or fermentation; nitrogen by nitrification, denitrification, or assimilation; and phosphorus in the form of polyphosphate polymers, stored as a source of energy for the
WW biome. Thus, functional properties of sludge microbiota help in avoiding
eutrophication and deterioration of recipient surface waters such as rivers and
streams. Within this anthropized ecosystem, prokaryotes live in tight association
with eukaryotes comprising protists, fungi, metazoans, metaphytes, and viruses.
They form a complex microbiome with a large part (>95–98%) still awaiting culture
and characterization [52–54].
Culture-independent molecular analysis of the sludge microbiome circumvents
conventional culture methods. It gives valuable information about microbiome
composition, community structure, and function. Thus, high-throughput sequencing
of 16S and 18S rRNA genes has depicted the high complexity of microbial
populations. Our most recent studies using 16S and 18S rDNA barcoding show
that at the phylum level, we found at least 40 and 15 prokaryotic (Archaea and
Bacteria domains) and eukaryotic phyla, respectively (Morin et al., 2020).
4.1 Eukaryotic Components
The eukaryotic compartment of the sludge microbiome is predominantly composed
of at least 15 phyla. The most predominant are Nucletmycea, Holozoa, Amoebozoa,
Rhizaria, Alveolata (Ciliophora, Apicomplexa), Stramenopiles, Discoba,
Chloroplastida, and Protalveolata, representing up to 90% of the total species, or
“operational taxonomic units (OTUs).” Unknown and multi-affiliation phyla are
making up to 10% of the total OTUs. The remaining six minor phyla affiliate with
Apusozoa, Rhodophyta, Cryptia, Haptisia, Metamonada, and Dinoflagellata. They
altogether totalize 1% of the total OTUs (Fig. 3a). In terms of abundance, seven
predominant phyla, Holozoa, Nucletmycea, Amoebozoa, Rhizaria, Ciliophora,
Discoba, and Stramenopiles, represent >98% of the total V9 18S rDNA sequence
reads (Fig. 3a, b). The remaining ten eukaryotic phyla made up only 1.20% of the
total eukaryotic V9 18S rDNA sequence reads (Morin et al., 2020). These phyla
comprise an abundance of non-cultivable species and lineages (60–90%).
Among novel lineages the phylum Cryptomycota, formerly known as LKM11
and LKM118, was found in abundance, making up to 76% of the total fungal
population within a domestic WWTP. The Cryptomycota are currently not
represented by only one cultivated species [54] (Fig. 3a, b; Morin et al., 2020).
Pathogenic fungi such as Olpidium, Paecilomyces, Aspergillus, Rhodotorula, Penicillium, Candida, Synchytrium, Phyllosticta, and Mucor have been isolated from
WWTPs and would be very dangerous to human health since treated WW in some
cases is not only used for irrigation but also to produce drinking water [55]. In our
study of domestic WWTP sludge, we detected 45 potential human fungal generacontaining pathogen species. Candida and Pichia were the two most important
genera reported for Ascomycota phylum, while Lichtheimia and Rhizopus were
observed for Mucoromycota phylum. These genera represent the most persistent
60
E. Ammar et al.
WW biome. Thus, functional properties of sludge microbiota help in avoiding
eutrophication and deterioration of recipient surface waters such as rivers and
streams. Within this anthropized ecosystem, prokaryotes live in tight association
with eukaryotes comprising protists, fungi, metazoans, metaphytes, and viruses.
They form a complex microbiome with a large part (>95–98%) still awaiting culture
and characterization [52–54].
Culture-independent molecular analysis of the sludge microbiome circumvents
conventional culture methods. It gives valuable information about microbiome
composition, community structure, and function. Thus, high-throughput sequencing
of 16S and 18S rRNA genes has depicted the high complexity of microbial
populations. Our most recent studies using 16S and 18S rDNA barcoding show
that at the phylum level, we found at least 40 and 15 prokaryotic (Archaea and
Bacteria domains) and eukaryotic phyla, respectively (Morin et al., 2020).
4.1 Eukaryotic Components
The eukaryotic compartment of the sludge microbiome is predominantly composed
of at least 15 phyla. The most predominant are Nucletmycea, Holozoa, Amoebozoa,
Rhizaria, Alveolata (Ciliophora, Apicomplexa), Stramenopiles, Discoba,
Chloroplastida, and Protalveolata, representing up to 90% of the total species, or
“operational taxonomic units (OTUs).” Unknown and multi-affiliation phyla are
making up to 10% of the total OTUs. The remaining six minor phyla affiliate with
Apusozoa, Rhodophyta, Cryptia, Haptisia, Metamonada, and Dinoflagellata. They
altogether totalize 1% of the total OTUs (Fig. 3a). In terms of abundance, seven
predominant phyla, Holozoa, Nucletmycea, Amoebozoa, Rhizaria, Ciliophora,
Discoba, and Stramenopiles, represent >98% of the total V9 18S rDNA sequence
reads (Fig. 3a, b). The remaining ten eukaryotic phyla made up only 1.20% of the
total eukaryotic V9 18S rDNA sequence reads (Morin et al., 2020). These phyla
comprise an abundance of non-cultivable species and lineages (60–90%).
Among novel lineages the phylum Cryptomycota, formerly known as LKM11
and LKM118, was found in abundance, making up to 76% of the total fungal
population within a domestic WWTP. The Cryptomycota are currently not
represented by only one cultivated species [54] (Fig. 3a, b; Morin et al., 2020).
Pathogenic fungi such as Olpidium, Paecilomyces, Aspergillus, Rhodotorula, Penicillium, Candida, Synchytrium, Phyllosticta, and Mucor have been isolated from
WWTPs and would be very dangerous to human health since treated WW in some
cases is not only used for irrigation but also to produce drinking water [55]. In our
study of domestic WWTP sludge, we detected 45 potential human fungal generacontaining pathogen species. Candida and Pichia were the two most important
genera reported for Ascomycota phylum, while Lichtheimia and Rhizopus were
observed for Mucoromycota phylum. These genera represent the most persistent
60
E. Ammar et al.