Time‐series metatranscriptomes reveal conserved patterns between phototrophic and heterotrophic microbes in diverse freshwater systems

Abstract

Microbial communities form the base of food webs in freshwater ecosystems, yet the interactions within these diverse assemblages are poorly understood. Based on evidence showing that primary production and respiration follow diurnal trends in lakes, we hypothesized that gene expression in freshwater microbes would have similar diel cycles. We used three 2‐d time series of metatranscriptomes to test this hypothesis in a eutrophic lake, an oligotrophic lake, and a humic lake. We identified prominent diel cycles in all three lakes, particularly in genes related to photosynthesis, sugar transport, and carbon fixation. The maximal time of expression for sugar transport genes tended to trail that of photosynthesis genes by several hours, indicating possible metabolic exchange between co‐occurring microbial lineages. These results provide an initial step in understanding sophisticated multispecies transcriptional organization within freshwater microbial communities.

Insights into the cyanosphere: capturing the respective metabolisms of cyanobacteria and chemotrophic bacteria in natural conditions?

“…This suggests that the dominant phyla might also be the most active ones. Consistency between mRNA, proteins and DNA-based diversities has also been observed for diverse ecosystems (Jiang et al, 2016;Russo et al, 2016;Linz et al, 2020), which confirms that short-read (100 bp here) data could be used to detect taxonomic information of mRNA. Nevertheless, some discrepancies were observed.…”

“…Besides the well‐known biases induced by the sampling strategy (e.g. during the collection and filtration of samples), and the short‐lives of mRNA (see Pascault et al ., 2015 for review; Steiner et al ., 2019), this issue of the lack of reference genomes in databases for environmental bacteria is one of the main limits when performing metatranscriptomic and metaproteomic analysis (Grossart et al ., 2020; Linz et al ., 2020). Thus, technological advances are still needed such as single‐cell omics, full‐genome reconstruction, and cultivated‐based approaches (Singer et al ., 2017; Rodriguez‐R et al ., 2020).…”

Metatranscriptomics From a Small Aquatic System: Microeukaryotic Community Functions Through the Diurnal Cycle

“…Additionally, chloroplasts were among the most abundant GO terms shared between day and night. A high abundance of chloroplast and photosynthesisrelated genes has been also reported in previous summer metatranscriptomic studies, with a higher expression around midday (Ji et al, 2018;Linz et al, 2019). Altogether, this shows the daily rhythmicity of photosynthetic organisms and suggests that, according to what we hypothesized, phototrophic microeukaryotes were more responsive to the day/night cycle than the heterotrophic microeukaryotes in the pond.…”

“…Photosynthesis and transporters-related transcripts, as well as transcripts involved in energy production and stress mechanisms, were preferentially expressed during the day. Whereas, carbon fixation, carbohydrates and amino acid synthesis, and cell division are processes that mainly occur during the night (Poretsky et al, 2009a;Vila-Costa et al, 2013;Aylward et al, 2015;Linz et al, 2019). Yet, most of these studies were done with communities from the open oceans and large lakes, while smaller aquatic ecosystems were so far overlooked.…”

Virus-associated organosulfur metabolism in human and environmental systems

“…Protein Reactions Enzymatic reactions, diagrams and pathways were created by referencing KEGG and MetaCyc (v22.6) (Caspi et al, 2012) annotations. Viral transcriptomics and growth rates Publicly available metatranscriptomic data from Lake Mendota, WI was assessed for AMGs by querying annotation names (Linz et al, 2020). This gene expression data comprises a two-day time series and is accompanied by metagenomic assemblies (IMG Taxon Object IDs 3300013004 and 3300013005).…”