Environmental microbiology最新文献

Developing N₂-fixing partnerships between diazotrophs and non-legumes can enhance soil fertility and reduce dependence on synthetic fertilisers. Unlike legumes, non-legumes lack the genetic ability to form root nodule symbiosis with rhizobia but can form facultative associations with free-living diazotrophs. Engineering these microbes by transferring key traits underlying efficient nodule formation and N₂-fixation from well-characterised rhizobia represents a central aim in synthetic biology to enhance biological nitrogen fixation in non-legumes. However, the lack of effective tools for identifying compatible and engineerable microbial partners is a key challenge. To address this, we have developed nodulation (nod) gene reporters to screen both rhizobia and non-rhizobia capable of expressing Sinorhizobium meliloti nod genes, which encode bacterial signals initiating nodule formation in legumes. The biosensors include a superfolder GFP reporter controlled by the inducible nod box promoter (PnodA), plant signal-dependent activators nodD1 and nodD2, and a constitutively mScarlet-I marker, named nodD1-PnodA and nodD2-PnodA. Their functionality was validated across diverse rhizobia and non-rhizobia using in vitro and in planta induction assays. This reporter system enables high-throughput identification of novel bacteria capable of recognising and responding to legume signalling molecules that coordinate symbiotic nitrogen fixation.

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 CO₂-rich, cold-water Geyser Andernach (Germany), using ultra-high-resolution mass spectrometry. We detected iGDGT-0, presumably derived from the dominant community member Candidatus Altiarchaeum, providing supporting evidence for its ability to synthesise tetraethers, as previously predicted from metagenomic data. Beyond the typical iGDGT-0 and acyclic glycerol trialkyl glycerol tetraether (iGTGT-0), we discovered novel structural derivatives, here referred to as extended iGDGTs and iGTGTs, characterised by the asymmetrical addition of up to two isoprenoid units to only one of their hydrocarbon side chains, analogous to those found in extended archaeols. The apparent absence of GDGT ring synthase A and B genes in the corresponding metagenome-assembled genome raises the possibility that the producing archaea may utilise extended iGDGTs as a membrane adaptation to cope with the nutrient-depleted conditions of the geyser environment, highlighting the adaptive flexibility of archaea to extreme physicochemical conditions.

The process of bacterial adaptation has a profound impact on human wellbeing and health, but our toolkit to modify evolution is limited. Here, we present a concept of how steering adaptation can be achieved by integration of bacterial evolution and microbial ecology. The fundamental question is how specific species bloom after community perturbation and subsequently evolve. We consider two kinds of traits-α-niche traits involved in partitioning resources (e.g., broadened resource consumption) and β-niche traits driven by changes in the abiotic environment (e.g., pH adaptation or resistance after antibiotic treatment). We suggest that the evolution of the second trait can be directed indirectly via the evolution of the first trait, exploiting specific interspecies interactions. Thus, understanding how these traits interact in co-evolving communities may offer unprecedented opportunities to deflect trait evolution. Summarising current knowledge, emphasising open questions and highlighting conceptual ideas, we hope to stimulate new studies that are needed to move this field forward.