Updated RDP taxonomy and RDP Classifier for more accurate taxonomic classification

Wang, Qiong; Cole, James R.

doi:10.1128/mra.01063-23

Cited by 7 publications

(1 citation statement)

References 10 publications

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“…To account for index bleed between samples, read counts in the OTU□×□sample matrices were adjusted using 1% as the filter percentage. To assign taxonomy, we used a hybrid algorithm integrating results from a USEARCH global alignment against the UNITE (v8, Nilsson et al 2019) and RDP (training set 19, Wang and Cole 2024) databases, including both UTAX and SINTAX classifiers. Data are deposited in the NCBI Short Read Archive (Bioproject # for bacteria PRJNA1094420 ; for fungi PRJNA1094416 ).…”

Section: Methodsmentioning

confidence: 99%

Necromass chemistry interacts with soil mineral and microbial properties to determine fungal carbon and nitrogen persistence in soils

Beidler,

Huenupi,

DeLancey

et al. 2024

Preprint

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Despite fungal necromass being increasingly recognized a major source of carbon (C) and nitrogen (N) in soils, understanding of how soil mineral and microbial properties interact with initial necromass chemistry to influence its accumulation and persistence remains limited. To track the fate of fungal C and N into mineral associated organic matter (MAOM), we generated dual-labeled 13C and 15N fungal necromass of high and low melanin phenotypes of Hyaloscypha bicolor. Necromass was incubated in live and sterile soils from six forests in Indiana, USA that differed in initial microbial and physiochemical characteristics. At the end of the 38-day incubation, considerably more initial fungal necromass N was incorporated into MAOM relative to necromass C and low melanin necromass contributed more to MAOM-C formation. Though soil iron oxide (FeOx) and clay content were positively correlated with MAOM-C formation from low melanin necromass, initial microbial community composition was the best predictor of MAOM-N formation for both high and low melanin necromass additions. In particular, soils with higher relative abundances of bacterial copiotrophs at the start of the study formed less fungal necromass-derived MAOM-N. We also used synthesized FeOx minerals to investigate how initial necromass chemistry impacts mineral sorption in vitro. We found higher adsorption of amide functionalities for low melanin necromass on goethite minerals after 24 hours. However, 30% less initial necromass-N was converted into MAOM-N in sterile soils regardless of necromass type. When considered together, our results indicate that the microbial synthesis pathway drives fungal necromass-derived MAOM-N formation and that microbial processing limits fungal necromass-derived MAOM-C formation, highlighting the importance of microbial controls on the preservation of fungal-derived SOM in soils.

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Section: Methodsmentioning

confidence: 99%