Department of Molecular Ecology

Inspiration and focus of our department

Microorganisms account for 70 % of the biomass in the oceans and are fundamental for the functioning of marine ecosystems. They play important roles in regulating organic matter and nutrient cycles and even influence the Earth's climate. Whereas only thou­sands of spe­cies of Bacteria and Archaea have been de­scribed by cul­tiv­a­tion-based meth­ods, we are identi­fy­ing mil­lions with mo­lecu­lar tech­niques. In our department, we use the most modern techniques in a multidisciplinary and polyphasic approach to ecologically characterise marine microbial communities from hydrothermal vents to coastal surface waters and from the tropics to the poles.

Uncultivated microbes in need of their own taxonomy

Taxonomy encompasses the identification, classification, and nomenclature of organisms. As such, taxonomy is a prerequisite for ecology. Only based on accurate taxonomic concepts and methods, can the diversity and composition of complex microbial communities be accurately described and monitored. Our department has a long tradition of developing and applying new taxonomic methods, from pioneering the in situ identification and quantification of not-yet cultivated bacteria and archaea through fluorescence in situ hybridization (FISH) to contributing to widely used standards of 16S rRNA gene classification. 

More recently, the developments in sequencing technologies provide a vast amounts of information on yet uncultivated microorganisms. By combining multiple methods, such as metagenomics and FISH, we have been able to describe several new marine taxa including the species Candidatus Prosiliicoccus vernus (Francis et al. 2019) and the genus Candidatus Abditibacter (Grieb et al. 2020). To find out more about our work on the taxonomy of yet-uncultivated bacteria and archaea visit our project page for taxonomy.

Diversity, visualisation and cultivation

One of the primary ques­tions of ecology is 'who or what is there?'. In mar­ine mi­cro­bial eco­logy, we typ­ic­ally em­ploy high-through­put se­quen­cing of the 16S rRNA gene to provide a win­dow into the di­versity of the microbial com­mu­nity. From this, we can de­term­ine the key mi­cro­bial taxa present and be­gin to for­mu­late hypotheses about eco­lo­gical pro­cesses tak­ing place. More re­cently, a sig­ni­fic­ant ad­vance­ment in long-read se­quen­cing tech­no­logy, with the advent of the PacBio Sequel II platform, now allows us to se­quence the ge­netic ma­ter­ial from en­vir­on­mental pop­u­la­tions (meta­ge­n­om­ics) and sim­ul­tan­eously re­trieve full-length 16S rRNA genes. In com­par­ison to short 16S rRNA gene amp­l­ic­ons, these full-length se­quences can be used in more ro­bust and ac­cur­ate phylo­gen­etic ana­lyses. 

The next fun­da­mental com­pon­ent of ecology is assessing the abund­ance of a spe­cific pop­u­la­tion in the en­vir­on­ment. Trivi­ally speak­ing, the more in­di­vidu­als there are, the more im­port­ant they are for the eco­sys­tem and the higher the im­pact on the nu­tri­ent cycle, re­source ex­plor­a­tion and meta­bolic in­ter­ac­tions. This is where our method FISH is an in­dis­pens­able tool for the enu­mer­a­tion of taxo­nom­ic­ally well-defined mi­croor­gan­isms. As most mi­crobes lack a con­spicu­ous mor­pho­logy, the only re­li­able marker to dis­tin­guish between them is the ri­bosomal RNA mo­lecule, which is highly con­served and abund­ant in every or­gan­ism. Us­ing small fluor­es­cently la­belled oli­go­nuc­leotides com­ple­ment­ary to the rRNA, we can tailor probes spe­cific for the taxa of in­terest to visu­al­ize and count them by epi­fluor­es­cence mi­cro­scopy. Be­sides a nu­mer­ical quan­ti­fic­a­tion, FISH provides a clue about cel­lu­lar struc­tures and phys­ical in­ter­ac­tions with other mi­crobes. We can use high-res­ol­u­tion mi­cro­scopy like Con­focal Laser Scan­ning Mi­cro­scopy (CLSM) and STim­u­lated Emis­sion De­ple­tion (STED) microscopy to study intracellular properties or the uptake of, e.g., substrates. Using FISH and high-resolution microscopy, we can determine accurate cell-sizes and biovolumes of uncultivated microbes.

Though we can ob­tain ample amounts of in­form­a­tion about the eco­logy of mi­croor­gan­isms from en­vir­on­mental samples, we ultimately still require pure cultures or enrichments in the lab. Cul­tiv­a­tion is still, in most cases, the only way to ex­per­i­ment­ally verify pre­dic­tions and hy­po­theses for­mu­lated from ge­n­omic se­quence in­form­a­tion. However, the isol­a­tion of mar­ine mi­croor­gan­isms can be a chal­len­ging task, as it is dif­fi­cult to re­cre­ate the nat­ural en­vir­on­ment and spe­cific con­di­tions re­quired for a pop­u­la­tion to grow. There­fore, we use li­quid me­di­ums and en­rich­ments along with phys­ical sep­ar­a­tion of in­di­vidual cells through di­lu­tion and mo­lecu­lar iden­ti­fic­a­tion meth­ods (in house de­veloped spe­cific PCR and in situ hy­brid­isa­tion probes) to isol­ate abund­ant mi­crobes from nat­ural com­munit­ies. Once a strain is in pure cul­ture, the source is un­lim­ited and physiolo­gical traits and in­di­vidual en­zymes can be stud­ied.

Functional characterization

The rapid development of massive sequencing technologies has unravelled a new era for the examination of the genetic potential of microbial communities. From the analyses of sequence discrete populations in nature to isolates in the lab, the use of multi-omic techniques allows us to integrate genetic information at the gene, transcript and also protein levels. Our goal is to bridge the gap between predicted function and measured microbial activity through the integration of these different levels of information. 

The mRNA of species within microbial communities tells us which genes are actively transcribed whilst metaproteomics identifies the abundant proteins. Combining these observations enables us to predict the metabolic processes, only hampered by the fact that for half of the proteins we do not know their function. But the accumulated knowledge of mankind allows us a first glance at novel ecosystems. With the observation of community responses to substrate additions and the study of novel strains, we aim at a full understanding of the major processes in nature. We are still explorers.