Biology subjects

Starke, R.

Publications and source records attributed to Starke, R..

3 recordsLinked to original sources

bioRxiv2020

Meta-analysis of 139 extant Tara ocean metagenomes to unveil the relationship between taxonomy and functionality in prokaryotes inhabiting aquatic ecosystems

The total microbiome functionality of bacteria was recently predicted to be 35.5 {+/-}0.2 million of KEGG functions. Logically, due to the limitation in space and resource availability of the local community, local functionality will only comprise a small subset of the total functionality but the relationship between taxonomy and functionality is still uncertain. Here, I used a meta-analysis of 139 extant Tara ocean seawater samples from 68 locations across to globe with information on prokaryotic taxonomy on species level from 16S metabarcoding and functionality of prokaryotes on eggNOG gene family level from metagenomes to unveil the relationship between taxonomy and functionality, and to predict the global distribution of functionality. Functional richness showed a statistically significant increase with increasing species richness (P <0.0001, R2 =0.64) and increasing species diversity (P <0.0001, R2 =0.26) while functional diversity was similar across the different waters, ranging from 2.96 to 3.22. Globally, the highest functional richness was found in the Northern Pacific Ocean and in the North Atlantic Ocean, and decreased at extreme latitudes. Taken together, I unveil the relationship between taxonomy and functionality, and predict the global distribution of functional richness in prokaryotes inhabiting aquatic ecosystems, implying more pronounced effects in terrestrial ecosystems due to larger differences in environmental parameters especially for functional diversity.

microbiology↗

bioRxiv2019

Gene copy normalization of the 16S rRNA gene cannot outweigh the methodological biases of sequencing

The 16S rRNA gene is the golden standard target of sequencing to uncover the composition of bacterial communities but the presence of multiple copies of the gene makes gene copy normalization (GCN) inevitable. Even though GCN resulted in abundances closer to the metagenome, it should be validated by communities with known composition as both amplicon and shotgun sequencing are prone to methodological biases. Here we compared the composition of three mock communities to the composition derived from 16S sequencing without and with GCN. In all of them, the 16S composition was different from the mock community and GCN improved the picture only in the community with the lowest Shannon diversity. Albeit with low abundance, half of the identified genera were not present in the mock communities. Our approach provides empirical evidence to the methodological biases introduced by sequencing that was only counteracted by GCN in the case of low -diversity, potentially due to the small number of bacterial taxa with known gene copy numbers. We thus cannot recommend the use of GCN moving forward and it is questionable whether a complete catalogue of 16S rRNA copy numbers can outweigh the methodological biases of sequencing.

microbiology↗

bioRxiv2019

The total fungal microbiome functionality

Unveiling the relationship between taxonomy and function of the microbiome is crucial to determine its contribution to ecosystem functioning. However, while there is a considerable amount of information on microbial taxonomic diversity, our understanding of its relationship to functional diversity is still scarce. Here we used a meta-analysis of 377 completely annotated and taxonomically different fungal genomes to predict the total fungal microbiome functionality on Earth with all known functions from level 3 of KEGG Orthology using both parametric and non-parametric estimations. The unsaturated model described the accumulation of functions with increasing species richness significantly better (P-value < 2.2e-16) than the saturated model suggesting the presence of widespread and rare functions. Consistent with the parametric approach, the non-parametric Chao-1 estimator that assumes a maximum functional richness did not reach a plateau. Based on previous estimates of fungal species richness on Earth, we propagated the unsaturated model to predict a total fungal microbiome functionality of 42.4 million. Of those, only 0.06% are known today since the vast majority belongs to yet unknown rare functions. Logically, our approach not only highlighted the presence of two types of functions but pointed towards the necessity of novel and more sophisticated methods to unveil the entirety of functions to fully understand the involvement of the fungal microbiome in ecosystem functioning.

ecology↗