Eco-system dynamics in the Arctic

How moss host genetics shape their microbiomes and function

After completing my PhD, I joined Dr. Stuart McDaniel’s group at the University of Florida as a postdoc. The goal of my postdoctoral project was to study rapidly changing Arctic ecosystems, focusing particularly on mosses, their microbiomes, and function. Why are mosses important in this context? Please read on to find out more…

Perks of the job: getting to visit these beautiful sites in Alaska was certainly a perk of my postdoc. On the left, a lake close to one of our sampling sites in Fairbanks, AK. Middle, Toolik Field Station in the distance. Toolik Field Station is a place where researchers from across the world gather to conduct field experiments and collect data in the Arctic Alaska. On the right, Arctic's beauty comes with its own set of challenges - swarms of mosquitoes surround us as we survey the field site.

Overview

My postdoctoral work was focused on investigating the roles of mosses (bryophytes) and their associated microbes in nitrogen (N) cycling within arctic tundra and boreal forest ecosystems. The Arctic is warming up twice as fast as rest of the world, therefore, to understand how ecosystems will respond to climate change, Arctic is a good place to start.

Mosses are an important component of these ecosystems because they account for approximately half of the net primary productivity of these regions and drive soil organic layer C accumulation. Additionally, moss-associated microbes are the primary source of biologically fixed N inputs in these nitrogen-limited environments.

Our long-term goal was to understand the ecosystem-scale consequences of climate change on community assembly and function and how this impacts biodiversity. We focused on how moss population genetics and species diversity shape the assembly and function of the moss microbiome, particularly the N-fixing microbiomes of feather mosses Hylocomium splendens and Pleurozium schreberi.

Additionally, we studied the evolutionary history of the genus Aulacomnium, an under-studied, yet an important contributor to the function of these ecosystems. Aulacomnium was selected as a study system owing to some key findings from our group’s previous work. We had observed that closely related species within this genus support distinct microbiome communities. This characteristic makes Aulacomnium a valuable model for identifying specific genetic variants that influence microbiome assembly, particularly in the context of gene flow between species.

Evolutionary history of the genus, Aulacomnium

This research project focused on the species within the Aulacomnium genus. Using ddRADseq and target capture sequencing data, we investigated the phylogenetic and population genetic relationships within this ecologically significant group of bryophytes in the Arctic. Specifically, we investigated three closely related species: Aulacomnium palustre, A. turgidum, and A. acuminatum. A. palustre exhibits a broad distribution, ranging from temperate forests to arctic tundra, while A. turgidum and A. acuminatum are sympatric with A. palustre in sub-arctic and arctic zones.

Our primary objectives regarding Aulacomnium were:

  • To test the hypothesis that A. acuminatum is a hybrid species resulting from the hybridization of A. palustre and _A. turgidum
  • To determine whether there is ongoing gene flow among these species in sympatric populations.
Another one of our moss collection sites near Toolik, overlooking the Brooks Range. In the distance, the treacherous Dalton highway snakes alongside the Trans-Alaska pipeline, cutting through the vast landscscape. Our truck, a tiny speck by the roadside, shows how far up we had had to climb to collect the samples.

Key findings

Collecting moss samples in the Arctic. We used these samples to conduct three types of experiments at three different labs: molecular analysis to investigate moss host genetics at the University of Florida, microbiome analysis at the University of Colorado, and measurements of N fixation with stable isotopes at the University of Northern Arizona. My responsibilities included generating ddRADseq and target capture sequencing data from these samples and conducting population genetic and phylogenetic data analysis.

Project contributions

  • Collected and processed ~600 moss samples (Aulacomnium and Hylocomium spp.)for DNA extraction and constructed NGS libraries (ddRADseq) for Illumina sequencing.
  • Built bioinformatic pipelines to process ddRADseq data and conduct downstream population genetic (e.g. STRUCTURE, Treemix) and phylogenetic (RAxML) analysis.
  • Developed bioinformatic pipelines for processing target-capture sequencing data generated from the GoFlag408 probe set. Conducted phylogenetic analysis (RAxML, ASTRAL), and assessed gene tree discordance and hybridization events (IQ-TREE, DENSITREE, PhyParts, PhyloNetworks).
  • Successfully constructed a well-supported phylogeny of the moss genus Aulacomnium using phylogenomic analyses of 399 targeted nuclear loci from the GoFlag408 probe se

I often say that, when it comes to rapidly changing Arctic eco-systems, mosses are tiny, but mighty! It is important to remember that mosses and their microbiomes are an important piece of the puzzle of predicting how Arctic ecosystems will respond to continued climate change.