Temperature and CO2 interactively drive shifts in the compositional and functional structure of peatland protist communities

Microbes affect the global carbon cycle that influences climate change and are in turn influenced by environmental change. Here, we use data from a long-term whole-ecosystem warming experiment at a boreal peatland to answer how temperature and CO2 jointly influence communities of abundant, diverse, yet poorly understood, non-fungi microbial Eukaryotes (protists). These microbes influence ecosystem function directly through photosynthesis and respiration, and indirectly, through predation on decomposers (bacteria and fungi). Using a combination of high-throughput fluid imaging and 18S amplicon sequencing, we report large climate-induced, community-wide shifts in the community functional composition of these microbes (size, shape, and metabolism) that could alter overall function in peatlands. Importantly, we demonstrate a taxonomic convergence but a functional divergence in response to warming and elevated CO2 with most environmental responses being contingent on organismal size: warming effects on functional composition are reversed by elevated CO2 and amplified in larger microbes but not smaller ones. These findings show how the interactive effects of warming and rising CO2 levels could alter the structure and function of peatland microbial food webs-a fragile ecosystem that stores upwards of 25% of all terrestrial carbon and is increasingly threatened by human exploitation.

Characterization of endophytic bacteriome diversity and associated beneficial bacteria inhabiting a macrophyte Eichhornia crassipes

Introduction

The endosphere of a plant is an interface containing a thriving community of endobacteria that can affect plant growth and potential for bioremediation. Eichhornia crassipes is an aquatic macrophyte, adapted to estuarine and freshwater ecosystems, which harbors a diverse bacterial community. Despite this, we currently lack a predictive understanding of how E. crassipes taxonomically structure the endobacterial community assemblies across distinct habitats (root, stem, and leaf).

Methods

In the present study, we assessed the endophytic bacteriome from different compartments using 16S rRNA gene sequencing analysis and verified the in vitro plant beneficial potential of isolated bacterial endophytes of E. crassipes.

Results and discussion

Plant compartments displayed a significant impact on the endobacterial community structures. Stem and leaf tissues were more selective, and the community exhibited a lower richness and diversity than root tissue. The taxonomic analysis of operational taxonomic units (OTUs) showed that the major phyla belonged to Proteobacteria and Actinobacteriota (> 80% in total). The most abundant genera in the sampled endosphere was Delftia in both stem and leaf samples. Members of the family Rhizobiaceae, such as in both stem and leaf samples. Members of the family Rhizobiaceae, such as Allorhizobium- Neorhizobium-Pararhizobium-Rhizobium were mainly associated with leaf tissue, whereas the genera Nannocystis and Nitrospira from the families Nannocystaceae and Nitrospiraceae, respectively, were statistically significantly associated with root tissue. Piscinibacter and Steroidobacter were putative keystone taxa of stem tissue. Most of the endophytic bacteria isolated from E. crassipes showed in vitro plant beneficial effects known to stimulate plant growth and induce plant resistance to stresses. This study provides new insights into the distribution and interaction of endobacteria across different compartments of E. crassipes Future study of endobacterial communities, using both culture-dependent and -independent techniques, will explore the mechanisms underlying the wide-spread adaptability of E. crassipesto various ecosystems and contribute to the development of efficient bacterial consortia for bioremediation and plant growth promotion.

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.

Endophytes from Halotolerant Plants Aimed to Overcome Salinity and Draught

The aim of our research was to study the endosphere of four halophytic plants: Salicornia europaea L., Salsola australis (R.Br.), Bassia sedoides (Pall.) and Kochia prostrata (L.) Schrad. from arid and saline areas of the Stavropol Territory, Russia. In total, 28 endophyte strains were isolated from the roots and stems of these halophytic plants. Most of the isolates (23 out of 28) were identified as Bacillus sp. while others belonged to the genera Oceanobacillus, Paenibacillus, Pantoea, Alcaligenes and Myroides. Three strains of Bacillus sp. (Se5R, Se1-1R, and Se1-3S), isolated from the S. europaea were capable of growth at 55 °C and in 10% of NaCl. Strains Se1-4S, Kp20-2S, and Bs11-2S Bacillus sp. (isolated from the S. australis, K. prostrata and B. sedoides, respectively) demonstrated strong plant growth promoting activity: 85-265% over control lettuce plants and a high degree of growth suppression (59.1-81.2%) of pathogenic fungi Fusarium oxysporum, Bipolaris sorokiniana and Rhizoctonia solani. Selected strains can be promising candidates for the development of bioinoculants to facilitate salt soil phytoremediation and be beneficial for mitigating the salt stress to the plants growing in salt-affected 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.

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

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

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.

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.

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.

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.

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.

Experimental warming alters the community composition, diversity, and N2 fixation activity of peat moss (Sphagnum fallax) microbiomes

Sphagnum-dominated peatlands comprise a globally important pool of soil carbon (C) and are vulnerable to climate change. While peat mosses of the genus Sphagnum are known to harbor diverse microbial communities that mediate C and nitrogen (N) cycling in peatlands, the effects of climate change on Sphagnum microbiome composition and functioning are largely unknown. We investigated the impacts of experimental whole-ecosystem warming on the Sphagnum moss microbiome, focusing on N2 fixing microorganisms (diazotrophs). To characterize the microbiome response to warming, we performed next-generation sequencing of small subunit (SSU) rRNA and nitrogenase (nifH) gene amplicons and quantified rates of N2 fixation activity in Sphagnum fallax individuals sampled from experimental enclosures over 2 years in a northern Minnesota, USA bog. The taxonomic diversity of overall microbial communities and diazotroph communities, as well as N2 fixation rates, decreased with warming (p < 0.05). Following warming, diazotrophs shifted from a mixed community of Nostocales (Cyanobacteria) and Rhizobiales (Alphaproteobacteria) to predominance of Nostocales. Microbiome community composition differed between years, with some diazotroph populations persisting while others declined in relative abundance in warmed plots in the second year. Our results demonstrate that warming substantially alters the community composition, diversity, and N2 fixation activity of peat moss microbiomes, which may ultimately impact host fitness, ecosystem productivity, and C storage potential in peatlands.

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.

Sunagoke Moss (Racomitrium japonicum) Used for Greening Roofs Is Severely Damaged by Sclerotium delphinii and Protected by a Putative Bacillus amyloliquefaciens Isolate

Mosses are ecologically important plants also used for greening, gardening, and decorative purposes. Knowledge of the microbial flora associated with mosses is expected to be important for control and preservation of global and local environments. However, the moss-associated microbial flora is often poorly known. Moss-associated fungi and bacteria may promote plant growth and pest control, but they may be alternative hosts for pathogens of vascular plants. In this study, the fungus Sclerotinia delphinii was identified for the first time as a pathogen that causes severe damage to Sunagoke moss (Racomitrium japonicum). This moss is used for greening roofs and walls of buildings in urban environments owing to its notable tolerance of environmental stresses. Inoculation with the S. delphinii strain SR1 of the mono- and dicotyledonous seed plants Hordeum vulgare, Brassica rapa var. pekinensis, Lactuca sativa, and Spinacia oleracea, in addition to the liverwort Marchantia polymorpha and the moss Physcomitrella patens, showed that the fungus has a wide host range. Colonization with SR1 progressed more rapidly in non-vascular than in vascular plant species. Studies with P. patens under controlled conditions showed that SR1 secreted a fluid during colonization. Treatment with the secretion induced production of reactive oxygen species in the moss. Endogenous peroxidase partially inhibited SR1 colonization of P. patens. A bacterial isolate, most likely Bacillus amyloliquefaciens, that coexists with R. japonicum was antagonistic to SR1 growth. Taken together, the present results suggest that fungal colonization of mosses may be prevented by a peroxidase secreted by the moss and an antagonistic bacterium coexisting in the moss habitat. The findings suggest that there is potential to apply biological control measures for protection of mosses against fungal pathogens.

Microbial communities associated with barley growing in an oil sands reclamation area in Alberta, Canada

Microbial communities that colonize the plant rhizosphere and the root interior can ameliorate plant stress and promote growth. These plant–microbe associations are being investigated to assist in reclamation soils in northern Alberta. This study assessed the diversity of bacterial species associated with barley plants growing at different cover managements and slope positions in an oil sands reclamation area. Phospholipid fatty acid analysis of the microbial communities indicated that both cover type and slope, in addition to soil total and organic carbon, NH4+, and organic matter, were significant determinants of microbial community composition. However, analysis of denaturing gel gradient electrophoresis (DGGE) banding patterns revealed that while most bulk and rhizosphere soils differentiated by cover management, no clustering was observed in endophytes. In addition, techniques to assess culture-dependent endophytic bacteria revealed a dominance of the class Gammaproteobacteria, in which Enterobacteriaceae (44%), Xanthomonaceae (30%), and Pseudomonaceae (26%) were the most abundant families in this class. Several endophytic isolates also matched those from DGGE profiles. The results of this study suggest that plants growing on oil sands reclamation covers host a wide range of bacterial endophytes, which should be assessed as to their potential to assist plant establishment and growth at such sites.

The influence of oxygen and methane on nitrogen fixation in subarctic Sphagnum mosses

Biological nitrogen fixation is an important source of bioavailable nitrogen in Sphagnum dominated peatlands. Sphagnum mosses harbor a diverse microbiome including nitrogen-fixing and methane (CH4) oxidizing bacteria. The inhibitory effect of oxygen on microbial nitrogen fixation is documented for many bacteria. However, the role of nitrogen-fixing methanotrophs in nitrogen supply to Sphagnum peat mosses is not well explored. Here, we investigated the role of both oxygen and methane on nitrogen fixation in subarctic Sphagnum peat mosses. Five species of Sphagnum mosses were sampled from two mesotrophic and three oligotrophic sites within the Lakkasuo peatland in Orivesi, central Finland. Mosses were incubated under either ambient or low oxygen conditions in the presence or absence of methane. Stable isotope activity assays revealed considerable nitrogen-fixing and methane-assimilating rates at all sites (1.4 ± 0.2 µmol 15N-N2 g-1 DW day-1 and 12.0 ± 1.1 µmol 13C-CH4 g-1 DW day-1, respectively). Addition of methane did not stimulate incorporation of 15N-nitrogen into biomass, whereas oxygen depletion increased the activity of the nitrogen-fixing community. Analysis of the 16S rRNA genes at the bacterial community level showed a very diverse microbiome that was dominated by Alphaproteobacteria in all sites. Bona fide methane-oxidizing taxa were not very abundant (relative abundance less than 0.1%). Based on our results we conclude that methanotrophs did not contribute significantly to nitrogen fixation in the investigated peatlands.

Long-Term Recovery of Microbial Communities in the Boreal Bryosphere Following Fire Disturbance

Our study used a ∼360-year fire chronosequence in northern Sweden to investigate post-fire microbial community dynamics in the boreal bryosphere (the living and dead parts of the feather moss layer on the forest floor, along with the associated biota). We anticipated systematic changes in microbial community structure and growth strategy with increasing time since fire (TSF) and used amplicon pyrosequencing to establish microbial community structure. We also recorded edaphic factors (relating to pH, C and N accumulation) and the physical characteristics of the feather moss layer. The molecular analyses revealed an unexpectedly diverse microbial community. The structure of the community could be largely explained by just two factors, TSF and pH, although the importance of TSF diminished as the forest recovered from disturbance. The microbial communities on the youngest site (TSF = 14 years) were clearly different from older locations (>100 years), suggesting relatively rapid post-fire recovery. A shift towards Proteobacterial taxa on older sites, coupled with a decline in the relative abundance of Acidobacteria, suggested an increase in resource availability with TSF. Saprotrophs dominated the fungal community. Mycorrhizal fungi appeared to decline in abundance with TSF, possibly due to changing N status. Our study provided evidence for the decadal-scale legacy of burning, with implications for boreal forests that are expected to experience more frequent burns over the course of the next century.

The Bacterial Signature of Leptospermum scoparium (Mānuka) Reveals Core and Accessory Communities with Bioactive Properties

Leptospermum scoparium or mānuka is a New Zealand native medicinal plant that produces an essential oil with antimicrobial properties. This is the first study to investigate the structure and bioactivity of endophytic bacteria in mānuka by using a combination of cultivation-independent (DGGE) and dependent approaches. A total of 23 plants were sampled across three sites. Plants were considered either immature (3-8 years) or mature (>20 years). The endophyte community structure and richness was affected by plant tissue and bacterial communities became more stable and uniform as plant maturity increased. A total of 192 culturable bacteria were recovered from leaves, stems and roots. Some bacterial isolates showed in vitro biocontrol activity against two fungal pathogens, Ilyonectria liriodendri and Neofusicoccum luteum and a bacterial pathogen, Pseudomonas syringae pv. actinidiae. A high proportion of bacterial endophytes could produce siderophores and solubilise phosphate in vitro. Gammaproteobacteria was the most variable class, representing the majority of cultivated bacteria with bioactivity.

The Sphagnum microbiome: new insights from an ancient plant lineage

57 I. 57 II. 58 III. 59 IV. 59 V. 61 VI. 62 63 References 63 SUMMARY: Peat mosses of the genus Sphagnum play a major role in global carbon storage and dominate many northern peatland ecosystems, which are currently being subjected to some of the most rapid climate changes on Earth. A rapidly expanding database indicates that a diverse community of microorganisms is intimately associated with Sphagnum, inhabiting the tissues and surface of the plant. Here we summarize the current state of knowledge regarding the Sphagnum microbiome and provide a perspective for future research directions. Although the majority of the microbiome remains uncultivated and its metabolic capabilities uncharacterized, prokaryotes and fungi have the potential to act as mutualists, symbionts, or antagonists of Sphagnum. For example, methanotrophic and nitrogen-fixing bacteria may benefit the plant host by providing up to 20-30% of Sphagnum carbon and nitrogen, respectively. Next-generation sequencing approaches have enabled the detailed characterization of microbiome community composition in peat mosses. However, as with other ecologically or economically important plants, our knowledge of Sphagnum-microbiome associations is in its infancy. In order to attain a predictive understanding of the role of the microbiome in Sphagnum productivity and ecosystem function, the mechanisms of plant-microbiome interactions and the metabolic potential of constituent microbial populations must be revealed.

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.

Endophytic microorganisms--promising applications in bioremediation of greenhouse gases

Bioremediation is a technique that uses microbial metabolism to remove pollutants. Various techniques and strategies of bioremediation (e.g., phytoremediation enhanced by endophytic microorganisms, rhizoremediation) can mainly be used to remove hazardous waste from the biosphere. During the last decade, this specific technique has emerged as a potential cleanup tool only for metal pollutants. This situation has changed recently as a possibility has appeared for bioremediation of other pollutants, for instance, volatile organic compounds, crude oils, and radionuclides. The mechanisms of bioremediation depend on the mobility, solubility, degradability, and bioavailability of contaminants. Biodegradation of pollutions is associated with microbial growth and metabolism, i.e., factors that have an impact on the process. Moreover, these factors have a great influence on degradation. As a result, recognition of natural microbial processes is indispensable for understanding the mechanisms of effective bioremediation. In this review, we have emphasized the occurrence of endophytic microorganisms and colonization of plants by endophytes. In addition, the role of enhanced bioremediation by endophytic bacteria and especially of phytoremediation is presented.