimatol. Palaeoecol. 367–368, 89–103 (2012).
Google Scholar 
Lindström, M., Jun-Yuan, C. & Jun-Ming, Z. Section at Daping reveals Sino-Baltoscandian parallelism of facies in the Ordovician. Geologiska Föreningen i Stockholm Förhandlingar 113, 189–205 (1991).
Google Scholar 
Edward, O. et al. A Baltic perspective on the early to early late ordovician δ13 C and δ18 O Records and its paleoenvironmental significance. Paleoceanog and Paleoclimatol 37, e2021PA004309 (2022).Pörtner, H. Climate change and temperature-dependent biogeography: oxygen limitation of thermal tolerance in animals. Naturwissenschaften 88, 137–146 (2001).
Google Scholar 
Gueguen, B. et al. The chromium isotope composition of reducing and oxic marine sediments. Geochimica et Cosmochimica Acta 184, 1–19 (2016).CAS 

Google Scholar 
Weyer, S. et al. Natural fractionation of 238U/235U. Geochimica et Cosmochimica Acta 72, 345–359 (2008).CAS 

Google Scholar 
Condon, D. J., McLean, N., Noble, S. R. & Bowring, S. A. Isotopic composition (238U/235U) of some commonly used uranium reference materials. Geochimica et Cosmochimica Acta 74, 7127–7143 (2010).CAS 

Google Scholar 
Wang, X., Planavsky, N. J., Reinhard, C. T., Hein, J. R. & Johnson, T. M. A cenozoic seawater redox record derived from 238U/235U in ferromanganese crusts. Am. J. Sci. 315, 64–83 (2016).
Google Scholar 
Trotter, J. A., Williams, I. S., Barnes, C. R., Männik, P. & Simpson, A. New conodont δ18O records of Silurian climate change: Implications for environmental and biological events. Palaeogeogr. Palaeoclimatol. Palaeoecol. 443, 34–48 (2016).
Google Scholar 
Scotese, C. R. Atlas of Silurian and Middle-Late Ordovician Paleogeographic Maps (Mollweide Projection), Maps 73-80, Volumes 5, The Early Paleozoic, PALEOMAP Atlas for ArcGIS, PALEOMAP Project, Evanston, IL. (2014). More

Zhang, Bo. et al. The influence of slope collapse on water exchange between a pit lake and a heterogeneous aquifer. Front. Environ. Sci. Eng. 13, 20 (2019).Article 

Google Scholar 
Li, Y. et al. Distribution and ecological risk assessment of heavy metals in sediments in Chinese collapsed lakes. Pol. J. Environ. Stud. 26, 181–188 (2017).CAS 
Article 

Google Scholar 
Li, J. et al. Analysis of heavy metal sources and health risk assessment of typical coal mine collapsed lakes in Huaibei Coalfield, Anhui Province, China. Polish J. Environ. Stud. 29, 3193–3202 (2020).CAS 
Article 

Google Scholar 
James, I. P. & Jennifer, B. H. M. Conceptual challenges in microbial community ecology. Philos. Trans. R. Soc. B 375, 20190241 (2020).Article 

Google Scholar 
Sunagawa, S. et al. Structure and function of the global ocean microbiome. Science 348, 1261359 (2015).PubMed 
Article 
CAS 

Google Scholar 
Falkowski Paul, G., Fenchel, T. & Delong Edward, F. The microbial engines that drive Earth’s biogeochemical cycles. Science 320, 1034–1039 (2008).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Whitman, W. B., Coleman, D. C. & Wiebe, W. J. Prokaryotes: The unseen majority. Proc. Natl. Acad. Sci. USA 95, 6578 (1998).ADS 
CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Parkes, R. J. et al. Deep sub-seafloor prokaryotes stimulated at interfaces over geological time. Nature 436, 390–394 (2005).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Wurzbacher, C. et al. Shifts among Eukaryota, Bacteria, and Archaea define the vertical organization of a lake sediment. Microbiome 5, 41 (2017).PubMed 
PubMed Central 
Article 

Google Scholar 
Nannipieri, P. & Eldor, P. The chemical and functional characterization of soil N and its biotic components. Soil Biol. Biochem. 41, 2357–2369 (2009).CAS 
Article 

Google Scholar 
Strauss, E. A., Mitchell, N. L. & Lamberti, G. A. Factors regulating nitrification in aquatic sediments: Effects of organic carbon, nitrogen availability, and pH. Can. J. Fish. Aquat. Sci. 59, 554–563 (2002).CAS 
Article 

Google Scholar 
Seymour, J. R., Seuront, L. & Mitchell, J. G. Microscale gradients of planktonic microbial communities above the sediment surface in a mangrove estuary. Estuar. Coast. Shelf Sci. 73, 651–666 (2007).ADS 
Article 

Google Scholar 
Aciego Pietri, J. C. & Brookes, P. C. Relationships between soil pH and microbial properties in a UK arable soil. Soil Biol. Biochem. 40, 1856–1861 (2008).CAS 
Article 

Google Scholar 
Pavloudi, C., Kristoffersen, J. B., Oulas, A., De Troch, M. & Arvanitidis, C. Sediment microbial taxonomic and functional diversity in a natural salinity gradient challenge Remane’s “species minimum” concept. PeerJ 5, e3687 (2017).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Wei, G., Li, M., Li, F., Li, H. & Gao, Z. Distinct distribution patterns of prokaryotes between sediment and water in the Yellow River estuary. Appl. Microbiol. Biotechnol. 100, 9683–9697 (2016).CAS 
PubMed 
Article 

Google Scholar 
van Dijk, E. L., Auger, H., Jaszczyszyn, Y. & Thermes, C. T. Ten years of next-generation sequencing technology. Trends Genet. 30, 418–426 (2014).PubMed 
Article 
CAS 

Google Scholar 
Sadaiappan, B., Prasannakumar, C., Subramanian, K. & Mahendran, S. Metagenomic data of vertical distribution and abundance of bacterial diversity in the hypersaline sediments of Mad Boon-mangrove ecosystem, Bay of Bengal. Data Brief 22, 716–721 (2019).PubMed 
Article 

Google Scholar 
Kim, K. Microbial diversity analysis of sediment from Nakdong River Estuary in the republic of Korea using 16s rRNA gene amplicon sequencing. Microbiol. Resour. Announc. 7, e01186-e11118 (2018).PubMed 
PubMed Central 

Google Scholar 
Deng, Y., Liu, Y., Dumont, M. & Conrad, R. Salinity affects the composition of the aerobic methanotroph community in alkaline lake sediments from the Tibetan Plateau. Microb. Ecol. 73, 101–110 (2017).PubMed 
Article 

Google Scholar 
Palmer, M. A., Covich, A. P., Lake, S., Biro, P. & Bund, W. JVd. Linkages between aquatic sediment biota and life above sediments as potential drivers of biodiversity. Bioscience 50, 1062–1075 (2000).Article 

Google Scholar 
Silveira, R. et al. Bacteria and archaea communities in Cerrado natural pond sediments. Microb. Ecol. 81, 563–578 (2021).CAS 
PubMed 
Article 

Google Scholar 
Galand, P. E. et al. Disturbance increases microbial community diversity and production in marine sediments. Front. Microbiol. 7, 1950 (2016).PubMed 
PubMed Central 
Article 

Google Scholar 
Dai, Y. et al. Spatiotemporal variation of planktonic and sediment bacterial assemblages in two plateau freshwater lakes at different trophic status. Appl. Microbiol. Biotechnol. 100, 4161–4175 (2016).CAS 
PubMed 
Article 

Google Scholar 
Dai, Y. et al. Macrophyte identity shapes water column and sediment bacterial community. Hydrobiologia https://doi.org/10.1007/s10750-019-3930-y (2019).Article 

Google Scholar 
Chaudhry, V., Rehman, A., Mishra, A., Chauhan, P. S. & Nautiyal, C. S. Changes in bacterial community structure of agricultural land due to long-term organic and chemical amendments. Microb. Ecol. 64, 450–460 (2012).PubMed 
Article 

Google Scholar 
Huang, W. et al. Comparison among the microbial communities in the lake, lake wetland, and estuary sediments of a plain river network. MicrobiologyOpen 8, e00644 (2019).PubMed 
Article 

Google Scholar 
Ji, B., Liang, J., Ma, Y., Zhu, L. & Liu, Y. Bacterial community and eutrophic index analysis of the East Lake. Environ. Pollut. 252, 682–688 (2019).CAS 
PubMed 
Article 

Google Scholar 
Song, H. et al. Bacterial communities in sediments of the shallow Lake Dongping in China. J. Appl. Microbiol. 112, 79–89 (2011).PubMed 
Article 
CAS 

Google Scholar 
Coleman, M. L., Hedrick, D. B., Lovley, D. R., White, D. C. & Pye, K. Reduction of Fe(III) in sediments by sulphate-reducing bacteria. Nature 361, 436–448 (1993).ADS 
CAS 
Article 

Google Scholar 
Zhang, L. et al. The molecular characteristics of dissolved organic matter in urbanized river sediments and their environmental impact under the action of microorganisms. Sci Total Environ 827, 154289 (2022).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Adhikari, N. P., Adhikari, S., Liu, X., Shen, L. & Gu, Z. Bacterial diversity in alpine lakes: A review from the third pole region. J. Earth Sci. 30, 387–396 (2019).CAS 
Article 

Google Scholar 
Wang, P. et al. Shift in bacterioplankton diversity and structure: Influence of anthropogenic disturbances along the Yarlung Tsangpo River on the Tibetan Plateau, China. Sci. Rep. 7, 12529 (2017).ADS 
PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Winters, A. D., Marsh, T. L., Brenden, T. O. & Faisal, M. Molecular characterization of bacterial communities associated with sediments in the Laurentian Great Lakes. J. Great Lakes Res. 40, 640–645 (2014).CAS 
Article 

Google Scholar 
Yang, J., Jiang, H., Dong, H. & Liu, Y. A comprehensive census of lake microbial diversity on a global scale. Sci. China Life Sci. 62, 1320–1331 (2019).PubMed 
Article 

Google Scholar 
Aida, M.-R. & Coker, J. A. The effects of extremes of pH on the growth and transcriptomic profiles of three haloarchaea. F1000Research 3, 168 (2014).Article 

Google Scholar 
Guo, H., Nasir, M., Lv, J., Dai, Y. & Gao, J. Understanding the variation of microbial community in heavy metals contaminated soil using high throughput sequencing. Ecotoxicol. Environ. Saf. 144, 300–306 (2017).CAS 
PubMed 
Article 

Google Scholar 
Kaci, A., Petit, F., Fournier, M., Cécillon, S. & Berthe, T. Diversity of active microbial communities subjected to long-term exposure to chemical contaminants along a 40-year-old sediment core. Environ. Sci. Pollut. Res. 23, 4095–4110 (2016).CAS 
Article 

Google Scholar 
Hamed, A. et al. Microbial community composition and functions are resilient to metal pollution along two forest soil gradients. FEMS Microbiol. Ecol. 91, 1–11 (2015).
Google Scholar 
Xu, M. et al. High microbial diversity stabilizes the responses of soil organic carbon decomposition to warming in the subsoil on the Tibetan Plateau. Glob. Change Biol. 27, 2061–2075 (2021).ADS 
CAS 
Article 

Google Scholar 
Li, Q., Zhao, X. & Hu, C. ISO10390: 2005 soil quality-determination of pH. Pollut. Control Technol. 1, 53–55 (2006).
Google Scholar 
Bremner, J. Total nitrogen. Methods of soil analysis: Part 2 chemical microbiological properties. Agron. Ser. 9, 1149–1178 (1965).CAS 

Google Scholar 
O’halloran, I. & Cade-Menun, B. Total and organic phosphorus. Soil Sampling Methods Anal. 2, 265–291 (2008).
Google Scholar 
Dennis, K. L. et al. Adenomatous polyps are driven by microbe-instigated focal inflammation and are controlled by IL-10-producing T cells. Can. Res. 73, 5905–5913 (2013).CAS 
Article 

Google Scholar 
Tanja, M. & Salzberg, S. L. FLASH: Fast length adjustment of short reads to improve genome assemblies. Bioinformatics 21, 2957–2963 (2011).
Google Scholar 
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C. & Knight, R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27, 2194 (2011).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Edgar, R. C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460 (2010).CAS 
PubMed 
Article 

Google Scholar 
Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7, 335–336 (2010).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Bokulich, N. A. et al. Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nat. Methods 10, 57–59 (2013).CAS 
PubMed 
Article 

Google Scholar 
Wang, Q., Garrity, G. M., Tiedje, J. M. & Cole, J. R. Nave Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73, 5261 (2007).ADS 
CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Quast, C., Pruesse, E., Yilmaz, P., Gerken, J. & Glckner, F. O. The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucleic Acids Res. 41, D590–D596 (2012).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Chen, H. & Boutros, P. C. VennDiagram: A package for the generation of highly-customizable Venn and Euler diagrams in R. Bioinformatics 12, 35–30 (2011).PubMed 
PubMed Central 

Google Scholar 
Schloss, P. D. et al. Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75, 7537–7541 (2009).ADS 
CAS 
PubMed 
PubMed Central 
Article 

Google Scholar  More