The dynamics of evolution - how horizontal gene transfer drives the diversification and adaptation of complex microbial communities in marine ecosystems
Final Report Abstract
Microorganisms are key players in ecosystem health and functioning. Consequently, assessing structural and functional dynamics of microbial communities towards changing environmental conditions is of crucial interest. One aim of my research project was to assess compositional and functional changes of endophyte communities in the plant holobiont as response towards agricultural management practices. Obtained results suggest that different plant species as observed responses were plant-species specific and differed among the years. Assessing composition and diversity of microbial communities by sequencing of 16S rRNA genes is a common approach in microbial ecology. Unfortunately, several questions in ecology require functional rather than taxonomic information. However, assessing functional capabilities of microbial communities, e.g., by sequencing of environmental DNA, is still very cost intensive. Hence, we developed a software package designated Tax4Fun2 to predict functional profiles from 16S rRNA gene data. A unique feature of Tax4Fun2 is the possibility to incorporate user-defined, habitat-specific data in the predictive process. We tested this novel feature using data derived from 90 seaweed microbiomes and obtained highly accurate functional profiles. This unique tool provides preliminary access to functional information and can be used to propose novel hypotheses related to ecosystem functioning. Understanding community assembly is one fundamental question in community ecology. Marine sponges are important ecosystem engineers. They host complex microbial communities which contribute to their health and survival. However, the mechanisms behind microbiome assembly in sponges are largely unknown. We identified abiotic factors as main drivers of community structuring of the sponge microbiome when considering all microbes present, but biotic interactions drove the assembly of more intimately associated ‘core’ microorganisms. To gain access to community functioning, we applied Tax4Fun2 and found that distinct functional patterns between different groups of sponges exist. Recent observations led to the assumption that horizontal gene transfer (HGT) is the driving force of microbial evolution. The second aim of my research project was to develop a strategy to detect horizontally transferred genes in microbial communities. We developed a bioinformatic pipeline designated MetaCHIP for HGT identification at community level. Obtained results indicate that genes for antibiotic resistance in the human gut and functions related to energy production and conversion as well as carbohydrate transport and metabolism in free-living marine microbes are potentially transferred by HGT. The third aim of my research project was to investigate the adaptation of microbial communities to their environment. Three metagenome-assembled genomes affiliated to the Thaumarchaeota were reconstructed from metagenomic datasets and compared to genomes of free-living members. Thaumarchaeota are commonly found as symbionts of marine sponges. Comparative genomic analysis of sponge-associated MAGs to genomes of free-living Thaumarchaeota revealed that functional adaptations to the symbiotic lifestyle are related to nutrient transport and metabolism, defense mechanisms and host interactions. Obtained results provide new evolutionary and ecological insights into the symbiosis between sponges and their thaumarchaeal symbionts.
Publications
- (2019) Comparative Genomics Reveals Ecological and Evolutionary Insights into Sponge-Associated Thaumarchaeota. mSystems 4 (4)
Zhang, Shan; Song, Weizhi; Wemheuer, Bernd; Reveillaud, Julie; Webster, Nicole; Thomas, Torsten
(See online at https://doi.org/10.1128/mSystems.00288-19) - Tax4Fun2: A R-based tool for the rapid prediction of habitat-specific functional profiles and functional redundancy based on 16S rRNA gene marker gene sequences
Franziska Wemheuer, Jessica Taylor, Rolf Daniel, Emma Johnston, Peter Meinicke, Bernd Wemheuer
(See online at https://doi.org/10.1101/490037) - Fungal Endophyte Communities of Three Agricultural Important Grass Species Differ in Their Response Towards Management Regimes. 01/2019; 7(2):37
Bernd Wemheuer, Torsten Thomas, Franziska Wemheuer
(See online at https://doi.org/10.3390/microorganisms7020037) - MetaCHIP: community-level horizontal gene transfer identification through the combination of best-match and phylogenetic approaches. Microbiome 03/2019; 7(1):36
Weizhi Song, Bernd Wemheuer, Shan Zhang, Kerrin Steensen, Torsten Thomas
(See online at https://doi.org/10.1186/s40168-019-0649-y) - Modularity and predicted functions of the global sponge-microbiome network. Nature Communications 12/2019; 10(1)
Miguel Lurgi, Torsten Thomas, Bernd Wemheuer, Nicole S. Webster, Jose M. Montoya
(See online at https://doi.org/10.1038/s41467-019-08925-4)
