Taxonomic and Functional Diversity Provides Insight into Microbial Pathways and Stress Responses in the Saline Qinghai Lake, China

Abstract

Microbe-mediated biogeochemical cycles contribute to the global climate system and have sensitive responses and feedbacks to environmental stress caused by climate change. Yet, little is known about the effects of microbial biodiversity (i.e., taxonmic and functional diversity) on biogeochemical cycles in ecosytems that are highly sensitive to climate change. One such sensitive ecosystem is Qinghai Lake, a high-elevation (3196 m) saline (1.4%) lake located on the Tibetan Plateau, China. This study provides baseline information on the microbial taxonomic and functional diversity as well as the associated stress response genes. Illumina metagenomic and metatranscriptomic datasets were generated from lake water samples collected at two sites (B and E). Autotrophic Cyanobacteria dominated the DNA samples, while heterotrophic Proteobacteria dominated the RNA samples at both sites. Photoheterotrophic Loktanella was also present at both sites. Photosystem II was the most active pathway at site B; while, oxidative phosphorylation was most active at site E. Organisms that expressed photosystem II or oxidative phosphorylation also expressed genes involved in photoprotection and oxidative stress, respectively. Assimilatory pathways associated with the nitrogen cycle were dominant at both sites. Results also indicate a positive relationship between functional diversity and the number of stress response genes. This study provides insight into the stress resilience of microbial metabolic pathways supported by greater taxonomic diversity, which may affect the microbial community response to climate change.

Bacterial community structure and function shift along a successional series of tidal flats in the Yellow River Delta

“…In addition, microbial community function has physiological plasticity to quickly respond to environmental changes and has the potential to acquire new genes through recombination91019. That is, stress resilience of microbial functional profiles supported by greater phylogenetic diversity51. PICRUSt cannot replace whole metagenome profiling and could be problematic when analyzing microbial communities with a large proportion of poorly characterized members.…”

Microbial functional diversity: From concepts to applications

“…This approach has been mostly reduced to the total abundance of genes, estimated as the number of sequences in the community (Burke et al, 2011;Souza et al, 2015), the signal intensity on a functional gene array (Bai et al, 2013;Bayer et al, 2014), or quantification using qPCR (Philippot et al, 2013;Powell, Welsh, Hallin, & Allison, 2015). A finer characterization of gene variants diversity is possible by considering their richness (Huang et al, 2014) or evenness (Powell et al, 2015) instead of their sheer abundance. For instance, denitrification rates were more strongly linked to the evenness of nir genes variants abundance distribution than to their richness or the total number of nir gene copies (Powell et al, 2015).…”

The transcriptional response of microbial communities in thawing Alaskan permafrost soils

“…Here, we performed a pilot study using ultrahigh throughput Illumina HiSeq sequencing of reverse transcribed mRNA (e.g., Orsi et al, 2013 ; Huang et al, 2014 ) to obtain a detailed overview of active metabolic pathways and responsible organisms in permafrost soils under pristine frozen conditions and transcriptional responses after 11 days of thaw. The permafrost soil horizons analyzed (up to 70-cm-deep) are expected to thaw in the Alaskan Arctic within decades as a result of continuing Arctic warming (Osterkamp, 2007 ).…”