Ammonia-oxidizing archaea are ubiquitous in marine and terrestrial environments and now thought to be significant contributors to carbon and nitrogen cycling. The isolation of Candidatus “ Nitrosopumilus maritimus ” strain SCM1 provided the opportunity for linking its chemolithotrophic physiology with a genomic inventory of the globally distributed archaea. Here we report the 1,645,259-bp closed genome of strain SCM1, revealing highly copper-dependent systems for ammonia oxidation and electron transport that are distinctly different from known ammonia-oxidizing bacteria. Consistent with in situ isotopic studies of marine archaea, the genome sequence indicates N. maritimus grows autotrophically using a variant of the 3-hydroxypropionate/4-hydroxybutryrate pathway for carbon assimilation, while maintaining limited capacity for assimilation of organic carbon. This unique instance of archaeal biosynthesis of the osmoprotectant ectoine and an unprecedented enrichment of multicopper oxidases, thioredoxin-like proteins, and transcriptional regulators points to an organism responsive to environmental cues and adapted to handling reactive copper and nitrogen species that likely derive from its distinctive biochemistry. The conservation of N. maritimus gene content and organization within marine metagenomes indicates that the unique physiology of these specialized oligophiles may play a significant role in the biogeochemical cycles of carbon and nitrogen.

The rate of production of methane in many environments depends upon mutualistic interactions between sulfate‐reducing bacteria and methanogens. To enhance our understanding of these relationships, we took advantage of the fully sequenced genomes of Desulfovibrio vulgaris and Methanococcus maripaludis to produce and analyze the first multispecies stoichiometric metabolic model. Model results were compared to data on growth of the co‐culture on lactate in the absence of sulfate. The model accurately predicted several ecologically relevant characteristics, including the flux of metabolites and the ratio of D. vulgaris to M. maripaludis cells during growth. In addition, the model and our data suggested that it was possible to eliminate formate as an interspecies electron shuttle, but hydrogen transfer was essential for syntrophic growth. Our work demonstrated that reconstructed metabolic networks and stoichiometric models can serve not only to predict metabolic fluxes and growth phenotypes of single organisms, but also to capture growth parameters and community composition of simple bacterial communities. ### Synopsis Biological communities present tremendous modeling challenges because of the complex network of diverse interactions between species. A class of communities that has not been extensively modeled—but is of particular interest from ecological, geological, and engineering perspectives—is represented by microbial communities that thrive in oxygen‐free (anoxic) environments. These communities are vital components in numerous environments ranging from freshwater sediments and guts of insects and animals to wastewater treatment plants. They play a significant role in global cycling of carbon. Unlike communities of macro‐organisms, the flow of carbon through anaerobic communities depends to a large extent on the transfer of metabolites between species. Thus, it is essential that modelers of these communities first consider the metabolic networks determining the interactions among species. We report here on a metabolic model of a simple anaerobic community. This simple community consists of a bacterium and an archaeon that cooperate in a special mutualistic interaction called ‘syntrophy’ to degrade lactate into acetate and methane as the sole means of gaining energy for growth. The cooperation is based on the transfer of electrons from the bacterium to the archaeon in the form of hydrogen or formate. The archaeon uses the electrons to reduce carbon dioxide into methane. If the electrons are not transferred, then the archaeon will not have an energy source for growth. In turn, the bacteria will be unable to gain energy by oxidizing lactate unless their metabolites, primarily hydrogen and acetate, are kept at sufficiently low concentrations to make the reaction thermodynamically favorable. Such methanogenic syntrophies often form the final step of anaerobic trophic cascades and are therefore necessary for maintaining a continuous flux of metabolites through the community ([Figure 1][1]). Although a variety of anaerobic syntrophic associations have been examined, they have been characterized primarily in terms of bulk system properties and not as an integrated metabolic network ([Schink and Stams, 2002][2]). To develop a foundation for a more mechanistic understanding of syntrophic growth, we established a syntrophic interaction between two species whose genomes have been sequenced— Desulfovibrio vulgaris and Methanococcus maripaludis. D. vulgaris is a bacterium that can oxidize and obtain energy from a wide variety of carbon sources by sulfate respiration. M. maripaludis is an archaeon that obtains energy for growth by producing methane from carbon dioxide and hydrogen. The complete genome sequences of these two organisms were used as a basis to construct flux‐balance models of the central metabolisms of each growing independently and in syntrophic association. The models consist of a series of linear equations, each expressing a relationship between metabolites and the rate of flux through the reaction ([Edwards et al , 2002][3]). Because of the number of unknowns in the model, fluxes were calculated using linear optimization of a specific reaction, usually biomass production ([Price et al , 2004][4]). The single‐organism flux‐balance models were first refined by comparing the predicted biomass yields to experimental observations. These analyses provided insight into the physiology of growth of each species. Specifically, analysis of the D. vulgaris submodel suggested that two protons must be translocated to produce one ATP during respiration of sulfate. The M. maripaludis model provided insight into the likely number of protons that must be translocated during methane production and generated predictions about the influence of acetate consumption on biomass yield. The two models were then combined to form one model describing growth and metabolite accumulation when the organisms were growing syntrophically. A flux diagram showing the metabolic networks contained in the combined two‐species model, and an example of a simulation result is shown in [Figure 2][5]. Experimental data for lactate and hydrogen uptake rates during growth of the syntrophic culture were used as inputs to the model to test whether it could accurately capture the main features of syntrophic growth. The model was able to predict fluxes of acetate, methane, and carbon dioxide. In addition, the model consistently predicted roughly two‐fold more D. vulgaris biomass than M. maripaludis biomass even when it was set to optimize M. maripaludis biomass. This result demonstrates the stoichiometric coupling of growth of this association and is consistent with our experimental data which showed a ratio of D. vulgaris to M. maripaludis cells of approximately 2–2.5 throughout growth in batch culture. The model and experimental studies...

Existing workflows for the analysis of multi-omic microbiome datasets are lab-specific and often result in sub-optimal data usage. Here we present IMP, a reproducible and modular pipeline for the integrated and reference-independent analysis of coupled metagenomic and metatranscriptomic data. IMP incorporates robust read preprocessing, iterative co-assembly, analyses of microbial community structure and function, automated binning, as well as genomic signature-based visualizations. The IMP-based data integration strategy enhances data usage, output volume, and output quality as demonstrated using relevant use-cases. Finally, IMP is encapsulated within a user-friendly implementation using Python and Docker. IMP is available at http://r3lab.uni.lu/web/imp/ (MIT license).

Tubulins, the protein constituents of the microtubule cytoskeleton, are present in all known eukaryotes but have never been found in the Bacteria or Archaea. Here we report the presence of two tubulin-like genes [bacterial tubulin a ( btuba ) and bacterial tubulin b ( btubb )] in bacteria of the genus Prosthecobacter (Division Verrucomicrobia). In this study, we investigated the organization and expression of these genes and conducted a comparative analysis of the bacterial and eukaryotic protein sequences, focusing on their phylogeny and 3D structures. The btuba and btubb genes are arranged as adjacent loci within the genome along with a kinesin light chain gene homolog. RT-PCR experiments indicate that these three genes are cotranscribed, and a probable promoter was identified upstream of btuba . On the basis of comparative modeling data, we predict that the Prosthecobacter tubulins are monomeric, unlike eukaryotic α and β tubulins, which form dimers and are therefore unlikely to form microtubule-like structures. Phylogenetic analyses indicate that the Prosthecobacter tubulins are quite divergent and do not support recent horizontal transfer of the genes from a eukaryote. The discovery of genes for tubulin in a bacterial genus may offer new insights into the evolution of the cytoskeleton.

Significance: Nature is full of species that cooperate in mutually beneficial interactions to survive. Some are completely dependent on such relationships. How and why does this specialization evolve? We show that as the bacterium Desulfovibrio vulgaris evolved for 1,000 generations in conditions forcing cooperation with the archaeon Methanococcus maripaludis , it lost a key metabolic trait that would be required for it to grow alone in most environments. Large subpopulations lacking the capacity to respire sulfate evolved in 13 of 21 replicates. Such striking parallel evolution suggests a trade-off between performance in the mutualistic environment and maintaining the flexibility to survive alone. This result may explain why sulfate reducers share a common ancestor with many species specialized for cooperation with methanogens.

Microbial communities are complex and dynamic systems that are primarily structured according to their members’ ecological niches. To investigate how niche breadth (generalist versus specialist lifestyle strategies) relates to ecological success, we develop and apply an integrative workflow for the multi-omic analysis of oleaginous mixed microbial communities from a biological wastewater treatment plant. Time- and space-resolved coupled metabolomic and taxonomic analyses demonstrate that the community-wide lipid accumulation phenotype is associated with the dominance of the generalist bacterium Candidatus Microthrix spp. By integrating population-level genomic reconstructions (reflecting fundamental niches) with transcriptomic and proteomic data (realised niches), we identify finely tuned gene expression governing resource usage by Candidatus Microthrix parvicella over time. Moreover, our results indicate that the fluctuating environmental conditions constrain the accumulation of genetic variation in Candidatus Microthrix parvicella likely due to fitness trade-offs. Based on our observations, niche breadth has to be considered as an important factor for understanding the evolutionary processes governing (microbial) population sizes and structures in situ.