Project description:Microbial enzymes alter marine biogeochemical cycles by catalyzing chemical transformations that bring elements into and out of particulate organic pools. These processes are traditionally studied through enzyme rate-based estimates and nutrient-amendment bioassays, but these approaches lack the ability to resolve species-level contributions to enzymatic rates. Molecular methods including proteomics have the potential to link the contributions of specific populations to the overall community enzymatic rate; this is important because organisms will have distinct enzyme characteristics, feedbacks, and responses to perturbations. Integrating molecular methods with rate measurements can be achieved quantitatively through absolute quantitative proteomics. Here, we use the subtropical North Atlantic as a model system to probe how absolute quantitative proteomics can provide a more comprehensive understanding of nutrient limitation in marine environments. The experimental system is characterized by phosphorus stress and potential metal-phosphorus co-limitation due to dependence of the organic phosphorus scavenging enzyme alkaline phosphatase on metal cofactors; we performed nutrient amendment incubation experiments to investigate how alkaline phosphatase abundance and activity is affected by trace metal additions. We show that the two most abundant picocyanobacteria, Prochlorocccus and Synechococcus are minor contributors to total alkaline phosphatase activity as assessed by a widely used enzyme assay. This was true even when trace metals were added, despite both species having the genetic potential to utilize both the Fe and Zn containing enzymes, PhoX and PhoA respectively. Serendipitously, we also found that the alkaline phosphatases responded to cobalt additions suggesting possible substitution of the metal center by Co in natural populations of Prochloroccocus (substitution for Fe in PhoX) and Synechococcus (substitution for Zn in PhoA). This integrated approach allows for a nuanced interpretation of how nutrient limitation affects marine biogeochemical cycles and highlights the benefit of building quantitative connections between rate and “-omics” based measurements.

Project description:Anthropogenic nutrient inputs alter soil biodiversity; however, it remains largely unknown whether changes in soil microeukaryotes (fungi and protists) are primarily driven by direct effects, such as modifications in soil properties, or by indirect effects, such as plant diversity loss. To disentangle these mechanisms, we investigated the long-term effects (11 years) of fertilization and manipulated plant diversity (1, 2, or 4 plant species) on soil microeukaryote communities in a temperate grassland experiment using long-amplicon rRNA sequencing. Our results indicate that fertilization generally had a stronger influence on microeukaryote communities than plant species richness. Fertilization altered the community composition of fungi and protists, increased OTU richness by 20.8% and 52.7%, respectively, and shifted community dominance from fungi to protists. Regarding plant diversity, we observed an effect exclusively on the protist community. Changes were primarily explained by increased plant biomass (driven by both fertilization and plant diversity) and by higher soil phosphorus and lower soil pH levels (driven exclusively by fertilization). Regarding life strategies, we observed synergistic treatment effects: fertilization primarily enhanced fungal saprophytes (only richness), fungal animal pathogens, and protist consumers, whereas plant diversity affected phototrophic protists (reduction) and protist animal pathogens (enhancement). Notably, fertilization and plant diversity decline together led to a cumulative increase in fungal plant pathogens. In conclusion, we highlight that fertilisation alone has a significant effect on soil microeukaryotes, while the additional decline in plant diversity affects different soil groups that are not directly affected by fertilisation. This synergistic pattern indicates that fertilization can influence the entire microeukaryote community through direct and indirect mechanisms, with a cumulative enhancement on certain groups, such as plant pathogens.

Project description:<p>Carbonate-type saline-alkaline stress severely constrains maize production; however, the synergistic response mechanisms between rhizosphere microorganisms and metabolites remain unclear. This study focused on maize fields in the carbonate chernozem region of the Songnen Plain in Northeast China. Through field experiments and the integration of soil chemical factor analysis, microbial high-throughput sequencing (16S rRNA and ITS), and non-targeted metabolomics (LC-MS), we systematically investigated the response mechanisms of the rhizosphere micro-ecosystem under saline-alkaline stress. The results indicated that saline-alkaline stress significantly increased soil pH and electrical conductivity (EC), and led to decreases in soil organic matter (SOM), total nitrogen (TN), and total phosphorus (TP) contents. However, the rhizosphere zone exhibited a certain buffering capacity, maintaining a higher cation exchange capacity (CEC). Microbial community analysis revealed that bacterial alpha diversity increased under stress. In contrast, fungal diversity significantly decreased, and the community structure shifted towards a pathogen-dominated community, primarily within Ascomycota, especially the genus Fusarium. Co-occurrence network analysis further revealed that saline-alkaline conditions enhanced the complexity and connectivity of bacterial networks but led to the contraction and structural simplification of fungal networks. Metabolite analysis showed that saline-alkaline stress induced significant reprogramming of the rhizosphere metabolic profile. Organophosphorus compounds, nucleotides, and their analogs were significantly enriched, while defensive secondary metabolites such as Cajanol specifically accumulated in the saline-alkaline rhizosphere. Pathway analysis indicated the activation of stress resistance and oxidative stress mitigation-related pathways, including Betalain biosynthesis, flavonoid biosynthesis, tryptophan metabolism, and arginine metabolism. Multi-omics integration analysis identified soil EC and total potassium (TK) as key environmental factors driving the differentiation of microbial and metabolite communities. Key differential metabolites showed significant positive correlations with saline-alkaline-enriched microbial taxa (e.g., Sphingomonas), revealing a metabolite-mediated microbial recruitment mechanism. This study, through multi-omics analysis, discovered that the maize rhizosphere, under saline-alkaline stress, undergoes metabolic reprogramming (e.g., enriching defensive metabolites like Cajanol) to directionally recruit beneficial bacteria such as Sphingomonas and maintains higher bacterial network complexity, while also leading to the pathologization of the fungal community. Our study reveals that maize recruits beneficial microbes via rhizosphere metabolic reprogramming, providing a mechanistic basis for microbiome-assisted saline-alkaline soil remediation.</p>

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