8.2.1 Compositional Changes of Bacterial Communities After
Vermicomposting
Vermicomposting led to significant changes in bacterial community composition at
phylum level (Fig. 8.1). The fresh plant materials and the respective vermicomposts
were found to group separately in two different clades (Fig. 8.1), as shown in the
phylogenetic tree inferred from the sequence data using FastTree 2.1 (Price et al.
2010). The raw plant materials were split into two additional clades (Fig. 8.1 top),
one comprised by the fresh samples of Scotch broom and acacia substrates and
another one by the initial samples of raw and distilled grape marcs. Within each of
these clades, there was also a clear differentiation between the two leguminous
shrubs and the two winemaking by-products (Fig. 8.1). The dissimilarity of bacterial
communities among samples at ASV levels was based on the relative abundance of
the dominant bacterial phyla in each sample (Fig. 8.1 barplot). Proteobacteria was
the most prevalent phylum in the four types of plant material accounting for almost
100% of the sequences in acacia and Scotch broom initial samples and nearly
60–70% of the sequences in the fresh samples of raw and distilled grape marcs
(Fig. 8.1). In the case of these two latter substrates, the bacterial community
composition was also composed of Firmicutes, with minor contributions of
Bacteroidetes and Actinobacteria (Fig. 8.1).
Proteobacteria continued to make up a significant proportion of the bacterial
communities within the vermicomposts’ microbial composition (Fig. 8.1). However,
at ASV level, we observed that 90% of ASVs were exclusively found in the
vermicomposts representing in average 90% of the sequences of each vermicompost.
Additionally, we tested for differentially abundant bacterial taxa between the fresh
plant materials and the respective vermicomposts by using the DESeq2 package
(Love et al. 2014). In particular, there was a pronounced reduction in the differential
abundance of Firmicutes in the vermicomposts derived from raw and distilled grape
marcs when compared to the initial samples (raw: mean of À9.51 log2 fold change,
p < 0.0001; distilled: mean of À8.56 log2 fold change, p < 0.0001, respectively). In
contrast, the differential abundance of Bacteroidetes (raw: mean of 1.50 log2 fold
change, p ¼ 0.029; distilled: mean of 1.79 log2 fold change, p ¼ 0.007);
Planctomycetes (raw: mean of 7.81 log2 fold change, p < 0.0001; distilled: mean
of 3.20 log2 fold change, p < 0.0001); and Verrucomicrobia (raw: mean of 4.86
log2 fold change, p < 0.0001; distilled: mean of 3.92 log2 fold change, p < 0.0001)
significantly increased after vermicomposting of both raw and distilled grape marcs.
Moreover, higher differential abundances of the phyla Bacteroidetes (mean: 1.69
log2 fold change, p ¼ 0.014), Verrucomicrobia (mean: 4.99 log2 fold change,
p < 0.0001) and Planctomycetes (mean: 5.17 log2 fold change, p < 0.0001) were
also found in the Scotch broom-derived vermicompost when compared to the fresh
plant material. Similarly, the acacia-derived vermicompost was characterized by
higher abundances of the phyla Verrucomicrobia (mean: 3.15 log2 fold change,
p < 0.0001) and Bacteroidetes (mean: 2.99 log2 fold change, p < 0.0001) and by
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M. Gómez-Brandón et al.
Vermicomposting
Vermicomposting led to significant changes in bacterial community composition at
phylum level (Fig. 8.1). The fresh plant materials and the respective vermicomposts
were found to group separately in two different clades (Fig. 8.1), as shown in the
phylogenetic tree inferred from the sequence data using FastTree 2.1 (Price et al.
2010). The raw plant materials were split into two additional clades (Fig. 8.1 top),
one comprised by the fresh samples of Scotch broom and acacia substrates and
another one by the initial samples of raw and distilled grape marcs. Within each of
these clades, there was also a clear differentiation between the two leguminous
shrubs and the two winemaking by-products (Fig. 8.1). The dissimilarity of bacterial
communities among samples at ASV levels was based on the relative abundance of
the dominant bacterial phyla in each sample (Fig. 8.1 barplot). Proteobacteria was
the most prevalent phylum in the four types of plant material accounting for almost
100% of the sequences in acacia and Scotch broom initial samples and nearly
60–70% of the sequences in the fresh samples of raw and distilled grape marcs
(Fig. 8.1). In the case of these two latter substrates, the bacterial community
composition was also composed of Firmicutes, with minor contributions of
Bacteroidetes and Actinobacteria (Fig. 8.1).
Proteobacteria continued to make up a significant proportion of the bacterial
communities within the vermicomposts’ microbial composition (Fig. 8.1). However,
at ASV level, we observed that 90% of ASVs were exclusively found in the
vermicomposts representing in average 90% of the sequences of each vermicompost.
Additionally, we tested for differentially abundant bacterial taxa between the fresh
plant materials and the respective vermicomposts by using the DESeq2 package
(Love et al. 2014). In particular, there was a pronounced reduction in the differential
abundance of Firmicutes in the vermicomposts derived from raw and distilled grape
marcs when compared to the initial samples (raw: mean of À9.51 log2 fold change,
p < 0.0001; distilled: mean of À8.56 log2 fold change, p < 0.0001, respectively). In
contrast, the differential abundance of Bacteroidetes (raw: mean of 1.50 log2 fold
change, p ¼ 0.029; distilled: mean of 1.79 log2 fold change, p ¼ 0.007);
Planctomycetes (raw: mean of 7.81 log2 fold change, p < 0.0001; distilled: mean
of 3.20 log2 fold change, p < 0.0001); and Verrucomicrobia (raw: mean of 4.86
log2 fold change, p < 0.0001; distilled: mean of 3.92 log2 fold change, p < 0.0001)
significantly increased after vermicomposting of both raw and distilled grape marcs.
Moreover, higher differential abundances of the phyla Bacteroidetes (mean: 1.69
log2 fold change, p ¼ 0.014), Verrucomicrobia (mean: 4.99 log2 fold change,
p < 0.0001) and Planctomycetes (mean: 5.17 log2 fold change, p < 0.0001) were
also found in the Scotch broom-derived vermicompost when compared to the fresh
plant material. Similarly, the acacia-derived vermicompost was characterized by
higher abundances of the phyla Verrucomicrobia (mean: 3.15 log2 fold change,
p < 0.0001) and Bacteroidetes (mean: 2.99 log2 fold change, p < 0.0001) and by
128
M. Gómez-Brandón et al.