considered to have low value and have usually been discarded, if properly treated,
they can be converted into high-nutrient biofertilizers and used as growing media for
vegetables and ornamentals (Cai et al. 2018; Gong et al. 2018). Their transformation
into green vermicomposts may therefore offer a dual purpose, i.e., environmental
protection and fertilizer production.
The purpose of this chapter is therefore to compare and provide a detailed
characterization of the microbiome of the green vermicomposts derived from raw
and distilled grape marcs of the grape variety Vitis vinifera v. Albariño and those
obtained from the leguminous shrubs Scotch broom and acacia. We evaluated the
taxonomic and functional diversity of bacterial communities and their metabolic
functions in the above-mentioned green vermicomposts and the respective raw
materials by applying 16S rRNA high-throughput sequencing.
The four types of plant material were separately processed in a pilot-scale
vermireactor (6 m
3 ) housed in a greenhouse with no temperature control located in
our research facilities using the epigeic earthworm Eisenia andrei. This earthworm
species has been widely used in vermicomposting facilities due to its high reproductive rate and its tolerance to a wide range of temperature and moisture conditions
(Domínguez and Edwards 2011). The vermireactor set-up and sampling procedure
were performed as described in Domínguez et al. (2019).
8.2 How Does Vermicomposting Influence Composition
of Bacterial Communities from Dead Plant Material?
For the evaluation of the bacterial community composition of the fresh materials and
the resulting vermicomposts, we amplified and sequenced a fragment ~250 bp long
of the 16S rRNA gene covering the V4 region using a dual-index sequencing
strategy as described by Kozich et al. (2013). DADA2 (version 1.9) was used to
infer the amplicon sequence variants (ASVs) present in each sample (Callahan et al.
2016). Default settings were used for ASV inference and chimera detection following the DADA2 pipeline tutorial (https://benjjneb.github.io/dada2/tutorial.html).
The taxonomic assignment was performed against the Silva v132 database using
the assignTaxonomy function in dada2, which implements RDP naive Bayesian
classifier (Wang et al. 2007; Quast et al. 2013). The minimum bootstrap confidence
for assigning taxonomy was 80. By using an ASV-based approach, it provides a
more accurate and reproducible description of amplicon-sequenced communities
than an OTU-based approach (Callahan et al. 2017). This relies on the fact that an
ASV is defined by a unique sequence that is different from sequences of other ASVs.
Moreover, ASVs could differ by as little as one base pair allowing a direct and more
straightforward comparison across studies whenever researchers use the same primer
set and procedure to obtain the ASVs.
8 Vermicomposts Are Biologically Different: Microbial and Functional Diversity of. . .
127
they can be converted into high-nutrient biofertilizers and used as growing media for
vegetables and ornamentals (Cai et al. 2018; Gong et al. 2018). Their transformation
into green vermicomposts may therefore offer a dual purpose, i.e., environmental
protection and fertilizer production.
The purpose of this chapter is therefore to compare and provide a detailed
characterization of the microbiome of the green vermicomposts derived from raw
and distilled grape marcs of the grape variety Vitis vinifera v. Albariño and those
obtained from the leguminous shrubs Scotch broom and acacia. We evaluated the
taxonomic and functional diversity of bacterial communities and their metabolic
functions in the above-mentioned green vermicomposts and the respective raw
materials by applying 16S rRNA high-throughput sequencing.
The four types of plant material were separately processed in a pilot-scale
vermireactor (6 m
3 ) housed in a greenhouse with no temperature control located in
our research facilities using the epigeic earthworm Eisenia andrei. This earthworm
species has been widely used in vermicomposting facilities due to its high reproductive rate and its tolerance to a wide range of temperature and moisture conditions
(Domínguez and Edwards 2011). The vermireactor set-up and sampling procedure
were performed as described in Domínguez et al. (2019).
8.2 How Does Vermicomposting Influence Composition
of Bacterial Communities from Dead Plant Material?
For the evaluation of the bacterial community composition of the fresh materials and
the resulting vermicomposts, we amplified and sequenced a fragment ~250 bp long
of the 16S rRNA gene covering the V4 region using a dual-index sequencing
strategy as described by Kozich et al. (2013). DADA2 (version 1.9) was used to
infer the amplicon sequence variants (ASVs) present in each sample (Callahan et al.
2016). Default settings were used for ASV inference and chimera detection following the DADA2 pipeline tutorial (https://benjjneb.github.io/dada2/tutorial.html).
The taxonomic assignment was performed against the Silva v132 database using
the assignTaxonomy function in dada2, which implements RDP naive Bayesian
classifier (Wang et al. 2007; Quast et al. 2013). The minimum bootstrap confidence
for assigning taxonomy was 80. By using an ASV-based approach, it provides a
more accurate and reproducible description of amplicon-sequenced communities
than an OTU-based approach (Callahan et al. 2017). This relies on the fact that an
ASV is defined by a unique sequence that is different from sequences of other ASVs.
Moreover, ASVs could differ by as little as one base pair allowing a direct and more
straightforward comparison across studies whenever researchers use the same primer
set and procedure to obtain the ASVs.
8 Vermicomposts Are Biologically Different: Microbial and Functional Diversity of. . .
127