Contrasting response of rice rhizosphere microbiomes to in situ cadmium-contaminated soil remediation

Changes in soil properties and microbial communities regulated rhizosphere protistan assemblages. • Bacterial community was more sensitive to soil amendments than protists and fungi. • Soil amendments trigger the role of specific protistan taxa Cercozoa on microbial interactions. Understanding the responses of different rhizosphere microbial lineages to soil amendments during in situ remediation of Cd-contaminated soil is of great importance in the assessment of the restoration and crop health. Here, we evaluated the effects of lime (LM), biochar (BC), pig manure (PM), and a commercial Mg-Ca-Si conditioner (CMC) on the rice rhizosphere soil physicochemical properties and community assembly of bacteria, fungi, and protists in a six-year consecutive application of soil amendments field trial. Our results indicated that among the four amendments, the BC and CMC had the best efficiency in increasing soil pH, which were 5.2% and 16.2%, respectively. Despite the differences in soil Cd concentrations is not noticeable, all the soil amendment treatments significantly decreased the proportion of available Cd in total Cd compared to the control. Soil amendments significantly altered the diversity of bacterial community, while they had no effect on fungal and protistan communities. Linear discriminant analysis effect size (LEfSe) showed that the bacteria was more sensitive to soil amendment-induced changes. For protists, treatments with LM and BC changed the groups of protistan consumers, while treatments with PM and CMC significantly increased the relative abundances of protistan phototrophs. Co-occurrence network analysis revealed that soil amendments increased microbial network complexity and triggered the role of protists, especially for the predatory protists Cercozoa, on microbial trophic interactions. Further variation partitioning analysis revealed that edaphic properties, bacterial and fungal communities compositions together explained the 77% of the total variation in protistan community, and the stronger correlations between diversity of bacterial and protistan communities suggested that the bacteria community was a more important biotic driver of the protistan community. Overall, our findings demonstrate the distinct responses of rice rhizosphere microbial communities to soil amendment applications, highlighting the interactive associations between microbiomes, which is vital for enhancing our ability to develop effective strategies for sustainable soil management. This study enhances our understanding of the ecological roles of protists under soil amendment applications and highlights their potential contributions in bioremediation and environmental applications for Cd-contaminated soil.

红球菌低分子量型腈水合酶的异源激活及激活子的结构域功能

腈水合酶激活子具有亚基自身交换伴随子或者金属离子伴随子的功能,能够辅助腈水合酶摄取金属离子,对于腈水合酶的活性表达必不可少。与腈水合酶自身相比,激活子的序列保守性低,研究其激活作用的特点,探索其结构与功能之间的关系,对于理解腈水合酶的成熟机制具有重要意义。将红球菌Rhodococcus rhodochrous J1低分子量型腈水合酶L-NHase分别与4种异源激活子组合共表达,测定异源激活子对L-NHase的激活作用,进一步对激活子进行序列分析和结构模拟,并研究关键结构域的功能。结果表明,4种异源激活子均能激活L-NHase,但激活后L-NHase的比酶活存在差异,激活子A对L-NHase的激活程度最高,激活后的L-NHase比酶活为出发酶的97.79%;激活子G对L-NHase的激活程度最低,激活后的L-NHase比酶活为出发酶的23.94%。激活子E和激活子G具有保守结构域TIGR03889,缺失其中部分序列会使两者的激活作用基本丧失。将激活子G的N端序列替换为激活子E的N端序列,并将激活子E的C端序列添加至激活子G的C端,能够使L-NHase的比酶活提高178.40%。激活子的激活作用具有普遍性和特异性,其保守结构域对激活作用至关重要,同时N端结构域和C端结构域也对激活作用产生重要影响。

Characterization of Lysine Monomethylome and Methyltransferase in Model Cyanobacterium Synechocystis sp.PCC 6803

Protein lysine methylation is a prevalent post-translational modification(PTM)and plays critical roles in all domains of life.However,its extent and function in photosynthetic organisms are still largely unknown.Cyanobacteria are a large group of prokaryotes that carry out oxygenic photosynthesis and are applied extensively in studies of photosynthetic mechanisms and environmental adaptation.Here we integrated propionylation of monomethylated proteins,enrichment of the modified peptides,and mass spectrometry(MS)analysis to identify monomethylated proteins in Synechocystis sp.PCC 6803(Synechocystis).Overall,we identified 376 monomethylation sites in270 proteins,with numerous monomethylated proteins participating in photosynthesis and carbon metabolism.We subsequently demonstrated that Cpc M,a previously identified asparagine methyltransferase in Synechocystis,could catalyze lysine monomethylation of the potential aspartate aminotransferase Sll0480 both in vivo and in vitro and regulate the enzyme activity of Sll0480.The loss of Cpc M led to decreases in the maximum quantum yield in primary photosystemⅡ(PSⅡ)and the efficiency of energy transfer during the photosynthetic reaction in Synechocystis.We report the first lysine monomethylome in a photosynthetic organism and present a critical database for functional analyses of monomethylation in cyanobacteria.The large number of monomethylated proteins and the identification of Cpc M as the lysine methyltransferase in cyanobacteria suggest that reversible methylation may influence the metabolic process and photosynthesis in both cyanobacteria and plants.

Global Profiling of the Lysine Crotonylome in Different Pluripotent States

Pluripotent stem cells(PSCs)can be expanded in vitro in different culture conditions,resulting in a spectrum of cell states with distinct properties.Understanding how PSCs transition from one state to another,ultimately leading to lineage-specific differentiation,is important for developmental biology and regenerative medicine.Although there is significant information regarding gene expression changes controlling these transitions,less is known about post-translational modifications of proteins.Protein crotonylation is a newly discovered post-translational modification where lysine residues are modified with a crotonyl group.Here,we employed affinity purification of crotonylated(LC–MS/MS)to systematically profile protein crotonylation in mouse PSCs in different states including ground,metastable,and primed states,as well as metastable PSCs undergoing early pluripotency exit.We successfully identified 3628 high-confidence crotonylated sites in 1426 proteins.These crotonylated proteins are enriched for factors involved in functions/processes related to pluripotency such as RNA biogenesis,central carbon metabolism,and proteasome function.Moreover,we found that increasing the cellular levels of crotonyl-coenzyme A(crotonyl-CoA)through crotonic acid treatment promotes proteasome activity in metastable PSCs and delays their differentiation,consistent with previous observations showing that enhanced proteasome activity helps to sustain pluripotency.Our atlas of protein crotonylation will be valuable for further studies of pluripotency regulation and may also provide insights into the role of metabolism in other cell fate transitions.