Exploring the under-investigated “microbial dark matter” of drinking water treatment plants

Bruno, Antonia; Sandionigi, Anna; Rizzi, Ermanno; Bernasconi, Marzia; Vicario, Saverio; Galimberti, Andrea; Cocuzza, Clementina; Labra, Massimo; Casiraghi, Maurizio

doi:10.1038/srep44350

Cited by 41 publications

(41 citation statements)

References 28 publications

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“…Fungal internal transcribed spacer (ITS) 1 loci were amplified with primers BITS and B58S3 [ 23 ], with the supplement of the Illumina overhang adapter sequences. Before amplification, DNA extracts were normalized by means of Quantitative real-time PCR (qPCR) Ct values with the same amplification primer pairs and the same protocols described by Bruno and colleagues [ 24 , 25 ]. Finally, the obtained libraries were submitted to Polo d’Innovazione Genomica, Genetica e Biologia Società Consortile R.L.…”

Section: Methodsmentioning

confidence: 99%

Grape microbiome as a reliable and persistent signature of field origin and environmental conditions in Cannonau wine production

et al. 2017

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Grape berries harbor a wide range of microbes originating from the vineyard environment, many of which are recognized for their role in the must fermentation process shaping wine quality. To better clarify the contribution of the microbiome of grape fruits during wine fermentation, we used high-throughput sequencing to identify bacterial and fungi communities associated with berries and musts of Cannonau. This is the most important cultivar-wine of Sardinia (Italy) where most vineyards are cultivated without phytochemical treatments. Results suggested that microbiomes of berries collected at four different localities share a core composition characterized by Enterobacteriales, Pseudomonadales, Bacillales, and Rhodospirillales. However, any area seems to enrich berries microbiome with peculiar microbial traits. For example, berries belonging to the biodynamic vineyards of Mamoiada were rich in Bacillales typical of manure (i.e. Lysinibacillus, Bacillus, and Sporosarcina), whereas in the Santadi locality, berries showed soil bacteria such as Pasteurellales and Bacteroidales as well as Rhodospirillales and Lactobacillales which are commonly involved in wine fermentation. In the case of fungi, the most abundant taxa were Dothioraceae, Pleosporaceae, and Saccharomycodaceae, and although the proportion of these families varied among localities, they occurred ubiquitously in all vineyards. During vinification processes performed at the same wine cellar under controlled conditions and without using any yeast starter, more than 50% of bacteria groups of berries reached musts, and each locality had its own private bacteria signature, even if Saccharomyces cerevisiae represented the most abundant fungal species. This work suggests that natural berries microbiome could be influenced by pedoclimatic and anthropologic conditions (e.g., farming management), and the fruits’ microorganisms persist during the fermentation process. For these reasons, a reliable wine genotyping should include the entire holobiont (plant and all its symbionts), and bioprospecting activities on grape microbiota could lead to improved viticulture yields and wine quality.

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Section: Methodsmentioning

confidence: 99%

Grape microbiome as a reliable and persistent signature of field origin and environmental conditions in Cannonau wine production

et al. 2017

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“…Overall, CPR and DPANN organisms are mostly detected in oxygen-limited or anaerobic environments. Although many CPR organisms seem to be dominant in untreated groundwater, the members of the Parcubacteria candidate superphylum can be selectively enriched in treated water 35 regardless of treatment and disinfectant type 36 and thus can persist in drinking water 37 . Both CPR and DPANN sometimes occur within the human microbiome (Supplementary Table 2).…”

Section: Introductionmentioning

confidence: 99%

Biosynthetic capacity, metabolic variety and unusual biology in the CPR and DPANN radiations

et al. 2018

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Candidate phyla radiation (CPR) bacteria and DPANN (an acronym of the names of the first included phyla) archaea are massive radiations of organisms that are widely distributed across Earth's environments, yet we know little about them. Initial indications are that they are consistently distinct from essentially all other bacteria and archaea owing to their small cell and genome sizes, limited metabolic capacities and often episymbiotic associations with other bacteria and archaea. In this Analysis, we investigate their biology and variations in metabolic capacities by analysis of approximately 1,000 genomes reconstructed from several metagenomics-based studies. We find that they are not monolithic in terms of metabolism but rather harbour a diversity of capacities consistent with a range of lifestyles and degrees of dependence on other organisms. Notably, however, certain CPR and DPANN groups seem to have exceedingly minimal biosynthetic capacities, whereas others could potentially be free living. Understanding of these microorganisms is important from the perspective of evolutionary studies and because their interactions with other organisms are likely to shape natural microbiome function.

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“…Advances in microbial dark matter research have the potential to alter our understanding of key tenets of evolutionary principles, such as the current debate over the phylogenetic position of the Asgard archaea, and the idea that the eukaryotic cell emerged from within the archaeal domain [ 6 – 8 ]. It is estimated that at least 80% of environmental genomic content could be considered as ‘genomic dark matter’ [ 5 , 9 – 11 ], with the majority found in subsurface environments [ 4 , 12 – 15 ]. Therefore, this prompted the desire to uncover unknown genes, functions and ecological roles of these novel groups in other microbial ecosystems [ 16 ], of particular interest for the present study, hypersaline microbial mats.…”

Section: Introductionmentioning

confidence: 99%

Microbial dark matter filling the niche in hypersaline microbial mats

Wong¹,

MacLeod²,

White³

et al. 2020

Microbiome

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Background Shark Bay, Australia, harbours one of the most extensive and diverse systems of living microbial mats that are proposed to be analogs of some of the earliest ecosystems on Earth. These ecosystems have been shown to possess a substantial abundance of uncultivable microorganisms. These enigmatic microbes, jointly coined as ‘microbial dark matter’ (MDM), are hypothesised to play key roles in modern microbial mats. Results We reconstructed 115 metagenome-assembled genomes (MAGs) affiliated to MDM, spanning 42 phyla. This study reports for the first time novel microorganisms (Zixibacterial order GN15) putatively taking part in dissimilatory sulfate reduction in surface hypersaline settings, as well as novel eukaryote signature proteins in the Asgard archaea. Despite possessing reduced-size genomes, the MDM MAGs are capable of fermenting and degrading organic carbon, suggesting a role in recycling organic carbon. Several forms of RuBisCo were identified, allowing putative CO2 incorporation into nucleotide salvaging pathways, which may act as an alternative carbon and phosphorus source. High capacity of hydrogen production was found among Shark Bay MDM. Putative schizorhodopsins were also identified in Parcubacteria, Asgard archaea, DPANN archaea, and Bathyarchaeota, allowing these members to potentially capture light energy. Diversity-generating retroelements were prominent in DPANN archaea that likely facilitate the adaptation to a dynamic, host-dependent lifestyle. Conclusions This is the first study to reconstruct and describe in detail metagenome-assembled genomes (MAGs) affiliated with microbial dark matter in hypersaline microbial mats. Our data suggests that these microbial groups are major players in these systems. In light of our findings, we propose H2, ribose and CO/CO2 as the main energy currencies of the MDM community in these mat systems.

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Exploring the under-investigated “microbial dark matter” of drinking water treatment plants

Cited by 41 publications

References 28 publications

Grape microbiome as a reliable and persistent signature of field origin and environmental conditions in Cannonau wine production

Grape microbiome as a reliable and persistent signature of field origin and environmental conditions in Cannonau wine production

Biosynthetic capacity, metabolic variety and unusual biology in the CPR and DPANN radiations

Microbial dark matter filling the niche in hypersaline microbial mats

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