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

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.

Comparisons of diazotrophic communities in native and agricultural desert ecosystems reveal plants as important drivers in diversity.

Diazotrophs provide the only biological source of fixed atmospheric nitrogen in the biosphere. Although they are the key player for plant-available nitrogen, less is known about their diversity and potential importance in arid ecosystems. We investigated the nitrogenase gene diversity in native and agricultural desert soil as well as within root-associated microbiota of medicinal plants grown in Egypt through the combination of nifH-specific qPCR, fingerprints, amplicon pyrosequencing and fluorescence in situ hybridization-confocal laser scanning microscopy. Although the diazotrophic microbiota were characterized by generally high abundances and diversity, statistically significant differences were found between both soils, the different microhabitats, and between the investigated plants (Matricaria chamomilla L., Calendula officinalis L. and Solanum distichum Schumach. and Thonn.). We observed a considerable community shift from desert to agriculturally used soil that demonstrated a higher abundance and diversity in the agro-ecosystem. The endorhiza was characterized by lower abundances and only a subset of species when compared to the rhizosphere. While the microbiomes of the Asteraceae were similar and dominated by potential root-nodulating rhizobia acquired primarily from soil, the perennial S. distichum generally formed associations with free-living nitrogen fixers. These results underline the importance of diazotrophs in desert ecosystems and additionally identify plants as important drivers in functional gene pool diversity.

The core microbiome bonds the Alpine bog vegetation to a transkingdom metacommunity.

Bog ecosystems fulfil important functions in Earth's carbon and water turnover. While plant communities and their keystone species Sphagnum have been well studied, less is known about the microbial communities associated with them. To study our hypothesis that bog plants share an essential core of their microbiome despite their different phylogenetic origins, we analysed four plant community plots with 24 bryophytes, vascular plants and lichen species in two Alpine bogs in Austria by 16S rDNA amplicon sequencing followed by bioinformatic analyses. The overall bog microbiome was classified into 32 microbial phyla, while Proteobacteria (30.8%), Verrucomicrobia (20.3%) and Planctomycetes (15.1%) belonged to the most abundant groups. Interestingly, the archaeal phylum Euryarcheota represented 7.2% of total microbial abundance. However, a high portion of micro-organisms remained unassigned at phylum and class level, respectively. The core microbiome of the bog vegetation contained 177 operational taxonomic units (OTUs) (150 526 seq.) and contributed to 49.5% of the total microbial abundance. Only a minor portion of associated core micro-organisms was host specific for examined plant groups (5.9-11.6%). Using our new approach to analyse plant-microbial communities in an integral framework of ecosystem, vegetation and microbiome, we demonstrated that bog vegetation harboured a core microbiome that is shared between plants and lichens over the whole ecosystem and formed a transkingdom metacommunity. All micro- and macro-organisms are connected to keystone Sphagnum mosses via set of microbial species, for example Burkholderia bryophila which was found associated with a wide spectrum of host plants and is known for a beneficial plant-microbe interaction.

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.

Sphagnum mosses harbour highly specific bacterial diversity during their whole lifecycle.

Knowledge about Sphagnum-associated microbial communities, their structure and their origin is important to understand and maintain climate-relevant Sphagnum-dominated bog ecosystems. We studied bacterial communities of two cosmopolitan Sphagnum species, which are well adapted to different abiotic parameters (Sphagnum magellanicum, which are strongly acidic and ombrotrophic, and Sphagnum fallax, which are weakly acidic and mesotrophic), in three Alpine bogs in Austria by a multifaceted approach. Great differences between bacterial fingerprints of both Sphagna were found independently from the site. This remarkable specificity was confirmed by a cloning and a deep sequencing approach. Besides the common Alphaproteobacteria, we found a discriminative spectrum of bacteria; although Gammaproteobacteria dominated S. magellanicum, S. fallax was mainly colonised by Verrucomicrobia and Planctomycetes. Using this information for fluorescent in situ hybridisation analyses, corresponding colonisation patterns for Alphaproteobacteria and Planctomycetes were detected. Bacterial colonies were found in high abundances inside the dead big hyalocytes, but they were always connected with the living chlorocytes. Using multivariate statistical analysis, the abiotic factors nutrient richness and pH were identified to modulate the composition of Sphagnum-specific bacterial communities. Interestingly, we found that the immense bacterial diversity was transferred via the sporophyte to the gametophyte, which can explain the high specificity of Sphagnum-associated bacteria over long distances. In contrast to higher plants, which acquire their bacteria mainly from the environment, mosses as the phylogenetically oldest land plants maintain their bacterial diversity within the whole lifecycle.

Similar diversity of alphaproteobacteria and nitrogenase gene amplicons on two related sphagnum mosses.

Sphagnum mosses represent a main vegetation component in ombrotrophic wetlands. They harbor a specific and diverse microbial community with essential functions for the host. To understand the extend of host specificity and impact of environment, Sphagnum fallax and Sphagnum angustifolium, two phylogenetically closely related species, which show distinct habitat preference with respect to the nutrient level, were analyzed by a multifaceted approach. Microbial fingerprints obtained by PCR-single-strand conformation polymorphism of 16S rRNA and nitrogenase-encoding (nifH) genes were highly similar for both Sphagnum species. Similarity was confirmed for colonization patterns obtained by fluorescence in situ hybridization (FISH) coupled with confocal laser scanning microscopy (CLSM): Alphaproteobacteria were the main colonizers inside the hyaline cells of Sphagnum leaves. A deeper survey of Alphaproteobacteria by 16S rRNA gene amplicon sequencing reveals a high diversity with Acidocella, Acidisphaera, Rhodopila, and Phenylobacterium as major genera for both mosses. Nitrogen fixation is an important function of Sphagnum-associated bacteria, which is fulfilled by microbial communities of Sphagna in a similar way. NifH libraries of Sphagnum-associated microbial communities were characterized by high diversity and abundance of Alphaproteobacteria but contained also diverse amplicons of other taxa, e.g., Cyanobacteria and Deltaproteobacteria. Statistically significant differences between the microbial communities of both Sphagnum species could not be discovered in any of the experimental approach. Our results show that the same close relationship, which exists between the physical, morphological, and chemical characteristics of Sphagnum mosses and the ecology and function of bog ecosystems, also connects moss plantlets with their associated bacterial communities.