Microbial nitrogen fixation and methane oxidation are strongly enhanced by light in Sphagnum mosses

Plant-mediated CH4 exchange in wetlands: A review of mechanisms and measurement methods with implications for modelling

Plant-mediated CH4 transport (PMT) is the dominant pathway through which soil-produced CH4 can escape into the atmosphere and thus plays an important role in controlling ecosystem CH4 emission. PMT is affected by abiotic and biotic factors simultaneously, and the effects of biotic factors, such as the dominant plant species and their traits, can override the effects of abiotic factors. Increasing evidence shows that plant-mediated CH4 fluxes include not only PMT, but also within-plant CH4 production and oxidation due to the detection of methanogens and methanotrophs attached to the shoots. Despite the inter-species and seasonal differences, and the probable contribution of within-plant microbes to total plant-mediated CH4 exchange (PME), current process-based ecosystem models only estimate PMT based on the bulk biomass or leaf area index of aerenchymatous plants. We highlight five knowledge gaps to which more research efforts should be devoted. First, large between-species variation, even within the same family, complicates general estimation of PMT, and calls for further work on the key dominant species in different types of wetlands. Second, the interface (rhizosphere-root, root-shoot, or leaf-atmosphere) and plant traits controlling PMT remain poorly documented, but would be required for generalizations from species to relevant functional groups. Third, the main environmental controls of PMT across species remain uncertain. Fourth, the role of within-plant CH4 production and oxidation is poorly quantified. Fifth, the simplistic description of PMT in current process models results in uncertainty and potentially high errors in predictions of the ecosystem CH4 flux. Our review suggest that flux measurements should be conducted over multiple growing seasons and be paired with trait assessment and microbial analysis, and that trait-based models should be developed. Only then we are capable to accurately estimate plant-mediated CH4 emissions, and eventually ecosystem total CH4 emissions at both regional and global scales.

Structure and Functions of Endophytic Bacterial Communities Associated with Sphagnum Mosses and Their Drivers in Two Different Nutrient Types of Peatlands

Sphagnum mosses are keystone plant species in the peatland ecosystems that play a crucial role in the formation of peat, which shelters a broad diversity of endophytic bacteria with important ecological functions. In particular, methanotrophic and nitrogen-fixing endophytic bacteria benefit Sphagnum moss hosts by providing both carbon and nitrogen. However, the composition and abundance of endophytic bacteria from different species of Sphagnum moss in peatlands of different nutrient statuses and their drivers remain unclear. This study used 16S rRNA gene amplicon sequencing to examine endophytic bacterial communities in Sphagnum mosses and measured the activity of methanotrophic microbial by the 13C-CH4 oxidation rate. According to the results, the endophytic bacterial community structure varied among Sphagnum moss species and Sphagnum capillifolium had the highest endophytic bacterial alpha diversity. Moreover, chlorophyll, phenol oxidase, carbon contents, and water retention capacity strongly shaped the communities of endophytic bacteria. Finally, Sphagnum palustre in Hani (SP) had a higher methane oxidation rate than S. palustre in Taishanmiao. This result is associated with the higher average relative abundance of Methyloferula an obligate methanotroph in SP. In summary, this work highlights the effects of Sphagnum moss characteristics on the endophytic bacteriome. The endophytic bacteriome is important for Sphagnum moss productivity, as well as for carbon and nitrogen cycles in Sphagnum moss peatlands.

Hot moment of N2O emissions in seasonally frozen peatlands

Since the start of the Anthropocene, northern seasonally frozen peatlands have been warming at a rate of 0.6 °C per decade, twice that of the Earth's average rate, thereby triggering increased nitrogen mineralization with subsequent potentially large losses of nitrous oxide (N2O) to the atmosphere. Here we provide evidence that seasonally frozen peatlands are important N2O emission sources in the Northern Hemisphere and the thawing periods are the hot moment of annual N2O emissions. The flux during the hot moment of thawing in spring was 1.20 ± 0.82 mg N2O m-2 d-1, significantly higher than that during the other periods (freezing, -0.12 ± 0.02 mg N2O m-2 d-1; frozen, 0.04 ± 0.04 mg N2O m-2 d-1; thawed, 0.09 ± 0.01 mg N2O m-2 d-1) or observed for other ecosystems at the same latitude in previous studies. The observed emission flux is even higher than those of tropical forests, the World's largest natural terrestrial N2O source. Furthermore, based on soil incubation with 15N and 18O isotope tracing and differential inhibitors, heterotrophic bacterial and fungal denitrification was revealed as the main source of N2O in peatland profiles (0-200 cm). Metagenomic, metatranscriptomic, and qPCR assays further revealed that seasonally frozen peatlands have high N2O emission potential, but thawing significantly stimulates expression of genes encoding N2O-producing protein complexes (hydroxylamine dehydrogenase (hao) and nitric oxide reductase (nor)), resulting in high N2O emissions during spring. This hot moment converts seasonally frozen peatlands into an important N2O emission source when it is otherwise a sink. Extrapolation of our data to all northern peatland areas reveals that the hot moment emissions could amount to approximately 0.17 Tg of N2O yr-1. However, these N2O emissions are still not routinely included in Earth system models and global IPCC assessments.

Understory species composition mediates soil greenhouse gas fluxes by affecting bacterial community diversity in boreal forests

Introduction

Plant species composition in forest ecosystems can alter soil greenhouse gas (GHG) budgets by affecting soil properties and microbial communities. However, little attention has been paid to the forest types characterized by understory vegetation, especially in boreal forests where understory species contribute significantly to carbon and nitrogen cycling.

Method

In the present study, soil GHG fluxes, soil properties and bacterial community, and soil environmental conditions were investigated among three types of larch forest [Rhododendron simsii-Larix gmelinii forest (RL), Ledum palustre-Larix gmelinii forest (LL), and Sphagnum-Bryum-Ledum palustre-Larix gmelinii forest (SLL)] in the typical boreal region of northeast China to explore whether the forest types characterized by different understory species can affect soil GHG fluxes.

Results

The results showed that differences in understory species significantly affected soil GHG fluxes, properties, and bacterial composition among types of larch forest. Soil CO₂ and N₂O fluxes were significantly higher in LL (347.12 mg m^-2 h^-1 and 20.71 μg m^-2 h^-1) and RL (335.54 mg m^-2 h^-1 and 20.73 μg m^-2 h^-1) than that in SLL (295.58 mg m^-2 h^-1 and 17.65 μg m^-2 h^-1), while lower soil CH₄ uptake (-21.07 μg m^-2 h^-1) were found in SLL than in RL (-35.21 μg m^-2 h^-1) and LL (-35.85 μg m^-2 h^-1). No significant differences between LL and RL were found in soil CO₂, CH₄, and N₂O fluxes. Soil bacterial composition was mainly dominated by Proteobacteria, Actinobacteria, Acidobacteria, and Chloroflexi among the three types of larch forest, while their abundances differed significantly. Soil environmental variables, soil properties, bacterial composition, and their interactions significantly affected the variations in GHG fluxes with understory species. Specifically, structural equation modeling suggested that soil bacterial composition and temperature had direct close links with variations in soil GHG fluxes among types of larch forest. Moreover, soil NO₃ ^--N and NH₄ ⁺ - N content also affected soil CO₂, CH₄, and N₂O fluxes indirectly, via their effects on soil bacterial composition.

Discussion

Our study highlights the importance of understory species in regulating soil GHG fluxes in boreal forests, which furthers our understanding of the role of boreal forests in sustainable development and climate change mitigation.

Organomineral fertilizer application enhances Perilla frutescens nutritional quality and rhizosphere microbial community stability in karst mountain soils

Introduction

Applications of organomineral fertilizer (OMF) are important measures for developing organic agriculture in karst mountain areas. However, the influence of OMF on the structure and function of soil microbial diversity and their relationship with crop yield and quality are still unclear.

Methods

Based on soil science, crop science, and high-throughput sequencing methods, we investigated the changes of rhizosphere soil microbial communities of Perilla frutescens under different fertilization measures. Then, the relationship between P. frutescens yield and quality with soil quality was analyzed.

Results

The results showed that the addition of OMF increased the amount of total carbon and total potassium in soil. OF, especially OMF, improved P. frutescens yield and quality (e.g., panicle number per plant, main panicle length, and unsaturated fatty acid contents). Both OF and OMF treatments significantly increased the enrichment of beneficial microorganism (e.g., Bacillus, Actinomadura, Candidatus_Solibacter, Iamia, Pseudallescheria, and Cladorrhinum). The symbiotic network analysis demonstrated that OMF strengthened the connection among the soil microbial communities, and the community composition became more stable. Redundancy analysis and structural equation modeling showed that the soil pH, available phosphorus, and available potassium were significantly correlated with soil microbial community diversity and P. frutescens yield and quality.

Discussion

Our study confirmed that OMF could replace CF or common OF to improve soil fertility, crop yield and quality in karst mountain soils.

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.

Defining the Sphagnum Core Microbiome across the North American Continent Reveals a Central Role for Diazotrophic Methanotrophs in the Nitrogen and Carbon Cycles of Boreal Peatland Ecosystems

Peat mosses of the genus Sphagnum are ecosystem engineers that frequently predominate over photosynthetic production in boreal peatlands. Sphagnum spp. host diverse microbial communities capable of nitrogen fixation (diazotrophy) and methane oxidation (methanotrophy), thereby potentially supporting plant growth under severely nutrient-limited conditions. Moreover, diazotrophic methanotrophs represent a possible “missing link” between the carbon and nitrogen cycles, but the functional contributions of the Sphagnum-associated microbiome remain in question. A combination of metagenomics, metatranscriptomics, and dual-isotope incorporation assays was applied to investigate Sphagnum microbiome community composition across the North American continent and provide empirical evidence for diazotrophic methanotrophy in Sphagnum-dominated ecosystems. Remarkably consistent prokaryotic communities were detected in over 250 Sphagnum SSU rRNA libraries from peatlands across the United States (5 states, 17 bog/fen sites, 18 Sphagnum species), with 12 genera of the core microbiome comprising 60% of the relative microbial abundance. Additionally, nitrogenase (nifH) and SSU rRNA gene amplicon analysis revealed that nitrogen-fixing populations made up nearly 15% of the prokaryotic communities, predominated by Nostocales cyanobacteria and Rhizobiales methanotrophs. While cyanobacteria comprised the vast majority (>95%) of diazotrophs detected in amplicon and metagenome analyses, obligate methanotrophs of the genus Methyloferula (order Rhizobiales) accounted for one-quarter of transcribed nifH genes. Furthermore, in dual-isotope tracer experiments, members of the Rhizobiales showed substantial incorporation of ¹³CH₄ and ¹⁵N₂ isotopes into their rRNA. Our study characterizes the core Sphagnum microbiome across large spatial scales and indicates that diazotrophic methanotrophs, here defined as obligate methanotrophs of the rare biosphere (Methyloferula spp. of the Rhizobiales) that also carry out diazotrophy, play a keystone role in coupling of the carbon and nitrogen cycles in nutrient-poor peatlands.

Response of a methane-driven interaction network to stressor intensification

Microorganisms may reciprocally select for specific interacting partners, forming a network with interdependent relationships. The methanotrophic interaction network, comprising methanotrophs and non-methanotrophs, is thought to modulate methane oxidation and give rise to emergent properties beneficial for the methanotrophs. Therefore, microbial interaction may become relevant for community functioning under stress. However, empirical validation of the role and stressor-induced response of the interaction network remains scarce. Here, we determined the response of a complex methane-driven interaction network to a stepwise increase in NH4Cl-induced stress (0.5-4.75 g L-1, in 0.25-0.5 g L-1 increments) using enrichment of a naturally occurring complex community derived from a paddy soil in laboratory-scale incubations. Although ammonium and intermediates of ammonium oxidation are known to inhibit methane oxidation, methanotrophic activity was unexpectedly detected even in incubations with high ammonium levels, albeit rates were significantly reduced. Sequencing analysis of the 16S rRNA and pmoA genes consistently revealed divergent communities in the reference and stressed incubations. The 16S rRNA-based co-occurrence network analysis revealed that NH4Cl-induced stress intensification resulted in a less complex and modular network, likely driven by less stable interaction. Interestingly, the non-methanotrophs formed the key nodes, and appear to be relevant members of the community. Overall, stressor intensification unravels the interaction network, with adverse consequences for community functioning.

The bacterial communities of Alaskan mosses and their contributions to N2-fixation

BACKGROUND

Mosses in high-latitude ecosystems harbor diverse bacterial taxa, including N2-fixers which are key contributors to nitrogen dynamics in these systems. Yet the relative importance of moss host species, and environmental factors, in structuring these microbial communities and their N2-fixing potential remains unclear. We studied 26 boreal and tundra moss species across 24 sites in Alaska, USA, from 61 to 69° N. We used cultivation-independent approaches to characterize the variation in moss-associated bacterial communities as a function of host species identity and site characteristics. We also measured N2-fixation rates via 15N2 isotopic enrichment and identified potential N2-fixing bacteria using available literature and genomic information.

RESULTS

Host species identity and host evolutionary history were both highly predictive of moss microbiome composition, highlighting strong phylogenetic coherence in these microbial communities. Although less important, light availability and temperature also influenced composition of the moss microbiome. Finally, we identified putative N2-fixing bacteria specific to some moss hosts, including potential N2-fixing bacteria outside well-studied cyanobacterial clades.

CONCLUSIONS

The strong effect of host identity on moss-associated bacterial communities demonstrates mosses' utility for understanding plant-microbe interactions in non-leguminous systems. Our work also highlights the likely importance of novel bacterial taxa to N2-fixation in high-latitude ecosystems. Video Abstract.