The growing research into the archaeal lipidome has uncovered a remarkable structural diversity in isoprenoidal glycerol dialkyl glycerol tetraethers (iGDGTs) and revealed complex membrane adaptations, especially in extreme environments. We performed a comprehensive analysis of the lipidome from the subsurface aquifer of the CO 2 ‐rich, cold‐water Geyser Andernach (Germany), using ultra‐high‐resolution mass spectrometry. We de...

There is growing evidence that morphological change is a widespread response to the warming climate. The empirical basis for understanding this process has, to date, largely been correlative analyses of morphological time series. However, it is not clear what constitutes sufficient temporal sampling for assessing long-term morphological change. We analyzed two long-term high-quality morphological datasets, one including 33 spe...

Metagenomics has become a standard technique for studying natural microbial communities, yet it cannot directly reveal microbial activity. Recent advances show that combining metagenomics with metaproteomics enables the identification of active community processes. Here, we highlight how metaproteomics can uncover key and keystone organisms, as well as provide constraints for predicting the lifestyles of both microbes and viru...

The rapid evolution of microbiology as a field of research has led to the introduction of new terminology and the adaptation of existing terms. However, inconsistencies in the use of these terms, including variations across different scientific disciplines, can lead to confusion and miscommunication within the scientific community. This article discusses the importance of precise terminology in microbiome research, highlightin...

The primary aim of the present study was to reveal the major differences between benzene-degrading bacterial communities evolve under aerobic versus microaerobic conditions and to reveal the diversity of those bacteria, which can relatively quickly degrade benzene even under microaerobic conditions. For this, parallel aerobic and microaerobic microcosms were set up by using groundwater sediment of a BTEX-contaminated site and...

Understanding intricate microbial interactions in the environment is crucial. This is especially true for the relationships between nutrients and bacteria, as phosphorus, nitrogen and organic carbon availability are known to influence bacterial population dynamics. It has been suggested that low nutrient conditions prompt the evolutionary process of genome streamlining. This process helps conserve scarce nutrients and allows f...

Resolving bacterial and archaeal genomes from metagenomes has revolutionized our understanding of Earth's biomes yet producing high‐quality genomes from assembled fragments has been an ever‐standing problem. While automated binning software and their combination produce prokaryotic bins in high throughput, their manual refinement has been slow, sometimes difficult or missing entirely facilitating error propagation in public da...

Diclofenac, ibuprofen, and carbamazepine are three of the most widely detected and most concerning pharmaceutical residues in aquatic ecosystems. The aim of this study was to identify bacteria that may be involved in their degradation from a bacterial biofilm. Selective enrichment cultures in mineral salt solution containing pharmaceutical compounds as sole source of carbon and energy were set up, and population dynamics were...

Symbiont relationships between corals and photosynthetic microorganisms sustain coral reef existence. However, the Great Amazon Reef System (GARS) stays under a plume layer that attenuates the entry of light, and instead of corals, sponges are the major reef epifauna, for which little is known about the function of the associated microbiome. Here, we used genome-resolved metagenomics to investigate how the sponge microbiome su...

Ants, an ecologically successful and numerically dominant group of animals, play key ecological roles as soil engineers, predators, nutrient recyclers, and regulators of plant growth and reproduction in most terrestrial ecosystems. Further, ants are widely used as bioindicators of the ecological impact of land use. We gathered information of ant species in the Atlantic Forest of South America. The ATLANTIC ANTS data set, which...

Aquaponic systems are sustainable solutions for food production combining fish growth ( aqua culture) and production of vegetables (hydro ponic ) in one recirculating system. In aquaponics, nitrogen-enriched wastewater from fish in the aquaculture serves as fertilizer for the plants in the hydroponics, while the nitrogen-depleted and detoxified water flows back to the aquaculture. To investigate bacterial nitrogen-cycling in s...

The aim of the present study was to reveal how different microbial communities evolve in diesel fuel/crude oil-contaminated environments under aerobic and microaerobic conditions. To investigate this question, aerobic and microaerobic bacterial enrichments amended with a diesel fuel/crude oil mixture were established and analysed. The representative aerobic enrichment community was dominated by Gammaproteobacteria (64.5%) with...

Summary Subsurface ecosystems like groundwater harbour diverse microbial communities, including small‐sized, putatively symbiotic organisms of the Candidate Phyla Radiation, yet little is known about their ecological preferences and potential microbial partners. Here, we investigated a member of the superphylum Microgenomates ( Cand . Roizmanbacterium ADI133) from oligotrophic groundwater using mini‐metagenomics and monitored...

Summary As in many deep underground environments, the microbial communities in subsurface high‐CO 2 ecosystems remain relatively unexplored. Recent investigations based on single‐gene assays revealed a remarkable variety of organisms from little studied phyla in Crystal Geyser (Utah, USA), a site where deeply sourced CO 2 ‐saturated fluids are erupted at the surface. To provide genomic resolution of the metabolisms of these or...