Limits...
Genomics of biological wastewater treatment.

Siezen RJ, Galardini M - Microb Biotechnol (2008)

View Article: PubMed Central - PubMed

Affiliation: Kluyver Centre for Genomics of Industrial Fermentation, TI Food and Nutrition, 6700AN Wageningen, the Netherlands. r.siezen@cmbi.ru.nl

AUTOMATICALLY GENERATED EXCERPT
Please rate it.

Biological wastewater treatment plants (WWTPs) employing sludge represent one of the most widely used biotechnological processes, with more than 120 billion litres treated daily in the USA alone (Fig.  1)... In addition, metagenome sequences have provided a first insight into metabolic requirements of specific microbes, allowing further optimization of enrichment conditions. 16S rRNA sequences from metagenome libraries have been used to identify new bacterial divisions and species and to visualize them using molecular techniques such as FISH... Starting from a metagenomic analysis of sludge microbes from such a digester, ) succeeded in reconstructing the complete genome of a WWE1 bacterium, represented by only 2% of the fosmid library reads, using a novel sequencing and assembly strategy specifically designed during this project... The reconstruction started with seed sequences (fully sequenced fosmids on which WWE1 16S rRNA sequences were found), to which > 99% identical fosmid paired‐end sequences from the metagenome library were added in an iterative fashion (Fig.  3)... This is the first time that such an iterative procedure had been used, and the first time ever a ‘complete’ genome from a previously unknown, uncultured and subdominant bacterium was reconstructed out of such a complex environment... Metaproteomics studies of sludge microbes from a similar EBPR reactor in the UK confirmed the activities of these EBPR processes, but also highlighted the importance of fatty acid cycling, denitrification and the glyoxylate bypass in EBPR... Many proteins were identified with the help of the template composite A.  phosphatis genome, but numerous protein variants were also found, which presumably came from related species and strains, highlighting the likely importance of genetic variation for overall community homeostasis... Metagenome sequencing was used to decipher the 4.2 Mb genome of the uncultured anammox bacterium Kuenenia stuttgartiensis; this bacterium dominated the complex community in a laboratory bioreactor 1 year after inoculation with wastewater sludge... A few genome sequences of some culturable members are available now (Table 1)... The ammonia‐oxidizing Nitrosomonas eutropha was found to have many genes for heavy metal and drug resistance, which could explain its presence in a polluted environment such as a WWTP... An environmental metagenomics approach was used to sequence, identify and assemble a 137 kb genome fragment of ‘Candidatus Nitrospira defluvii’, which had been enriched from activated sludge from a domestic WWTP... This contig, harbouring a 16S rRNA gene of N.  defluvii, was surprisingly found to encode a chlorite dismutase, which converts chlorite (ClO2) to chloride (Cl) and O2... Survival of this species in a nitrifying WWTP may depend on this somewhat unique activity, as (per)chlorate‐containing fertilizers, disinfectants and bleaching agents are all discharged into the environment... Furthermore, hypochlorite (ClO) is often added to activated sludge to reduce the outgrowth of filamentous bacteria.

Show MeSH
Iterative assembly process of fosmid paired‐end sequences used for reconstruction of the complete genome of Candidatus Cloacamonas acidaminovorans. Reprinted with permission from Pelletier and colleagues (2008); for details see their paper. Copyright 2008, American Society for Microbiology.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC3815239&req=5

f3: Iterative assembly process of fosmid paired‐end sequences used for reconstruction of the complete genome of Candidatus Cloacamonas acidaminovorans. Reprinted with permission from Pelletier and colleagues (2008); for details see their paper. Copyright 2008, American Society for Microbiology.

Mentions: Metagenomics projects involve not only species that are predominant in the wastewater treatment, but also minor members of the population. For instance, a new bacterial division (WWE1) belonging to the Spirochaetes, with no cultured representative, has been characterized (Chouari et al., 2005b). Members of this division are present in anaerobic digesters, generally as a subdominant group (< 10% of the population), where they perform the decomposition of organic matter into methane and CO2. Starting from a metagenomic analysis of sludge microbes from such a digester, Pelletier and colleagues (2008) succeeded in reconstructing the complete genome of a WWE1 bacterium, represented by only 2% of the fosmid library reads, using a novel sequencing and assembly strategy specifically designed during this project. The reconstruction started with seed sequences (fully sequenced fosmids on which WWE1 16S rRNA sequences were found), to which > 99% identical fosmid paired‐end sequences from the metagenome library were added in an iterative fashion (Fig. 3). A circular genome of 2.2 Mb was then obtained by standard finishing techniques; its reconstruction was probably made possible by the extremely low sequence polymorphism of the dominant phylotype (Pelletier et al., 2008). This is the first time that such an iterative procedure had been used, and the first time ever a ‘complete’ genome from a previously unknown, uncultured and subdominant bacterium was reconstructed out of such a complex environment. Their procedure clearly shows promise for application to other wastewater‐sequencing projects as well as to other environmental samples.


Genomics of biological wastewater treatment.

Siezen RJ, Galardini M - Microb Biotechnol (2008)

Iterative assembly process of fosmid paired‐end sequences used for reconstruction of the complete genome of Candidatus Cloacamonas acidaminovorans. Reprinted with permission from Pelletier and colleagues (2008); for details see their paper. Copyright 2008, American Society for Microbiology.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3815239&req=5

f3: Iterative assembly process of fosmid paired‐end sequences used for reconstruction of the complete genome of Candidatus Cloacamonas acidaminovorans. Reprinted with permission from Pelletier and colleagues (2008); for details see their paper. Copyright 2008, American Society for Microbiology.
Mentions: Metagenomics projects involve not only species that are predominant in the wastewater treatment, but also minor members of the population. For instance, a new bacterial division (WWE1) belonging to the Spirochaetes, with no cultured representative, has been characterized (Chouari et al., 2005b). Members of this division are present in anaerobic digesters, generally as a subdominant group (< 10% of the population), where they perform the decomposition of organic matter into methane and CO2. Starting from a metagenomic analysis of sludge microbes from such a digester, Pelletier and colleagues (2008) succeeded in reconstructing the complete genome of a WWE1 bacterium, represented by only 2% of the fosmid library reads, using a novel sequencing and assembly strategy specifically designed during this project. The reconstruction started with seed sequences (fully sequenced fosmids on which WWE1 16S rRNA sequences were found), to which > 99% identical fosmid paired‐end sequences from the metagenome library were added in an iterative fashion (Fig. 3). A circular genome of 2.2 Mb was then obtained by standard finishing techniques; its reconstruction was probably made possible by the extremely low sequence polymorphism of the dominant phylotype (Pelletier et al., 2008). This is the first time that such an iterative procedure had been used, and the first time ever a ‘complete’ genome from a previously unknown, uncultured and subdominant bacterium was reconstructed out of such a complex environment. Their procedure clearly shows promise for application to other wastewater‐sequencing projects as well as to other environmental samples.

View Article: PubMed Central - PubMed

Affiliation: Kluyver Centre for Genomics of Industrial Fermentation, TI Food and Nutrition, 6700AN Wageningen, the Netherlands. r.siezen@cmbi.ru.nl

AUTOMATICALLY GENERATED EXCERPT
Please rate it.

Biological wastewater treatment plants (WWTPs) employing sludge represent one of the most widely used biotechnological processes, with more than 120 billion litres treated daily in the USA alone (Fig.  1)... In addition, metagenome sequences have provided a first insight into metabolic requirements of specific microbes, allowing further optimization of enrichment conditions. 16S rRNA sequences from metagenome libraries have been used to identify new bacterial divisions and species and to visualize them using molecular techniques such as FISH... Starting from a metagenomic analysis of sludge microbes from such a digester, ) succeeded in reconstructing the complete genome of a WWE1 bacterium, represented by only 2% of the fosmid library reads, using a novel sequencing and assembly strategy specifically designed during this project... The reconstruction started with seed sequences (fully sequenced fosmids on which WWE1 16S rRNA sequences were found), to which > 99% identical fosmid paired‐end sequences from the metagenome library were added in an iterative fashion (Fig.  3)... This is the first time that such an iterative procedure had been used, and the first time ever a ‘complete’ genome from a previously unknown, uncultured and subdominant bacterium was reconstructed out of such a complex environment... Metaproteomics studies of sludge microbes from a similar EBPR reactor in the UK confirmed the activities of these EBPR processes, but also highlighted the importance of fatty acid cycling, denitrification and the glyoxylate bypass in EBPR... Many proteins were identified with the help of the template composite A.  phosphatis genome, but numerous protein variants were also found, which presumably came from related species and strains, highlighting the likely importance of genetic variation for overall community homeostasis... Metagenome sequencing was used to decipher the 4.2 Mb genome of the uncultured anammox bacterium Kuenenia stuttgartiensis; this bacterium dominated the complex community in a laboratory bioreactor 1 year after inoculation with wastewater sludge... A few genome sequences of some culturable members are available now (Table 1)... The ammonia‐oxidizing Nitrosomonas eutropha was found to have many genes for heavy metal and drug resistance, which could explain its presence in a polluted environment such as a WWTP... An environmental metagenomics approach was used to sequence, identify and assemble a 137 kb genome fragment of ‘Candidatus Nitrospira defluvii’, which had been enriched from activated sludge from a domestic WWTP... This contig, harbouring a 16S rRNA gene of N.  defluvii, was surprisingly found to encode a chlorite dismutase, which converts chlorite (ClO2) to chloride (Cl) and O2... Survival of this species in a nitrifying WWTP may depend on this somewhat unique activity, as (per)chlorate‐containing fertilizers, disinfectants and bleaching agents are all discharged into the environment... Furthermore, hypochlorite (ClO) is often added to activated sludge to reduce the outgrowth of filamentous bacteria.

Show MeSH