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Characterization of leaf blade- and leaf sheath-associated bacterial communities and assessment of their responses to environmental changes in CO₂, temperature, and nitrogen levels under field conditions.

Ikeda S, Tokida T, Nakamura H, Sakai H, Usui Y, Okubo T, Tago K, Hayashi K, Sekiyama Y, Ono H, Tomita S, Hayatsu M, Hasegawa T, Minamisawa K - Microbes Environ. (2015)

Bottom Line: Rice shoot-associated bacterial communities at the panicle initiation stage were characterized and their responses to elevated surface water-soil temperature (ET), low nitrogen (LN), and free-air CO2 enrichment (FACE) were assessed by clone library analyses of the 16S rRNA gene.The most significant effect of FACE was also observed on leaf blade-associated bacteria under the LN condition, which was explained by decreases and increases in Agrobacterium and Pantoea, respectively.Thus, the combined effects of environmental factors need to be considered in order to realistically assess the effects of environmental changes on microbial community structures.

View Article: PubMed Central - PubMed

Affiliation: Memuro Research Station, Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization.

ABSTRACT
Rice shoot-associated bacterial communities at the panicle initiation stage were characterized and their responses to elevated surface water-soil temperature (ET), low nitrogen (LN), and free-air CO2 enrichment (FACE) were assessed by clone library analyses of the 16S rRNA gene. Principal coordinate analyses combining all sequence data for leaf blade- and leaf sheath-associated bacteria revealed that each bacterial community had a distinct structure, as supported by PC1 (61.5%), that was mainly attributed to the high abundance of Planctomycetes in leaf sheaths. Our results also indicated that the community structures of leaf blade-associated bacteria were more sensitive than those of leaf sheath-associated bacteria to the environmental factors examined. Among these environmental factors, LN strongly affected the community structures of leaf blade-associated bacteria by increasing the relative abundance of Bacilli. The most significant effect of FACE was also observed on leaf blade-associated bacteria under the LN condition, which was explained by decreases and increases in Agrobacterium and Pantoea, respectively. The community structures of leaf blade-associated bacteria under the combination of FACE and ET were more similar to those of the control than to those under ET or FACE. Thus, the combined effects of environmental factors need to be considered in order to realistically assess the effects of environmental changes on microbial community structures.

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Phylogenetic distribution of OTUs for Bacilli responding to environmental factors in 16S rRNA gene clone libraries of rice leaf blade- and leaf sheath-associated bacteria under ambient and FACE conditions. The dendrogram indicates the phylogenetic relationships among the representative sequences of OTUs (defined by ≥97% identity). The table indicates the relative abundance of clones belonging to each OTU in each library and the results of a BLAST search using the representative sequences. ** and * indicate significant differences between the control (ambient CO2 with normal temperature and standard nitrogen level) and other samples at P<0.01 and P<0.05, respectively. Shading indicates OTUs described in the main text.
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f4-30_51: Phylogenetic distribution of OTUs for Bacilli responding to environmental factors in 16S rRNA gene clone libraries of rice leaf blade- and leaf sheath-associated bacteria under ambient and FACE conditions. The dendrogram indicates the phylogenetic relationships among the representative sequences of OTUs (defined by ≥97% identity). The table indicates the relative abundance of clones belonging to each OTU in each library and the results of a BLAST search using the representative sequences. ** and * indicate significant differences between the control (ambient CO2 with normal temperature and standard nitrogen level) and other samples at P<0.01 and P<0.05, respectively. Shading indicates OTUs described in the main text.

Mentions: Firmicutes was also a dominant taxon in rice shoots (Table 5). Both Bacilli and Clostridia were more abundant in leaf blades than in leaf sheaths. Within Bacilli, Bacillus, Paenibacillus, Staphylococcus, and Exiguobacterium were more abundant in leaf blades (Table S2). The clustering analyses identified two dominant OTUs (BA6 and BA10 corresponding to Staphylococcus and Exiguobacterium, respectively, in Fig. 4). Clostridia, which are obligate anaerobic bacteria, were also slightly more abundant in leaf blades (Table 5), which are generally considered to be an aerobic environment due to photosynthesis. Planctomycetes, which have rarely been reported in association with the aerial tissues of plants, were exclusively present in leaf sheaths at a high abundance under all conditions examined (20.0–30.5% in Table 5). Although the Planctomycete community in rice leaf sheaths appeared to be phylogenetically diverse, relatively dominant OTUs were identified by clustering analyses (Fig. 5). In the genus Planctomyces, OTUs PL1, PL2, PL4, and PL16 were detected under most environmental conditions examined, except for OTU PL1 in AMBI-NT. In the genus Pirellula, OTUs PL25, PL31, and PL32 were detected under most conditions examined, except for OTU 31 in AMBI-NT. OTU PL25 was identified as the most dominant and stable OTU in the Planctomycete community (Fig. 5). A prominent feature of this community in rice leaf sheaths was that the representative sequences of 16S rRNA genes for most OTUs had less than 95% identity to known species (Fig. 5). A phylogenetic tree analysis revealed the presence of three unique clusters for rice leaf sheaths (clusters A–C in Fig. 7). Clusters A and B were distantly related to the known species of two genera, Pirellula and Rhodopirellula, whereas cluster C was located within the cluster of known Planctomyces species.


Characterization of leaf blade- and leaf sheath-associated bacterial communities and assessment of their responses to environmental changes in CO₂, temperature, and nitrogen levels under field conditions.

Ikeda S, Tokida T, Nakamura H, Sakai H, Usui Y, Okubo T, Tago K, Hayashi K, Sekiyama Y, Ono H, Tomita S, Hayatsu M, Hasegawa T, Minamisawa K - Microbes Environ. (2015)

Phylogenetic distribution of OTUs for Bacilli responding to environmental factors in 16S rRNA gene clone libraries of rice leaf blade- and leaf sheath-associated bacteria under ambient and FACE conditions. The dendrogram indicates the phylogenetic relationships among the representative sequences of OTUs (defined by ≥97% identity). The table indicates the relative abundance of clones belonging to each OTU in each library and the results of a BLAST search using the representative sequences. ** and * indicate significant differences between the control (ambient CO2 with normal temperature and standard nitrogen level) and other samples at P<0.01 and P<0.05, respectively. Shading indicates OTUs described in the main text.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4356464&req=5

f4-30_51: Phylogenetic distribution of OTUs for Bacilli responding to environmental factors in 16S rRNA gene clone libraries of rice leaf blade- and leaf sheath-associated bacteria under ambient and FACE conditions. The dendrogram indicates the phylogenetic relationships among the representative sequences of OTUs (defined by ≥97% identity). The table indicates the relative abundance of clones belonging to each OTU in each library and the results of a BLAST search using the representative sequences. ** and * indicate significant differences between the control (ambient CO2 with normal temperature and standard nitrogen level) and other samples at P<0.01 and P<0.05, respectively. Shading indicates OTUs described in the main text.
Mentions: Firmicutes was also a dominant taxon in rice shoots (Table 5). Both Bacilli and Clostridia were more abundant in leaf blades than in leaf sheaths. Within Bacilli, Bacillus, Paenibacillus, Staphylococcus, and Exiguobacterium were more abundant in leaf blades (Table S2). The clustering analyses identified two dominant OTUs (BA6 and BA10 corresponding to Staphylococcus and Exiguobacterium, respectively, in Fig. 4). Clostridia, which are obligate anaerobic bacteria, were also slightly more abundant in leaf blades (Table 5), which are generally considered to be an aerobic environment due to photosynthesis. Planctomycetes, which have rarely been reported in association with the aerial tissues of plants, were exclusively present in leaf sheaths at a high abundance under all conditions examined (20.0–30.5% in Table 5). Although the Planctomycete community in rice leaf sheaths appeared to be phylogenetically diverse, relatively dominant OTUs were identified by clustering analyses (Fig. 5). In the genus Planctomyces, OTUs PL1, PL2, PL4, and PL16 were detected under most environmental conditions examined, except for OTU PL1 in AMBI-NT. In the genus Pirellula, OTUs PL25, PL31, and PL32 were detected under most conditions examined, except for OTU 31 in AMBI-NT. OTU PL25 was identified as the most dominant and stable OTU in the Planctomycete community (Fig. 5). A prominent feature of this community in rice leaf sheaths was that the representative sequences of 16S rRNA genes for most OTUs had less than 95% identity to known species (Fig. 5). A phylogenetic tree analysis revealed the presence of three unique clusters for rice leaf sheaths (clusters A–C in Fig. 7). Clusters A and B were distantly related to the known species of two genera, Pirellula and Rhodopirellula, whereas cluster C was located within the cluster of known Planctomyces species.

Bottom Line: Rice shoot-associated bacterial communities at the panicle initiation stage were characterized and their responses to elevated surface water-soil temperature (ET), low nitrogen (LN), and free-air CO2 enrichment (FACE) were assessed by clone library analyses of the 16S rRNA gene.The most significant effect of FACE was also observed on leaf blade-associated bacteria under the LN condition, which was explained by decreases and increases in Agrobacterium and Pantoea, respectively.Thus, the combined effects of environmental factors need to be considered in order to realistically assess the effects of environmental changes on microbial community structures.

View Article: PubMed Central - PubMed

Affiliation: Memuro Research Station, Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization.

ABSTRACT
Rice shoot-associated bacterial communities at the panicle initiation stage were characterized and their responses to elevated surface water-soil temperature (ET), low nitrogen (LN), and free-air CO2 enrichment (FACE) were assessed by clone library analyses of the 16S rRNA gene. Principal coordinate analyses combining all sequence data for leaf blade- and leaf sheath-associated bacteria revealed that each bacterial community had a distinct structure, as supported by PC1 (61.5%), that was mainly attributed to the high abundance of Planctomycetes in leaf sheaths. Our results also indicated that the community structures of leaf blade-associated bacteria were more sensitive than those of leaf sheath-associated bacteria to the environmental factors examined. Among these environmental factors, LN strongly affected the community structures of leaf blade-associated bacteria by increasing the relative abundance of Bacilli. The most significant effect of FACE was also observed on leaf blade-associated bacteria under the LN condition, which was explained by decreases and increases in Agrobacterium and Pantoea, respectively. The community structures of leaf blade-associated bacteria under the combination of FACE and ET were more similar to those of the control than to those under ET or FACE. Thus, the combined effects of environmental factors need to be considered in order to realistically assess the effects of environmental changes on microbial community structures.

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