Metagenomics and Microbiology at large has experienced a boom thanks to the high throughput sequencing (mostly Illumina) as illustrated by the GTDB, a novel genomic taxonomy that collects more than 200,000 microbes, most of them metagenome assembled genomes (MAGs). However, our knowledge of the astounding diversity of microbes is still biased. Most of these genomes are incomplete “drafts” produced by bioinformatic assembly. These drafts tend to be incomplete and suffer from major limitations: i) they do not work for the most abundant, often microdiverse microbes that are largely unrepresented as MAGs, ii) even the ones that assemble miss the variable (flexible) part of the genomes that is often the most ecologically and biotechnologically relevant iii) assemblies are often fragmented so that the overall synteny supra-operonic organization is lost. Fortunately, third generation, high fidelity sequencing provides novel platforms from which we can get complete MAGs (cMAGs) with which a more realistic view of microbial genomes can be obtained. Not only that, but more complete genomes coupled to better annotation tools could lead a much more realistic view of the Biology of microbes. Some examples from different aquatic environments including freshwater and marine will be presented.

Members of the phylum Planctomycetes occur ubiquitously but can dominate bacterial communities on the surface of macroscopic aquatic phototrophs, e.g., algae or seagrasses. An observed abundance in the range of 60-85% of the epiphytic bacterial community on such surfaces is quite astonishing when considering that planctomycetes grow considerably slower than other heterotrophic bacteria occupying the same ecological niches. The observed dominance is suggested to result from complex phototroph-planctomycete allelopathic interactions that likely involve secondary metabolite biosynthesis. Despite genome- and lifestyle-based evidence, neither the interaction of planctomycetes with bacterial competitors nor their suspected bioactive compound repertoire have been studied on the molecular level so far. As a model system we currently investigate the interaction of the planctomycete Stieleria maiorica with Phaeobacter inhibens, a member of the ‘Roseobacter group’. The production of stieleriacines, a class of long-chain N-acyl tyrosines, by S. maiorica is potentially relevant for altering physicochemical properties of marine biotic surfaces, ultimately leading to active shaping of microbial communities by S. maiorica.

As part of the molecular toolbox that is required to investigate the role of secondary metabolite biosynthetic gene clusters and other structural genes, the research also focuses on the development of tools for the targeted modification of planctomycetal genomes. Especially the construction of replicative plasmids and strategies for the marker-free introduction of genomic modifications by two-step homologous recombination are urgently required to push the research field forward. In addition, we continue to explore the planctomycetal diversity by the description of novel members of the phylum and optimize long-read sequencing techniques by tailor-made bioinformatic algorithms for the phylum.

The discovery and harnessing of the anammox bacteria is a triumph of predictive microbiology and engineering ingenuity . The harnessing is achieved by hitching ammonia oxidation to nitrite by ammonia oxidisers to the production of to nitrogen gas from ammonia and nitrite by anammox bacteria.  The anammox treatment process holds the promise of excellent nitrogen removal with lower cost and lower greenhouse gas emissions.  However, annamox bacteria grow very slowly, making experimentation time consuming and expensive. Consequently has proven difficult to extend the anammox treatment process to the normal domestic wastewater. Considerable experimentation is required to get the right balance between the ammonia, nitrite and anammox bacteria. One possible solution is simulation. Using powerful individual based models in combination with high performance computers it is possible to conduct extensive trials “in silico” improving research efficiency by orders of magnitude.  However, we also wish the process, once developed, to be as stable as possible.  The underlying diversity of the annamox bacteria is therefore also of interest.  There are systematic patterns in microbial diversity that can give us clues about diversity.  One such pattern is the relationship between metabolic energy and diversity.  On this basis it would appear that anammox bacteria (DGcat  -363 kJmol-1) should be more diverse than either ammonia oxidisers or nitrite oxidisers (DGcat  -283 and -79 kJmol-1). If this is the case, then it might imply that something other than niches were controlling the  diversity of autotrophs. Whilst we are not sure what that thing might be, one possibility is that energy places intrinsic limits on diversity. A plausible mechanism for this could be the drift barrier hypothesis which relates the number of selectable alleles to the steepness of selection gradients. Thus if metabolic energy controlled selection gradients, directly or indirectly, it could also control microbial diversity.  A theoretical understanding of what controls microbial diversity would be both intellectually satisfying and of great help in the “a priori” engineering of microbial communities.

Members of the Planctomycetes-Verrucomicrobia-Chlamydiae (PVC) bacterial superphylum play diverse and important ecological roles in many environments. While PVC bacteria are primarily free-living, the phylum Chlamydiae is an exception. This group of highly successful intracellular symbionts of eukaryotes ranges from animal pathogens to relatives with microbial or unknown hosts from diverse environments. Despite their conserved lifestyle, it is unclear how chlamydial symbiosis evolved. Here, we studied chlamydial evolution by performing large-scale phylogenomic analyses and gene-tree aware ancestral state reconstruction using a wide sampling of PVC genomic diversity. Unexpectedly for strict intracellular symbionts, we found that Chlamydiae evolution was characterized not just by extensive loss, but also by genome expansion from diverse horizontal gene transfer events. The Chlamydiae ancestor gained the genetic capability to infect eukaryotic hosts, indicating that the chlamydial symbiotic lifestyle has prevailed over a billion years of evolutionary history and diversification. This chlamydial ancestor was a facultative anaerobe, with the potential to transition between oxic and anoxic environments. Key differences in underlying energy metabolism and aerobiosis later emerged along a major split within Chlamydiae underpinned by complex genome dynamics. Host-associated lifestyles are widespread among bacteria, and together our analyses provide a blueprint for understanding major transitions in their evolution.