Vitamin interdependencies predicted by metagenomics-informed network analyses and validated in microbial community microcosms

Maize associated bacterial and fungal microbiomes show contrasting conformation patterns dependent on plant compartment and water availability

Plant-associated microorganisms can help crops to alleviate stress and increase the resilience of agricultural ecosystems to climate change. However, we still lack knowledge on the dynamics of soil and plant microbiomes and their response to changing conditions. This information is essential for the development of microbiome-based solutions to improve crop resilience to stressors associated with climate change. In this work, we explored: (i) the conformation of the bacterial and fungal assemblages of different soil and plant compartments (bulk soil, rhizosphere, roots, leaves and grains) along the crop cycle of maize in an open field trial; and (ii) the effect of water restriction on the maize microbiome, comparing optimal irrigation with a 30% reduction of water supply. Our results show a dynamic compartment-driven recruitment of microorganisms with contrasting patterns for bacteria and fungi that were intensified towards the end of the plant cycle. Roots showed the most differentiated bacterial assemblage while fungi conformed a very distinct community in the leaves, suggesting a relevant contribution of aerial fungal propagules to the microbiome of this plant organ. Regarding the grain, bacterial communities looked closer to those in the leaves, while fungal communities were more like those in the root. Despite the reductions in plant growth and yield, the microbiome of limited-watered plants did not show severe alterations. Still, significant impacts were observed within compartments, being fungi more responsive to limited watering than bacteria, with hallmark fungal ASVs for each compartment and irrigation regime. Network analysis suggests that bacteria and fungi may play different roles in the shifts observed under water limitation. Our study highlights the importance of conducting multikingdom analyses for a holistic understanding of the dynamics and evolution of the microbial assemblages in the whole plant and their roles in plant response to environmental stressors.

Influences of fluctuating nutrient loadings on nitrate-reducing microorganisms in rivers

Rivers serve important functions for human society and are significantly impacted by anthropogenic nutrient inputs (e.g. organic and sulfur compounds). Reduced organic and sulfur compounds influence the nitrogen cycle as they are electron donors of microbial nitrate reduction. Water pollution caused by individual nutrients and the mechanisms have been studied, but how the variation in multiple nutrient loadings influences nitrate-reducing microorganisms is less understood. Two sets of microcosms were established and exposed to nitrate, along with either acetate or thiosulfate, at different times. Nutrient concentrations responded to the loading pollutant. The nutrient loading order was more important in shaping microbial community structure and microbial interactions through the exchange of growth-required substances. This indicated that upstream or historical nutrient inflows impacted current nitrate reduction by changing the seeding microbial community, highlighting the importance of river connectivity. Based on metatranscriptome analysis, although the order and type of nutrient loadings were equally important in regulating global transcriptomes, transcripts of enzymes for key metabolisms (nitrate reduction, sulfur oxidation, etc.) more actively responded to the nutrient type. The regulation of a small set of genes was sufficient to make the transition, while most transcripts were not degraded and regenerated. These insights are important for understanding the varying pollution status of rivers and for developing effective solutions, such as remediation.

Impact of extreme rainfall and flood events on harmful cyanobacterial communities and ecological safety in the Baiyangdian Lake Basin, China

Globally, climate change has intensified extreme rainfall events, leading to substantial hydrological changes in aquatic ecosystems. These changes, in turn, have increased the frequency of harmful algal blooms, particularly those of cyanobacteria. This study examines cyanobacterial community dynamics in the Baiyangdian Lake Basin, China, after heavy rainfall and flooding events. The aim was to clarify how such extreme hydrological events affect cyanobacterial populations in floodplain ecosystems and assess related ecological risks. The results demonstrated a significant increase in cyanobacterial diversity, exemplified by an increase of the Shannon diversity index from an average of 1.72 to 2.1 (p < 0.05). Following heavy rainfall and subsequent flooding, the average relative abundance of cyanobacteria in the microbial community increased from 7.59 % to 9.62 %, along a notable rise in the abundance of harmful cyanobacteria. The community structure exhibited notable differences after flooding, showing an increase in species richness, but a decrease in community tightness and clustering, as well as a reduction in niche overlap among harmful cyanobacteria. Environmental factors such as dissolved oxygen, water temperature, and pH were identified as crucial predictors of harmful cyanobacterial community differences and abundance variations resulting from flooding. These findings provide a critical framework for predicting ecological risks associated with the expansion of bloom-forming cyanobacteria in large shallow lake basins, particularly under intensified rainfall and flooding events. This insight is essential to anticipate potential ecological disruptions in sensitive aquatic ecosystems.

Efficient carbon flux allocation towards D-pantothenic acid production via growth-decoupled strategy in Escherichia coli

For industrial strain construction, rational allocation of carbon flux is of paramount importance especially for decoupling cell growth and chemical productions to get maximum titer, rate, yield (TRY), which become Gordian Knot. Here, a temperature-sensitive switch and genetic circuits was used for effectively decoupling cell growth from D-pantothenic acid (DPA) production, along with systematically metabolic engineering including blocking redundant pathways of pyruvate and enhancing DPA driving force. Afterwards, rapid biomass accumulation only happened during growth stage, and subsequent high-efficient DPA production was initiated with reducing fermentation temperature. Finally, 97.20 g/L DPA and 0.64 g/g glucose conversion rate were achieved in 5-liter fed-batch fermentation. These undisputedly represent a milestone for the biosynthesis of DPA. With using strategies for decoupling cell growth from chemical productions, it would serve as "Alexander's sword" to cut Gordian Knot to get industrial chassis cells with excellent TRY for de novo biosynthesis of valuable chemicals.

Metabolic Regulation of Microbiota and Tissue Response

The microbiota in our gut regulates the sophisticated metabolic system that the human body has, essentially converting food into energy and the building blocks for various bodily functions. In this review, we discuss the multifaceted impact of the microbiota on host nutritional status by producing short-chain fatty acids, influencing gut hormones and mediating bile acid metabolism, and the key role in maintaining intestinal barrier integrity and immune homeostasis. Understanding and leveraging the power of the gut microbiome holds tremendous potential for enhancing human health and preventing various diseases.

Effect of rainfall in shaping microbial community during Microcystis bloom in Nakdong River, Korea

Various environmental factors play a role in the formation and collapse of Microcystis blooms. This study investigates the impact of heavy rainfall on cyanobacterial abundance, microbial community composition, and functional dynamics in the Nakdong River, South Korea, during typical and exceptionally rainy years. The results reveal distinct responses to rainfall variations, particularly in cyanobacterial dominance and physicochemical characteristics. In 2020, characterized by unprecedented rainfall from mid-July to August, Microcystis blooms were interrupted significantly, exhibiting lower cell densities and decreased water temperature, compared to normal bloom patterns in 2019. Moreover, microbial community composition varied, with increases in Gammaproteobacteria and notably in genera of Limnohabitans and Fluviicola. These alterations in environmental conditions and bacterial community were similar to those of the post-bloom period in late September 2019. It shows that heavy rainfall during summer leads to changes in environmental factors, consequently causing shifts in bacterial communities akin to those observed during the autumn-specific post-bloom period in typical years. These changes also accompany shifts in bacterial functions, primarily involved in the degradation of organic matter such as amino acids, fatty acids, and terpenoids, which are assumed to have been released due to the significant collapse of cyanobacteria. Our results demonstrate that heavy rainfall in early summer induces changes in the environmental factors and subsequently microbial communities and their functions, similar to those of the post-bloom period in autumn, leading to the earlier breakdown of Microcystis blooms.

Functional fractions of Astragalus polysaccharides as a potential prebiotic to alleviate ulcerative colitis

Ulcerative colitis (UC) is a chronic inflammatory disease of the intestine that is significantly influenced by an imbalance in the gut microbiota. Astragalus membranaceus, particularly its polysaccharide components, has shown therapeutic potential for the treatment of UC, although the specific active constituents and their mechanistic pathways remain to be fully elucidated. In this study, we investigated two molecular weight fractions of Astragalus polysaccharides (APS), APS1 (Mw < 10 kDa) and APS2 (10 kDa < Mw < 50 kDa), isolated by ultrafiltration, focusing on their prebiotic effects, effects on UC, and the underlying mechanism. Our results showed that both APS1 and APS2 exhibit prebiotic properties, with APS1 significantly outperforming APS2 in ameliorating UC symptoms. APS1 significantly attenuated weight loss and UC manifestations, reduced colonic pathology, and improved intestinal mucosal barrier integrity. In addition, APS1 significantly reduced the levels of inflammatory cytokines in the serum and colonic tissue, and downregulated colonic chemokines. Furthermore, APS1 ameliorated dextran sulfate sodium salt (DSS)-induced intestinal dysbiosis by promoting the growth of beneficial microbes and inhibiting the proliferation of potential pathogens, leading to a significant increase in short-chain fatty acids. In conclusion, this study highlights the potential of APS1 as a novel prebiotic for the prevention and treatment of UC.

Genome-scale community modelling reveals conserved metabolic cross-feedings in epipelagic bacterioplankton communities

Marine microorganisms form complex communities of interacting organisms that influence central ecosystem functions in the ocean such as primary production and nutrient cycling. Identifying the mechanisms controlling their assembly and activities is a major challenge in microbial ecology. Here, we integrated Tara Oceans meta-omics data to predict genome-scale community interactions within prokaryotic assemblages in the euphotic ocean. A global genome-resolved co-activity network revealed a significant number of inter-lineage associations across diverse phylogenetic distances. Identified co-active communities include species displaying smaller genomes but encoding a higher potential for quorum sensing, biofilm formation, and secondary metabolism. Community metabolic modelling reveals a higher potential for interaction within co-active communities and points towards conserved metabolic cross-feedings, in particular of specific amino acids and group B vitamins. Our integrated ecological and metabolic modelling approach suggests that genome streamlining and metabolic auxotrophies may act as joint mechanisms shaping bacterioplankton community assembly in the global ocean surface.

Bacterial growth and environmental adaptation via thiamine biosynthesis and thiamine-mediated metabolic interactions

Understanding the ancestral transition from anaerobic to aerobic lifestyles is essential for comprehending life's early evolution. However, the biological adaptations occurring during this crucial transition remain largely unexplored. Thiamine is an important cofactor involved in central carbon metabolism and aerobic respiration. Here, we explored the phylogenetic and global distribution of thiamine-auxotrophic and thiamine-prototrophic bacteria based on the thiamine biosynthetic pathway in 154 838 bacterial genomes. We observed strong coincidences of the origin of thiamine-synthetic bacteria with the "Great Oxygenation Event," indicating that thiamine biosynthesis in bacteria emerged as an adaptation to aerobic respiration. Furthermore, we demonstrated that thiamine-mediated metabolic interactions are fundamental factors influencing the assembly and diversity of bacterial communities by a global survey across 4245 soil samples. Through our newly established stable isotope probing-metabolic modeling method, we uncovered the active utilization of thiamine-mediated metabolic interactions by bacterial communities in response to changing environments, thus revealing an environmental adaptation strategy employed by bacteria at the community level. Our study demonstrates the widespread thiamine-mediated metabolic interactions in bacterial communities and their crucial roles in setting the stage for an evolutionary transition from anaerobic to aerobic lifestyles and subsequent environmental adaptation. These findings provide new insights into early bacterial evolution and their subsequent growth and adaptations to environments.

Metabolic exchanges are ubiquitous in natural microbial communities

Microbial communities drive global biogeochemical cycles and shape the health of plants and animals-including humans. Their structure and function are determined by ecological and environmental interactions that govern the assembly, stability and evolution of microbial communities. A widely held view is that antagonistic interactions such as competition predominate in microbial communities and are ecologically more important than synergistic interactions-for example, mutualism or commensalism. Over the past decade, however, a more nuanced picture has emerged, wherein bacteria, archaea and fungi exist within interactive networks in which they exchange essential and non-essential metabolites. These metabolic interactions profoundly impact not only the physiology, ecology and evolution of the strains involved, but are also central to the functioning of many, if not all, microbiomes. Therefore, we advocate for a balanced view of microbiome ecology that encompasses both synergistic and antagonistic interactions as key forces driving the structure and dynamics within microbial communities.