High specificity but contrasting biodiversity of Sphagnum-associated bacterial and plant communities in bog ecosystems independent of the geographical region

Reviewing bryophyte-microorganism association: insights into environmental optimization

Bryophytes, the second-largest group of plants, play a crucial role as early colonizers of land and are a prolific source of naturally occurring substances with significant economic potential. Microorganisms, particularly bacteria, cyanobacteria, fungi form intricate associations with plants, notably bryophytes, contributing to the ecological functioning of terrestrial ecosystems and sometimes it gives negative impact also. This review elucidates the pivotal role of endophytic bacteria in promoting plant growth, facilitating nutrient cycling, and enhancing environmental health. It comprehensively explores the diversity and ecological significance of fungal and bacterial endophytes across various ecosystems. Furthermore, it highlights the moss nitrogen dynamics observed in select moss species. Throughout the review, emphasis is placed on the symbiotic interdependence between bryophytes and microorganisms, offering foundational insights for future research endeavors. By shedding light on the intricate bryophyte-microorganism associations, this study advances our understanding of the complex interplay between plants, microbes, and their environment, paving the way for further research and applications in environmental and biotechnological realms.

Impact of changing climate on bryophyte contributions to terrestrial water, carbon, and nitrogen cycles

Bryophytes, including the lineages of mosses, liverworts, and hornworts, are the second-largest photoautotroph group on Earth. Recent work across terrestrial ecosystems has highlighted how bryophytes retain and control water, fix substantial amounts of carbon (C), and contribute to nitrogen (N) cycles in forests (boreal, temperate, and tropical), tundra, peatlands, grasslands, and deserts. Understanding how changing climate affects bryophyte contributions to global cycles in different ecosystems is of primary importance. However, because of their small physical size, bryophytes have been largely ignored in research on water, C, and N cycles at global scales. Here, we review the literature on how bryophytes influence global biogeochemical cycles, and we highlight that while some aspects of global change represent critical tipping points for survival, bryophytes may also buffer many ecosystems from change due to their capacity for water, C, and N uptake and storage. However, as the thresholds of resistance of bryophytes to temperature and precipitation regime changes are mostly unknown, it is challenging to predict how long this buffering capacity will remain functional. Furthermore, as ecosystems shift their global distribution in response to changing climate, the size of different bryophyte-influenced biomes will change, resulting in shifts in the magnitude of bryophyte impacts on global ecosystem functions.

Habitat conditions and not moss composition mediate microbial community structure in Swiss peatlands

Peatlands, one of the oldest ecosystems, globally store significant amounts of carbon and freshwater. However, they are under severe threat from human activities, leading to changes in water, nutrient and temperature regimes in these delicate systems. Such shifts can trigger a substantial carbon flux into the atmosphere and diminish the water-holding capacity of peatlands. Microbes associated with moss in peatlands play a crucial role in providing these ecosystem services, which are at risk due to global change. Therefore, understanding the factors influencing microbial composition and function is vital. Our study focused on five peatlands along an altitudinal gradient in Switzerland, where we sampled moss on hummocks containing Sarracenia purpurea. Structural equation modelling revealed that habitat condition was the primary predictor of community structure and directly influenced other environmental variables. Interestingly, the microbial composition was not linked to the local moss species identity. Instead, microbial communities varied significantly between sites due to differences in acidity levels and nitrogen availability. This finding was also mirrored in a co-occurrence network analysis, which displayed a distinct distribution of indicator species for acidity and nitrogen availability. Therefore, peatland conservation should take into account the critical habitat characteristics of moss-associated microbial communities.

The microbiome of Riccia liverworts is an important reservoir for microbial diversity in temporary agricultural crusts

BACKGROUND

The microbiota of liverworts provides an interesting model for plant symbioses; however, their microbiome assembly is not yet understood. Here, we assessed specific factors that shape microbial communities associated with Riccia temporary agricultural crusts in harvested fields by investigating bacterial, fungal and archaeal communities in thalli and adhering soil from different field sites in Styria and Burgenland, Austria combining qPCR analyses, amplicon sequencing and advanced microscopy.

RESULTS

Riccia spec. div. was colonized by a very high abundance of bacteria (10¹⁰ 16S rRNA gene copies per g of thallus) as well as archaea and fungi (10⁸ ITS copies per g of thallus). Each Riccia thallus contain approx. 1000 prokaryotic and fungal ASVs. The field type was the main driver for the enrichment of fungal taxa, likely due to an imprint on soil microbiomes by the cultivated crop plants. This was shown by a higher fungal richness and different fungal community compositions comparing liverwort samples collected from pumpkin fields, with those from corn fields. In contrast, bacterial communities linked to liverworts are highly specialized and the soil attached to them is not a significant source of these bacteria. Specifically, enriched Cyanobacteria, Bacteroidetes and Methylobacteria suggest a symbiotic interaction. Intriguingly, compared to the surrounding soil, the thallus samples were shown to enrich several well-known bacterial and fungal phytopathogens indicating an undescribed role of liverworts as potential reservoirs of crop pathogens.

CONCLUSIONS

Our results provide evidence that a stable bacterial community but varying fungal communities are colonizing liverwort thalli. Post-harvest, temporary agricultural biocrusts are important reservoirs for microbial biodiversity but they have to be considered as potential reservoirs for pathogens as well.

Missing symbionts – emerging pathogens? Microbiome management for sustainable agriculture

Plant diversification and co-evolution shaped the plant microbiome and vice versa. This resulted in a specific composition of the plant microbiome and a strong connection with the host in terms of functional interplay. Symbionts are part of the microbiota, and important for the plant’s germination and growth, nutrition, as well as stress protection. However, human activities in the Anthropocene are linked to a significant shift of diversity, evenness and specificity of the plant microbiota. In addition, and very importantly, many plant symbionts are missing or no longer functional. It will require targeted microbiome management to support and reintroduce them. In future agriculture, we should aim at replacing harmful chemicals in the field, as well as post-harvest, by using precision microbiome engineering. This is because the plant microbiome is connected across systems and crucial for human and planetary health. This commentary aims to inspire holistic studies for the development of solutions for sustainable agriculture in framework of the One Health and the Planetary Health concepts.

Mites (Oribatida and Mesostigmata) and vegetation as complementary bioindicators in peatlands

Vegetation is widely used in the assessment of the quality of peatlands, while the invertebrate fauna of peatlands is relatively poorly studied. We compared the bioindicator values of vegetation with two arthropod groups widespread in peatlands, saprophagous Oribatida (Acariformes) and predatory Mesostigmata (Parasitiformes) mites. Samples were collected from ecotones at the edges of peatland ponds in Poland, including four in near-natural condition (i.e., peatlands unaffected by human activity) and three in previously disturbed but now recovering peatlands. A set of abiotic parameters was measured at each site: pond area, mean annual temperature, annual precipitation, and water parameters (pH, conductivity, colour, total nitrogen, phosphorus, calcium, and organic carbon). Overall, 63,635 specimens of Oribatida and 448 of Mesostigmata were recovered in the sampling. Species richness of Oribatida (56 species) was higher than that of flora (46) and Mesostigmata (15). Vegetation was significantly associated with annual precipitation in the years 1998-2007 which accounted for 29.1 % of the variation in vegetation communities. Oribatida variability was significantly associated with the content of organic carbon in water accounting for 32.4 % of variation. In contrast, variation in the Mesostigmata was not significantly associated with any of the abiotic parameters. Vegetation at ponds in previously disturbed and now recovering peatlands had higher bush cover than at near-natural ponds and the pond in the cutaway peat had lowest moss cover and the highest number of associate species (i.e., species with wide tolerance not characteristic of the certain community). Mite communities did not differ consistently between near-natural and recovering peatlands. Sphagnum divinum Flatberg et Hassel was recorded from Poland for the first time.

Inclusion of juvenile stages improves diversity assessment and adds to our understanding of mite ecology - A case study from mires in Norway

Arachnid orders, Mesostigmata, Trombidiformes, and Sarcoptiformes, commonly known as 'mites', are abundant in mires, both as adults and as juveniles. However, due to the challenges of identification, the juvenile forms are often excluded from analyses. This is the first study in mires that included all three mite orders identified to the species level, including juvenile instars. We aimed to compare how diversity and the response to ecological variables differed if only the adults (ad) vs. the total number of specimens (ad+juv) are considered. Samples of 20 Sphagnum species (five subgenera) were collected and mites were extracted using Berlese funnels. Overall, nearly 60,000 mites were analyzed; of these Mesostigmata made up 1.87% of the total, Trombidiformes -0.27%, and Sarcoptiformes -97.86%. The study revealed 154 species (33 Mesostigmata, 24 Trombidiformes, and 97 Sarcoptiformes), the highest diversity of mites ever reported from mires. The inclusion of juveniles increased observed species richness by 6%, with 10 species (one Mesostigmata, six Trombidiformes, and three Sarcoptiformes) represented only by juvenile forms. Seventeen species are new to Norway (four Mesostigmata, one Sarcoptiformes, and 12 Trombidiformes, including five undescribed species of Stigmaeidae and Cunaxidae). Four of these were represented in the samples only by juveniles. Including the juveniles explained a greater amount of the variability of Trombidiformes (explanatory variables account for 23.60% for ad, and 73.74% for ad+juv) and Mesostigmata (29.23% - ad, 52.91% - ad+juv), but had less of an impact for Sarcoptiformes (38.48% - ad, 39.26% - ad+juv). Locality, Sphagnum subgenus and species, wetness, and trophic state significantly affected the mite communities and should be taken into consideration when studying mires. Since juvenile stages contribute significantly to mite diversity in mires, they should also be included in mite studies in other habitats.

Keystone Taxa and Predictive Functional Analysis of Sphagnum palustre Tank Microbiomes in Erxianyan Peatland, Central China

Sphagnum is a fundamental ecosystem of engineers, including more than 300 species around the world. These species host diverse microbes, either endosymbiotic or ectosymbiotic, and are key to carbon sequestration in peatland ecosystems. However, the linkages between different types of Sphagnum and the diversity and ecological functions of Sphagnum-associated microbiomes are poorly known, and so are their joint responses to ecological functions. Here, we systematically investigated endophytes in Sphagnum palustre via next-generation sequencing (NGS) techniques in the Erxianyan peatland, central China. The total bacterial microbiome was classified into 38 phyla and 55 classes, 122 orders and 490 genera. The top 8 phyla of Proteobacteria (33.69%), Firmicutes (11.94%), Bacteroidetes (9.42%), Actinobacteria (6.53%), Planctomycetes (6.37%), Gemmatimonadetes (3.05%), Acidobacteria (5.59%) and Cyanobacteria (1.71%) occupied 78.31% of total OTUs. The core microbiome of S. palustre was mainly distributed mainly in 7 phyla, 9 classes, 15 orders, 22 families and 43 known genera. There were many differences in core microbiomes compared to those in the common higher plants. We further demonstrate that the abundant functional groups have a substantial potential for nitrogen fixation, carbon cycle, nitrate metabolism, sulfate respiration and chitinolysis. These results indicate that potential ecological function of Sphagnum palustre in peatlands is partially rooted in its microbiomes, and that incorporating into functional groups of Sphagnum-associated microbiomes can promote mechanistic understanding of Sphagnum ecology in subalpine peatlands.

Photosynthetic microorganisms effectively contribute to bryophyte CO2 fixation in boreal and tropical regions

Photosynthetic microbes are omnipresent in land and water. While they critically influence primary productivity in aquatic systems, their importance in terrestrial ecosystems remains largely overlooked. In terrestrial systems, photoautotrophs occur in a variety of habitats, such as sub-surface soils, exposed rocks, and bryophytes. Here, we study photosynthetic microbial communities associated with bryophytes from a boreal peatland and a tropical rainforest. We interrogate their contribution to bryophyte C uptake and identify the main drivers of that contribution. We found that photosynthetic microbes take up twice more C in the boreal peatland (~4.4 mg CO2.h-1.m-2) than in the tropical rainforest (~2.4 mg CO2.h-1.m-2), which corresponded to an average contribution of 4% and 2% of the bryophyte C uptake, respectively. Our findings revealed that such patterns were driven by the proportion of photosynthetic protists in the moss microbiomes. Low moss water content and light conditions were not favourable to the development of photosynthetic protists in the tropical rainforest, which indirectly reduced the overall photosynthetic microbial C uptake. Our investigations clearly show that photosynthetic microbes associated with bryophyte effectively contribute to moss C uptake despite species turnover. Terrestrial photosynthetic microbes clearly have the capacity to take up atmospheric C in bryophytes living under various environmental conditions, and therefore potentially support rates of ecosystem-level net C exchanges with the atmosphere.

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.

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.

Influence of environmental factors on the tropical peatlands diazotrophic communities from the Southern Brazilian Atlantic Rain Forest

The tropical peatlands of southern Brazil are essential for the maintenance of the Atlantic Rain Forest, one of the 25 hotspots of biodiversity in the world. Although diazotrophic microorganisms are essential for the maintenance of this nitrogen limited ecosystem, so far studies have focused only on microorganisms involved in the carbon cycle. In this work, peat samples were collected from three tropical peatland regions during dry and rainy seasons and their chemical and microbial characteristics were evaluated. Our results showed that the structure of the diazotrophic communities in the Brazilian tropical peatlands differs in the evaluated seasons. The abundance of the genus Bradyrhizobium showed to be affected by rainfall and peat pH. Despite the shifts of the nitrogen fixing population in the tropical peatland caused by seasonality it showed to be constantly dominated by α-Proteobacteria followed by Cyanobacteria. In addition, more than 50% of nifH gene sequences have not been classified, indicating the necessity for more studies in tropical peatland, since the reduction of N supply in the peatlands stimulates the recalcitrant organic matter decomposition performed by peatland microorganisms, influencing the C stock.

Bog ecosystems as a playground for plant-microbe coevolution: bryophytes and vascular plants harbour functionally adapted bacteria

BACKGROUND

Bogs are unique ecosystems inhabited by distinctive, coevolved assemblages of organisms, which play a global role for carbon storage, climate stability, water quality and biodiversity. To understand ecology and plant-microbe co-occurrence in bogs, we selected 12 representative species of bryophytes and vascular plants and subjected them to a shotgun metagenomic sequencing approach. We explored specific plant-microbe associations as well as functional implications of the respective communities on their host plants and the bog ecosystem.

RESULTS

Microbial communities were shown to be functionally adapted to their plant hosts; a higher colonization specificity was found for vascular plants. Bryophytes that commonly constitute the predominant Sphagnum layer in bogs were characterized by a higher bacterial richness and diversity. Each plant group showed an enrichment of distinct phylogenetic and functional bacterial lineages. Detailed analyses of the metabolic potential of 28 metagenome-assembled genomes (MAGs) supported the observed functional specification of prevalent bacteria. We found that novel lineages of Betaproteobacteria and Actinobacteria in the bog environment harboured genes required for carbon fixation via RuBisCo. Interestingly, several of the highly abundant bacteria in both plant types harboured pathogenicity potential and carried similar virulence factors as found with corresponding human pathogens.

CONCLUSIONS

The unexpectedly high specificity of the plant microbiota reflects intimate plant-microbe interactions and coevolution in bog environments. We assume that the detected pathogenicity factors might be involved in coevolution processes, but the finding also reinforces the role of the natural plant microbiota as a potential reservoir for human pathogens. Overall, the study demonstrates how plant-microbe assemblages can ensure stability, functioning and ecosystem health in bogs. It also highlights the role of bog ecosystems as a playground for plant-microbe coevolution. Video abstract.

Plant resistome profiling in evolutionary old bog vegetation provides new clues to understand emergence of multi-resistance

The expanding antibiotic resistance crisis calls for a more in depth understanding of the importance of antimicrobial resistance genes (ARGs) in pristine environments. We, therefore, studied the microbiome associated with Sphagnum moss forming the main vegetation in undomesticated, evolutionary old bog ecosystems. In our complementary analysis of culture collections, metagenomic data and a fosmid library from different geographic sites in Europe, we identified a low abundant but highly diverse pool of resistance determinants, which targets an unexpectedly broad range of 29 antibiotics including natural and synthetic compounds. This derives both, from the extraordinarily high abundance of efflux pumps (up to 96%), and the unexpectedly versatile set of ARGs underlying all major resistance mechanisms. Multi-resistance was frequently observed among bacterial isolates, e.g. in Serratia, Rouxiella, Pandoraea, Paraburkholderia and Pseudomonas. In a search for novel ARGs, we identified the new class A β-lactamase Mm3. The native Sphagnum resistome comprising a highly diversified and partially novel set of ARGs contributes to the bog ecosystem´s plasticity. Our results reinforce the ecological link between natural and clinically relevant resistomes and thereby shed light onto this link from the aspect of pristine plants. Moreover, they underline that diverse resistomes are an intrinsic characteristic of plant-associated microbial communities, they naturally harbour many resistances including genes with potential clinical relevance.

Environmental patterns of brown moss- and Sphagnum-associated microbial communities

Northern peatlands typically develop through succession from fens dominated by the moss family Amblystegiaceae to bogs dominated by the moss genus Sphagnum. How the different plants and abiotic environmental conditions provided in Amblystegiaceae and Sphagnum peat shape the respective moss associated microbial communities is unknown. Through a large-scale molecular and biogeochemical study spanning Arctic, sub-Arctic and temperate regions we assessed how the endo- and epiphytic microbial communities of natural northern peatland mosses relate to peatland type (Sphagnum and Amblystegiaceae), location, moss taxa and abiotic environmental variables. Microbial diversity and community structure were distinctly different between Amblystegiaceae and Sphagnum peatlands, and within each of these two peatland types moss taxon explained the largest part of microbial community variation. Sphagnum and Amblystegiaceae shared few (< 1% of all operational taxonomic units (OTUs)) but strikingly abundant (up to 65% of relative abundance) OTUs. This core community overlapped by one third with the Sphagnum-specific core-community. Thus, the most abundant microorganisms in Sphagnum that are also found in all the Sphagnum plants studied, are the same OTUs as those few shared with Amblystegiaceae. Finally, we could confirm that these highly abundant OTUs were endophytes in Sphagnum, but epiphytes on Amblystegiaceae. We conclude that moss taxa and abiotic environmental variables associate with particular microbial communities. While moss taxon was the most influential parameter, hydrology, pH and temperature also had significant effects on the microbial communities. A small though highly abundant core community is shared between Sphagnum and Amblystegiaceae.

Dynamics of microbial populations and diversity in NAPL contaminated peat soil under varying water table conditions

Despite the risks that hydrocarbon contamination from pipeline leaks or train derailments impose on the health of peatlands in hydrocarbon production areas and transportation corridors, assessing the effect of such contaminations on the health and sustainability of peatlands has received little attention. This study investigates the impacts of hydrocarbons on peat microbial communities. Column experiments were conducted on non-aqueous phase liquid (NAPL) contaminated undisturbed peat core (0-35 cm) under static and fluctuating water table conditions. Water table fluctuations reduced residual NAPL saturation from 8.1-11.3% to 7.7-9.5%. Biodegradation of n-C₈ and n-C₁₂ along with oxidation of CH₄ together produced high CO₂ concentrations in the headspace. Clear patterns in dynamics in the microbial community structure were observed, with a more pronounced population growth. However, a significant loss of microbial richness was observed in contaminated columns. The result indicates that the phylum Proteobacteria benefited most from NAPL; however, their families differed between static and fluctuating water table conditions. This study established strong evidence that peat microbes and water table fluctuation can be an excellent tool for hydrocarbon removal and its control in peatlands.

A New High-Throughput Screening Method to Detect Antimicrobial Volatiles from Metagenomic Clone Libraries

The ever-growing spread of resistance in medicine and agriculture highlights the need to identify new antimicrobials. Microbial volatile organic compounds (VOCs) are one of the most promising groups of chemicals to meet this need. These rarely exploited molecules exhibit antimicrobial activity and their high vapour pressure makes them ideal for application in surface sterilisation, and in particular, in biofumigation. Therefore, we adapted the previously developed Two Clamp VOCs Assay (TCVA) to a new high-throughput screening for the detection of novel antifungal VOCs from metagenomic clone libraries. As a proof of concept, we tested the new high-throughput TCVA (htTCVA) by sourcing a moss metagenomic library against Fusarium culmorum. This led to the identification of five clones that inhibited the growth of mycelium and spores in vitro by up to 8% and 30% and subsequently, to the identification of VOCs that are potentially, and in part responsible for the clones’ antifungal activity. For these VOCs, the in vitro effect of the pure compounds was as high as 100%. These results demonstrate the robustness and feasibility of the htTCVA, which provides access to completely new and unexplored biosynthetic pathways and their secondary metabolites.

Temporal dynamics in the taxonomic and functional profile of the Sphagnum-associated fungi (mycobiomes) in a Sphagnum farming field site in Northwestern Germany

The drainage of peatlands for their agricultural use leads to huge emissions of greenhouse gases. One sustainable alternative is the cultivation of peat mosses after rewetting ('Sphagnum farming'). Environmental parameters of such artificial systems may differ from those of natural Sphagnum ecosystems which host a rich fungal community. We studied the fungal community at a 4 ha Sphagnum farming field site in Northwestern Germany and compared it with that of natural Sphagnum ecosystems. Additionally, we asked if any fungi occur with potentially negative consequences for the commercial production and/or use of Sphagnum biomass. Samples were collected every 3 months within 1 year. High-throughput sequencing of the fungal ITS2 barcode was used to obtain a comprehensive community profile of the fungi. The dominant taxa in the fungal community of the Sphagnum farming field site were all commonly reported from natural Sphagnum ecosystems. While the taxonomic composition showed clear differences between seasons, a stable functional community profile was identified across seasons. Additionally, nutrient supply seems to affect composition of fungal community. Despite a rather high abundance of bryophyte parasites, and the occurrence of both Sphagnum-species-specific and general plant pathogens, their impact on the productivity and usage of Sphagnum biomass as raw material for growing media was considered to be low.

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

Nitrogen (N₂ )-fixing moss microbial communities play key roles in nitrogen cycling of boreal forests. Forest type and leaf litter inputs regulate moss abundance, but how they control moss microbiomes and N₂ -fixation remains understudied. We examined the impacts of forest type and broadleaf litter on microbial community composition and N₂ -fixation rates of Hylocomium splendens and Pleurozium schreberi. We conducted a moss transplant and leaf litter manipulation experiment at three sites with paired paper birch (Betula neoalaskana) and black spruce (Picea mariana) stands in Alaska. We characterized bacterial communities using marker gene sequencing, determined N₂ -fixation rates using stable isotopes (¹⁵ N₂ ) and measured environmental covariates. Mosses native to and transplanted into spruce stands supported generally higher N₂ -fixation and distinct microbial communities compared to similar treatments in birch stands. High leaf litter inputs shifted microbial community composition for both moss species and reduced N₂ -fixation rates for H. splendens, which had the highest rates. N₂ -fixation was positively associated with several bacterial taxa, including cyanobacteria. The moss microbiome and environmental conditions controlled N₂ -fixation at the stand and transplant scales. Predicted shifts from spruce- to deciduous-dominated stands will interact with the relative abundances of mosses supporting different microbiomes and N₂ -fixation rates, which could affect stand-level N inputs.

Reconstruction of Bacterial Metagenome-Assembled Genome Sequences from Alpine Bog Vegetation

Bacteria are essential constituents of bog ecosystems. Here, we report 44 bacterial genome sequences reconstructed from metagenomes sampled across 12 plant species representing Alpine bog vegetation. This resource will facilitate further exploration of the genetic potential of these bacteria and allow researchers to refine their ecological roles in association with their plant hosts.

Effect of Bacterial and Fungal Microbiota Removal on the Survival and Development of Bryophagous Beetles

Insect microbiota may play a wide range of roles in host physiology. Among others, microbiota can be involved in diet processing or protection against pathogens, both of which are potentially important in bryophagous (moss-feeding) insects, which survive on extreme diets and live in the stable environment of moss clumps suitable for the growth of fungi and bacteria. We treated Cytilus sericeus (Forster, 1771) (Coleoptera: Byrrhidae) as a model organism with bactericides and fungicides to test the effect of bacterial and fungal removal on egg hatching and larval development. Furthermore, we supplied larvae with adult feces to determine whether feces is a source of beneficial microbiota or pathogens. Bactericides had a positive effect, but fungicides had a negative effect on beetle fitness, both of which manifested during egg hatching. The feces did not play a positive role. Our conclusions indicate the presence of beneficial fungal microbiota associated with eggs but not transmitted through feces. Based on preliminary cultivation and fungicide tests, Fusarium or Penicillium may be important for suppressing pathogens, but their exact role needs to be further studied.

Microbiome definition re-visited: old concepts and new challenges

The field of microbiome research has evolved rapidly over the past few decades and has become a topic of great scientific and public interest. As a result of this rapid growth in interest covering different fields, we are lacking a clear commonly agreed definition of the term "microbiome." Moreover, a consensus on best practices in microbiome research is missing. Recently, a panel of international experts discussed the current gaps in the frame of the European-funded MicrobiomeSupport project. The meeting brought together about 40 leaders from diverse microbiome areas, while more than a hundred experts from all over the world took part in an online survey accompanying the workshop. This article excerpts the outcomes of the workshop and the corresponding online survey embedded in a short historical introduction and future outlook. We propose a definition of microbiome based on the compact, clear, and comprehensive description of the term provided by Whipps et al. in 1988, amended with a set of novel recommendations considering the latest technological developments and research findings. We clearly separate the terms microbiome and microbiota and provide a comprehensive discussion considering the composition of microbiota, the heterogeneity and dynamics of microbiomes in time and space, the stability and resilience of microbial networks, the definition of core microbiomes, and functionally relevant keystone species as well as co-evolutionary principles of microbe-host and inter-species interactions within the microbiome. These broad definitions together with the suggested unifying concepts will help to improve standardization of microbiome studies in the future, and could be the starting point for an integrated assessment of data resulting in a more rapid transfer of knowledge from basic science into practice. Furthermore, microbiome standards are important for solving new challenges associated with anthropogenic-driven changes in the field of planetary health, for which the understanding of microbiomes might play a key role. Video Abstract.

Rare Species Shift the Structure of Bacterial Communities Across Sphagnum Compartments in a Subalpine Peatland

Sphagnum-associated microbiomes are crucial to Sphagnum growth and peatland ecological functions. However, roles of rare species in bacterial communities across Sphagnum compartments are poorly understood. Here the structures of rare taxa (RT) and conditionally abundant and rare taxa (CART) from Sphagnum palustre peat (SP), S. palustre ectosphere (Ecto) and S. palustre endosphere (Endo) were investigated in the Dajiuhu Peatland, central China. Our results showed that plant compartment effects significantly altered the diversities and structures of bacterial communities. The Observed species and Simpson indices of RT and CART in alpha diversity significantly increased from Endo to SP, with those of Ecto in-between. The variations of community dissimilarities of RT and CART among compartments were consistent with those of whole bacterial communities (WBC). Network analysis indicated a non-random co-occurrence pattern of WBC and all keystone species are affiliated with RT and CART, indicating their important role in sustaining the WBC. Furthermore, the community structures of RT and CART in SP were significantly shaped by water table and total nitrogen content, which coincided with the correlations between WBC and environmental factors. Collectively, our results for the first time confirm the importance of rare species to bacterial communities through structural and predicted functional analyses, which expands our understanding of rare species in Sphagnum-associated microbial communities in subalpine peatlands.

Effects of Sphagnum Leachate on Competitive Sphagnum Microbiome Depend on Species and Time

Plant specialized metabolites play an important role in soil carbon (C) and nutrient fluxes. Through anti-microbial effects, they can modulate microbial assemblages and associated microbial-driven processes, such as nutrient cycling, so to positively or negatively cascade on plant fitness. As such, plant specialized metabolites can be used as a tool to supplant competitors. These compounds are little studied in bryophytes. This is especially notable in peatlands where Sphagnum mosses can dominate the vegetation and show strong interspecific competition. Sphagnum mosses form carpets where diverse microbial communities live and play a crucial role in Sphagnum fitness by regulating C and nutrient cycling. Here, by means of a microcosm experiment, we assessed to what extent moss metabolites of two Sphagnum species (S. fallax and S. divinum) modulate the competitive Sphagnum microbiome, with particular focus on microbial respiration. Using a reciprocal leachate experiment, we found that interactions between Sphagnum leachates and microbiome are species-specific. We show that both Sphagnum leachates differed in compound richness and compound relative abundance, especially sphagnum acid derivates, and that they include microbial-related metabolites. The addition of S. divinum leachate on the S. fallax microbiome immediately reduced microbial respiration (−95%). Prolonged exposition of S. fallax microbiome to S. divinum leachate destabilized the food web structure due to a modulation of microbial abundance. In particular, leachate addition decreased the biomass of testate amoebae and rotifers but increased that of ciliates. These changes did not influence microbial CO₂ respiration, suggesting that the structural plasticity of the food web leads to its functional resistance through the replacement of species that are functionally redundant. In contrast, S. fallax leachate neither affected S. divinum microbial respiration, nor microbial biomass. We, however, found that S. fallax leachate addition stabilized the food web structure associated to S. divinum by changing trophic interactions among species. The differences in allelopathic effects between both Sphagnum leachates might impact their competitiveness and affect species distribution at local scale. Our study further paves the way to better understand the role of moss and microbial specialized metabolites in peatland C dynamics.

Structural Variations of Bacterial Community Driven by Sphagnum Microhabitat Differentiation in a Subalpine Peatland

Sphagnum microbiomes play an important role in the northern peatland ecosystems. However, information about above and belowground microbiomes related to Sphagnum at subtropical area remains largely limited. In this study, microbial communities from Sphagnum palustre peat, S. palustre green part, and S. palustre brown part at the Dajiuhu Peatland, in central China were investigated via 16S rRNA gene amplicon sequencing. Results indicated that Alphaproteobacteria was the dominant class in all samples, and the classes Acidobacteria and Gammaproteobacteria were abundant in S. palustre peat and S. palustre brown part samples, respectively. In contrast, the class Cyanobacteria dominated in S. palustre green part samples. Microhabitat differentiation mainly contributes to structural differences of bacterial microbiome. In the S. palustre peat, microbial communities were significantly shaped by water table and total nitrogen content. Our study is a systematical investigation on above and belowground bacterial microbiome in a subalpine Sphagnum peatland and the results offer new knowledge about the distribution of bacterial microbiome associated with different microhabitats in subtropical area.

Plant Phenotypic Traits Eventually Shape Its Microbiota: A Common Garden Test

Plant genotype drives the development of plant phenotypes and the assembly of plant microbiota. The potential influence of the plant phenotypic characters on its microbiota is not well characterized and the co-occurrence interrelations for specific microbial taxa and plant phenotypic characters are poorly understood. We established a common garden experiment, which quantifies prokaryotic and fungal communities in the phyllosphere and rhizosphere of six spruce (Picea spp.) tree species, through Illumina amplicon sequencing. We tested for relationships between bacterial/archaeal and fungal communities and for the phenotypic characters of their plant hosts. Host phenotypic characters including leaf length, leaf water content, leaf water storage capacity, leaf dry mass per area, leaf nitrogen content, leaf phosphorous content, leaf potassium content, leaf δ¹³C values, stomatal conductance, net photosynthetic rate, intercellular carbon dioxide concentration, and transpiration rate were significantly correlated with the diversity and composition of the bacterial/archaeal and fungal communities. These correlations between plant microbiota and suites of host plant phenotypic characters suggest that plant genotype shape its microbiota by driving the development of plant phenotypes. This will advance our understanding of plant-microbe associations and the drivers of variation in plant and ecosystem function.

What Is the Role of Archaea in Plants? New Insights from the Vegetation of Alpine Bogs

Archaea are still an underdetected and little-studied part of the plant microbiome. We provide first and novel insights into Archaea as a functional component of the plant microbiome obtained by metagenomic analyses. Archaea were found to have the potential to interact with plants by (i) plant growth promotion through auxin biosynthesis, (ii) nutrient supply, and (iii) protection against abiotic stress.

The Archaea represent a significant component of the plant microbiome, whereas their function is still unclear. Different plant species representing the natural vegetation of alpine bogs harbor a substantial archaeal community originating from five phyla, 60 genera, and 334 operational taxonomic units (OTUs). We identified a core archaeome for all bog plants and ecosystem-specific, so far unclassified Archaea. In the metagenomic data set, Archaea were found to have the potential to interact with plants by (i) possible plant growth promotion through auxin biosynthesis, (ii) nutrient supply, and (iii) protection against abiotic (especially oxidative and osmotic) stress. The unexpectedly high degree of plant specificity supports plant-archaeon interactions. Moreover, functional signatures of Archaea reveal genetic capacity for the interplay with fungi and an important role in the carbon and nitrogen cycle: e.g., CO₂ and N₂ fixation. These facts reveal an important, yet unobserved role of the Archaea for plants as well as for the bog ecosystem.

IMPORTANCEArchaea are still an underdetected and little-studied part of the plant microbiome. We provide first and novel insights into Archaea as a functional component of the plant microbiome obtained by metagenomic analyses. Archaea were found to have the potential to interact with plants by (i) plant growth promotion through auxin biosynthesis, (ii) nutrient supply, and (iii) protection against abiotic stress.

Moss habitats distinctly affect their associated bacterial community structures as revealed by the high-throughput sequencing method

To better understand the factors that influence the distribution of bacteria associated with mosses, the communities inhabiting in five moss species from two different habitats in Beijing Songshan National Nature Reserve were investigated using the high-throughput sequencing method. The sequencing was performed based on the bacterial 16S rRNA and 16S rDNA libraries. Results showed that there are abundant bacteria inhabiting in all the mosses sampled. The taxonomic analysis of these bacteria showed that they mainly consisted of those in the phyla Proteobacteria and Actinobacteria, and seldom were from phylum Armatimonadetes, Bacteroidetes and Firmicutes. The hierarchical cluster tree, based on the OTU level, divided the bacteria associated with all samples into two branches according to the habitat types of the host (terrestrial and aquatic). The PCoA diagram further divided the bacterial compositions into four groups according to both types of habitats and the data sources (DNA and RNA). There were larger differences in the bacterial community composition in the mosses collected from aquatic habitat than those of terrestrial one, whether at the DNA or RNA level. Thus, this survey supposed that the habitat where the host was growing was a relevant factor influencing bacterial community composition. In addition, the bacterial community detected at the RNA level was more sensitive to the habitat of the growing host, which could also be proved by the significantly differences in the predicted function by PICRUSt and the metabolically active dominant genera between different groups. This study expands the knowledge about the interactions between mosses and microbes.

Infection of Soybean Plants with the Insect Bacterial Symbiont Burkholderia gladioli and Evaluation of Plant Fitness

To investigate the establishment and consequences of host-microbe interactions, it is important to develop controlled infection assays suitable for each system, as well as appropriate methods to evaluate successful infection and its associated effects. Here, we describe a procedure for bacterial inoculation of soybean plants, followed by the assessment of systemic infection and impact on plant fitness. Soybean (Glycine max) seedlings were mechanically wounded using a device that mimics insect herbivory and inoculated with known cell numbers of Burkholderia gladioli bacteria previously isolated from an insect host. The impact on the plants was evaluated by monitoring changes in height, time to flowering and chlorophyll content during plant development, and by quantifying seed production in comparison to plants inoculated with sterile water. The presence and proliferation of bacterial infection were examined in tissues from developed plants using quantitative PCR and fluorescence in situ hybridization (FISH).

Diverse fen plant communities enhance carbon-related multifunctionality, but do not mitigate negative effects of drought

Global change, like droughts, can destabilize the carbon sink function of peatlands, either directly or indirectly through changes in plant community composition. While the effects of drought and plant community composition on individual carbon (C) related processes are well understood, their effect on multiple C-related processes simultaneously-multifunctionality-is poorly known. We studied the effect of drought on four C-related processes (net and gross CO₂ exchange, methane fluxes, and dissolved organic carbon content) in a plant removal experiment. Plant functional type (PFT) removal (graminoids, herbs, Polytrichum spp., incl. combinations) negatively affected multifunctionality; most markedly when all PFTs were removed. Our results corroborate a negative drought effect on C-related multifunctionality. Drought reduced multifunctionality, and this reduction was again largest when all PFTs were removed. Our data further indicate that much of these negative drought effects were carried over and maintained from the initial removal treatment. These results suggest that while a high diversity in plant functional types is associated to high C-related multifunctionality, plant community assembly does not drive the ability of peatlands to withstand the negative impacts of drought on multifunctionality. Hence, to safeguard the carbon cycling function in intact peatlands, the effects of climate change on the functional composition of the peatland plant community needs to be minimized.

Diverse fen plant communities enhance carbon-related multifunctionality, but do not mitigate negative effects of drought

Global change, like droughts, can destabilize the carbon sink function of peatlands, either directly or indirectly through changes in plant community composition. While the effects of drought and plant community composition on individual carbon (C) related processes are well understood, their effect on multiple C-related processes simultaneously-multifunctionality-is poorly known. We studied the effect of drought on four C-related processes (net and gross CO₂ exchange, methane fluxes, and dissolved organic carbon content) in a plant removal experiment. Plant functional type (PFT) removal (graminoids, herbs, Polytrichum spp., incl. combinations) negatively affected multifunctionality; most markedly when all PFTs were removed. Our results corroborate a negative drought effect on C-related multifunctionality. Drought reduced multifunctionality, and this reduction was again largest when all PFTs were removed. Our data further indicate that much of these negative drought effects were carried over and maintained from the initial removal treatment. These results suggest that while a high diversity in plant functional types is associated to high C-related multifunctionality, plant community assembly does not drive the ability of peatlands to withstand the negative impacts of drought on multifunctionality. Hence, to safeguard the carbon cycling function in intact peatlands, the effects of climate change on the functional composition of the peatland plant community needs to be minimized.

Symbiont dynamics and strain diversity in the defensive mutualism between Lagria beetles and Burkholderia

Defensive mutualisms are often facultative in nature, and their evolutionary dynamics can be shaped by changes in local antagonist communities or arms races with coevolving antagonists. Under these conditions, selection may favour hosts that flexibly acquire symbionts producing compounds with bioactivity against current antagonists. Here, we study the prevalence, dynamics and strain diversity of Burkholderia gladioli bacteria in Lagria beetles, a recently described protective symbiosis involving vertical transmission and antifungal defense for the host eggs. In Lagria hirta, we investigate the fate of the bacteria during the host life cycle. Despite a transmission route relying solely on the females, the bacteria are present in both sexes during the larval stage, suggesting a potentially multifaceted defensive role. In L. hirta and L. villosa adults, culture-dependent and -independent techniques revealed that individual beetles harbour diverse Burkholderia strains from at least two different phylogenetic clades, yet all closely related to free-living B. gladioli. Interestingly, rearing the beetles in the laboratory strongly impacted symbiont strain profiles in both beetle species. Our findings highlight the dynamic nature of the B. gladioli-Lagria symbiosis and present this as a valuable system for studying multiple strain coinfections, as well as the evolutionary and ecological factors regulating defensive symbiosis.

Molybdenum-Based Diazotrophy in a Sphagnum Peatland in Northern Minnesota

Microbial N₂ fixation (diazotrophy) represents an important nitrogen source to oligotrophic peatland ecosystems, which are important sinks for atmospheric CO₂ and are susceptible to the changing climate. The objectives of this study were (i) to determine the active microbial group and type of nitrogenase mediating diazotrophy in an ombrotrophic Sphagnum-dominated peat bog (the S1 peat bog, Marcell Experimental Forest, Minnesota, USA); and (ii) to determine the effect of environmental parameters (light, O₂, CO₂, and CH₄) on potential rates of diazotrophy measured by acetylene (C₂H₂) reduction and ¹⁵N₂ incorporation. A molecular analysis of metabolically active microbial communities suggested that diazotrophy in surface peat was primarily mediated by Alphaproteobacteria (Bradyrhizobiaceae and Beijerinckiaceae). Despite higher concentrations of dissolved vanadium ([V] 11 nM) than molybdenum ([Mo] 3 nM) in surface peat, a combination of metagenomic, amplicon sequencing, and activity measurements indicated that Mo-containing nitrogenases dominate over the V-containing form. Acetylene reduction was only detected in surface peat exposed to light, with the highest rates observed in peat collected from hollows with the highest water contents. Incorporation of ¹⁵N₂ was suppressed 90% by O₂ and 55% by C₂H₂ and was unaffected by CH₄ and CO₂ amendments. These results suggest that peatland diazotrophy is mediated by a combination of C₂H₂-sensitive and C₂H₂-insensitive microbes that are more active at low concentrations of O₂ and show similar activity at high and low concentrations of CH₄ IMPORTANCE Previous studies indicate that diazotrophy provides an important nitrogen source and is linked to methanotrophy in Sphagnum-dominated peatlands. However, the environmental controls and enzymatic pathways of peatland diazotrophy, as well as the metabolically active microbial populations that catalyze this process, remain in question. Our findings indicate that oxygen levels and photosynthetic activity override low nutrient availability in limiting diazotrophy and that members of the Alphaproteobacteria (Rhizobiales) catalyze this process at the bog surface using the molybdenum-based form of the nitrogenase enzyme.

Antibiotic-producing symbionts dynamically transition between plant pathogenicity and insect-defensive mutualism

Pathogenic and mutualistic bacteria associated with eukaryotic hosts often lack distinctive genomic features, suggesting regular transitions between these lifestyles. Here we present evidence supporting a dynamic transition from plant pathogenicity to insect-defensive mutualism in symbiotic Burkholderia gladioli bacteria. In a group of herbivorous beetles, these symbionts protect the vulnerable egg stage against detrimental microbes. The production of a blend of antibiotics by B. gladioli, including toxoflavin, caryoynencin and two new antimicrobial compounds, the macrolide lagriene and the isothiocyanate sinapigladioside, likely mediate this defensive role. In addition to vertical transmission, these insect symbionts can be exchanged via the host plant and retain the ability to initiate systemic plant infection at the expense of the plant's fitness. Our findings provide a paradigm for the transition between pathogenic and mutualistic lifestyles and shed light on the evolution and chemical ecology of this defensive mutualism.

Adaptation Mechanisms in the Evolution of Moss Defenses to Microbes

Bryophytes, including mosses, liverworts and hornworts are early land plants that have evolved key adaptation mechanisms to cope with abiotic stresses and microorganisms. Microbial symbioses facilitated plant colonization of land by enhancing nutrient uptake leading to improved plant growth and fitness. In addition, early land plants acquired novel defense mechanisms to protect plant tissues from pre-existing microbial pathogens. Due to its evolutionary stage linking unicellular green algae to vascular plants, the non-vascular moss Physcomitrella patens is an interesting organism to explore the adaptation mechanisms developed in the evolution of plant defenses to microbes. Cellular and biochemical approaches, gene expression profiles, and functional analysis of genes by targeted gene disruption have revealed that several defense mechanisms against microbial pathogens are conserved between mosses and flowering plants. P. patens perceives pathogen associated molecular patterns by plasma membrane receptor(s) and transduces the signal through a MAP kinase (MAPK) cascade leading to the activation of cell wall associated defenses and expression of genes that encode proteins with different roles in plant resistance. After pathogen assault, P. patens also activates the production of ROS, induces a HR-like reaction and increases levels of some hormones. Furthermore, alternative metabolic pathways are present in P. patens leading to the production of a distinct metabolic scenario than flowering plants that could contribute to defense. P. patens has acquired genes by horizontal transfer from prokaryotes and fungi, and some of them could represent adaptive benefits for resistance to biotic stress. In this review, the current knowledge related to the evolution of plant defense responses against pathogens will be discussed, focusing on the latest advances made in the model plant P. patens.

Illumina sequencing-based community analysis of bacteria associated with different bryophytes collected from Tibet, China

Background

Previous studies on the bacteria associated with the bryophytes showed that there were abundant bacteria inhabited in/on these hosts. However, the type of bacteria and whether these discriminate between different bryophytes based on a particular factor remains largely unknown.

Results

This study was designed to analyze the biodiversity and community of the bacteria associated with ten liverworts and ten mosses using Illumina-sequencing techniques based on bacterial 16S rRNA gene. A total of 125,762 high quality sequences and 437 OTUs were obtained from twenty bryophytes. Generally, there were no obvious differences between the richness of bacteria associated with liverworts and mosses; however, the diversity was significantly higher in liverworts than in mosses. The taxonomic analyses showed that there were abundant bacteria inhabited with each bryophyte and those primarily detected in all samples were within the phyla Proteobacteria, Actinobacteria, Acidobacteria, Bacteroidetes, Armatimonadetes and Planctomycetes. In addition, bacteria assigned to Chloroflexi, Fibrobacteres, Gemmatimonadetes, Chlamydiae, group of TM6 and WCHB1-60 also appeared in part of the bryophytes. The assigned bacteria included those adapted to aquatic, anaerobic and even extreme drought environments, which is consistent with the bryophyte transition from aquatic to terrestrial conditions. Of them, approximately 10 recognized genera were shared by all the samples in a higher proportion, such as Burkholderia, Novosphingobium, Mucilaginibacter, Sorangium, Frankia, Frondihatitans, Haliangium, Rhizobacter, Granulicella and Hafnia, and 11 unclassified genera were also detected in all samples, which exhibited that large amounts of unclassified bacteria could interact with the bryophytes. The Heatmap and Principle Coordinate Analyses showed that bacteria associated with six mosses displayed a higher community similarity. Notably, the bacteria associated with another four mosses exhibited higher similarity with the ten liverworts.

Conclusions

The result of further analysis of the bacterial community in different bryophytes revealed that the phylogeny of hosts might portray a strong influence on the associated bacterial community and that niche also played important roles when the hosts were phylogenetically more similar. Further studies are needed to confirm the role of phylogeny on bacterial communities and determine the level of influence on predicting which bacteria is associated with the host.

Relative importance of local habitat complexity and regional factors for assemblages of oribatid mites (Acari: Oribatida) in Sphagnum peat bogs

We investigated communities of oribatid mites in five peat bogs in the north-west of the East European plain. We aimed to determine the extent to which geographic factors (latitude, separation distance), local environment (Sphagnum moss species, ground water level, biogeochemistry) and local habitat complexity (diversity of vascular plants and bryophytes in the surrounding plant community) influence diversity and community composition of Oribatida. There was a significant north-to-south increase in Oribatida abundance. In the variance partitioning, spatial factors explained 33.1 % of variability in abundance across samples; none of the environmental factors were significant. Across all bogs, Oribatida species richness and community composition were similar in Sphagnum rubellum and Sphagnum magellanicum, but significantly different and less diverse in Sphagnum cuspidatum. Sphagnum microhabitat explained 52.2 % of variability in Oribatida species richness, whereas spatial variables explained only 8.7 %. There was no distance decay in community similarity between bogs with increased geographical distance. The environmental variables explained 34.9 % of the variance in community structure, with vascular plants diversity, bryophytes diversity, and ground water level all contributing significantly; spatial variables explained 15.1 % of the total variance. Overall, only 50 % of the Oribatida community variance was explained by the spatial structure and environmental variables. We discuss relative importance of spatial and local environmental factors, and make general inferences about the formation of fauna in Sphagnum bogs.

Habitat heterogeneity and connectivity shape microbial communities in South American peatlands

Bacteria play critical roles in peatland ecosystems. However, very little is known of how habitat heterogeneity affects the structure of the bacterial communities in these ecosystems. Here, we used amplicon sequencing of the 16S rRNA and nifH genes to investigate phylogenetic diversity and bacterial community composition in three different sub-Antarctic peat bog aquatic habitats: Sphagnum magellanicum interstitial water, and water from vegetated and non-vegetated pools. Total and putative nitrogen-fixing bacterial communities from Sphagnum interstitial water differed significantly from vegetated and non-vegetated pool communities (which were colonized by the same bacterial populations), probably as a result of differences in water chemistry and biotic interactions. Total bacterial communities from pools contained typically aquatic taxa, and were more dissimilar in composition and less species rich than those from Sphagnum interstitial waters (which were enriched in taxa typically from soils), probably reflecting the reduced connectivity between the former habitats. These results show that bacterial communities in peatland water habitats are highly diverse and structured by multiple concurrent factors.

Dynamics of Viral Abundance and Diversity in a Sphagnum-Dominated Peatland: Temporal Fluctuations Prevail Over Habitat

Viruses impact microbial activity and carbon cycling in various environments, but their diversity and ecological importance in Sphagnum-peatlands are unknown. Abundances of viral particles and prokaryotes were monitored bi-monthly at a fen and a bog at two different layers of the peat surface. Viral particle abundance ranged from 1.7 x 10⁶ to 5.6 x 10⁸ particles mL^-1, and did not differ between fen and bog but showed seasonal fluctuations. These fluctuations were positively correlated with prokaryote abundance and dissolved organic carbon, and negatively correlated with water-table height and dissolved oxygen. Using shotgun metagenomics we observed a shift in viral diversity between winter/spring and summer/autumn, indicating a seasonal succession of viral communities, mainly driven by weather-related environmental changes. Based on the seasonal asynchrony between viral and microbial diversity, we hypothesize a seasonal shift in the active microbial communities associated with a shift from lysogenic to lytic lifestyles. Our results suggest that temporal variations of environmental conditions rather than current habitat differences control the dynamics of virus-host interactions in Sphagnum-dominated peatlands.

Nitrous oxide emission potentials of Burkholderia species isolated from the leaves of a boreal peat moss Sphagnum fuscum*

Using a culture-based nitrous oxide (N2O) emission assay, three active N2O emitters were isolated from Sphagnum fuscum leaves and all identified as members of Burkholderia. These isolates showed N2O emission in the medium supplemented with but not with , and Burkholderia sp. SF-E2 showed the most efficient N2O emission (0.20 μg·vial−1·day−1) at 1.0 mM KNO3. In Burkholderia sp. SF-E2, the optimum pH for N2O production was 5.0, close to that of the phyllosphere of Sphagnum mosses, while the optimum temperature was uniquely over 30 °C. The stimulating effect of additional 1.5 mM sucrose on N2O emission was ignorable, but Burkholderia sp. SF-E2 upon exposure to 100 mg·L−1  E-caffeic acid showed uniquely 67-fold higher N2O emission. All of the three N2O emitters were negative in both acetylene inhibition assay and PCR assay for nosZ-detection, suggesting that N2O reductase or the gene itself is missing in the N2O-emitting Burkholderia.

Mining for Nonribosomal Peptide Synthetase and Polyketide Synthase Genes Revealed a High Level of Diversity in the Sphagnum Bog Metagenome

Sphagnum bog ecosystems are among the oldest vegetation forms harboring a specific microbial community and are known to produce an exceptionally wide variety of bioactive substances. Although the Sphagnum metagenome shows a rich secondary metabolism, the genes have not yet been explored. To analyze nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs), the diversity of NRPS and PKS genes in Sphagnum-associated metagenomes was investigated by in silico data mining and sequence-based screening (PCR amplification of 9,500 fosmid clones). The in silico Illumina-based metagenomic approach resulted in the identification of 279 NRPSs and 346 PKSs, as well as 40 PKS-NRPS hybrid gene sequences. The occurrence of NRPS sequences was strongly dominated by the members of the Protebacteria phylum, especially by species of the Burkholderia genus, while PKS sequences were mainly affiliated with Actinobacteria. Thirteen novel NRPS-related sequences were identified by PCR amplification screening, displaying amino acid identities of 48% to 91% to annotated sequences of members of the phyla Proteobacteria, Actinobacteria, and Cyanobacteria. Some of the identified metagenomic clones showed the closest similarity to peptide synthases from Burkholderia or Lysobacter, which are emerging bacterial sources of as-yet-undescribed bioactive metabolites. This report highlights the role of the extreme natural ecosystems as a promising source for detection of secondary compounds and enzymes, serving as a source for biotechnological applications.

Understanding diversity patterns in bacterioplankton communities from a sub-Antarctic peatland

Bacterioplankton communities inhabiting peatlands have the potential to influence local ecosystem functions. However, most microbial ecology research in such wetlands has been done in ecosystems (mostly peat soils) of the Northern Hemisphere, and very little is known of the factors that drive bacterial community assembly in other regions of the world. In this study, we used high-throughput sequencing to analyse the structure of the bacterial communities in five pools located in a sub-Antarctic peat bog (Tierra del Fuego, Argentina), and tested for relationships between bacterial communities and environmental conditions. Bacterioplankton communities in peat bog pools were diverse and dominated by members of the Proteobacteria, Actinobacteria, Bacteroidetes and Verrucomicrobia. Community structure was largely explained by differences in hydrological connectivity, pH and nutrient status (ombrotrophic versus minerotrophic pools). Bacterioplankton communities in ombrotrophic pools showed phylogenetic clustering, suggesting a dominant role of deterministic processes in shaping these assemblages. These correlations between habitat characteristics and bacterial diversity patterns provide new insights into the factors regulating microbial populations in peatland ecosystems.

Linking soil microbial communities to vascular plant abundance along a climate gradient

The ongoing expansion of shrub cover in response to climate change represents a unique opportunity to explore the link between soil microbial communities and vegetation changes. This link is particularly important in peatlands where shrub expansion is expected to feed back negatively on the carbon sink capacity of these ecosystems. Microbial community structure and function were measured seasonally in four peatlands located along an altitude gradient representing a natural gradient of climate and associated vascular plant abundance. We show that increased soil temperature and reduced water content are associated with greater vascular plant biomass, in particular that of ericoids, and that this, in turn, is correlated with greater microbial biomass. More specifically, microbial community structure is characterized by an increasing dominance of fungi over bacteria with improved soil oxygenation. We also found that the carbon and nitrogen stoichiometry of microbial biomass differs in relation to soil microbial community structure and that this is ultimately associated with a different investment in extracellular enzymatic activity. Our findings highlight the fact that the determination of the structural identity of microbial communities can help to explain the biogeochemical dynamics of organic matter and provide a better understanding of ecosystem response to environmental changes.

Bacterial networks and co-occurrence relationships in the lettuce root microbiota

Lettuce is one of the most common raw foods worldwide, but occasionally also involved in pathogen outbreaks. To understand the correlative structure of the bacterial community as a network, we studied root microbiota of eight ancient and modern Lactuca sativa cultivars and the wild ancestor Lactuca serriola by pyrosequencing of 16S rRNA gene amplicon libraries. The lettuce microbiota was dominated by Proteobacteria and Bacteriodetes, as well as abundant Chloroflexi and Actinobacteria. Cultivar specificity comprised 12.5% of the species. Diversity indices were not different between lettuce cultivar groups but higher than in L. serriola, suggesting that domestication lead to bacterial diversification in lettuce root system. Spearman correlations between operational taxonomic units (OTUs) showed that co-occurrence prevailed over co-exclusion, and complementary fluorescence in situ hybridization-confocal laser scanning microscopy (FISH-CLSM) analyses revealed that this pattern results from both potential interactions and habitat sharing. Predominant taxa, such as Pseudomonas, Flavobacterium and Sphingomonadaceae rather suggested interactions, even though these are not necessarily part of significant modules in the co-occurrence networks. Without any need for complex interactions, single organisms are able to invade into this microbial network and to colonize lettuce plants, a fact that can influence the susceptibility to pathogens. The approach to combine co-occurrence analysis and FISH-CLSM allows reliably reconstructing and interpreting microbial interaction networks.

The Sphagnum microbiome supports bog ecosystem functioning under extreme conditions

Sphagnum-dominated bogs represent a unique yet widely distributed type of terrestrial ecosystem and strongly contribute to global biosphere functioning. Sphagnum is colonized by highly diverse microbial communities, but less is known about their function. We identified a high functional diversity within the Sphagnum microbiome applying an Illumina-based metagenomic approach followed by de novo assembly and MG-RAST annotation. An interenvironmental comparison revealed that the Sphagnum microbiome harbours specific genetic features that distinguish it significantly from microbiomes of higher plants and peat soils. The differential traits especially support ecosystem functioning by a symbiotic lifestyle under poikilohydric and ombrotrophic conditions. To realise a plasticity-stability balance, we found abundant subsystems responsible to cope with oxidative and drought stresses, to exchange (mobile) genetic elements, and genes that encode for resistance to detrimental environmental factors, repair and self-controlling mechanisms. Multiple microbe-microbe and plant-microbe interactions were also found to play a crucial role as indicated by diverse genes necessary for biofilm formation, interaction via quorum sensing and nutrient exchange. A high proportion of genes involved in nitrogen cycle and recycling of organic material supported the role of bacteria for nutrient supply. 16S rDNA analysis indicated a higher structural diversity than that which had been previously detected using PCR-dependent techniques. Altogether, the diverse Sphagnum microbiome has the ability to support the life of the host plant and the entire ecosystem under changing environmental conditions. Beyond this, the moss microbiome presents a promising bio-resource for environmental biotechnology - with respect to novel enzymes or stress-protecting bacteria.

Insights into functional bacterial diversity and its effects on Alpine bog ecosystem functioning

Plant-associated bacteria are important for the growth and health of their host, but little is known about its functional diversity and impact on ecosystem functioning. We studied bacterial nitrogen fixation and methane oxidation from indicator Sphagnum mosses in Alpine bogs to test a hypothesis that the plant microbiome contained different functional patterns depending on their functions within the ecosystem. A high abundance and diversity of nitrogenase genes were detected, mostly specific for each Sphagnum. In contrast, methanotrophs formed highly similar patterns despite a high abundance and diversity of methane monooxygenase genes. Our hypothesis was supported by these contrasting functional patterns together with the result that the Sphagnum sporophyte contained a high proportion of specific diazotrophs (45.5%) but no potential methanotrophs. While essential for plant growth under nutrient-limited conditions, nitrogen-fixing bacteria were highly specific and transferred with the sporophyte unlike the ubiquitous methanotrophs which are important for the climate-relevant ecosystem itself.

Vertical transmission explains the specific Burkholderia pattern in Sphagnum mosses at multi-geographic scale

The betaproteobacterial genus Burkholderia is known for its versatile interactions with its hosts that can range from beneficial to pathogenic. A plant-beneficial-environmental (PBE) Burkholderia cluster was recently separated from the pathogen cluster, yet still little is known about burkholderial diversity, distribution, colonization, and transmission patterns on plants. In our study, we applied a combination of high-throughput molecular and microscopic methods to examine the aforementioned factors for Burkholderia communities associated with Sphagnum mosses - model plants for long-term associations - in Austrian and Russian bogs. Analysis of 16S rRNA gene amplicons libraries revealed that most of the Burkholderia are part of the PBE group, but a minor fraction was closely related to B. glathei and B. andropogonis from the pathogen cluster. Notably, Burkholderia showed highly similar composition patterns for each moss species independent of the geographic region, and Burkholderia-specific fluorescent in situ hybridization of Sphagnum gametophytes exhibited similar colonization patterns in different Sphagnum species at multi-geographic scales. To explain these patterns, we compared the compositions of the surrounding water, gametophyte-, and sporophyte-associated microbiome at genus level and discovered that Burkholderia were present in the Sphagnum sporophyte and gametophyte, but were absent in the flark water. Therefore, Burkholderia is a part of the core microbiome transmitted from the moss sporophyte to the gametophyte. This suggests a vertical transmission of Burkholderia strains, and thus underlines their importance for the plants themselves.