resulted in a total of ten and seven phyla that differed in abundance for the pairs
distilled marc-Scotch broom and distilled marc-acacia vermicompost samples,
respectively. Some of these phyla including Acidobacteria, Spirochaetes,
Nitrospirae and Gemmatimonadetes had lower differential abundances in the distilled grape marc-derived vermicompost compared to acacia and Scotch broom
vermicomposts. Others like Chloroflexi, Verrucomicrobia, Patescibacteria and
Actinobacteria reached higher abundances in the vermicompost samples from distilled grape marc according to DESeq results.
While lower differential abundances of Verrucomicrobia (mean: À2.02 log2 fold
change, p ¼ 0.002) and Patescibacteria (mean: À6.92 log2 fold change, p ¼ 0.024)
were recorded in Scotch broom vermicompost samples, higher abundances of
Actinobacteria (mean: 2.08 log2 fold change, p ¼ 0.003) and Firmicutes (mean:
2.75 log2 fold change, p ¼ 0.003) were found in these vermicompost samples
compared to those obtained from the acacia plant material.
8.3 How Does Vermicomposting Influence Alphaand Beta-Diversity of Bacterial Communities from
Dead Plant Material?
In this chapter taxonomic α-diversity of bacterial communities was calculated as the
number of observed ASVs, while phylogenetic diversity was assessed as Faith’s
phylogenetic diversity (Faith 1992). An increase in α-diversity was reported for all
of the four vermicomposts in comparison with the respective fresh materials at both
taxonomic and phylogenetic levels (Fig. 8.3a, b). The Scotch broom-derived
vermicompost harboured the highest α-diversity at taxonomic level (689 Æ 35),
being 17 times greater than in the initial substrate (Fig. 8.3a), while no differences
were observed among the other three vermicomposts (Fig. 8.3a). A similar pattern
emerged for the Faith phylogenetic diversity (Fig. 8.3b), and in this case the highest
values were reported for both the Scotch broom- and acacia-derived vermicomposts
(Fig. 8.3b).
The increase in α-diversity was reflected in different patterns of taxonomic and
phylogenetic β-diversity (Fig. 8.4a, b). Taxonomic β-diversity at the ASV level was
estimated as the difference in the composition of the bacterial taxonomic community
between the fresh plant materials and the respective vermicomposts. This was done
by coupling principal coordinate analysis (PCoA) with distance matrices that take
the abundance of ASVs into account (Bray–Curtis). Phylogenetic β-diversity was
estimated by PCoA of weighted (considering abundance of ASVs) UniFrac matrix
distances (Lozupone and Knight 2005) by using the phyloseq library (Love et al.
2014). Principal coordinate analysis showed that the fresh plant materials differed
from each other in terms of β-diversity at both taxonomic and phylogenetic levels
(Fig. 8.4a, b). In addition, they also grouped separately from the respective
vermicomposts (Fig. 8.4a, b). This implies that the bacterial community present in
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distilled marc-Scotch broom and distilled marc-acacia vermicompost samples,
respectively. Some of these phyla including Acidobacteria, Spirochaetes,
Nitrospirae and Gemmatimonadetes had lower differential abundances in the distilled grape marc-derived vermicompost compared to acacia and Scotch broom
vermicomposts. Others like Chloroflexi, Verrucomicrobia, Patescibacteria and
Actinobacteria reached higher abundances in the vermicompost samples from distilled grape marc according to DESeq results.
While lower differential abundances of Verrucomicrobia (mean: À2.02 log2 fold
change, p ¼ 0.002) and Patescibacteria (mean: À6.92 log2 fold change, p ¼ 0.024)
were recorded in Scotch broom vermicompost samples, higher abundances of
Actinobacteria (mean: 2.08 log2 fold change, p ¼ 0.003) and Firmicutes (mean:
2.75 log2 fold change, p ¼ 0.003) were found in these vermicompost samples
compared to those obtained from the acacia plant material.
8.3 How Does Vermicomposting Influence Alphaand Beta-Diversity of Bacterial Communities from
Dead Plant Material?
In this chapter taxonomic α-diversity of bacterial communities was calculated as the
number of observed ASVs, while phylogenetic diversity was assessed as Faith’s
phylogenetic diversity (Faith 1992). An increase in α-diversity was reported for all
of the four vermicomposts in comparison with the respective fresh materials at both
taxonomic and phylogenetic levels (Fig. 8.3a, b). The Scotch broom-derived
vermicompost harboured the highest α-diversity at taxonomic level (689 Æ 35),
being 17 times greater than in the initial substrate (Fig. 8.3a), while no differences
were observed among the other three vermicomposts (Fig. 8.3a). A similar pattern
emerged for the Faith phylogenetic diversity (Fig. 8.3b), and in this case the highest
values were reported for both the Scotch broom- and acacia-derived vermicomposts
(Fig. 8.3b).
The increase in α-diversity was reflected in different patterns of taxonomic and
phylogenetic β-diversity (Fig. 8.4a, b). Taxonomic β-diversity at the ASV level was
estimated as the difference in the composition of the bacterial taxonomic community
between the fresh plant materials and the respective vermicomposts. This was done
by coupling principal coordinate analysis (PCoA) with distance matrices that take
the abundance of ASVs into account (Bray–Curtis). Phylogenetic β-diversity was
estimated by PCoA of weighted (considering abundance of ASVs) UniFrac matrix
distances (Lozupone and Knight 2005) by using the phyloseq library (Love et al.
2014). Principal coordinate analysis showed that the fresh plant materials differed
from each other in terms of β-diversity at both taxonomic and phylogenetic levels
(Fig. 8.4a, b). In addition, they also grouped separately from the respective
vermicomposts (Fig. 8.4a, b). This implies that the bacterial community present in
132
M. Gómez-Brandón et al.