Project description:Metagenome data from soil samples were collected at 0 to 10cm deep from 2 avocado orchards in Channybearup, Western Australia, in 2024. Amplicon sequence variant (ASV) tables were constructed based on the DADA2 pipeline with default parameters.
Project description:Lotus japonicus is a model legume broadly used to study transcriptome regulation under different stress conditions and microorganism interaction. Understanding how this model plant respond gainst alkaline stress will certainly help to develop more tolerant cultivars in economically important Lotus species as well as in other legumes. In order to uncover the most important response mechanisms activated during alkaline stress, we explored by microarray analysis the transcriptome regulation occurring in the phenotypically contrasting ecotypes MG-20 and Gifu B-129 of L. japonicus after 21 days of alkaline stress.
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:To investigate the rapid adaptation mechanism of Bacillus thuringiensis in an alkaline environment, we have employed whole genome microarray expression profiling as a discovery platform to identify the difference of gene expression between normal condition and alkaline condition.
Project description:Cyanobacteria are able to grow at a wide pH range and for many strains their growth is enhanced in alkaline environment. In this study, we investigated the proteomic response of the cyanobacterium of Synechocystis sp. PCC 6803 to alkaline pH. The proteomes of Synechocystis grown in BG-11 medium buffered at pH 7.5, pH 8.2 and pH 9.2 were analysed by a mass spectrometry-based (LC-MS/MS) data-dependent acquisition (DDA) method. Total proteins (membrane and soluble) from unfractionated Synechocystis cell lysates were investigated.