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Characterization of microbial community structure during continuous anaerobic digestion of straw and cow manure.

Sun L, Pope PB, Eijsink VG, Schnürer A - Microb Biotechnol (2015)

Bottom Line: Compared with manure itself, digestion of manure resulted in a higher abundance of an uncultured class WWE1 and lower abundance of Bacilli.Adding straw to the digesters increased the level of Bacteroidia, while increasing the operating temperature decreased the level of this class and instead increased the relative abundance of an uncultured genus affiliated to order MBA08 (Clostridia).A considerable fraction of bacterial sequences could not be allocated to genus level, indicating that novel phylotypes are resident in these communities.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology, Swedish University of Agricultural Science, Uppsala BioCenter, P.O. Box 7025, SE-750 07, Uppsala, Sweden.

No MeSH data available.


(A) Archaeal and (B) bacterial phylogenetic distances between samples as determined by unweighted UniFrac principal coordinate analysis (red = manure; blue = digester RM; orange = digester RTcSS and R37SS; green = digester R44SS; purple = digester R52SS).
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fig01: (A) Archaeal and (B) bacterial phylogenetic distances between samples as determined by unweighted UniFrac principal coordinate analysis (red = manure; blue = digester RM; orange = digester RTcSS and R37SS; green = digester R44SS; purple = digester R52SS).

Mentions: Amplicon pyrosequencing of 25 samples yielded 77 791 and 64 731 non-chimeric reads for archaea and bacteria respectively. The number of operational taxonomic units (OTUs) per sample ranged from 12 to 25 for archaea and from 112 to 277 for bacteria (Table 1). The phylogenetic compositions as determined by principal coordinate analysis (PCoA) of unweighted UniFrac matrices (Fig. 1) for the archaeal and bacterial communities within the same digester at multiple sampling points over time were similar. For instance, the four sampling points of the parallel digesters RTcSS (reactors operated with steam-exploded straw and manure at 37°C, Risberg et al., 2013) were clustered closely together, indicating comparable phylogenetic structures within a total period of 91 days. Moreover, the communities in all parallel digesters running under the same conditions were also comparable, e.g. the community in duplicate reactors running with steam-exploded straw and manure at different temperatures (R37SS, R44SS and R52SS) was also similar at individual time points. The estimated richness for all samples analysed at all sampling points based on the Chao1 index indicated that the observed phylotypes covered 23–93% and 48–82% of the archaeal and bacterial populations respectively (Table 1). In general, the species richness expressed as the number of observed OTUs decreased as the operating temperature increased for both bacteria and archaea (Table 1 and Fig. S1). For bacterial reads, no species richness difference was observed between manure itself and the digester operated with manure alone (RM). However, a slightly lower bacterial species richness was observed in digesters that received straw in the substrate (digesters RTcSS and R37SS) than that operated with manure alone (RM) (Welch’s t-test, P < 0.01). In contrast, for archaea, no clear trend in species richness was observed when comparing the manure itself and the mesophilic digesters operating with manure, alone or combined with straw. The Simpson diversity index ranged from 0.53 to 0.78 for archaea and from 0.72 to 0.98 for bacteria (Table 1). For the bacterial community, a lower Simpson index was observed during the increase in operating temperature, suggesting lower community evenness in these digesters (R44SS and R52SS, digesters processing straw and manure at 44°C and 52°C). Compared with the bacterial community, the Simpson index was generally lower for the archaeal community, and with the lowest value in R44SS compared with R37SS and R52SS (Welch’s t-test, P < 0.05). The Shannon diversity index varied from 1.46 to 2.64 for archaea and from 3.45 to 6.36 for bacteria (Table 1). Within the bacterial community, the Shannon index was comparably lower in digesters operating with straw at higher temperatures, i.e. at 44°C and 52°C compared with 37°C (Welch’s t-test, P < 0.05). For the archaeal community, a lower Shannon diversity index was observed in R44SS compared with R37/TcSS and R52SS (Welch’s t-test, P < 0.05), and in RM compared with R37/TcSS (Welch’s t-test, P < 0.01).


Characterization of microbial community structure during continuous anaerobic digestion of straw and cow manure.

Sun L, Pope PB, Eijsink VG, Schnürer A - Microb Biotechnol (2015)

(A) Archaeal and (B) bacterial phylogenetic distances between samples as determined by unweighted UniFrac principal coordinate analysis (red = manure; blue = digester RM; orange = digester RTcSS and R37SS; green = digester R44SS; purple = digester R52SS).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
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fig01: (A) Archaeal and (B) bacterial phylogenetic distances between samples as determined by unweighted UniFrac principal coordinate analysis (red = manure; blue = digester RM; orange = digester RTcSS and R37SS; green = digester R44SS; purple = digester R52SS).
Mentions: Amplicon pyrosequencing of 25 samples yielded 77 791 and 64 731 non-chimeric reads for archaea and bacteria respectively. The number of operational taxonomic units (OTUs) per sample ranged from 12 to 25 for archaea and from 112 to 277 for bacteria (Table 1). The phylogenetic compositions as determined by principal coordinate analysis (PCoA) of unweighted UniFrac matrices (Fig. 1) for the archaeal and bacterial communities within the same digester at multiple sampling points over time were similar. For instance, the four sampling points of the parallel digesters RTcSS (reactors operated with steam-exploded straw and manure at 37°C, Risberg et al., 2013) were clustered closely together, indicating comparable phylogenetic structures within a total period of 91 days. Moreover, the communities in all parallel digesters running under the same conditions were also comparable, e.g. the community in duplicate reactors running with steam-exploded straw and manure at different temperatures (R37SS, R44SS and R52SS) was also similar at individual time points. The estimated richness for all samples analysed at all sampling points based on the Chao1 index indicated that the observed phylotypes covered 23–93% and 48–82% of the archaeal and bacterial populations respectively (Table 1). In general, the species richness expressed as the number of observed OTUs decreased as the operating temperature increased for both bacteria and archaea (Table 1 and Fig. S1). For bacterial reads, no species richness difference was observed between manure itself and the digester operated with manure alone (RM). However, a slightly lower bacterial species richness was observed in digesters that received straw in the substrate (digesters RTcSS and R37SS) than that operated with manure alone (RM) (Welch’s t-test, P < 0.01). In contrast, for archaea, no clear trend in species richness was observed when comparing the manure itself and the mesophilic digesters operating with manure, alone or combined with straw. The Simpson diversity index ranged from 0.53 to 0.78 for archaea and from 0.72 to 0.98 for bacteria (Table 1). For the bacterial community, a lower Simpson index was observed during the increase in operating temperature, suggesting lower community evenness in these digesters (R44SS and R52SS, digesters processing straw and manure at 44°C and 52°C). Compared with the bacterial community, the Simpson index was generally lower for the archaeal community, and with the lowest value in R44SS compared with R37SS and R52SS (Welch’s t-test, P < 0.05). The Shannon diversity index varied from 1.46 to 2.64 for archaea and from 3.45 to 6.36 for bacteria (Table 1). Within the bacterial community, the Shannon index was comparably lower in digesters operating with straw at higher temperatures, i.e. at 44°C and 52°C compared with 37°C (Welch’s t-test, P < 0.05). For the archaeal community, a lower Shannon diversity index was observed in R44SS compared with R37/TcSS and R52SS (Welch’s t-test, P < 0.05), and in RM compared with R37/TcSS (Welch’s t-test, P < 0.01).

Bottom Line: Compared with manure itself, digestion of manure resulted in a higher abundance of an uncultured class WWE1 and lower abundance of Bacilli.Adding straw to the digesters increased the level of Bacteroidia, while increasing the operating temperature decreased the level of this class and instead increased the relative abundance of an uncultured genus affiliated to order MBA08 (Clostridia).A considerable fraction of bacterial sequences could not be allocated to genus level, indicating that novel phylotypes are resident in these communities.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology, Swedish University of Agricultural Science, Uppsala BioCenter, P.O. Box 7025, SE-750 07, Uppsala, Sweden.

No MeSH data available.