lower abundances of the phylum Firmicutes (mean: À5.14 log2 fold change,
p < 0.0001).
These differences in microbial community composition between the
vermicomposts and the respective raw materials might be a consequence of the
successional changes that take place over the course of the vermicomposting process. Such changes will be inextricably linked to the quantity and quality of the
available nutrient supplies and constitute an example of heterotrophic ecological
succession (Fierer et al. 2010). During vermicomposting, early microbial colonizers
(often assimilated to copiotrophs) are characterized by high nutritional requirements
and will preferentially consume rich and soluble substrates. As succession progresses, late decomposers (often assimilated to oligotrophs) will take over and will
exhibit low growth rates and higher substrate utilization efficiency to metabolize
complex carbon compounds (Ho et al. 2017). This could explain why oligotrophic
bacterial groups such as Planctomycetes and Verrucomicrobia had higher differential abundances in the vermicomposts compared to the fresh plant materials while the
abundance of Firmicutes that is considered as a fast-growing copiotroph group was
lower in the vermicomposts. The phylum Bacteroidetes is also associated with
copiotrophic environments (Yang et al. 2019), but unlike Firmicutes, Bacteroidetes
mostly comprise Gram-negative bacteria. Earlier studies based on phospholipid fatty
acid (PLFA) analysis have shown that the passage of organic material through the
gut of E. andrei reduced the abundance of Gram-positive bacteria to a greater extent
than Gram-negative bacteria (Gómez-Brandón et al. 2011, 2012). This feature could
have favoured that Bacteroidetes, in contrast to Firmicutes, appeared in higher
abundances in the vermicomposts than in the initial substrates.
8.2.2 Compositional Changes of Bacterial Communities
Among Vermicomposts
The vermicomposts could be differentiated from each other at phylum level in line
with the type of plant material (Fig. 8.1 bottom). The percentage of shared ASVs and
sequences between each pair of vermicomposts is shown in Fig. 8.2. Testing for
differentially abundant bacterial taxa between pairs of vermicomposts was also
achieved using the DESeq2 package. When comparing the bacterial community
composition of the vermicompost samples derived from the raw grape marc to those
obtained from distilled marc, we found that five bacterial phyla significantly differed
in abundance. They comprised the phyla Patescibacteria (mean: À8.85 log2 fold
change, p ¼ 0.003), Acidobacteria (mean: 2.34 log2 fold change, p ¼ 0.006),
Nitrospirae (mean: 5.95 log2 fold change, p ¼ 0.011), Gemmatimonadetes (mean:
3.71 log2 fold change, p ¼ 0.010) and Armatimonadetes (mean: 5.09 log2 fold
change, p ¼ 0.003). The mean log2 fold change values were either positive or
negative depending whether the above-mentioned phyla appeared in higher or lower
differential abundances in the raw grape marc vermicompost samples.
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M. Gómez-Brandón et al.
p < 0.0001).
These differences in microbial community composition between the
vermicomposts and the respective raw materials might be a consequence of the
successional changes that take place over the course of the vermicomposting process. Such changes will be inextricably linked to the quantity and quality of the
available nutrient supplies and constitute an example of heterotrophic ecological
succession (Fierer et al. 2010). During vermicomposting, early microbial colonizers
(often assimilated to copiotrophs) are characterized by high nutritional requirements
and will preferentially consume rich and soluble substrates. As succession progresses, late decomposers (often assimilated to oligotrophs) will take over and will
exhibit low growth rates and higher substrate utilization efficiency to metabolize
complex carbon compounds (Ho et al. 2017). This could explain why oligotrophic
bacterial groups such as Planctomycetes and Verrucomicrobia had higher differential abundances in the vermicomposts compared to the fresh plant materials while the
abundance of Firmicutes that is considered as a fast-growing copiotroph group was
lower in the vermicomposts. The phylum Bacteroidetes is also associated with
copiotrophic environments (Yang et al. 2019), but unlike Firmicutes, Bacteroidetes
mostly comprise Gram-negative bacteria. Earlier studies based on phospholipid fatty
acid (PLFA) analysis have shown that the passage of organic material through the
gut of E. andrei reduced the abundance of Gram-positive bacteria to a greater extent
than Gram-negative bacteria (Gómez-Brandón et al. 2011, 2012). This feature could
have favoured that Bacteroidetes, in contrast to Firmicutes, appeared in higher
abundances in the vermicomposts than in the initial substrates.
8.2.2 Compositional Changes of Bacterial Communities
Among Vermicomposts
The vermicomposts could be differentiated from each other at phylum level in line
with the type of plant material (Fig. 8.1 bottom). The percentage of shared ASVs and
sequences between each pair of vermicomposts is shown in Fig. 8.2. Testing for
differentially abundant bacterial taxa between pairs of vermicomposts was also
achieved using the DESeq2 package. When comparing the bacterial community
composition of the vermicompost samples derived from the raw grape marc to those
obtained from distilled marc, we found that five bacterial phyla significantly differed
in abundance. They comprised the phyla Patescibacteria (mean: À8.85 log2 fold
change, p ¼ 0.003), Acidobacteria (mean: 2.34 log2 fold change, p ¼ 0.006),
Nitrospirae (mean: 5.95 log2 fold change, p ¼ 0.011), Gemmatimonadetes (mean:
3.71 log2 fold change, p ¼ 0.010) and Armatimonadetes (mean: 5.09 log2 fold
change, p ¼ 0.003). The mean log2 fold change values were either positive or
negative depending whether the above-mentioned phyla appeared in higher or lower
differential abundances in the raw grape marc vermicompost samples.
130
M. Gómez-Brandón et al.