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Series GSE268149 Query DataSets for GSE268149
Status Public on May 29, 2024
Title Transcriptomic analyses of bacterial growth on fungal necromass reveals different microbial community niches during degradation
Organisms Serratia marcescens; Chitinophaga pinensis; Cellvibrio japonicus
Experiment type Expression profiling by high throughput sequencing
Summary Bacteria are major drivers of organic matter decomposition and play crucial roles in global nutrient cycling. Although the degradation of dead fungal biomass (necromass) is increasingly recognized as an important contributor to soil carbon (C) and nitrogen (N) cycling, the genes and metabolic pathways involved in necromass degradation are under characterized. In particular, how bacteria degrade necromass containing different quantities of melanin, which largely control rates of necromass decomposition in situ, is largely unknown. To address this gap, we conducted a multi-timepoint transcriptomic analysis using three Gram-negative, bacterial species grown on low or high melanin necromass of Hyaloscypha bicolor. The bacterial species, Cellvibrio japonicus, Chitinophaga pinensis, and Serratia marcescens, belong to genera known to degrade necromass in situ. We found that while bacterial growth was consistently higher on low than high melanin necromass, the CAZyme-encoding gene expression response of the three species was similar between the two necromass types. Interestingly, this trend was not shared for genes encoding nitrogen utilization, which varied in C. pinensis and S. marcescens during growth on high versus low melanin necromass. Additionally, this study tested the metabolic capabilities of these bacterial species to grow on a diversity of C and N sources and found that the three bacteria have substantially different abilities to utilize carbon and nitrogen compounds. Collectively, our data suggests that as necromass changes chemically over the course of degradation, certain bacterial species are favored based on their differential metabolic capacities.
Overall design Bacterial cell pellets were collected during exponential growth or stationary phase in biolgical triplicate during the degradation of high or low melanin fungal necromass. Reference conditon was growth using glucose as sole carbon source.
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Submission date May 22, 2024
Last update date May 29, 2024
Contact name Jeffrey G. Gardner
Organization name University of Maryland - Baltimore County
Department Department of Biological Sciences
Street address 1000 Hilltop Circle
City Baltimore
State/province MD
ZIP/Postal code 21250
Country USA
Platforms (3)
GPL34518 Illumina HiSeq 1000 (Cellvibrio japonicus)
GPL34519 Illumina HiSeq 1000 (Chitinophaga pinensis)
GPL34520 Illumina HiSeq 1000 (Serratia marcescens)
Samples (48)
GSM8286399 Cj_NecHi_Log_Rep1
GSM8286400 Cj_NecHi_Log_Rep2
GSM8286401 Cj_NecHi_Log_Rep3
BioProject PRJNA1114768

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Supplementary file Size Download File type/resource
GSE268149_Cj_NecHi_TPM.csv.gz 94.4 Kb (ftp)(http) CSV
GSE268149_Cj_NecLo_TPM.csv.gz 95.4 Kb (ftp)(http) CSV
GSE268149_Cp_Glc_TPM.csv.gz 173.5 Kb (ftp)(http) CSV
GSE268149_Cp_NecHi_TPM.csv.gz 168.9 Kb (ftp)(http) CSV
GSE268149_Cp_NecLo_TPM.csv.gz 166.4 Kb (ftp)(http) CSV
GSE268149_Necromass_DEG.xlsx 1.2 Mb (ftp)(http) XLSX
GSE268149_Sm_Glc_TPM.csv.gz 184.1 Kb (ftp)(http) CSV
GSE268149_Sm_NecHi_TPM.csv.gz 119.3 Kb (ftp)(http) CSV
GSE268149_Sm_NecLo_TPM.csv.gz 118.9 Kb (ftp)(http) CSV
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