Experimental assessment of tree canopy and leaf litter controls on the microbiome and nitrogen fixation rates of two boreal mosses

Boreal moss-microbe interactions are revealed through metagenome assembly of novel bacterial species

Moss-microbe interactions contribute to ecosystem processes in boreal forests. Yet, how host-specific characteristics and the environment drive the composition and metabolic potential of moss microbiomes is still poorly understood. In this study, we use shotgun metagenomics to identify the taxonomy and metabolic potential of the bacteria of four moss species of the boreal forests of Northern Québec, Canada. To characterize moss bacterial community composition and diversity, we assembled the genomes of 110 potentially novel bacterial species. Our results highlight that moss genus, species, gametophyte section, and to a lesser extent soil pH and soil temperature, drive moss-associated bacterial community composition and diversity. In the brown gametophyte section, two Stigonema spp. showed partial pathway completeness for photosynthesis and nitrogen fixation, while all brown-associated Hyphomicrobiales had complete assimilatory nitrate reduction pathways and many nearly complete carbon fixation pathways. Several brown-associated species showed partial to complete pathways for coenzyme M and F420 biosynthesis, important for methane metabolism. In addition, green-associated Hyphomicrobiales (Methylobacteria spp.) displayed potential for the anoxygenic photosystem II pathway. Overall, our findings demonstrate how host-specific characteristics and environmental factors shape the composition and metabolic potential of moss bacteria, highlighting their roles in carbon fixation, nitrogen cycling, and methane metabolism in boreal forests.

Exploring the Metatranscriptome of Bacterial Communities of Two Moss Species Thriving in Different Environments-Terrestrial and Aquatic

Mosses host diverse bacterial communities essential for their fitness, nutrient acquisition, stress tolerance, and pathogen defense. Understanding the microbiome's taxonomic composition is the first step, but unraveling their functional capabilities is crucial for grasping their ecological significance. Metagenomics characterizes microbial communities by composition, while metatranscriptomics explores gene expression, providing insights into microbiome functionality beyond the structure. Here, we present for the first time a metatranscriptomic study of two moss species, Hypnum cupressiforme (Hedw.) and Platyhypnidium riparioides (Hedw.) Dixon., renowned as key biomonitors of atmospheric and water pollution. Our investigation extends beyond taxonomic profiling and offers a profound exploration of moss bacterial communities. Pseudomonadota and Actinobacteria are the dominant bacterial phyla in both moss species, but their proportions differ. In H. cupressiforme, Actinobacteria make up 62.45% and Pseudomonadota 32.48%, while in P. riparioides, Actinobacteria account for only 25.67% and Pseudomonadota 69.08%. This phylum-level contrast is reflected in genus-level differences. Our study also shows the expression of most genes related to nitrogen cycling across both microbiomes. Additionally, functional annotation highlights disparities in pathway prevalence, including carbon dioxide fixation, photosynthesis, and fatty acid biosynthesis, among others. These findings hint at potential metabolic distinctions between microbial communities associated with different moss species, influenced by their specific genotypes and habitats. The integration of metatranscriptomic data holds promise for enhancing our understanding of bryophyte-microbe partnerships, opening avenues for novel applications in conservation, bioremediation, and sustainable agriculture.

Out of site, out of mind: Changes in feather moss phyllosphere microbiota in mine offsite boreal landscapes

Plant-microbe interactions play a crucial role in maintaining biodiversity and ecological services in boreal forest biomes. Mining for minerals, and especially the emission of heavy metal-enriched dust from mine sites, is a potential threat to biodiversity in offsite landscapes. Understanding the impacts of mining on surrounding phyllosphere microbiota is especially lacking. To investigate this, we characterized bacterial and fungal communities in the phyllosphere of feather moss Pleurozium schreberi (Brid). Mitt in boreal landscapes near six gold mine sites at different stages of the mine lifecycle. We found that (1) both mining stage and ecosystem type are drivers of the phyllosphere microbial community structure in mine offsite landscapes; (2) Bacterial alpha diversity is more sensitive than fungal alpha diversity to mining stage, while beta diversity of both groups is impacted; (3) mixed and deciduous forests have a higher alpha diversity and a distinct microbial community structure when compared to coniferous and open canopy ecosystems; (4) the strongest effects are detectable within 0.2 km from operating mines. These results confirmed the presence of offsite effects of mine sites on the phyllosphere microbiota in boreal forests, as well as identified mining stage and ecosystem type as drivers of these effects. Furthermore, the footprint was quantified at 0.2 km, providing a reference distance within which mining companies and policy makers should pay more attention during ecological assessment and for the development of mitigation strategies. Further studies are needed to assess how these offsite effects of mines affect the functioning of boreal ecosystems.

Nitrogen fixation and nifH gene diversity in cyanobacteria living on feather mosses in a subalpine forest of Mt. Fuji

In the boreal forests, feather mosses such as Hylocomium splendens and Pleurozium schreberi are colonized by cyanobacteria, which provide large amounts of nitrogen to forest ecosystems through nitrogen fixation. Although these feather mosses are also ubiquitous in subalpine forests of East Asia, little is known regarding their associated cyanobacteria and their ability to fix nitrogen. In this study, we investigated (1) whether cyanobacteria co-exist and fix nitrogen in the two species of feather mosses that cover the ground surface in a subalpine forest of Mt. Fuji, (2) whether cyanobacteria belonging to a common cluster with boreal forests are found in feather mosses in Mt. Fuji, and (3) whether moss-associated nitrogen fixation rates differed among moss growing substrates, canopy openness, and moss nitrogen concentrations in the same forest area. Our results showed that cyanobacteria colonized feather mosses in the subalpine forests of Mt. Fuji and acetylene reduction rates as an index of nitrogen fixation tended to be higher in H. splendens than in P. schreberi. Based on analysis of the nifH gene, 43 bacterial operational taxonomic units (OTUs) were identified, 28 of which represented cyanobacteria. Among the five clusters of cyanobacteria classified based on their nifH gene and identified in northern Europe, four (Nostoc cluster I, Nostoc cluster II, Stigonema cluster, and nifH2 cluster) were also found at Mt. Fuji. The acetylene reduction rate differed depending on the moss growing substrate and the total nitrogen concentration of moss shoots, and a strong negative correlation was observed with the total nitrogen concentration.

Unraveling global and diazotrophic bacteriomes of boreal forest floor feather mosses and their environmental drivers at the ecosystem and at the plant scale in North America

Feather mosses are abundant cryptogams of the boreal forest floor and shelter a broad diversity of bacteria who have important ecological functions (e.g., decomposition, nutrient cycling). In particular, nitrogen (N₂-) fixation performed by feather moss-associated diazotrophs constitutes an important entry of nitrogen in the boreal forest ecosystem. However, the composition of the feather moss bacteriome and its environmental drivers are still unclear. Using cDNA amplicon sequencing of the 16S rRNA and nifH genes and cyanobacterial biomass quantification, we explored the active global and diazotrophic bacterial communities of two dominant feather moss species (i) at the ecosystem scale, along a 500-km climatic and nutrient deposition gradient in the North American boreal forest, and (ii) at the plant scale, along the moss shoot senescence gradient. We found that cyanobacteria were major actors of the feather moss bacteriome, accounting for 33% of global bacterial communities and 65% of diazotrophic communities, and that several cyanobacterial and methanotrophic genera were contributing to N₂-fixation. Moreover, we showed that bacteria were occupying ecological niches along the moss shoot, with phototrophs being dominant in the apical part and methanotrophs being dominant in the basal part. Finally, climate (temperature, precipitation), environmental variables (moss species, month, tree density) and nutrients (nitrogen, phosphorus, molybdenum, vanadium, iron) strongly shaped global and diazotrophic bacteriomes. In summary, this work presents evidence that the feather moss bacteriome plays crucial roles in supporting moss growth, health, and decomposition, as well as in the boreal forest carbon and nitrogen cycles. This study also highlights the substantial effects of climate and nutrients on the feather moss bacteriome, suggesting the importance of understanding the impacts of global change on moss-associated bacterial growth and activity.

Biotic and abiotic controls of nitrogen fixation in cyanobacteria-moss associations

Most mosses are colonized by nitrogen (N)-fixing cyanobacteria. This discovery is relatively recent, which can explain the large knowledge gaps the field is now tackling. For instance, while we have a good understanding of the abiotic controls (e.g. nutrient availability, increased temperature), we still do not know much about the biotic controls of N₂ fixation in mosses. I propose here that we should endeavour to position moss-cyanobacteria associations along the mutualism-parasitism continuum under varying abiotic conditions (e.g. nutrient availability). This would finally unravel the nature of the relationship between the partners and will be a big leap in our understanding of the evolution of plant-bacteria interactions using moss-cyanobacteria associations as a model system.

Unraveling host-microbe interactions and ecosystem functions in moss-bacteria symbioses

Mosses are non-vascular plants usually found in moist and shaded areas, with great ecological importance in several ecosystems. This is especially true in northern latitudes, where mosses are responsible for up to 100% of primary production in some ecosystems. Mosses establish symbiotic associations with unique bacteria that play key roles in the carbon and nitrogen cycles. For instance, in boreal environments, more than 35% of the nitrogen fixed by diazotrophic symbionts in peatlands is transferred to mosses, directly affecting carbon fixation by the hosts, while moss-associated methanotrophic bacteria contribute 10-30% of moss carbon. Further, half of ecosystem N input may derive from moss-cyanobacteria associations in pristine ecosystems. Moss-bacteria interactions have consequences on a global scale since northern environments sequester 20% of all the carbon generated by forests in the world and stock at least 32% of global terrestrial carbon. Different moss hosts influence bacteria in distinct ways, which suggests that threats to mosses also threaten unique microbial communities with important ecological and biogeochemical consequences. Since their origin ~500 Ma, mosses have interacted with bacteria, making these associations ideal models for understanding the evolution of plant-microbe associations and their contribution to biogeochemical cycles.

Long-term warming effects on the microbiome and nifH gene abundance of a common moss species in sub-Arctic tundra

Bacterial communities form the basis of biogeochemical processes and determine plant growth and health. Mosses harbour diverse bacterial communities that are involved in nitrogen fixation and carbon cycling. Global climate change is causing changes in aboveground plant biomass and shifting species composition in the Arctic, but little is known about the response of moss microbiomes in these environments. Here, we studied the total and potentially active bacterial communities associated with Racomitrium lanuginosum in response to a 20-yr in situ warming in an Icelandic heathland. We evaluated the effect of warming and warming-induced shrub expansion on the moss bacterial community composition and diversity, and nifH gene abundance. Warming changed both the total and the potentially active bacterial community structure, while litter abundance only affected the total bacterial community structure. The abundance of nifH genes was negatively affected by litter abundance. We also found shifts in the potentially nitrogen-fixing community, with Nostoc decreasing and noncyanobacterial diazotrophs increasing in relative abundance. Our data suggest that the moss microbial community and potentially nitrogen fixing taxa will be sensitive to future warming, partly via changes in litter and shrub abundance.

Succession comprises a sequence of threshold-induced community assembly processes towards multidiversity

Research on successions and community assembly both address the same processes such as dispersal, species sorting, and biotic interactions but lack unifying concepts. Recent theoretical advances integrated both research lines proposing a sequence of stochastic and deterministic processes along successional gradients. Shifts in ecosystem states along successional gradients are predicted to occur abruptly once abiotic and biotic factors dominate over dispersal as main driver. Considering the multidiversity composed of five organismal groups including plants, animals, and microbes, our results imply that stochastic, likely dispersal-dominated, processes are replaced by rather deterministic processes such as environmental filtering and biotic interactions after around 60 years of succession in a glacier forefield. The niche-based character of later successional processes is further supported by a decline in multi-beta-diversity. Our results may update concepts of community assembly by considering multiple taxa, help to bridge the gap between research on successions and community assembly, and provide insights into the emergence of multidiverse and complex ecosystems.

Dominance of coniferous and broadleaved trees drives bacterial associations with boreal feather mosses

The composition of ecologically important moss-associated bacterial communities seems to be mainly driven by host species but may also be shaped by environmental conditions related with tree dominance. The moss phyllosphere has been studied in coniferous forests while broadleaf forests remain understudied. To determine if host species or environmental conditions defined by tree dominance drives the bacterial diversity in the moss phyllosphere, we used 16S rRNA gene amplicon sequencing to quantify changes in bacterial communities as a function of host species (Pleurozium schreberi and Ptilium crista-castrensis) and forest type (coniferous black spruce versus deciduous broadleaf trembling aspen) in eastern Canada. The overall composition of moss phyllosphere was defined by the interaction of both factors, though most of bacterial phyla were determined by a strong effect of forest type. Bacterial α-diversity was highest in spruce forests, while there was greater turnover (β-diversity) and higher γ-diversity in aspen forests. Unexpectedly, Cyanobacteria were much more relatively abundant in aspen than in spruce forests, with the cyanobacteria family Nostocaceae differing the most between forest types. Our results advance the understanding of moss-associated microbial communities among coniferous and broadleaf deciduous forests, which are important with the increasing changes in tree dominance in the boreal system. This article is protected by copyright. All rights reserved.

The moss traits that rule cyanobacterial colonization

BACKGROUND AND AIMS

Cyanobacteria associated with mosses represent a main nitrogen (N) source in pristine, high-latitude and -altitude ecosystems due to their ability to fix N2. However, despite progress made regarding moss-cyanobacteria associations, the factors driving the large interspecific variation in N2 fixation activity between moss species remain elusive. The aim of the study was to identify the traits of mosses that determine cyanobacterial colonization and thus N2 fixation activity.

METHODS

Four moss species varying in N2 fixation activity were used to assess cyanobacterial abundance and activity to correlate it with moss traits (morphological, chemical, water-balance traits) for each species.

KEY RESULTS

Moss hydration rate was one of the pivotal traits, explaining 56 and 38 % of the variation in N2 fixation and cyanobacterial colonization, respectively, and was linked to morphological traits of the moss species. Higher abundance of cyanobacteria was found on shoots with smaller leaves, and with a high frequency of leaves. High phenol concentration inhibited N2 fixation but not colonization. These traits driving interspecific variation in cyanobacterial colonization, however, are also affected by the environment, and lead to intraspecific variation. Approximately 24 % of paraphyllia, filamentous appendages on Hylocomium splendens stems, were colonized by cyanobacteria.

CONCLUSIONS

Our findings show that interspecific variations in moss traits drive differences in cyanobacterial colonization and thus, N2 fixation activity among moss species. The key traits identified here that control moss-associated N2 fixation and cyanobacterial colonization could lead to improved predictions of N2 fixation in different moss species as a function of their morphology.

Indirect effects of climate change inhibit N2 fixation associated with the feathermoss Hylocomium splendens in subarctic tundra

Mosses can be responsible for up to 100% of net primary production in arctic and subarctic tundra, and their associations with diazotrophic cyanobacteria have an important role in increasing nitrogen (N) availability in these pristine ecosystems. Predictions about the consequences of climate change in subarctic environments point to increased N mineralization in soil and higher litter deposition due to warming. It is not clear yet how these indirect climate change effects impact moss-cyanobacteria associations and N₂ fixation. This work aimed to evaluate the effects of increased N and litter input on biological N₂ fixation rates associated with the feathermoss Hylocomium splendens from a tundra heath. H. splendens samples were collected near Abisko, northern Sweden, from a field experiment with annual additions of ammonium chloride and dried birch litter and the combination of both for three years. Samples were analyzed for N₂ fixation, cyanobacterial colonization, C and N content and pH. Despite the high N additions, no significant differences in moss N content were found. However, differences between treatments were observed in N₂ fixation rates, cyanobacterial colonization and pH, with the combined ammonium+litter treatment causing a significant reduction in the number of branch-colonizing cyanobacteria and N₂ fixation, and ammonium additions significantly lowering moss pH. A significant, positive relationship was found between N₂ fixation rates, moss colonization by cyanobacteria and pH levels, showing a clear drop in N₂ fixation rates at lower pH levels even if larger cyanobacterial populations were present. These results suggest that increased N availability and litter deposition resulting from climate change not only interferes with N₂ fixation directly, but also acidifies moss microhabitats and reduces the abundance of associated cyanobacteria, which could eventually impact the N cycle in the Subarctic.

The relationship of C and N stable isotopes to high-latitude moss-associated N2 fixation

Moss-associated N₂ fixation by epiphytic microbes is a key biogeochemical process in nutrient-limited high-latitude ecosystems. Abiotic drivers, such as temperature and moisture, and the identity of host mosses are critical sources of variation in N₂ fixation rates. An understanding of the potential interaction between these factors is essential for predicting N inputs as moss communities change with the climate. To further understand the drivers and results of N₂ fixation rate variation, we obtained natural abundance values of C and N isotopes and an associated rate of N₂ fixation with ¹⁵N₂ gas incubations in 34 moss species collected in three regions across Alaska, USA. We hypothesized that δ¹⁵N values would increase toward 0‰ with higher N₂ fixation to reflect the increasing contribution of fixed N₂ in moss biomass. Second, we hypothesized that δ¹³C and N₂ fixation would be positively related, as enriched δ¹³C signatures reflect abiotic conditions favorable to N₂ fixation. We expected that the magnitude of these relationships would vary among types of host mosses, reflecting differences in anatomy and habitat. We found little support for our first hypothesis, with only a modest positive relationship between N₂ fixation rates and δ¹⁵N in a structural equation model. We found a significant positive relationship between δ¹³C and N₂ fixation only in Hypnales, where the probability of N₂ fixation activity reached 95% when δ¹³C values exceeded - 30.4‰. We conclude that moisture and temperature interact strongly with host moss identity in determining the extent to which abiotic conditions impact associated N₂ fixation rates.

The genetic architecture of sexual dimorphism in the moss Ceratodon purpureus

A central problem in evolutionary biology is to identify the forces that maintain genetic variation for fitness in natural populations. Sexual antagonism, in which selection favours different variants in males and females, can slow the transit of a polymorphism through a population or can actively maintain fitness variation. The amount of sexually antagonistic variation to be expected depends in part on the genetic architecture of sexual dimorphism, about which we know relatively little. Here, we used a multivariate quantitative genetic approach to examine the genetic architecture of sexual dimorphism in a scent-based fertilization syndrome of the moss Ceratodon purpureus. We found sexual dimorphism in numerous traits, consistent with a history of sexually antagonistic selection. The cross-sex genetic correlations (rmf) were generally heterogeneous with many values indistinguishable from zero, which typically suggests that genetic constraints do not limit the response to sexually antagonistic selection. However, we detected no differentiation between the female- and male-specific trait (co)variance matrices (Gf and Gm, respectively), meaning the evolution of sexual dimorphism may be constrained. The cross-sex cross-trait covariance matrix B contained both symmetric and asymmetric elements, indicating that the response to sexually antagonistic or sexually concordant selection, and the constraint to sexual dimorphism, are highly dependent on the traits experiencing selection. The patterns of genetic variances and covariances among these fitness components is consistent with partly sex-specific genetic architectures having evolved in order to partially resolve multivariate genetic constraints (i.e. sexual conflict), enabling the sexes to evolve towards their sex-specific multivariate trait optima.