A transcriptomics approach to compare transcriptomes of individual methylotrophs from Lake Washington sediment in artificial communities and in pure cultures.

We established simple synthetic microbial communities in a microcosm model system to determine the mechanisms that underlay cross-feeding in microbial methane-consuming communities. Co-occurring strains from Lake Washington sediment were used that are involved in methane consumption, a methanotroph and two non-methanotrophic methylotrophs. Overall design: RNAseq profiles of methanotrophs and non-methanotrophic methylotrophs in pure culture and in two species mixtures. Duplicate samples (total N = 10) were submitted for transcriptomics analysis to GENEWIZ (Seattle, USA). 1 x 50 bp were sequenced in single-read configuration in Rapid Run mode on a HiSeq 2500 System.

本研究通过微宇宙模型系统构建了简单的合成微生物群落，旨在解析甲烷降解微生物群落中交叉营养互养（cross-feeding）的潜在机制。实验所用菌株分离自华盛顿湖沉积物，均参与甲烷代谢过程，包含1株甲烷氧化菌（methanotroph）与2株非甲烷氧化型甲基营养菌（non-methanotrophic methylotroph）。
实验设计：对纯培养及双菌株混合培养体系中的甲烷氧化菌与非甲烷氧化型甲基营养菌进行RNA-seq转录组分析。设置生物学重复样本（总样本量N=10），将其提交至美国西雅图的GENEWIZ公司开展转录组学检测。测序采用HiSeq 2500测序系统，以快速运行模式（Rapid Run mode）进行单端测序，读取长度为1×50 bp。