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454 Pyrosequencing-based assessment of bacterial diversity and community structure in termite guts, mounds and surrounding soils.

Makonde HM, Mwirichia R, Osiemo Z, Boga HI, Klenk HP - Springerplus (2015)

Bottom Line: The results indicated significant difference in bacterial community composition and structure between the gut and corresponding soil samples.The results not only demonstrated a high level of bacterial diversity in the gut and surrounding soil environments, but also presence of distinct bacterial communities that are yet to be cultivated.Therefore, combined efforts using both culture and culture-independent methods are suggested to comprehensively characterize the bacterial species and their specific roles in these environments.

View Article: PubMed Central - PubMed

Affiliation: Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Brunswick, Germany ; Pure and Applied Sciences, Technical University of Mombasa, P.O.Box 90420-80100, Mombasa, Kenya.

ABSTRACT
Termites constitute part of diverse and economically important termite fauna in Africa, but information on gut microbiota and their associated soil microbiome is still inadequate. In this study, we assessed and compared the bacterial diversity and community structure between termites' gut, their mounds and surrounding soil using the 454 pyrosequencing-based analysis of 16S rRNA gene sequences. A wood-feeder termite (Microcerotermes sp.), three fungus-cultivating termites (Macrotermes michaelseni, Odontotermes sp. and Microtermes sp.), their associated mounds and corresponding savannah soil samples were analyzed. The pH of the gut homogenates and soil physico-chemical properties were determined. The results indicated significant difference in bacterial community composition and structure between the gut and corresponding soil samples. Soil samples (Chao1 index ranged from 1359 to 2619) had higher species richness than gut samples (Chao1 index ranged from 461 to 1527). The bacterial composition and community structure in the gut of Macrotermes michaelseni and Odontotermes sp. were almost identical but different from that of Microtermes and Microcerotermes species, which had unique community structures. The most predominant bacterial phyla in the gut were Bacteroidetes (40-58 %), Spirochaetes (10-70 %), Firmicutes (17-27 %) and Fibrobacteres (13 %) while in the soil samples were Acidobacteria (28-45 %), Actinobacteria (20-40 %) and Proteobacteria (18-24 %). Some termite gut-specific bacterial lineages belonging to the genera Dysgonomonas, Parabacteroides, Paludibacter, Tannerella, Alistipes, BCf9-17 termite group and Termite Treponema cluster were observed. The results not only demonstrated a high level of bacterial diversity in the gut and surrounding soil environments, but also presence of distinct bacterial communities that are yet to be cultivated. Therefore, combined efforts using both culture and culture-independent methods are suggested to comprehensively characterize the bacterial species and their specific roles in these environments.

No MeSH data available.


Rarefaction curves indicating the observed number of operational taxonomic units (OTUs). The samples are marked by different colors. MCG8Microcerotermes sp. gut homogenate, MIG7 Microtermes sp. gut homogenate, OTG1Odontotermes sp. gut homogenate, MTG4M. michaelseni gut homogenate, OTN2 soil from mound C of Odontotermes sp., MTN5 soil from mound D of M.michaelseni, MTS6 soil collected 3 m away from mound D, OTS3 soil collected 3 m away from mound C
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Fig4: Rarefaction curves indicating the observed number of operational taxonomic units (OTUs). The samples are marked by different colors. MCG8Microcerotermes sp. gut homogenate, MIG7 Microtermes sp. gut homogenate, OTG1Odontotermes sp. gut homogenate, MTG4M. michaelseni gut homogenate, OTN2 soil from mound C of Odontotermes sp., MTN5 soil from mound D of M.michaelseni, MTS6 soil collected 3 m away from mound D, OTS3 soil collected 3 m away from mound C

Mentions: Bacterial diversity and richness for the selected sequences from each sample (Table 1) was evaluated by rarefaction as shown in Fig. 4 and Additional file 1b. At 3, 5 and 10 % sequence divergence, most rarefaction curves did not reach saturation, indicating that the surveying efforts did not fully cover the extent of taxonomic diversity at these genetic distances, but a substantial fraction of the bacterial diversity within individual samples was assessed. The diversity measures indicated that MTN5 had the most genus-level taxa (645, Table 1) and MCG8 the least (261, Table 1), that OTN2 was richest (Chao 1 index), while MCG8 was poorest. Despite variation in community composition, Simpson (1/D) and Shannon indices were similar across communities, ranging from 0.9 to 1.0 and 4.0 to 5.4, respectively. Comparison between any pair of bacterial communities using unweighted UniFrac PCoA (Fig. 3) showed a distinct clustering by environment but the p value of 0.283 and R value of 0.091 indicated that the grouping of samples is weak. For instance, samples OTG1 and MTG4 clustered together (Fig. 3), indicating similarities in the two guts. Sample MIG7 was slightly away from OTG1 and MTG4 meaning that its bacterial communities and community structure are different from the two. Sample MCG8 was very distinct and far away from the other gut samples, implying that its bacterial communities are unique to those of fungus-cultivating termites. Likewise, the mound samples (OTN2 and MTN5) and soils samples (OTS3 and MTS6) clustered together (Figs. 2a, 3), indicating that the bacterial community structure of the sample types was almost identical. The PCA (Fig. 2b), indicated that the relative abundances of Alistipes, Treponema, Bryobacter and Frankia are the major effect determining the overall variance of the genus compositions in the samples. Differences regarding the other genera detected in the samples are minimal. Alistipes abundance increases in the direction of the M. michaelseni (sample MTG4) and Odontotermes sp. (sample OTG1), while abundance of Treponema increases towards Microcerotermes sp. (sample MCG8) and Microtermes sp. (sample MIG7). Bryobacter and Frankia, however, increases towards the mounds (samples OTN2 and MTN5) and soil (samples OTS3 and MTS6).Fig. 4


454 Pyrosequencing-based assessment of bacterial diversity and community structure in termite guts, mounds and surrounding soils.

Makonde HM, Mwirichia R, Osiemo Z, Boga HI, Klenk HP - Springerplus (2015)

Rarefaction curves indicating the observed number of operational taxonomic units (OTUs). The samples are marked by different colors. MCG8Microcerotermes sp. gut homogenate, MIG7 Microtermes sp. gut homogenate, OTG1Odontotermes sp. gut homogenate, MTG4M. michaelseni gut homogenate, OTN2 soil from mound C of Odontotermes sp., MTN5 soil from mound D of M.michaelseni, MTS6 soil collected 3 m away from mound D, OTS3 soil collected 3 m away from mound C
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4556716&req=5

Fig4: Rarefaction curves indicating the observed number of operational taxonomic units (OTUs). The samples are marked by different colors. MCG8Microcerotermes sp. gut homogenate, MIG7 Microtermes sp. gut homogenate, OTG1Odontotermes sp. gut homogenate, MTG4M. michaelseni gut homogenate, OTN2 soil from mound C of Odontotermes sp., MTN5 soil from mound D of M.michaelseni, MTS6 soil collected 3 m away from mound D, OTS3 soil collected 3 m away from mound C
Mentions: Bacterial diversity and richness for the selected sequences from each sample (Table 1) was evaluated by rarefaction as shown in Fig. 4 and Additional file 1b. At 3, 5 and 10 % sequence divergence, most rarefaction curves did not reach saturation, indicating that the surveying efforts did not fully cover the extent of taxonomic diversity at these genetic distances, but a substantial fraction of the bacterial diversity within individual samples was assessed. The diversity measures indicated that MTN5 had the most genus-level taxa (645, Table 1) and MCG8 the least (261, Table 1), that OTN2 was richest (Chao 1 index), while MCG8 was poorest. Despite variation in community composition, Simpson (1/D) and Shannon indices were similar across communities, ranging from 0.9 to 1.0 and 4.0 to 5.4, respectively. Comparison between any pair of bacterial communities using unweighted UniFrac PCoA (Fig. 3) showed a distinct clustering by environment but the p value of 0.283 and R value of 0.091 indicated that the grouping of samples is weak. For instance, samples OTG1 and MTG4 clustered together (Fig. 3), indicating similarities in the two guts. Sample MIG7 was slightly away from OTG1 and MTG4 meaning that its bacterial communities and community structure are different from the two. Sample MCG8 was very distinct and far away from the other gut samples, implying that its bacterial communities are unique to those of fungus-cultivating termites. Likewise, the mound samples (OTN2 and MTN5) and soils samples (OTS3 and MTS6) clustered together (Figs. 2a, 3), indicating that the bacterial community structure of the sample types was almost identical. The PCA (Fig. 2b), indicated that the relative abundances of Alistipes, Treponema, Bryobacter and Frankia are the major effect determining the overall variance of the genus compositions in the samples. Differences regarding the other genera detected in the samples are minimal. Alistipes abundance increases in the direction of the M. michaelseni (sample MTG4) and Odontotermes sp. (sample OTG1), while abundance of Treponema increases towards Microcerotermes sp. (sample MCG8) and Microtermes sp. (sample MIG7). Bryobacter and Frankia, however, increases towards the mounds (samples OTN2 and MTN5) and soil (samples OTS3 and MTS6).Fig. 4

Bottom Line: The results indicated significant difference in bacterial community composition and structure between the gut and corresponding soil samples.The results not only demonstrated a high level of bacterial diversity in the gut and surrounding soil environments, but also presence of distinct bacterial communities that are yet to be cultivated.Therefore, combined efforts using both culture and culture-independent methods are suggested to comprehensively characterize the bacterial species and their specific roles in these environments.

View Article: PubMed Central - PubMed

Affiliation: Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Brunswick, Germany ; Pure and Applied Sciences, Technical University of Mombasa, P.O.Box 90420-80100, Mombasa, Kenya.

ABSTRACT
Termites constitute part of diverse and economically important termite fauna in Africa, but information on gut microbiota and their associated soil microbiome is still inadequate. In this study, we assessed and compared the bacterial diversity and community structure between termites' gut, their mounds and surrounding soil using the 454 pyrosequencing-based analysis of 16S rRNA gene sequences. A wood-feeder termite (Microcerotermes sp.), three fungus-cultivating termites (Macrotermes michaelseni, Odontotermes sp. and Microtermes sp.), their associated mounds and corresponding savannah soil samples were analyzed. The pH of the gut homogenates and soil physico-chemical properties were determined. The results indicated significant difference in bacterial community composition and structure between the gut and corresponding soil samples. Soil samples (Chao1 index ranged from 1359 to 2619) had higher species richness than gut samples (Chao1 index ranged from 461 to 1527). The bacterial composition and community structure in the gut of Macrotermes michaelseni and Odontotermes sp. were almost identical but different from that of Microtermes and Microcerotermes species, which had unique community structures. The most predominant bacterial phyla in the gut were Bacteroidetes (40-58 %), Spirochaetes (10-70 %), Firmicutes (17-27 %) and Fibrobacteres (13 %) while in the soil samples were Acidobacteria (28-45 %), Actinobacteria (20-40 %) and Proteobacteria (18-24 %). Some termite gut-specific bacterial lineages belonging to the genera Dysgonomonas, Parabacteroides, Paludibacter, Tannerella, Alistipes, BCf9-17 termite group and Termite Treponema cluster were observed. The results not only demonstrated a high level of bacterial diversity in the gut and surrounding soil environments, but also presence of distinct bacterial communities that are yet to be cultivated. Therefore, combined efforts using both culture and culture-independent methods are suggested to comprehensively characterize the bacterial species and their specific roles in these environments.

No MeSH data available.