{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T00:02:34Z","timestamp":1791849754303,"version":"4.3.4"},"reference-count":118,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2022,10,13]],"date-time":"2022-10-13T00:00:00Z","timestamp":1665619200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31530087"],"award-info":[{"award-number":["31530087"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32001227"],"award-info":[{"award-number":["32001227"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>Nest materials are a major heat source due to rotting promoted by microbial activity. Additionally, they are a potential microbial source given their direct contact with eggshells. Microbial dynamics during incubation have been studied in wild birds; however, similar studies in reptiles remain elusive. Here, the study characterized microbial communities in the nest materials of Chinese alligator (<jats:italic>Alligator sinensis<\/jats:italic>) using high-throughput sequencing of bacterial 16S rRNA genes and fungal internal transcribed spacer (ITS) region sequences. The results showed that significant changes in the diversity and structure of microbial communities according to different incubation periods. The diversity and richness of bacterial species increased significantly over time, but the relative abundance of the most dominant bacteria in pre-incubation period, including some pathogenic bacteria, declined after incubation. In contrast, fungal species diversity and richness decreased significantly with time. Additionally, nest material composition significantly influenced microbial community structure rather than species diversity and richness. Notably, the fungal community structure showed a stronger response than bacteria to nest material composition, which varied due to differences in plant litter composition. Our results demonstrate the significant response of microbial community diversity and structure to differences in incubation periods and nest material composition in reptiles. It is further emphasized that the importance of incubation period in the conservation of the Chinese alligator and could inform similar studies in other reptiles and birds.<\/jats:p>","DOI":"10.3389\/fmicb.2022.983808","type":"journal-article","created":{"date-parts":[[2022,10,13]],"date-time":"2022-10-13T07:44:55Z","timestamp":1665647095000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":6,"title":["Incubation determines favorable microbial communities in Chinese alligator nests"],"prefix":"10.3389","volume":"13","author":[{"given":"Qin-Zhang","family":"Yu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Meng-Yuan","family":"Hu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Li","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jian-Qing","family":"Lin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sheng-Guo","family":"Fang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2022,10,13]]},"reference":[{"key":"B1","first-page":"83","article-title":"The nest environment and the embryonic development of sea turtles","author":"Ackerman","year":"2017","journal-title":"The Biology of Sea Turtles"},{"key":"B2","doi-asserted-by":"crossref","first-page":"500","DOI":"10.1159\/000151575","article-title":"Pantoea agglomerans bloodstream infection in preterm neonates.","volume":"17","author":"Aly","year":"2008","journal-title":"Med. Princ. Pract."},{"key":"B3","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2180-10-189","article-title":"ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases.","volume":"10","author":"Bellemain","year":"2010","journal-title":"BMC Microbiol."},{"key":"B4","doi-asserted-by":"publisher","first-page":"542","DOI":"10.1007\/BF00317161","article-title":"Interactions between fungi, bacteria and beech leaves in a stream microcosm.","volume":"89","author":"Bengtsson","year":"1992","journal-title":"Oecologia"},{"key":"B5","doi-asserted-by":"crossref","first-page":"453","DOI":"10.1097\/01.inf.0000261200.83869.92","article-title":"Pantoea agglomerans septicemia in three newborn infants.","volume":"26","author":"Bergman","year":"2007","journal-title":"Pediatr. Infect. Dis. J."},{"key":"B6","doi-asserted-by":"publisher","first-page":"1450","DOI":"10.1016\/j.soilbio.2011.03.012","article-title":"The under-recognized dominance of Verrucomicrobia in soil bacterial communities.","volume":"43","author":"Bergmann","year":"2011","journal-title":"Soil Biol. Biochem."},{"key":"B7","doi-asserted-by":"publisher","first-page":"57","DOI":"10.1038\/nmeth.2276","article-title":"Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing.","volume":"10","author":"Bokulich","year":"2013","journal-title":"Nat. Methods"},{"key":"B8","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0114861","article-title":"Composition of bacterial assemblages in different components of Reed warbler nests and a possible role of egg incubation in pathogen regulation.","volume":"9","author":"Brandl","year":"2014","journal-title":"PLoS One"},{"key":"B9","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1007\/978-1-4615-3060-2_4","article-title":"Trans-shell transmission","author":"Bruce","year":"1994","journal-title":"Microbiology of the Avian Egg"},{"key":"B10","doi-asserted-by":"publisher","first-page":"889","DOI":"10.1094\/PDIS.2002.86.8.889","article-title":"Interactions between Myxobacteria, plant pathogenic fungi, and biocontrol agents.","volume":"86","author":"Bull","year":"2002","journal-title":"Plant Dis."},{"key":"B11","doi-asserted-by":"publisher","DOI":"10.1016\/j.scitotenv.2020.137717","article-title":"Bacterial diversity of the green turtle (Chelonia mydas) nest environment.","volume":"720","author":"Candan","year":"2020","journal-title":"Sci. Total Environ."},{"key":"B12","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1038\/nmeth.f.303","article-title":"QIIME allows analysis of high-throughput community sequencing data.","volume":"7","author":"Caporaso","year":"2010","journal-title":"Nat. Methods"},{"key":"B13","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0062671","article-title":"Leaf litter mixtures alter microbial community development: mechanisms for non-additive effects in litter decomposition.","volume":"8","author":"Chapman","year":"2018","journal-title":"PLoS One"},{"key":"B14","author":"Chen","year":"2003","journal-title":"Research on Chinese alligator."},{"key":"B15","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-020-00896-9","article-title":"Maternal gut microbes shape the early-life assembly of gut microbiota in passerine chicks via nests.","volume":"8","author":"Chen","year":"2020","journal-title":"Microbiome"},{"key":"B16","first-page":"287","article-title":"Bacteremia caused by Pantoea agglomerans and Enterococcus faecalis in a patient with colon cancer.","volume":"12","author":"Christakis","year":"2007","journal-title":"J. BUON"},{"key":"B17","doi-asserted-by":"publisher","first-page":"169","DOI":"10.1007\/BF00384280","article-title":"Use of nest material as insecticidal and anti-pathogenic agents by the European starling.","volume":"67","author":"Clark","year":"1985","journal-title":"Oecologia"},{"key":"B18","doi-asserted-by":"crossref","first-page":"238","DOI":"10.2307\/1935180","article-title":"Temperature distribution and calorimetric determination of heat production in the nest of the Wood ant, Formica Polyctena (Hymenoptera, Formicidae).","volume":"61","author":"Coenen-Strass","year":"1980","journal-title":"Ecology"},{"key":"B19","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1111\/j.1469-8137.1996.tb01153.x","article-title":"A comparison of the extracellular enzyme activities of two ectomycorrhizal and a leaf-saprotrophic basidiomycete colonizing beech leaf litter.","volume":"134","author":"Colpaert","year":"1996","journal-title":"New Phytol."},{"key":"B20","doi-asserted-by":"publisher","first-page":"532","DOI":"10.1111\/j.1461-0248.2005.00748.x","article-title":"Incubation reduces microbial growth on eggshells and the opportunity for trans-shell infection.","volume":"8","author":"Cook","year":"","journal-title":"Ecol. Lett."},{"key":"B21","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1093\/beheco\/arh131","article-title":"Microbial infection affects egg viability and incubation behavior in a tropical passerine.","volume":"16","author":"Cook","year":"","journal-title":"Behav. Ecol."},{"key":"B22","doi-asserted-by":"publisher","first-page":"2233","DOI":"10.1098\/rspb.2003.2508","article-title":"Trans-shell infection by pathogenic micro-organisms reduces the shelf life of non-incubated bird\u2019s eggs: a constraint on the onset of incubation?","volume":"270","author":"Cook","year":"2003","journal-title":"Proc. R. Soc. B Biol. Sci."},{"key":"B23","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1111\/j.1574-6976.2000.tb00548.x","article-title":"Biology and global distribution of myxobacteria in soils.","volume":"24","author":"Dawid","year":"2000","journal-title":"FEMS Microbiol. Rev."},{"key":"B24","doi-asserted-by":"publisher","first-page":"4393","DOI":"10.1128\/JCM.42.9.4393-4395.2004","article-title":"Bacteremic infection with Pantoea ananatis.","volume":"42","author":"De Baere","year":"2004","journal-title":"J. Clin. Microbiol."},{"key":"B25","doi-asserted-by":"publisher","first-page":"795","DOI":"10.1016\/j.femsre.2004.11.005","article-title":"Living in a fungal world: impact of fungi on soil bacterial niche development.","volume":"29","author":"De Boer","year":"2005","journal-title":"FEMS Microbiol. Rev."},{"key":"B26","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1016\/S0038-0717(97)00100-4","article-title":"Anti-fungal properties of chitinolytic dune soil bacteria.","volume":"30","author":"De Boer","year":"1998","journal-title":"Soil Biol. Biochem."},{"key":"B27","doi-asserted-by":"crossref","first-page":"1291","DOI":"10.1111\/j.1461-0248.2005.00828.x","article-title":"Diversity of locust gut bacteria protects against pathogen invasion.","volume":"8","author":"Dillon","year":"2005","journal-title":"Ecol. Lett."},{"key":"B28","doi-asserted-by":"publisher","first-page":"996","DOI":"10.1038\/nmeth.2604","article-title":"UPARSE: highly accurate OTU sequences from microbial amplicon reads.","volume":"10","author":"Edgar","year":"2013","journal-title":"Nat. Methods"},{"key":"B29","doi-asserted-by":"crossref","DOI":"10.3390\/genes10090637","article-title":"Profiling the functional diversity of termite mound soil bacteria as revealed by shotgun sequencing.","volume":"10","author":"Enagbonma","year":"2019","journal-title":"Genes"},{"key":"B30","doi-asserted-by":"crossref","first-page":"75","DOI":"10.15446\/rfmvz.v62n3.54943","article-title":"Distocia en una serpiente ratonera amarilla (Coelognathus flavolineatus, Schlegel 1837) - Reporte de caso.","volume":"62","author":"Estrada","year":"2015","journal-title":"Rev. Facultad Med. Vet. Zootecnia"},{"key":"B31","doi-asserted-by":"publisher","first-page":"262","DOI":"10.1097\/00007611-198902000-00027","article-title":"Initial antibiotic therapy for Alligator bites: characterization of the oral flora of Alligator mississippiensis.","volume":"82","author":"Flandry","year":"1989","journal-title":"South Med. J."},{"key":"B32","doi-asserted-by":"crossref","DOI":"10.1001\/archinte.1978.03630290076024","article-title":"Septic arthritis caused by Enterobacter agglomerans.","volume":"138","author":"Flatauer","year":"1978","journal-title":"Arch. Intern. Med."},{"key":"B33","doi-asserted-by":"publisher","first-page":"996","DOI":"10.1017\/s0953756203008177","article-title":"Enzyme production by Mycena galopus mycelium in artificial media and in Picea sitchensis F-1 horizon needle litter.","volume":"107","author":"Ghosh","year":"2003","journal-title":"Mycol. Res."},{"key":"B34","doi-asserted-by":"crossref","first-page":"133","DOI":"10.3354\/dao016133","article-title":"Studies on an ulcerative stomatitis obstructive rhinitis pneumonia disease complex in hatching and juvenile sea-turtles Chelonia mydas and Caretta caretta.","volume":"16","author":"Glazebrook","year":"1993","journal-title":"Dis. Aquat. Organ."},{"key":"B35","doi-asserted-by":"crossref","DOI":"10.1071\/9781486300679","author":"Grigg","year":"2015","journal-title":"Biology and Evolution of Crocodylians."},{"key":"B36","doi-asserted-by":"publisher","first-page":"1140","DOI":"10.1002\/ece3.1011","article-title":"Dynamics of bacterial and fungal communities associated with eggshells during incubation.","volume":"4","author":"Grizard","year":"2014","journal-title":"Ecol. Evol."},{"key":"B37","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0121716","article-title":"Shifts in bacterial communities of eggshells and antimicrobial activities in eggs during incubation in a ground-nesting passerine.","volume":"10","author":"Grizard","year":"2015","journal-title":"PLoS One"},{"key":"B38","doi-asserted-by":"publisher","DOI":"10.3390\/microorganisms8101482","article-title":"Seasonal variations in soil microbiota profile of termite (Syntermes wheeleri) mounds in the Brazilian tropical savanna.","volume":"8","author":"Guimaraes","year":"2020","journal-title":"Microorganisms"},{"key":"B39","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1007\/s10336-005-0012-x","article-title":"European starlings: nestling condition, parasites and green nest material during the breeding season.","volume":"146","author":"Gwinner","year":"2005","journal-title":"J. Ornithol."},{"key":"B40","doi-asserted-by":"publisher","first-page":"494","DOI":"10.1101\/gr.112730.110","article-title":"Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons.","volume":"21","author":"Haas","year":"2011","journal-title":"Genome Res."},{"key":"B41","doi-asserted-by":"crossref","DOI":"10.1016\/j.ejsobi.2020.103190","article-title":"Litter composition has stronger influence on the structure of soil fungal than bacterial communities.","volume":"98","author":"Habtewold","year":"2020","journal-title":"Eur. J. Soil Biol."},{"key":"B42","doi-asserted-by":"crossref","first-page":"1045","DOI":"10.1007\/s10336-017-1462-7","article-title":"Use of anthropogenic material affects bird nest arthropod community structure: influence of urbanisation, and consequences for ectoparasites and fledging success.","volume":"158","author":"Hanmer","year":"2017","journal-title":"J. Ornithol."},{"key":"B43","doi-asserted-by":"publisher","first-page":"125","DOI":"10.7164\/antibiotics.57.125","article-title":"Isolation and structural characterization of siderophores, madurastatins, produced by a pathogenic Actinomadura madurae.","volume":"57","author":"Harada","year":"2004","journal-title":"J. Antibiot."},{"key":"B44","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.8614","article-title":"Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites.","volume":"8","author":"Herv\u00e9","year":"2020","journal-title":"PeerJ"},{"key":"B45","doi-asserted-by":"crossref","DOI":"10.1016\/j.funeco.2020.100964","article-title":"Nest microbiota and pathogen abundance in sea turtle hatcheries.","volume":"47","author":"Hoh","year":"2020","journal-title":"Fungal Ecol."},{"key":"B46","doi-asserted-by":"crossref","first-page":"743","DOI":"10.1006\/anbe.1994.1296","article-title":"Female mate choice and nest desertion in penduline tits, Remiz pendulinus: the importance of nest quality.","volume":"48","author":"Hoi","year":"1994","journal-title":"Anim. Behav."},{"key":"B47","doi-asserted-by":"crossref","first-page":"464","DOI":"10.1006\/anbe.1996.0046","article-title":"Nest size variation and its importance for mate choice in penduline tits, Remiz pendulinus.","volume":"51","author":"Hoi","year":"1996","journal-title":"Anim. Behav."},{"key":"B48","doi-asserted-by":"publisher","first-page":"328","DOI":"10.7589\/0090-3558-33.2.328","article-title":"Aerobic bacterial flora of addled raptor eggs in Saskatchewan.","volume":"33","author":"Houston","year":"1997","journal-title":"J. Wildlife Dis."},{"key":"B49","first-page":"169","author":"Huchzermeyer","year":"1997","journal-title":"Diseases of Farmed Crocodiles."},{"key":"B50","doi-asserted-by":"crossref","first-page":"265","DOI":"10.20506\/rst.21.2.1334","article-title":"Diseases of farmed crocodiles and ostriches.","volume":"21","author":"Huchzermeyer","year":"2002","journal-title":"Rev. Sci. Tech. Off. Int. Epiz."},{"key":"B51","author":"Huchzermeyer","year":"2003","journal-title":"Crocodiles: Biology, Husbandry and Diseases."},{"key":"B52","doi-asserted-by":"crossref","first-page":"1719","DOI":"10.1128\/AEM.72.3.1719-1728.2006","article-title":"Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes.","volume":"72","author":"Janssen","year":"2006","journal-title":"Appl. Environ. Microbiol."},{"key":"B53","doi-asserted-by":"crossref","first-page":"148","DOI":"10.1094\/Phyto-60-148","article-title":"Mechanism of lysis of fungal mycelia in soil.","volume":"60","author":"Ko","year":"1970","journal-title":"Phytopathology"},{"key":"B54","first-page":"121","article-title":"The effect of microorganisms on the mortality of house sparrow (Passer domesticus) and tree sparrow (Passer montanus) embryos","author":"Kozlowski","year":"1991","journal-title":"Nestling Mortality of Granivorous Birds Due to Microorganisms and Toxic Substances"},{"key":"B55","doi-asserted-by":"crossref","first-page":"E252","DOI":"10.3928\/01477447-20130122-32","article-title":"Osteomyelitis caused by Pantoea agglomerans in a closed fracture in a child.","volume":"36","author":"Labianca","year":"2013","journal-title":"Orthopedics"},{"key":"B56","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1002\/jez.1402700105","article-title":"Temperature-dependent sex determination in crocodilians.","volume":"270","author":"Lang","year":"1994","journal-title":"J. Exp. Zool."},{"key":"B57","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0103959","article-title":"Effect of incubation on bacterial communities of eggshells in a temperate bird, the Eurasian magpie (Pica pica).","volume":"9","author":"Lee","year":"2014","journal-title":"PLoS One"},{"key":"B58","doi-asserted-by":"publisher","DOI":"10.1139\/m70-087","article-title":"New Herpetosiphon species (Flexibacterales).","volume":"16","author":"Lewin","year":"1970","journal-title":"Can. J. Microbiol."},{"key":"B59","first-page":"871","article-title":"Lysis of fungal mycelium by Streptomyces spp and their chitinase systems.","volume":"55","author":"Lloyd","year":"1965","journal-title":"Phytopathology"},{"key":"B60","doi-asserted-by":"publisher","first-page":"66","DOI":"10.1016\/j.jtherbio.2015.01.006","article-title":"Effect of nesting environment on incubation temperature and hatching success of Morelet\u2019s crocodile (Crocodylus moreletii) in an urban lake of Southeastern Mexico.","author":"L\u00f3pez-Luna","year":"2015","journal-title":"J. Therm. Biol."},{"key":"B61","doi-asserted-by":"crossref","first-page":"11436","DOI":"10.1073\/pnas.0611525104","article-title":"Global patterns in bacterial diversity.","volume":"104","author":"Lozupone","year":"2007","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"B62","doi-asserted-by":"crossref","first-page":"506","DOI":"10.1128\/MMBR.66.3.506-577.2002","article-title":"Microbial cellulose utilization: fundamentals and biotechnology.","volume":"66","author":"Lynd","year":"2002","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"B63","doi-asserted-by":"publisher","first-page":"703","DOI":"10.1603\/EN12159","article-title":"Actinomycetes with antimicrobial activity isolated from Paper wasp (Hymenoptera: Vespidae: Polistinae) nests.","volume":"42","author":"Madden","year":"2013","journal-title":"Environ. Entomol."},{"key":"B64","doi-asserted-by":"publisher","first-page":"71","DOI":"10.1016\/0168-1605(93)90009-6","article-title":"Microbial flora of frozen tail meat from captive Nile crocodiles (Crocodylus niloticus).","volume":"18","author":"Madsen","year":"1993","journal-title":"Int. J. Food Microbiol."},{"key":"B65","doi-asserted-by":"crossref","first-page":"439","DOI":"10.2307\/1563479","article-title":"Maintenance of temperature of crocodile nests (Reptilia, Crocodilidae).","volume":"13","author":"Magnusson","year":"1979","journal-title":"J. Herpetol."},{"key":"B66","doi-asserted-by":"crossref","first-page":"199","DOI":"10.2307\/1564173","article-title":"Sources of heat for nests of Paleosuchus trigonatus and a review of crocodilian nest temperatures.","volume":"19","author":"Magnusson","year":"1985","journal-title":"J. Herpetol."},{"key":"B67","doi-asserted-by":"publisher","first-page":"2957","DOI":"10.1093\/bioinformatics\/btr507","article-title":"FLASH: fast length adjustment of short reads to improve genome assemblies.","volume":"27","author":"Mago\u010d","year":"2011","journal-title":"Bioinformatics"},{"key":"B68","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1111\/j.1462-5822.2010.01549.x","article-title":"Breathing life into pathogens: the influence of oxygen on bacterial virulence and host responses in the gastrointestinal tract.","volume":"13","author":"Marteyn","year":"2011","journal-title":"Cell Microbiol."},{"key":"B69","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0158158","article-title":"Nest bacterial environment affects microbiome of Hoopoe eggshells, but not that of the uropygial secretion.","volume":"11","author":"Mart\u00ednez-Garc\u00eda","year":"2016","journal-title":"PLoS One"},{"key":"B70","doi-asserted-by":"publisher","first-page":"622","DOI":"10.7164\/antibiotics.56.622","article-title":"Chandrananimycins AapproxC: production of novel anticancer antibiotics from a marine Actinomadura sp. Isolate M048 by variation of medium composition and growth conditions.","volume":"56","author":"Maskey","year":"2003","journal-title":"J. Antibiot."},{"key":"B71","doi-asserted-by":"publisher","DOI":"10.1098\/rspb.2013.2460","article-title":"Does sex-ratio selection influence nest-site choice in a reptile with temperature-dependent sex determination?","volume":"280","author":"Mitchell","year":"2013","journal-title":"Proc. Biol. Sci."},{"key":"B72","doi-asserted-by":"crossref","first-page":"367","DOI":"10.1016\/S0038-0717(98)00138-2","article-title":"Fungal\u2013bacterial interaction on beech leaves: influence on decomposition and dissolved organic carbon quality.","volume":"31","author":"M\u00f8ller","year":"1999","journal-title":"Soil Biol. Biochem."},{"key":"B73","doi-asserted-by":"crossref","first-page":"6920","DOI":"10.1128\/AEM.00414-10","article-title":"Comparative analysis of myxococcus predation on soil bacteria.","volume":"76","author":"Morgan","year":"2010","journal-title":"Appl. Environ. Microbiol."},{"key":"B74","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1080\/01490451.2013.820236","article-title":"Bacterial communities in soil under moss and lichen-moss crusts.","volume":"31","author":"Navarro-Noya","year":"2014","journal-title":"Geomicrobiol. J."},{"key":"B75","doi-asserted-by":"publisher","DOI":"10.1016\/j.syapm.2021.126222","article-title":"The bacterial and fungal nest microbiomes in populations of the social spider Stegodyphus dumicola.","volume":"44","author":"Nazipi","year":"2021","journal-title":"Syst. Appl. Microbiol."},{"key":"B76","doi-asserted-by":"publisher","first-page":"182","DOI":"10.3389\/fmicb.2020.615659","article-title":"Relationship between soil fungal diversity and temperature in the maritime Antarctic.","volume":"6","author":"Newsham","year":"2016","journal-title":"Nat. Clim. Change"},{"key":"B77","doi-asserted-by":"crossref","first-page":"72","DOI":"10.1111\/brv.12333","article-title":"Developmental temperatures and phenotypic plasticity in reptiles: a systematic review and meta-analysis.","volume":"93","author":"Noble","year":"2018","journal-title":"Biol. Rev. Camb. Philos. Soc."},{"key":"B78","doi-asserted-by":"publisher","first-page":"2477","DOI":"10.1128\/JCM.02371-07","article-title":"Molecular phylogenetic diversity, multilocus haplotype nomenclature, and in vitro antifungal resistance within the Fusarium solani species complex.","volume":"46","author":"O\u2019Donnell","year":"2008","journal-title":"J. Clin. Microbiol."},{"key":"B79","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-019-43025-9","article-title":"Fungal elevational Rapoport pattern from a high mountain in Japan.","volume":"9","author":"Ogwu","year":"2019","journal-title":"Sci. Rep."},{"key":"B80","doi-asserted-by":"publisher","first-page":"955","DOI":"10.1139\/w06-023","article-title":"Ecology of ligninolytic fungi associated with leaf litter decomposition.","volume":"22","author":"Osono","year":"2007","journal-title":"Ecol. Res."},{"key":"B81","doi-asserted-by":"crossref","first-page":"517","DOI":"10.1016\/j.soilbio.2005.05.022","article-title":"Immobilization of avian excreta-derived nutrients and reduced lignin decomposition in needle and twig litter in a temperate coniferous forest.","volume":"38","author":"Osono","year":"2005","journal-title":"Soil Biol. Biochem."},{"key":"B82","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1007\/s00248-015-0692-6","article-title":"Bacterial communities in termite fungus combs are comprised of consistent gut deposits and contributions from the environment.","volume":"71","author":"Otani","year":"2016","journal-title":"Microb. Ecol."},{"key":"B83","doi-asserted-by":"crossref","first-page":"32","DOI":"10.2174\/1874453220130815001","article-title":"An assessment of the microbial diversity present on the surface of naturally incubated House wren eggs.","volume":"6","author":"Potter","year":"2013","journal-title":"Open Ornithol. J."},{"key":"B84","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.29594","article-title":"The genome of an intranuclear parasite, Paramicrosporidium saccamoebae, reveals alternative adaptations to obligate intracellular parasitism.","volume":"6","author":"Quandt","year":"2017","journal-title":"eLife"},{"key":"B85","doi-asserted-by":"publisher","first-page":"D590","DOI":"10.1093\/nar\/gks1219","article-title":"The SILVA ribosomal RNA gene database project: improved data processing and web-based tools.","volume":"41","author":"Quast","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"B86","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.2584","article-title":"VSEARCH: a versatile open source tool for metagenomics.","volume":"4","author":"Rognes","year":"2016","journal-title":"PeerJ"},{"key":"B87","doi-asserted-by":"publisher","first-page":"1340","DOI":"10.1038\/ismej.2010.58","article-title":"Soil bacterial and fungal communities across a pH gradient in an arable soil.","volume":"4","author":"Rousk","year":"2010","journal-title":"ISME J."},{"key":"B88","doi-asserted-by":"publisher","DOI":"10.1093\/femsec\/fiz052","article-title":"Antimicrobial activity of nest-lining feathers is enhanced by breeding activity in avian nests.","volume":"95","author":"Ruiz-Castellano","year":"2019","journal-title":"FEMS Microbiol. Ecol."},{"key":"B89","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0148894","article-title":"Nest material shapes eggs bacterial environment.","volume":"11","author":"Ruiz-Castellano","year":"2016","journal-title":"PLoS One"},{"key":"B90","doi-asserted-by":"publisher","first-page":"3652","DOI":"10.1128\/aem.57.12.3652-3655.1991","article-title":"Limited bacterial mineralization of fungal degradation intermediates from synthetic lignin.","volume":"57","author":"R\u00fcttimann","year":"1991","journal-title":"Appl. Environ. Microbiol."},{"key":"B91","doi-asserted-by":"publisher","first-page":"192","DOI":"10.1111\/j.1574-6968.2010.02116.x","article-title":"Fusarium solani is responsible for mass mortalities in nests of loggerhead sea turtle, Caretta caretta, in Boavista, Cape Verde.","volume":"312","author":"Sarmiento-Ram\u00edrez","year":"2010","journal-title":"FEMS Microbiol. Lett."},{"key":"B92","doi-asserted-by":"crossref","DOI":"10.1186\/gb-2011-12-6-r60","article-title":"Metagenomic biomarker discovery and explanation.","volume":"12","author":"Segata","year":"2011","journal-title":"Genome Biol."},{"key":"B93","doi-asserted-by":"crossref","first-page":"473","DOI":"10.1128\/mr.54.4.473-501.1990","article-title":"Social and developmental biology of the myxobacteria.","volume":"54","author":"Shimkets","year":"1990","journal-title":"Microbiol. Rev."},{"key":"B94","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1007682","article-title":"Unraveling the ecology and epidemiology of an emerging fungal disease, sea turtle egg fusariosis (STEF).","volume":"15","author":"Smyth","year":"2019","journal-title":"PLoS Pathog."},{"key":"B95","doi-asserted-by":"publisher","DOI":"10.1007\/s00248-021-01927-0","article-title":"Dynamics of bacterial communities on eggshells and on nest materials during incubation in the Oriental tit (Parus minor).","author":"Song","year":"2022","journal-title":"Microb. Ecol."},{"key":"B96","doi-asserted-by":"publisher","first-page":"447","DOI":"10.1016\/j.resmic.2007.04.002","article-title":"Differential degradation of oak (Quercus petraea) leaf litter by litter-decomposing basidiomycetes.","volume":"158","author":"Steffen","year":"2007","journal-title":"Res. Microbiol."},{"key":"B97","doi-asserted-by":"publisher","first-page":"819","DOI":"10.1007\/s002530000473","article-title":"Mineralisation of 14C-labelled synthetic lignin and ligninolytic enzyme activities of litter-decomposing basidiomycetous fungi.","volume":"54","author":"Steffen","year":"2000","journal-title":"Appl. Microbiol. Biotechnol."},{"key":"B98","doi-asserted-by":"publisher","DOI":"10.1098\/rsbl.2012.0931","article-title":"Incorporation of cigarette butts into nests reduces nest ectoparasite load in urban birds: new ingredients for an old recipe?","volume":"9","author":"Su\u00e1rez-Rodr\u00edguez","year":"2013","journal-title":"Biol. Lett."},{"key":"B99","doi-asserted-by":"publisher","first-page":"211","DOI":"10.1264\/jsme2.me13183","article-title":"Termite nests as an abundant source of cultivable Actinobacteria for biotechnological purposes.","volume":"29","author":"Sujada","year":"2014","journal-title":"Microbes Environ."},{"key":"B100","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1007\/s13225-019-00422-9","article-title":"Fungicolous fungi: terminology, diversity, distribution, evolution, and species checklist.","volume":"95","author":"Sun","year":"2019","journal-title":"Fungal Divers."},{"key":"B101","doi-asserted-by":"crossref","first-page":"594","DOI":"10.1080\/00275514.1973.12019473","article-title":"Isolation of thermophilic fungi from Alligator nesting material.","volume":"65","author":"Tansey","year":"1973","journal-title":"Mycologia"},{"key":"B102","doi-asserted-by":"crossref","first-page":"S1325","DOI":"10.1139\/b95-394","article-title":"Interactions of wood decay fungi with other microorganisms, with emphasis on the degradation of cell walls.","volume":"73","author":"Tsuneda","year":"1995","journal-title":"Can. J. Bot."},{"key":"B103","doi-asserted-by":"publisher","first-page":"251","DOI":"10.1007\/s11259-018-9728-y","article-title":"Identification of bacteria present in ulcerative stomatitis lesions of captive sea turtles Chelonia mydas.","volume":"42","author":"Vega-Manriquez","year":"2018","journal-title":"Vet. Res. Commun."},{"key":"B104","doi-asserted-by":"publisher","first-page":"465","DOI":"10.3928\/0147-7447-19880301-11","article-title":"Enterobacter agglomerans osteomyelitits of the hand from a rose thorn: a case report.","volume":"11","author":"Vincent","year":"1988","journal-title":"Orthopedics"},{"key":"B105","doi-asserted-by":"publisher","first-page":"975","DOI":"10.1007\/s00248-011-9987-4","article-title":"Exploring the potential for Actinobacteria as defensive symbionts in fungus-growing termites.","volume":"63","author":"Visser","year":"2012","journal-title":"Microb. Ecol."},{"key":"B106","doi-asserted-by":"crossref","first-page":"828","DOI":"10.1038\/nrmicro2910","article-title":"Microbial life in the phyllosphere.","volume":"10","author":"Vorholt","year":"2012","journal-title":"Nat. Rev. Microbiol."},{"key":"B107","doi-asserted-by":"publisher","first-page":"968","DOI":"10.1093\/femsre\/fuv027","article-title":"Pantoea: insights into a highly versatile and diverse genus within the Enterobacteriaceae.","volume":"39","author":"Walterson","year":"2015","journal-title":"FEMS Microbiol. Rev."},{"key":"B108","doi-asserted-by":"crossref","first-page":"827","DOI":"10.1016\/S0038-0717(03)00118-4","article-title":"Determinants of litter mixing effects in a Swedish boreal forest.","volume":"35","author":"Wardle","year":"2003","journal-title":"Soil Biol. Biochem."},{"key":"B109","doi-asserted-by":"crossref","first-page":"424","DOI":"10.1046\/j.1365-2656.2002.00611.x","article-title":"Interactive effects of concealment, parental behaviour and predators on the survival of open passerine nests.","volume":"71","author":"Weidinger","year":"2002","journal-title":"J. Anim. Ecol."},{"key":"B110","doi-asserted-by":"publisher","first-page":"309","DOI":"10.1146\/annurev.phyto.40.030402.110010","article-title":"Microbial populations responsible for specific soil suppressiveness to plant pathogens.","volume":"40","author":"Weller","year":"2002","journal-title":"Annu. Rev. Phytopathol."},{"key":"B111","doi-asserted-by":"publisher","first-page":"1385","DOI":"10.1039\/b817073h","article-title":"The impact of genomics on the exploitation of the myxobacterial secondary metabolome.","volume":"26","author":"Wenzel","year":"2009","journal-title":"Nat. Prod. Rep."},{"key":"B112","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1023\/A:1020592802234","article-title":"The consequences of volatile organic compound mediated bacterial and fungal interactions.","volume":"81","author":"Wheatley","year":"2002","journal-title":"Antonie Van Leeuwenhoek"},{"key":"B113","doi-asserted-by":"crossref","first-page":"487","DOI":"10.1093\/jxb\/52.suppl_1.487","article-title":"Microbial interactions and biocontrol in the rhizosphere.","volume":"52","author":"Whipps","year":"2001","journal-title":"J. Exp. Bot."},{"key":"B114","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1111\/j.1472-765X.1990.tb00268.x","article-title":"Bacteria in the gular and paracloacal glands of the American alligator (Alligator mississippiensis; Reptila, Crocodilia).","volume":"10","author":"Williams","year":"1990","journal-title":"Lett. Appl. Microbiol."},{"key":"B115","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-020-00824-x","article-title":"A predatory myxobacterium controls cucumber Fusarium wilt by regulating the soil microbial community.","volume":"8","author":"Ye","year":"2020","journal-title":"Microbiome"},{"key":"B116","doi-asserted-by":"publisher","first-page":"1792","DOI":"10.1099\/ijsem.0.000939","article-title":"Psychrobacter glaciei sp. nov., isolated from the ice core of an Arctic glacier.","volume":"66","author":"Zeng","year":"2016","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"B117","doi-asserted-by":"crossref","first-page":"574","DOI":"10.1093\/jpe\/rtaa045","article-title":"Characteristics of fungal community structure during the decomposition of mixed foliage litter from Pinus massoniana and broadleaved tree species in southwestern China.","volume":"13","author":"Zhang","year":"2020","journal-title":"Chin. J. Plant Ecol."},{"key":"B118","doi-asserted-by":"crossref","first-page":"725","DOI":"10.1093\/czoolo\/59.6.725","article-title":"The sex ratio of wild Chinese alligators Alligator sinensis.","volume":"59","author":"Zhao","year":"2013","journal-title":"Curr. Zool."}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2022.983808\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,10,13]],"date-time":"2022-10-13T07:45:51Z","timestamp":1665647151000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2022.983808\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,10,13]]},"references-count":118,"alternative-id":["10.3389\/fmicb.2022.983808"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2022.983808","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,10,13]]},"article-number":"983808"}}