Summary: iTOL is a powerful and comprehensive phylogenetic tree visualization engine. However, adjusting to new templates can be time-consuming, especially when many templates are available. We developed an R package namely itol.toolkit to help users generate all 23 types of annotation files in iTOL. This R package also provides an all-in-one data structure to store data and themes, accelerating the step from metadata to annotation files of iTOL visualizations through automatic workflows. Availability and implementation: The manual and source code are available at https://github.com/TongZhou2017/itol.toolkit

The conversion of intrinsic lands to anthropogenic uses has increased nutrient inputs for lake microbes, profoundly influencing biogeochemical processes, particularly carbon cycling. Microbial carbon utilization is crucial in lake carbon sequestration, but its general changes under anthropogenic disturbances remain controversial. We combined carbon utilization assays with Biolog EcoPlates and 16S rRNA gene amplicon sequencing to examine microbial carbon utilization and carbon loss in lakes along a 3369 km gradient of land-use intensities spanning the Yangtze River and its front basin across China. Our results demonstrated that >30% land-use conversions from intrinsic to anthropogenic lands (farmland and built areas) resulted in >50% carbon loss in lakes. The large carbon loss was primarily driven by elevated nutrient concentrations, which stimulated microbial carbon utilization. Microbes in water were more responsive to environmental changes than those in sediment. We further identified distinct preferences of microbial carbon utilization driven by compositional shifts in core species. Specifically, nutrient-sensitive species (Roseomonas and Methylocystis) were replaced by nutrient-preferential species (Desertimonas and Clostridium sensu stricto), which collectively enhanced the utilization of substrates such as itaconic acid, phenylethyl-amine and glycerol, thereby accelerating carbon loss. This study quantifies the relationship between microbial carbon utilization and carbon loss, emphasizing the importance of regulating land-use changes and nutrient inputs to mitigate their impacts on lakes.

The sclerotium of the edible mushroom Polyporus umbellatus (Zhuling) exhibits various medicinal properties. However, given its long growth cycle and overexploitation, wild resources are facing depletion. Macrofungal growth depends on diverse microbial communities; however, the impact of soil bacteria on P. umbellatus development is unknown. Here, we combined high-throughput sequencing and pure culturing to characterize the diversity and potential function of bacteria and fungi inhabiting the P. umbellatus sclerotium and tested the bioactivities of their isolates. Fungal operational taxonomic units (OTUs) were clustered and classified, revealing 1275 genera. Bacterial OTUs yielded 891 genera. Additionally, 81 bacterial and 15 fungal strains were isolated from P. umbellatus sclerotia. Antagonism assays revealed three bacterial strains (FN2, FL19, and CL15) promoting mycelial growth by producing indole-3-acetic acid, solubilizing phosphate, and producing siderophores, suggesting their role in regulating growth, development, and production of active compounds in P. umbellatus. FN2-CL15 combined with bacterial liquid promoted growth and increased the polysaccharide content of P. umbellatus mycelia. This study reports new bioactive microbial resources for fertilizers or pesticides to enhance the growth and polysaccharide accumulation of P. umbellatus mycelia and offers guidance for exploring the correlation between medicinal macrofungi and associated microbial communities.

Murraya paniculate, is traditionally used for management of gut, air way and cardiovascular disorders. In this study, we sequenced the complete chloroplast genome of M. paniculata based on next-generation sequencing and used the data to assess genomic resources. The chloroplast genome of M. paniculata is 160,280 bp in length consisting of large and small single-copy regions of length 87,605 and 18,609 bp, separated by two IR regions of 27,033 bp. The overall GC content was 38.61%. De novo assembly and annotation showed the presence of unique genes with 85 protein-coding genes, 29 tRNA genes, and eight rRNA genes. A maximum-likelihood phylogenomic analysis showed that M. paniculata was closely related to M. caloxylon.