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Ann Microbiol (2017) 67:313–319 DOI 10.1007/s13213-017-1262-6 ORIGINAL ARTICLE Diversity and composition of bacterial community in the rhizosphere sediments of submerged macrophytes revealed by 454 pyrosequencing 1,2 1,2,3 1,2,3 3 2 Dayong Zhao & Sichen Wang & Rui Huang & Jin Zeng & Feng Huang & 1,2 Zhongbo Yu Received: 2 November 2016 /Accepted: 27 February 2017 /Published online: 17 March 2017 Springer-Verlag Berlin Heidelberg and the University of Milan 2017 Abstract Freshwater lake sediments support a variety of sub- Introduction merged macrophytes that may host groups of bacteria exerting important ecological functions. We collected three kinds of The rhizosphere is the narrow zone of soil containing numerous commonly found submerged macrophyte species bacteria and under the direct influence of the root exudates of (Ceratophyllum demersum, Vallisneria spiralis and Elodea plant. It is considered to be one of the most dynamic interfaces on nuttallii) to investigate the bacterial community associated Earth (Philippot et al. 2013). Many studies have investigated the with their rhizosphere sediments. High-throughput 454 pyro- bacterial community located in the rhizosphere of terrestrial sequencing and bioinformatics analyses were performed to plants, including its diversity (Teixeira et al. 2010), composition examine the diversity and composition of the bacterial com- (Bulgarelli et al. 2012; DeAngelis et al. 2009; Peiffer et al. 2013; munity. The results obtained indicated that the diversity of the Uroz et al. 2010), activity (Chaparro et al. 2014; Ofek-Lalzar bacterial community associated with the rhizosphere sedi- et al. 2014), variations according to plant species (Garbeva ments of submerged macrophytes was significantly lower than et al. 2008; Berg and Smalla 2009) and variations according to that of the bulk sediment. Remarkable differences in the bac- plant development (Chaparro et al. 2014). However, little is terial community composition between the rhizosphere and known about the bacterial communities living in close associa- bulk sediments were also observed. tion with freshwater macrophytes, such as submerged macro- phytes. Submerged plants could repair the environment by ab- sorbing nutrient elements, such as nitrogen and phosphorus, and . . Keywords Submergedmacrophytes Rhizospheresediment are a crucial component of the lake ecosystem (Chmielewski Bacterial community High-throughput pyrosequencing et al. 1997;Jeppesenet al. 1998;Lembi 2001). Additionally, various buffering mechanisms that keep water in its clear state, including bicarbonate utilization, nutrient uptake and allelopathy, are maintained by submerged macrophytes (Jatin et al. 2008). Zeng et al. (2012) reported that macrophytes can influence shifts in the bacterioplankton community in Lake Taihu. Dayong Zhao and Sichen Wang contributed equally to this work. Hempel et al. (2008) also demonstrated that the composition of the epiphytic bacterial community was affected by sub- * Dayong Zhao email@example.com merged macrophytes. However, there have been only a few studies which have targeted the overall bacterial community in the rhizosphere of submerged macrophytes in the freshwater State Key Laboratory of Hydrology—Water Resources and ecosystem. Hydraulic Engineering, Hohai University, Nanjing 210098, China In the study reported here, we collected three species of College of Hydrology and Water Resources, Hohai University, submerged macrophytes (Ceratophyllum demersum, Nanjing 210098, China Vallisneria spiralis and Elodea nuttallii) from the water of State Key Laboratory of Lake Science and Environment, Nanjing Huashen Lake, Nanjing, China. Microcosms for culturing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China the submerged macrophytes were constructed. Sediment 314 Ann Microbiol (2017) 67:313–319 samples were collected from the rhizosphere sediment, bulk samples were homogenized. Sediment samples were stored sediment and surface sediment of each microcosm. Bacterial at −70 °C for further analysis. community composition was investigated using 454 high- throughput pyrosequencing of the 16S ribosomal RNA (16S DNA extraction and PCR amplification rRNA) gene. The aim of our investigation was to determine whether the diversity and composition of the bacterial com- DNA was extracted from duplicate soil samples (0.25 g) with munity associated with the rhizosphere sediment of sub- the PowerSoil DNA Isolation kit (MoBio Laboratories, merged macrophytes differed from those of the bulk sediment. Solana Beach, CA) according to the manufacturer’sinstruc- tions. The quality of the extracted DNA was measured using a biophotometer (Eppendorf, Hamburg, Germany). The extract- ed DNA was stored at −70 °C for further analysis. Materials and methods PCR analyses were performed to amplify the bacterial 16S rRNA gene with the primers 27 F (5′-AGAGTTTGATCCTG Microcosm construction and sample collection GCTCAG-3′) and 533R (5′-TTACCGCGGCTGCTGGCAC −3′) (Lu et al. 2012;Zhao etal. 2014a;Zenget al. 2016). The In July of 2012, sediment samples were collected from PCR primers were fixed with the Roche 454 pyrosequencing Huashen Lake using a core sampler (model DM60; China adapter (Roche Applied Science, Penzberg, Germany), and an Mingyu Holdings Group, Shanghai). At the same time, sam- individual 10-bp barcode nucleotide for each sample was at- ples of lake water and of three species of submerged plants tached to the reverse primer 533R. The PCR reaction mixture (Ceratophyllum demersum, Vallisneria spiralis and Elodea with a total volume of 50 μlincluded 10 μl of 5× PrimeSTAR 2+ nuttallii) were collected. All samples were brought back to Buffer (plus Mg ), 0.2 mM dNTPs, 0.4 μM each of the for- the laboratory immediately after collection and prepared for ward and reverse primers, 2.0 U TaKaRa PrimeSTAR HS construction of the microcosm systems. DNA Polymerase, 10–20 ng of DNA template and ddH O. Microcosms were constructed in plexiglass tubes (internal The thermal cycling conditions for PCR amplification diameter 40 cm, length 25 cm) to simulate the natural lake consisted of a 5-min initial denaturation at 95 °C followed environment. The top 12 cm of the collected sediment cores by 24 cycles of denaturation at 94 °C for 30 s, annealing at were sectioned into 2-cm intervals, and sediment samples col- 55 °C for 30 s and extension at 72 °C for 30 s, with a final lected at the same depth were pooled together. The sediments extension at 72 °C for 5 min. Each sample was amplified in were then sieved through mesh to remove the macrofauna and triplicate, and the combined PCR products were verified by large particles before being fully homogenized and placed in 2% (w/v) agarose gel electrophoresis and purified with the plexiglass tubes with 2-cm intervals corresponding to their AxyPrep DNA gel purification kit (Axygen Biotechnology original depths. Filtered lake water was added to the plexiglass Hangzhou Ltd., Hangzhou, China). columns with intravenous needles. The height of the lake sed- Equal amounts of PCR products amplified from each sam- iment in the plexiglass tubes was 12 cm and that of the over- ple were sent to the Majorbio Company in Shanghai for py- lying water was 10 cm in the constructed microcosms. The rosequencing on the Roche 454 FLX Titanium platform microcosms were pre-incubated for 2 days, then the above- (Roche Applied Science). The obtained raw sequences have mentioned three kinds of commonly found submerged mac- been deposited in the Genbank database under the accession rophytes, C. demersum, V. spiralis and E. nuttallii,were added number SRP091979. into the microcosm separately. Each kind of submerged mac- rophyte was cultivated in three replicate columns, and each Sequence processing and data analysis column contained one submerged plant. Two control columns (with no submerged macrophytes) were also prepared. The Raw sequence reads were denoised and trimmed according to microcosms were incubated at 25 °C and light was provided the online 454 standard operating procedure of the Mothur 12 h a day. software package (Schloss et al. 2011). Sequences shorter than After incubation for 80 days, the surface sediments (top 0– 200 nucleotides (excluding the primer and barcode), se- 1 cm) and bulk sediments (depth 5–10 cm) were collected quences containing ambiguous base calls to the primer se- from each microcosm with a self-made sampler. The bulk quences and homopolymers longer than 8 nucleotides were sediment was collected at least 15 cm away from the planted excluded from further analysis (Victor et al. 2010). The re- submerged macrophytes in order to avoid contact with the maining sequences were transformed to the reverse comple- roots. The rhizosphere sediment associated with each kind of ments and aligned using the nearest alignment space termina- submerged macrophyte was collected from all over the root tion algorithm against a bacterial SILVA 16S rRNA gene tem- zone by shaking off sediment that was loosely adhering to the plate (Schloss et al. 2011). Putative chimeric sequences with roots, as described by Herrmann et al. (2009). Replicate potential pyrosequencing errors were removed with the Ann Microbiol (2017) 67:313–319 315 command ‘chimera.uchime’ in Mothur. The command comparable with those of the rhizosphere samples (P>0.05), ‘pre.cluster’ was further employed to prune the dataset and but they were significantly different from those of the bacterial accelerate the distance-running procedure (Huse et al. 2010). community in the bulk sediment samples. The PD was com- The subsampled sequences were used to analyze the alpha parable among the three groups. diversity, including number of operational taxonomic units The diversity of the bacterial community associated with (OTUs) and Chao1 indices, using the command the rhizosphere sediments of submerged macrophytes was ‘summary.single’ in Mothur. The phylogenetic diversity significantly lower than that of the bulk sediment (P<0.05; (PD) was estimated using Faith’s index (Faith 1992). Table 1). Peiffer et al. ( 2013) also reported a significant re- Nonmetric multidimensional scaling (NMDS) analysis was duction in the α-diversity of the bacterial community for the carried out using the vegan package in R (version 2.15.0) to maize rhizosphere microbiome under field conditions investigate the similarities in bacterial community composi- (P < 0.05). Although a number of studies have reported de- tion. The Bray–Curtis metric (Bray and Curtis 1957)was creased bacterial community diversity in the rhizosphere soils employed to calculate the dissimilarities in community com- of terrestrial plants, due to variations in these studies, such as position for each pair of samples. Duncan’s multiple range test the growth of the plants and the different sampling strategies, was performed to test the differences in bacterial community it is difficult to obtain a general description of the rhizosphere composition among different sediment groups (e.g., the sur- microbiome (for more detail, see Philippot et al. 2013). face sediments, bulk sediments and rhizosphere sediments) using the SPSS 17.0 software package (IBM Corp., Differences in bacterial community composition Armonk, NY). Heatmaps were implemented with HemI among the different sediment samples (Heatmap Illustrator, version 1.0) to compare the bacterial community of the most abundant genera in each sample The classifier results of the taxon assignments at the phylum level (Deng et al. 2014). for each sample are shown in Fig. 1. Proteobacteria, which accounted for 18.97–36.09% of the total effective sequences, was the most abundant phylum in all samples except for the surface sediment of V. spiralis and the bulk sediment of the Results and discussion control group. Other phyla or subphyla, including Chloroflexi Richness and diversity of the bacterial communities (14.9% ± 0.06), Deltaproteobacteria (11.15% ± 0.04), in different sediment groups Bacteroidetes (9.92% ± 0.02) and Betaproteobacteria (8.51%±0.03), were also dominant phyla in our study (Fig. 1). After denoising, filtering out chimeras and removing the archaeal Duncan’s multiple range test was performed to compare differ- sequences, the remained number of sequences ranged from 5679 ences in the taxonomic groups of bacteria among surface sedi- to 8037 for each sample. The obtained sequences in each sample ments, bulk sediments and rhizosphere sediments (Table 2). At were subsampled to the minimum number (5679) of sequences the phylum level, the relative abundances of Actinobacteria and for comparing the richness and diversity in samples. Firmicutes were found to be significantly higher in the bulk sedi- For the richness and alpha diversity analyses the sediment ment than in the surface and rhizosphere sediments (P<0.05) samples collected from the microcosms planted with the sub- (Table 2). However, the bacterial community derived from the merged macrophytes were divided into the following three surface and rhizosphere sediments maintained a higher relative groups: surface sediment (depth 0–1cm),bulksediment abundance of the Proteobacteria group (P<0.05). Relative abun- (depth 5–10 cm) and rhizosphere sediment (Table 1). The dances in the classes of Actinobacteria, KD4-96 and Clostridia differences among the groups were compared using analysis were significantly higher in bulk sediments (P<0.05). At the order of variance. The numbers of OTUs and Chao1 indexes of the level, the percentages of Acidimicrobidae, Rubrobacteridae, bacterial community in the surface sediment samples were Clostridiales and Myxococcales were significantly higher in the Table 1 Richness and diversity Parameters of richness and diversity of Surface sediment Bulk sediment Rhizosphere of the bacterial community bacteria community (depth 0–1cm) (depth 5–10 cm) sediment derived from the surface, bulk and rhizosphere sediments collected Number of OTUs 2731.33 ± 87.79 a 3209.67 ± 227.1 b 2419.33 ± 320.15 a for analysis Chao1 index 5238.86 ± 137.68 a 6307.36 ± 477.75 b 5072.26 ± 346.89 a PD 215.74 ± 3.36 a 232.43 ± 15.08 a 219.96 ± 10.9 a Values in table are given as the mean ± standard deviation (SD) of triplicate (n = 3) samples. Values in each row (different sediment groups) followed by different lowercase letters are significantly different (P<0.05) OTU, Operational taxonomic unit; PD, phylogenetic diversity 316 Ann Microbiol (2017) 67:313–319 Fig. 1 Relative abundance of the dominant bacterial taxa (phyla and subphyla) in each bacterial community. C.D Ceratophyllum demersum, V.S Vallisneria spiralis, E.N Elodea nuttallii, SS surface sediment (depth 0–1cm), BS bulk sediment (depth 5–10 cm), RS rhizosphere sediment, CN control bulk sediments than in the surface and rhizosphere sediments samples, whereas the genera Acidimicrobineae (affiliated with (P<0.05); however, the Xanthomonadale group was significantly Actinobacteria), Clostridium (affiliated with Firmicutes) and less abundant in the bulk sediments (P<0.05). At the family level, Caldilinea (affiliated with Chloroflexi) were abundant in the bulk Acidimicrobiales, Actinomycetales, AKIW543 and Clostridiaceae sediment samples of both inoculated and uninoculated micro- were more abundant in the bulk sediments (P<0.05). The relative cosms. Two genera Nitrospira (affiliated with Nitrospirae) and abundances of Comamonadaceae were higher in the bacterial Opitutus (affiliated with Verrucomicrobia) were abundant in the community derived from the surface and rhizosphere sediments. rhizosphere and surface sediments of the uninoculated The top ten abundant genera in each sample were selected (a microcosms. total of 30 genera), and their abundancess were compared to At the phylum level, the percentages of phyla Firmicutes, those in other samples using the heatmap analysis (Fig. 2). The Actinobacteria and Proteobacteria in the rhizosphere sediments sig- genera Rubrivivax, Sulfuricurvum and Thiobacillus (all affiliated nificantly differed from those in the bulk sediments (P<0.05). with Proteobacteria) were abundant in the surface sediment These results are consistent with those reported by DeAngelis Table 2 Differentially abundant Taxonomic level Taxon Surface sediment (%) Bulk sediment (%) Rhizosphere (%) taxa among bacterial communities derived from the Phylum Actinobacteria 3.73 ± 0.85 a 10.23 ± 0.88 b 3.12 ± 1.18 a surface, bulk and rhizosphere sediments collected for analysis Firmicutes 2.76 ± 0.3 a 4.74 ± 0.85 b 1.35 ± 0.75 a Proteobacteria 30.68 ± 2.98 ab 22.38 ± 2.29 a 32.66 ± 5.66 b Class Actinobacteria 3.73 ± 0.85 a 10.23 ± 0.88 b 3.12 ± 1.18 a KD4-96 1.35 ± 0.37 b 1.78 ± 0.17 b 0.56 ± 0.39 a Clostridia 2.23 ± 0.31 b 3.79 ± 0.69 c 1.16 ± 0.63 a Order Actinobacteridae 1.21 ± 0.18 a 2.46 ± 0.20 b 1.17 ± 0.30 a Rubrobacteridae 0.65 ± 0.35 a 2.45 ± 0.34 b 0.45 ± 0.26 a Clostridiales 2.23 ± 0.31 b 3.78 ± 0.69 c 1.16 ± 0.63 a Rhodospirillales 1.24 ± 0.42 a 0.73 ± 0.18 a 1.14 ± 0.03 a Myxococcales 1.27 ± 0.11 a 2.43 ± 0.3 b 1.82 ± 0.36 a Xanthomonadales 1.86 ± 0.36 b 0.89 ± 0.11 a 2.04 ± 0.64 b Family Acidimicrobiales 0.98 ± 0.42 a 2.01 ± 0.25 b 0.89 ± 0.42 a Actinomycetales 1.21 ± 0.18 a 2.46 ± 0.2 b 1.17 ± 0.30 a AKIW543 0.62 ± 0.33 a 2.24 ± 0.29 b 0.41 ± 0.23 a vadinHA17 1.29 ± 0.25 b 1.32 ± 0.05 b 0.69 ± 0.08 a Clostridiaceae 0.95 ± 0.11 b 1.97 ± 0.29 c 0.26 ± 0.15 a Comamonadaceae 1.33 ± 0.11 b 0.6 ± 0.11 a 1.93 ± 0.19 b Values in table are given as the mean ± SD of triplicate (n = 3) samples. Values in each row (different sediment groups) followed by different lowercase letters are significantly different (P < 0.05) Ann Microbiol (2017) 67:313–319 317 Fig. 2 Heatmap of the ten most abundant genera in each sample. The color intensity in each box indicates the relative percentage of a genus in each sample. For abbreviations, see caption to Fig. 1 et al. (2009) for the bacterial community associated with the wild from the bulk sediment of the microcosms with submerged oat root. These authors found that the relative abundances of 7% of macrophytes clustered together (Fig. 3a). Bacterial communi- ties in the surface sediments of the microcosms with sub- the bacterial taxa derived from the wild oat root were significantly different from those in the bulk soil. They also reported that merged macrophytes were also similar. However, remarkable Firmicutes, Actinobacteria or Alphaproteobacteria was the domi- differences in the composition of the bacterial community nant group in the bacterial communities studied, with significantly were observed for the rhizosphere sediments of the three kinds different relative abundances between the rhizosphere and bulk of submerged macrophytes (Fig. 3a). The composition of the soils. Several previous studies have found that some genera of bacterial community derived from the bulk sediment of the Proteobacteria were the dominant bacterial community members control columns was similar to that of the bulk sediment in the rhizosphere of Avena fatua (DeAngelis et al. 2009), maize planted with submerged macrophytes, whereas different bac- (Gomes et al. 2001) and grain legumes (Sharma et al. 2005). One terial community compositions were found in the surface sed- explanation may be the presence of fast-growing r-strategists of the iments between the inoculated and uninoculated microcosms Proteobacteria that are able to absorb a broad range of root-derived (Fig. 3a). carbon substrates (Philippot et al. 2013). To further investigate the composition of the bacterial com- The results of the heatmap analysis indicated that the relative munity for the general and rare bacterial groups, we further abundance of Nitrospira was remarkably higher in the rhizo- divided the overall bacterial community into the following three sphere sediments than in the bulk sediments of both inoculated ecological categories: general OTUs (the OTUs which contain- and uninoculated microcosms. Nitrospira plays an important role ing≥ 11 sequences in all samples), rare OTUs (the OTUs which in the process of ammonia oxidation, which is a vital step of contained only one sequence in all samples) and other OTUs nitrification (Purkhold et al. 2000). Previous studies have found (the OTUs beyond general and rare OTUs). The NMDS anal- significantly elevated abundances of the bacterial amoA gene, ysis was conducted for the general and rare bacterial groups which encodes the active site of ammonia monooxygenase, in separately (Fig. 3b, c). The results showed that the composition the rhizosphere sediment of C. demersum and V. spinulosa of the bacterial community of the general OTUs was similar to (P<0.05) (Zhao et al. 2014b). The process of ammonia oxida- that of the overall bacterial community (Fig. 3b). However, the tion requires oxygen (Kowalchuk and Stephen 2001). It is there- bacterial community composition of rare OTUs was clearly fore possible that the higher relative abundance of Nitrospira different from that of the overall bacterial community found in the rhizosphere sediment may be attributable to the (Fig. 3c). It was evident that the bacterial community derived oxygen released from the rhizosphere of submerged from the rhizosphere sediments of different submerged macro- macrophytes. phytes clustered together (Fig. 3c), suggesting that the rare bac- terial groups associated with the rhizosphere sediments of dif- ferent submerged macrophytes were similar. Non-metric multi-dimensional scaling analysis The results of the NMDS analysis indicated that the composition of the bacterial community in the bulk sed- The results of the NMDS analysis clearly indicated that the bacterial community composition was strongly related to the iment of both the uninoculated microcosm systems and different sediment groups. The bacterial communities derived those with the three kinds of submerged macrophytes 318 Ann Microbiol (2017) 67:313–319 Fig. 3 Nonmetric multidimensional scaling analysis of bacterial community composition in 11 sediment samples based on total operational taxonomic units (OTUs) (a), based on general OTUs (b) and based on rare OTUs (c) clustered together and was clearly different from that of suggesting that the rare bacterial groups associated with the bacterial community derived from the rhizosphere the rhizosphere sediments of the different submerged sediment samples (Fig. 3a). Many previous studies have macrophytes were similar. reported different relative abundances of microbial pop- The results of our study indicate that the diversity of ulations in the rhizosphere of crops and of cultivated the bacterial community associated with the rhizosphere and native plant species (Garbeva et al. 2008;Oh sediments of the submerged macrophytes was significant- et al. 2012;Teixeiraetal. 2010). Plants may influence ly lower than that of the bulk sediment. Remarkable dif- the microorganisms associated with their rhizosphere ferences in the composition of the bacterial community through the release of exudates by the roots. Terrestrial between the rhizosphere and bulk sediments were also plants have been shown to release secondary com- observed. Further studies are needed to investigate the pounds, such as phenols and alkaloids, which could af- functional characterization of the bacterial community fect the bacterial communities (Berg and Smalla 2009). colonizing in the rhizosphere sediments of submerged Further comparison of the NMDS patterns of the abun- macrophytes. The results of such studies would improve dant and rare bacterial groups revealed remarkably differ- our understanding of the ecological functions of sub- ent patterns in the NMDS plot (Fig. 3b, c). Most bacterial merged macrophytes in the freshwater ecosystem. communities include a great number of species. Only a few of these bacterial species are very abundant, and a great number of bacterial species contain only a few indi- viduals (Sogin et al. 2006). In recent years, the rare bio- Acknowledgments We thank Mr. Feng Shen his help in the data anal- sphere of bacteria has been examined, revealing that the ysis. This work was supported by the National Natural Science distribution patterns of rare and abundant taxa are seldom Foundation of China (41371098, 41571108 and 41671078), Natural Science Foundation of Jiangsu Province, China (BK20151614), the similar (Galand et al. 2009; Gobet et al. 2012). In our Special Fund of State Key Laboratory of Hydrology-Water Resources study, the bacterial community derived from the rhizo- and Hydraulic Engineering (20145027312, 20155019012), the sphere sediments of different submerged macrophytes Fundamental Research Funds for the Central Universities clustered together for the rare bacterial groups (Fig. 3c), (2015B14214) and Qing Lan Project of Jiangsu Province. Ann Microbiol (2017) 67:313–319 319 Lu L, Xing DF, Ren NQ (2012) Pyrosequencing reveals highly diverse References microbial communities in microbial electrolysis cells involved in enhanced H production from waste activated sludge. 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Annals of Microbiology – Springer Journals
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