Strong Regionality and Dominance of Anaerobic Bacterial Taxa Characterize Diazotrophic Bacterial Communities of the Arcto-Alpine Plant Species Oxyria digyna and Saxifraga oppositifolia

This is an electronic reprint of the original article. This reprint may differ from the original in pagination and typographic detail. Author(s): Title: Year: Version: Please cite the original version: All material supplied via JYX is protected by copyright and other intellectual property rights, and duplication or sale of all or part of any of the repository collections is not permitted, except that material may be duplicated by you for your research use or educational purposes in electronic or print form. You must obtain permission for any other use. Electronic or print copies may not be offered, whether for sale or otherwise to anyone who is not an authorised user. Strong Regionality and Dominance of Anaerobic Bacterial Taxa Characterize Diazotrophic Bacterial Communities of the Arcto-Alpine Plant Species Oxyria digyna and Saxifraga oppositifolia Gopala Krishnan, Manoj Kumar; van Elsas, Jan Dirk; Nissinen, Riitta Gopala Krishnan, M. K., van Elsas, J. D., & Nissinen, R. (2017). Strong Regionality and Dominance of Anaerobic Bacterial Taxa Characterize Diazotrophic Bacterial Communities of the Arcto-Alpine Plant Species Oxyria digyna and Saxifraga oppositifolia. Frontiers in Microbiology, 8, Article 1972. https://doi.org/10.3389/fmicb.2017.01972 2017 ORIGINAL RESEARCH published: 13 October 2017 doi: 10.3389/fmicb.2017.01972 Frontiers in Microbiology | www.frontiersin.org 1October 2017 | Volume 8 | Article 1972 Edited by: Davide Bulgarelli, University of Dundee, United Kingdom Reviewed by: Adrian Ho, Leibniz University of Hanover, Germany Silvia Proietti, Università degli Studi della Tuscia, Italy *Correspondence: Riitta Nissinen [email protected] Specialty section: This article was submitted to Plant Microbe Interactions, a section of the journal Frontiers in Microbiology Received: 01 June 2017 Accepted: 25 September 2017 Published: 13 October 2017 Citation: Kumar M, van Elsas JD and Nissinen R (2017) Strong Regionality and Dominance of Anaerobic Bacterial Taxa Characterize Diazotrophic Bacterial Communities of the Arcto-Alpine Plant Species Oxyria digyna and Saxifraga oppositifolia. Front. Microbiol. 8:1972. doi: 10.3389/fmicb.2017.01972 Strong Regionality and Dominance of Anaerobic Bacterial Taxa Characterize Diazotrophic Bacterial Communities of the Arcto-Alpine Plant Species Oxyria digyna and Saxifraga oppositifolia Manoj Kumar1, 2, Jan Dirk van Elsas2and Riitta Nissinen1* 1Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland, 2Department of Microbial Ecology, University of Groningen, Groningen, Netherlands Arctic and alpine biomes are most often strongly nitrogen-limited, and hence biological nitrogen fixation is a strong driver of these ecosystems. Both biomes are characterized by low temperatures and short growing seasons, but they differ in seasonality of solar radiation and in soil water balance due to underlying permafrost in the Arctic. Arcto-alpine plant species are well-adapted to the low temperatures that prevail in their habitats, and plant growth is mainly limited by the availability of nutrients, in particular nitrogen, due to slow mineralization. Nitrogen fixing bacteria are likely important for plant growth in these habitats, but very little is known of these bacteria or forces shaping their communities. In this study, we characterized the potential nitrogen fixing bacterial (PNFB) communities associated with two arcto-alpine pioneer plant species, Oxyria digyna (mountain sorrel) and Saxifraga oppositifolia (blue saxifrage), in three climate regions. Both of these plants readily colonize low nutrient mineral soils. Our goal was to investigate how climate (region) and, on the other hand, host plant and plant species shape these communities. To our knowledge, this is the first comprehensive study describing PNFB communities associated with pioneer plants in different arcto-alpine biomes. Replicate samples were taken from two arctic regions, Kilpisjärvi and Ny-Ålesund, and one alpine region, Mayrhofen. In these, the PNFB communities in the bulk and rhizosphere soils and the plant endospheres were characterized by nifH-targeted PCR and massive parallel sequencing. The data revealed strong effects of climatic region on the dominating nitrogen fixers. Specifically, nifH sequences related to Geobacter (δ-Proteobacteria) were present in high relative abundances in the nitrogen-fixing communities in the Mayrhofen and Kilpisjärvi regions, while members of the Clostridiales prevailed in the Kilpisjärvi and Ny-Ålesund regions. The bulk and rhizosphere soil as well as the endosphere communities in the Mayrhofen region were all characterized by high relative abundances of nifH sequences related to Geobacter. In contrast, the endosphere and soil (bulk or rhizosphere soil) communities in the High Arctic were highly divergent: endosphere communities in the arctic regions were shaped by Clostridium spp., Kumar et al. Diazotrophs in Arcto-Alpine Plants while nifH sequences representing δ-Proteobacteria, β-Proteobacteria, Cyanobacteria (in Ny-Ålesund), and Verrucomicrobia (in Kilpisjärvi) dominated the soil communities. Interestingly, the major PNFB genera identified in this study have been previously identified as members of conserved core microbiomes in the endospheres and seeds of these plants by 16S rRNA gene based analyses combined with bacterial isolation, suggesting a very tight interaction between diazotrophic bacteria and these arctic pioneer plants. Overall, anaerobic bacterial taxa dominated the PNFB communities of the endospheres and rhizospheres of the two plant species in all study sites. This could indicate anoxic conditions in and around plant roots at the time of sampling (early growth season), created by melting snow and underlying permafrost. Keywords: nifH, pioneer plants, Geobacter,Clostridium, endophytic bacteria INTRODUCTION Nitrogen (N) is considered to be the major limiting factor for both microbial and plant growth in arctic and alpine biomes (Chapin et al., 1986; Wallenstein et al., 2009; Sistla et al., 2012). In particular, the amount of available soil nitrogen is very low in low organic content mineral-rich tundra soils. One example is given by recently deglaciated soils with low levels of (mineralizable) nitrogen and carbon that are colonized by patchy pioneer plant communities (Brankatschk et al., 2011). In these soils, nitrogen fixation is the primary source of bioavailable nitrogen (N) for plants (Chapin et al., 1992). Furthermore, the levels of nitrogen fixation and N cycling were shown to be correlated with vegetation cover by Brankatschk et al. (2011). These authors observed no N-fixation activity, and extremely low denitrification and nitrification rates, coupled to low nifH gene copy numbers, in the youngest (10-year old) soils in glacier forefields. In contrast, a densely plant-covered 120year old soil in the same chronosequence showed both higher enzyme activities and higher copy numbers of the nifH, next to nirK and nirS, genes. Clearly, the older soils had gained the capacity to cycle nitrogen on the basis of a pioneer-species-based ecosystem build-up, in which plants found capacities to grow and, in turn, supported the evolved microbial communities and activity. Arctic plants are well-adapted to low temperatures during the growing season. In fact, the photosynthesis rates in the Arctic are comparable to those at lower latitudes (Central Europe) (Chapin et al., 1987). However, to compensate for the slower enzyme kinetics at low temperatures, higher amounts of enzymes are required. For example, arctic plants have significantly higher numbers of the key photosynthesis enzyme RuBisCO (ribulose1, 5 bisphosphate-carboxylase-oxygenase). Consequently, the tissues of arctic plants contain more N than those of plants in warmer climates (Weintraub and Schimel, 2005), underlining the demand for N availability. Biological nitrogen fixation thus constitutes a key strategy involved in initial primary production. In the emerged systems, with plants in place as primary producers, the key nitrogen input will mainly come from plantsymbiotic and/or associative nitrogen fixers. The fixed nitrogen may then be recycled/mineralized via deamination (yielding ammonia), followed by nitrification and denitrification reactions. Associative nitrogen fixing bacteria are likely vital for plant growth in the arcto-alpine pioneer communities. Yet, very little is known about these bacteria, their diversity, or forces shaping their communities. In previous studies, we focused on two arcto-alpine pioneer plant species, Oxyria digyna and Saxifraga oppositifolia, as “models” of the primary colonizers of the nutrient-poor mineral soils that abound in arctic and alpine regions. Preliminary evidence was found for the contention that the soil bacterial communities in different arcto-alpine regions are region-specific, whereas endophytic bacterial communities (using the 16S rRNA gene sequence as a proxy) are host plant specific (Kumar et al., 2017). However, these communities also share a group of bacterial taxa (core microbiome), which are apparently associated with the host plants in all three climatic regions, including several potential nitrogen fixers (Kumar et al., 2017). In this study, we examined the factors shaping the communities of potential nitrogen fixing bacteria (PNFB) in the two selected arcto-alpine pioneer plants and the associated soils in different climate zones. We hypothesized that the bacterial taxa with known nitrogen fixers, which we had previously identified as major members of the core microbiomes of these pioneer plants are also major part of the nifH communities of these plants. Further, we hypothesized, that, like the total bacterial communities, the PNFB communities are host plant specific, and additionally shaped by climatic regions. MATERIALS AND METHODS Sampling and DNA Isolation The plant and DNA samples used to characterize total bacterial communities (Kumar et al., 2017) were also used in this study, and details of sampling sites can be found in the supplemental data in Kumar et al. (2017). Samples were collected using random sampling strategy in June 2012 from eight sampling sites in three different geographic regions: Kilpisjärvi, Northern Finland (KJ), Ny-Ålesund, Svalbard (NÅ), and Mayrhofen, Austria (MA) (Figure 1). NÅ is located in the high Arctic climatic region, where the mean annual temperature is −6.4 and soil temperatures do not rise above 10◦C. The vegetation in NÅ region is arctic tundra, and plant growing season typically 60– 90 days. Sampling sites in KJ represent the low Arctic climate Frontiers in Microbiology | www.frontiersin.org 2October 2017 | Volume 8 | Article 1972 Kumar et al. Diazotrophs in Arcto-Alpine Plants FIGURE 1 | Sampling locations: Mayrhofen in Austrian Alps, Kilpisjärvi in low-arctic Finnish Lapland and Ny-Ålesund in high-arctic Svalbard. region. The mean annual temperatures in KJ is −2.1◦C, with high seasonal temperature fluctuations. Growing season in the tundra vegetation zone in KJ is up to 90 days. The MA sites represent alpine climate, and are located in the alpine tundra vegetation zone, above the tree-line in the Austrian Alps, at an elevation of ca. 2,400 m. Coordinates of the sampling sites can be found at: http://journal.frontiersin.org/article/10.3389/fmicb. 2017.00012/full#supplementary-material. Six replicates of bulk soil and plant samples of each O. digyna and S. oppositifolia (with adhering rhizosphere soil) were collected from all sites and transported to the laboratory. All samples were processed as described in Kumar et al. (2017). In brief, after removing rhizosphere soil parts, plant roots were thoroughly washed with water and surface-sterilized by immersion into 3% sodium hypochlorite (3min), followed by rinses in sterile double-distilled water (3 ×90 s). 80–100 mg of processed root sample were snap-frozen with liquid nitrogen and stored at −80◦C for DNA extraction and analysis. nifH Library Preparation and Sequencing The MoBio Power soil kit (MoBio, Carlsbad, CA, USA) and Invisorb Spin plant Midi kit (STRATEC, Biomedical AG, Germany) were used to extract DNA from soil and plant samples, respectively, as described in Kumar et al. (2017). Libraries for sequencing were prepared using the M-13 linker method by Mäki et al. (2016). The nifH gene was amplified using an optimized nested approach. The first PCR was done with primers 19f/nifH3 (Yeager et al., 2004) and the second one with one forward primer nifH1f (as described by Zehr and McReynolds, 1989) with M13 linker and equimolar concentration of two reverse primers, nifH2r (Zehr and McReynolds, 1989) and nifH2 (Izquierdo and Nüsslein, 2006). The first PCR reaction had 2 µl of template DNA, 1x PCR buffer, 2.5 mM of MgCl2, 1 mg/ml of bovine serum albumin (BSA), 0.4mM dNTP’s, 0.9µM of each primer, and 2,500 U/ml of GoTaq DNA ploymerase (Promega, WI, USA) in a 30 µl reaction volume. For the second PCR, 1 µl of amplified product from the first PCR was added along with 1x PCR buffer, 1mM of MgCl2, 1 mg/ml of BSA, 0.2mM dNTP’s, 0.9 µM of each primer and 1250 U/ml of GoTaq DNA ploymerase (Promega) in a 30 µl reaction volume. Amplifications for both PCR reactions were performed as follows: 2 min denaturation at 95◦C followed by 35 cycles of denaturing, annealing and extension at 95◦C for 1min, 51◦C (first PCR)/53◦C (second PCR) for 1 min and 72◦C for 1 min, respectively. Final extension was carried out at 72◦C for 2min. Samples were barcoded using a third PCR round, where an aliquot (1 µl) of the second PCR was re-amplified using the barcode-M13 as forward primer and nifH2r/nifH2-P1 with adaptor A as reverse primer. PCR mix and conditions were similar to those described for the second PCR, except that only eight cycles were used for amplification. The products were purified using the Agencourt AMPure XP PCR purification system (Beckman Coulter, CA, USA), followed by quantification with a Qubit Fluorometer (Invitrogen). Equivalent DNA quantities of each sample were then pooled and sizefractionated (size selection range of 350–550 bp) using Pippin Prep (Sage Science, MA, USA) with 2% agarose gel cassette (Marker E) according to the manufacturer’s protocol. The libraries were sequenced using an Ion 314 chip kit V2 BC on an Ion Torrent PGM machine (Life Technologies, MA, USA) in the Biocenter, Oulu, Finland. Nucleotide sequence data has been submitted to the ENA database with accession number PRJEB20618. Bioinformatics and Statistical Analysis All reads from the Ion Torrent sequencing were processed using QIIME (Quantitative Insights Into Microbial Ecology, Caporaso et al., 2010) and Fungene pipelines (Fish et al., 2013), as described by Zhang et al. (2015). All sequences with quality scores below 22 and lengths below 240 bp were removed. USEARCH (Edgar, 2010) algorithm was used for chimera removal. After chimera removal, all nucleotide sequences were translated into protein sequences. Frameshifts were detected and corrected with Framebot (length cutoff =80 AAs), aligned using HMMER3 Aligner (with nifH as representative gene) and then clustered by RDP mcClust (90% similarity) in the Fungene pipeline at RDP (fungene.cme.msu.edu). The resulting cluster file was converted into an OTU table by a RDP cluster file formatter in R (version 3.2.5; https://www.r-project.org/). OTUs were assigned to the nearest neighbor by FrameBot in Fungene pipeline. The OTUs were grouped into OPUs (operating phylogenetic units) based on clustering with the same reference sequence. Taxonomic affiliations of 12 OPUs were complemented by P-BLAST at NCBI (blast.ncbi.nlm.nih.gov). Prior to community analysis, the sample reads werestandardized by subsampling all the samples with read counts above dataset median to the median. The samples with reads below median were included as such, as described in Cárcer et al. (2011). OPU abundances were square-root transformed prior to community analyses. ANOVA (analysis of variance), and PERMANOVA (permutational multivariate analysis of variance) and PCoA (Principal Co-Ordinate Analysis) were used Frontiers in Microbiology | www.frontiersin.org 3October 2017 | Volume 8 | Article 1972 Kumar et al. Diazotrophs in Arcto-Alpine Plants to test and visualize the differences between the sample groups. The impact of OPUs to similarities within and dissimilarities between sample groups was estimated with SIMPER (Similarity Percentages–species contributions). Community analyses were all performed in the Primer 6.1. software package (http://www. primer-e.com/). RESULTS Regions (350 bp long) of the nifH genes were amplified from microbial community DNA isolated from the bulk and rhizosphere soils and endospheres from O. digyna and S. oppositifolia in the three regions (Figure 1) using the optimized PCR approach (described in Materials and Methods). The quality-trimmed and translated nifH sequences were used for clustering, resulting in a total of 296 OTUs (at 90% amino acid sequence identity). These 296 OTUs were further clustered based on alignments with NifH protein reference sequences in the RDP FunGene NifH database. This resulted in 97 units, denoted “operational phylogenetic units” (OPUs). Considering all the OPU data, a high diversity of nifH gene sequences was detected in our soil and plant microbial communities. Thus, a suite of nifH genes, affiliated with the bacterial phyla Proteobacteria (classes α-, β-, δ-, and γProteobacteria and Acidithiobacillia),Firmicutes,Actinobacteria, Chlorobi,Bacteroidetes,Cyanobacteria, and Verrucomicrobia, was detected (Figure 2). The most abundant reads in the dataset clustered with nifH gene sequences from the δProteobacteria (genera Geobacter and Desulfotignum), γ-Proteobacteria (Bradyrhizobium), Firmicutes (genera Clostridium, Desulfosporosinus and Acetobacterium) and βProteobacteria (Burkholderia [Burkholderiales] and Leptothrix [Comamonadaceae]) (Figure 2). In the further text, we use these partial sequences to characterize the populations of “PNFB.” FIGURE 2 | Taxonomic distribution of the nifH gene sequences in the three geographic regions at phylum level, except for phylum Proteobacteria which is presented at class level. The Species Richness and Diversity of PNFB Communities Is Lowest in the High Arctic The species richness (SR) and Shannon diversity values (SD) of the PNFB communities (based on the nifH gene amplicon OPUs as a proxy) were highest in the bulk soils, followed by the rhizosphere soils and the endosphere samples. Specifically, the SR and SD values in the endosphere were significantly lower than those in the two soil compartments (P<0.05; Figure 3). Then, the richness and diversity values of the communities from the three climate regions were compared separately for each compartment. The SR and SD values of the bulk soil communities were both highest in the MA, but the differences were not significant. In the plant-associated compartments (rhizoand endospheres), the values of both parameters were highest in the KJ in both plant-associated compartments, but the differences between KJ and other regions were significant only in the rhizosphere communities (P<0.05; Figure 3). Community Structures of PNFB Are Driven by Compartment and Region The community structures of the PNFB were analyzed at the OPU level across all samples. Compartment, region and sampling site all had significant impacts on the PNFB community structures, with compartment being the most important factor (Table 1). The endosphere PNFB communities were significantly different from those from both soil compartments (P=0.003), while we detected no significant differences between bulk and rhizosphere soil community structures (Table 1) in region-wide analyses. This was also evident in the PCoA ordination, which showed that the endosphere communities grouped separately from the soil-derived ones (Figure 4). In addition to compartment, a clear trend for grouping according to region was also visible in the PCoA, with NÅ and MA samples clustering at opposite sites on the first PCO (Figure 4). The communities in the three climatic regions differed significantly from each other in both global analysis and when different compartments were analyzed separately (Table 1). The plant-associated KJ communities were more similar to both the NÅ and MA communities than the latter two to each other, while the opposite was true for the bulk soil communities (Table 1). Different Bacteria Dominate the PNFB Communities in Different Regions and Compartments We next investigated the taxonomic composition of the PNFB communities across the different compartments and regions. The bulk and rhizosphere soil PNFB communities were characterized by high relative abundances of nifH sequences representing the Betaproteobacterial taxa Leptothrix and Burkholderia, as well as the Deltaproteobacterial genus Geobacter in all three regions (Figure 5). Several taxa, however, were highly unevenly distributed between the different regions. Geobacter-type nifH sequences dominated the bulk and rhizosphere soils in MA and were also abundant in KJ soils, but they were detected only at very Frontiers in Microbiology | www.frontiersin.org 4October 2017 | Volume 8 | Article 1972 Kumar et al. Diazotrophs in Arcto-Alpine Plants FIGURE 3 | Species richness and Shannon diversity of PNFB communities in different regions and compartments. Diversity indices were calculated using nifH gene OPUs as a proxy. Compartment or regions with differ significantly from other groups are marked by asterisk. low relative abundances in NÅ (Figure 5,Table 2). In contrast, Acetobacterium bakii (Clostridiales), and Cyanobacteria-related nifH sequences (Nostoc, Nodularia, Synechococcus) were more abundant in the NÅ region than in the other regions (Figure 5C). Furthermore, OPUs clustering with nifH sequences from the Opitutaceae (Verrucomicrobia) were highly abundant in the KJ soils (Figure 5). These taxa also defined the region-specific soil communities (Table 2). The endosphere PNFB communities were dominated by nifH OPUs representing the genera Burkholderia, Bradyrhizobium, Geobacter (Deltaproteobacteria), and Clostridium (Firmicutes) (Figure 5A). Clostridium OPUs were mostly restricted to the endosphere, while Burkholderia and Geobacter were present in all comparments (Figure 5B). However, the latter two taxa were highly unevenly distributed across the climatic regions. While the MA communities were strongly dominated by OPUs related to several Geobacter species, including G. lovleyi, G. bemidjiensis, and G. uraniireducens, the NÅ endosphere communities were strongly shaped by the genus Clostridium (3 OPUs;Figure 5A,Table 2). Such Clostridiumlike OPUs were virtually absent from the MA endosphere communities, and, likewise, Geobacter-type OPUs in NÅ (Figure 5C). Moreover, the major nifH OPUs in the KJ endosphere communities were affiliated with both the genera Clostridium and Geobacter, next to Bradyrhizobium, and Burkholderia (Figure 5,Table 2). The endosphere and soil communities were more dissimilar from each other in NÅ (pseudo-F =9.79, P=0.001) than in the other regions (pseudo-F =7.80 P=0.001 and 5.56 P=0.001 for KJ and MA, respectively). While in the MA and— to a lesser extent—in the KJ microbiomes, the major PNFB OPUs (representing Geobacter, Burholderiales, and Leptothrix) were found in all compartments, the OPUs dominating the endosphere in NÅ (Clostridum) were barely detectable in the corresponding soil communities. Moreover, several of the major soil OPUs (e.g., Acetobacter) were virtually absent from the endosphere (Figure 5B,Table 2). Geobacter and Bradyrhizobium Diazotrophs Are Differentially Enriched in the S. oppositifolia and O. digyna Endospheres Compartment (in particular the endosphere-soil division), followed by region and sampling site, were the major determinants of the plant-associated PNFBs, with no strong host plant specificity. However, we detected small but significant impacts of host plant species on the endosphere PNFB Frontiers in Microbiology | www.frontiersin.org 5October 2017 | Volume 8 | Article 1972 Kumar et al. Diazotrophs in Arcto-Alpine Plants TABLE 1 | Impact of different factors on PNFB community structures. PERMANOVA GLOBAL ANALYSIS (ALL SAMPLES) Factor F P q S Co 8.5428 0.001 23.367 Re 3.63731 0.01 20.308 Si(re) 4.3384 0.001 17.751 co ×re 2.0550 0.002 14.932 co ×si(re) 1.9712 0.001 16.432 PAIR-WISE ANALYSES Compartments Bulk vs. Rhizo t (P) Bulk vs. Endo t (P) Rhizo vs. Endo t (P) All regions NS (0.189) 3.0884 (0.003) 3.3799 (0.003) Mayrhofen 1.4788 (0.019) 2.2824 (0.001) 2.7259 (0.001) Kilpisjärvi 1.6801 (0.014) 3.2609 (0.001) 2.9407 (0.001) Ny-Ålesund 1.5336 (0.018) 3.1962 (0.001) 3.6902 (0.001) Regions Mayrhofenx Kilpisjärvi t (P) Mayrhofenx Ny-Ålesund t (P) Kilpisjärvix Ny-Ålesund t (P) All compartments 3.0703 (0.001) 4.000 (0.001) 3.0815 (0.001) Bulk soil 2.3047 (0.002) 2.155 (0.001) 2.8326 (0.001) Rhizosphere 2.9113 (0.001) 3.8324 (0.001) 3.1553 (0.001) Endosphere 2.1865 (0.001) 2.9723 (0.001) 1.9935 (0.001) RHIZOSPHERE AND ENDOSPHERE Factor F P sqS Co 21.769 0.001 27.875 Pl 5.0168 0.001 12.259 Re 12.096 0.001 24.787 co ×pl 3.2908 0.001 13.092 co ×re 3.9875 0.001 18.189 pl ×re 1.7684 0.015 9.2244 co ×pl ×re 1.9635 0.009 14.608 The PERMANOVA is based on Bray-Curtis dissimilarity matrixes of square-root transformed relative abundances of PNFB OPUs. Co, compartment; re, region; si, site; pl, plant species. Nested factors are denoted in brackets () and test for interaction between factors is denoted with x. communities (Table 1), and trends in the affiliation of several OPUs with particular plant species were visible. Thus, OPUs representing Bradyrhizobium and Burkholderia were consistently present in relatively higher abundances in the O. digyna endosphere samples than in the S. oppositifolia ones (Figure 6). In contrast, the S. oppositifolia endosphere communities were more enriched with Geobacter related OPUs, in the MA and KJ regions. Furthermore, the latter communities harbored relatively more OPUs related to Desulfosporosinus (Clostridiales) in KJ and Clostridium and Desulfuromonas related OPUs in NÅ, in comparison to O. digyna (Figure 6). Several of these OPUs were important determinants in shaping the local host plant specific communities (Supplemental Table S1). DISCUSSION Using the nifH gene as a proxy, we analyzed the diversity and community composition of PNFB in two pioneer plant FIGURE 4 | Principal Coordinate Analysis (PCoA) of PNFB communities, from bulk soils, rhizosphere soils, and endospheres of Oxyria digyna and Saxifraga oppositifolia from three regions, based on Bray-Curtis similarity matrix of square root transformed relative abundances of nifH-based OPUs. Symbol shapes correspond to different compartments, and symbol colors to different regions. species growing in low-nutrient soils in three arcto-alpine climate regions. Based on our previous work, we were aware of the presence of many PNFB taxa representing Firmicutes and δproteobacteria, that are routinely missed by many nifH-targeting primer combinations (Gaby and Buckley, 2012), in the bacterial communities associated with O. digyna and S. oppositifolia (Nissinen et al., 2012; Kumar et al., 2017). Thus, we optimized a nested PCR approach with primers 19f/nifH3 (1st round, Yeager et al., 2004) and nifH1f/ nifH2r+nifhH2 (Zehr and McReynolds, 1989; Izquierdo and Nüsslein, 2006). The amplification system was chosen, as it reportedly yields the highest phylogenetic coverage of diazotrophic bacterial groups (Gaby and Buckley, 2012). Overall, we detected high diversities of PNFB across all samples. Our libraries had good phylogenetic coverage, with the collective PNFB OPUs representing seven phyla (Figure 2), including representatives from nifH clusters I, II, and III. This indicates that the selected PCR approach enabled maximal coverage from all the nifH phylogenetic groupings (Gaby and Buckley, 2012). In particular, the PNFB communities in our soils were dominated by nifH gene types from the α-, β-, γ-, and δProteobacteria and the Clostridiales. The δ-proteobacterial genus Geobacter and the β-proteobacterial genera Burkholderia and Leptothrix constituted the most abundant PNFB taxa in the soil communities across all regions. The phylogenetic composition of the PNFB in our data set differs from those reported for high-organic-matter tundra soils from Arctic or alpine sites, in which aerobic proteobacterial diazotrophs dominated (Deslippe and Egger, 2006; Tai et al., 2013). Frontiers in Microbiology | www.frontiersin.org 6October 2017 | Volume 8 | Article 1972 Kumar et al. Diazotrophs in Arcto-Alpine Plants FIGURE 5 | Average relative abundances (A) and distribution of OPUs (B,C) in different sample compartments and geographic regions. (A) Average relative abundances (four biological replicates) of PNFB communities in different sample compartments and geographic regions. Compartments: B, bulk soil; R, rhizosphere soil; E, endosphere; MA, Mayrhofen; the Alps; KJ, Kilpisjärvi; Low Arctic, NÅ, Ny-Ålesund; High Arctic. Only major PNFB OPUs (relative abundance above 1%) are indicated, OPUs with <1% relative abundance are grouped together (“others”). (B) Ternary plot of distribution of OPUs across different compartments. Each circle represents one OPU. The size of the circle represents the average relative abundance of the OPU in the dataset. The circle color corresponds to OPUs taxonomic affiliation. Location of the circle in the plot in relation to different compartments indicates the contribution of each compartment to the OPU’s total relative abundance, with the dotted grid inside the plot area indicating 20% increments of contribution. (C) Ternary plot of distribution of OPUs across different regions. Similar to (B), the size, the color and the location of each circle indicates the average relative abundance, taxonomic affiliation and association with different regions of the corresponding OPU. Frontiers in Microbiology | www.frontiersin.org 7October 2017 | Volume 8 | Article 1972 Kumar et al. Diazotrophs in Arcto-Alpine Plants TABLE 2 | Top OPUs contributing up to 90% (endosphere) or 60% (rhizosphere and endosphere) cumulative similarity of PNFB communities in different regions are shown. Species Av.Ab Av.Sim Sim/SD Contrib (%) Cum. (%) BULK SOIL Group Mayrhofen Geobacter_lovleyi_SZ 3.73 6.44 2.09 12.32 12.32 Geobacter_uraniireducens_Rf4 3.26 5.47 1.74 10.48 22.80 Burkholderia_sp_CCGE1002_plasmid_pBC201 3.07 4.66 1.47 8.91 31.71 Burkholderia_sp_Ch1-1_ctg00023 2.45 4.17 2.43 7.98 39.69 Leptothrix_cholodnii_SP-6 1.56 3.19 9.31 6.11 45.80 Desulfotignum balticum 2.02 2.92 1.52 5.60 51.40 Rhizobium_sp_ANU289 1.88 2.85 1.35 5.46 56.85 Geobacter uraniireducens sp 1.66 2.50 1.52 4.79 61.64 Group Kilpisjärvi Burkholderia_sp_Ch1-1_ctg00023 3.58 6.75 2.44 16.64 16.64 Opitutaceae_bacterium_TAV2_ctg796 3.55 4.90 1.15 12.57 29.21 Bradyrhizobium_sp_ORS278 1.70 2.59 1.27 6.37 35.58 Burkholderia_sp_CCGE1002_plasmid_pBC201 1.68 2.48 1.57 6.12 41.70 Geobacter_uraniireducens_Rf4 1.74 2.03 1.06 5.00 46.70 Leptothrix 1.02 1.70 1.52 4.20 50.90 Unidentified_bacterium_nif_cluster 1.46 1.35 0.65 3.33 54.23 Desulfovibrio_sp_FW1012B_ctg00046 1.28 1.34 0.65 3.31 57.54 Geobacter_lovleyi_SZ 1.48 1.17 0.47 2.88 60.42 Group Ny-Ålesund Burkholderia_sp_Ch1-1_ctg00023 3.39 6.56 2.12 15.30 15.30 Burkholderia_sp_CCGE1002_plasmid_pBC201 3.19 6.15 2.32 14.33 29.63 Leptothrix 2.36 4.25 1.92 9.92 39.55 Synechococcus_sp_PCC_7335 1.41 2.23 1.41 5.19 44.74 Leptothrix_cholodnii_SP-6 1.12 1.86 1.49 4.32 49.06 Nostoc_punctiforme_PCC_73102 1.59 1.71 0.75 3.98 53.04 Acetobacterium bakii 1.74 1.65 0.60 3.84 56.87 Polaromonas_naphthalenivorans_CJ2 1.25 1.62 1.03 3.78 60.65 RHIZOSPHERE SOIL Group Mayrhofen Geobacter_uraniireducens_Rf4 3.80 8.09 2.86 14.08 14.08 Geobacter_lovleyi_SZ 3.88 7.67 2.30 13.36 27.44 Burkholderia_sp_CCGE1002_plasmid_pBC201 3.51 7.06 1.99 12.30 39.73 Geobacter uraniireducens sp 2.73 5.80 3.07 10.09 49.82 Burkholderia_sp_Ch1-1_ctg00023 2.11 3.96 2.79 6.89 56.71 Rhizobium_sp_ANU289 1.66 2.67 1.36 4.65 61.37 Group Kilpisjärvi Burkholderia_sp_Ch1-1_ctg00023 3.30 6.00 2.53 14.96 14.96 Geobacter_bemidjiensis_Bem 2.17 3.55 1.42 8.86 23.82 Geobacter_uraniireducens_Rf4 2.58 3.40 1.17 8.50 32.32 Geobacter_lovleyi_SZ 2.33 2.94 0.91 7.34 39.66 Burkholderia_sp_CCGE1002_plasmid_pBC201 1.55 2.67 2.32 6.67 46.34 Desulfobacterium_autotrophicum_HRM2 1.90 2.64 1.08 6.58 52.91 Opitutaceae_bacterium_TAV2_ctg796 1.41 1.23 0.50 3.06 55.98 Bradyrhizobium_sp_ORS278 0.89 1.18 1.03 2.94 58.91 Leptothrix_cholodnii_SP-6 0.95 1.15 0.99 2.87 61.79 Group Ny-Ålesund Burkholderia_sp_Ch1-1_ctg00023 3.77 7.83 2.68 17.78 17.78 Acetobacterium bakii 2.94 4.36 0.95 9.90 27.68 (Continued) Frontiers in Microbiology | www.frontiersin.org 8October 2017 | Volume 8 | Article 1972