<i>Casimicrobium huifangae</i>
            gen. nov., sp. nov., a Ubiquitous “Most-Wanted” Core Bacterial Taxon from Municipal Wastewater Treatment Plants

Song, Yang; Jiang, Cheng‐Ying; Liang-gang, Zong; Wang, Baojun; Jiang, Yong; Yin, Ye; Zhu, Hai-Zhen; Qin, Ya-Ling; Cheng, Rui-Xue; Liu, Zhi-Pei; Liu, Yao; Jin, Tao; Corvini, Philippe F.-X.; Rabaey, Korneel; Wang, Aijie; Liu, Shuang‐Jiang

doi:10.1128/aem.02209-19

Cited by 31 publications

(7 citation statements)

References 75 publications

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“…For example, we did not find evidence for the presence of the recently isolated organism Casimicrobium huifangae, which might play a role in phosphate removal and nitrate reduction. Our activated sludge communities also did not contain any members of the genus Nitrospira (42). While the Global Water Microbiome Consortium reported on the ubiquitous presence of Nitrospira in a global survey of WWTPs (4), the most abundant known nitrite oxidizers in the SBR samples in this study were Nitrotoga (0.2% Ϯ 0.2%) and Nitrobacter (0.3% Ϯ 0.2%) (43).…”

Section: Discussionmentioning

confidence: 48%

Seasonal Dynamics of the Activated Sludge Microbiome in Sequencing Batch Reactors, Assessed Using 16S rRNA Transcript Amplicon Sequencing

Johnston

Behrens

2020

Appl Environ Microbiol

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Activated sludge is comprised of diverse microorganisms which remediate wastewater. Previous research has characterized activated sludge using 16S rRNA gene amplicon sequencing which can help to address questions on the relative abundance of microorganisms. In this study we use 16S rRNA transcript sequencing in order to characterize “active” populations (via protein synthesis potential) and gain a deeper understanding of microbial activity patterns within activated sludge. Seasonal abundances of individual populations in activated sludge change over time, yet a persistent group of core microorganisms remains throughout the year which are traditionally classified on presence or absence without monitoring their activity or growth. The goal of this study was to further our understanding of how the activated sludge microbiome changes between seasons with respect to population abundance, activity, and growth. Triplicate sequencing batch reactors were sampled in 10-minute intervals throughout reaction cycles during all four seasons. We quantified the gene and transcript copy numbers of 16S rRNA amplicons using real-time PCR and sequenced the products to reveal community abundance and activity changes. We identified 108 OTUs with stable abundance, activity, and growth throughout the year. Non-proliferating OTUs were commonly human-health related, while OTUs that showed seasonal abundance changes have previously been identified as being associated with floc formation and bulking. We observed significant differences in 16S rRNA transcript copy numbers, particularly at lower temperatures in winter and spring. The study provides an analysis of the seasonal dynamics of microbial activity variations in activated sludge based on quantifying and sequencing 16S rRNA transcripts. Importance Sequencing batch reactors are a common design for wastewater treatment plants, particularly in smaller municipalities due to their low footprint and ease of operations. However, like most treatment plants in temperate/continental climates, the microbial community involved in water treatment is highly seasonal and their biological processes can be sensitive to cold temperatures. The seasonality of these microbial communities has been explored primarily in conventional treatment plants, but not in sequencing batch reactors. Furthermore, most studies often only address “which organisms are present?”. However, the activated sludge microbial community is very diverse that it is often hard to discern which organisms are “active” and which organisms are simply “present”. In this study we are applying additional sequencing techniques to also address “which organisms are active?” and “which organisms are growing?” By addressing these three questions, we gain new insights into seasonal microbial populations dynamics and activity patterns affecting wastewater treatment.

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Section: Discussionmentioning

confidence: 48%

Seasonal Dynamics of the Activated Sludge Microbiome in Sequencing Batch Reactors, Assessed Using 16S rRNA Transcript Amplicon Sequencing

Johnston

Behrens

2020

Appl Environ Microbiol

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“…Demultiplexed sequences were merged with FLASH (v1.2.11) [42] and quality filtered with fastp (v0.19.6) [43] according to the criteria previously described [44] . Usearch (v8.1.1861) [45] algorithm was used for removal of the chimeric sequences and OTU clustering with a similarity threshold of 97%.…”

Section: Methodsmentioning

confidence: 99%

Contribution of sample processing to gut microbiome analysis in the model Lepidoptera, silkworm Bombyx mori

Zhang

Sun

et al. 2021

Computational and Structural Biotechnology Journal

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“…The global-scale “wanted list” could facilitate various types of research in microbial ecology by specifying key targets. In 2020, a research team successfully isolated a new strain Casimicrobium huifangae which showed the ability to degrade complex organic matters [ 72 ] and belonged to 28 core OTUs mentioned above [ 12 ]. In our 71 “wanted list” OTUs, 15 OTUs are still in “darkness” with no isolates or genomes and 36 OTUs have genomes but lack isolates.…”

Section: Discussionmentioning

confidence: 99%

The microbial dark matter and “wanted list” in worldwide wastewater treatment plants

et al. 2023

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Background Wastewater treatment plants (WWTPs) are one of the largest biotechnology applications in the world and are of critical importance to modern urban societies. An accurate evaluation of the microbial dark matter (MDM, microorganisms whose genomes remain uncharacterized) proportions in WWTPs is of great value, while there is no such research yet. This study conducted a global meta-analysis of MDM in WWTPs with 317,542 prokaryotic genomes from the Genome Taxonomy Database and proposed a “wanted list” for priority targets in further investigations of activated sludge. Results Compared with the Earth Microbiome Project data, WWTPs had relatively lower genome-sequenced proportions of prokaryotes than other ecosystems, such as the animal related environments. Analysis showed that the median proportions of the genome-sequenced cells and taxa (100% identity and 100% coverage in 16S rRNA gene region) in WWTPs reached 56.3% and 34.5% for activated sludge, 48.6% and 28.5% for aerobic biofilm, and 48.3% and 28.5% for anaerobic digestion sludge, respectively. This result meant MDM had high proportions in WWTPs. Besides, all of the samples were occupied by a few predominant taxa, and the majority of the sequenced genomes were from pure cultures. The global-scale “wanted list” for activated sludge contained four phyla that have few representatives and 71 operational taxonomic units with the majority of them having no genome or isolate yet. Finally, several genome mining methods were verified to successfully recover genomes from activated sludge such as hybrid assembly of the second- and third-generation sequencing. Conclusions This work elucidated the proportion of MDM in WWTPs, defined the “wanted list” of activated sludge for future investigations, and certified potential genome recovery methods. The proposed methodology of this study can be applied to other ecosystems and improve understanding of ecosystem structure across diverse habitats.

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Casimicrobium huifangae gen. nov., sp. nov., a Ubiquitous “Most-Wanted” Core Bacterial Taxon from Municipal Wastewater Treatment Plants

Cited by 31 publications

References 75 publications

Seasonal Dynamics of the Activated Sludge Microbiome in Sequencing Batch Reactors, Assessed Using 16S rRNA Transcript Amplicon Sequencing

Seasonal Dynamics of the Activated Sludge Microbiome in Sequencing Batch Reactors, Assessed Using 16S rRNA Transcript Amplicon Sequencing

Contribution of sample processing to gut microbiome analysis in the model Lepidoptera, silkworm Bombyx mori

The microbial dark matter and “wanted list” in worldwide wastewater treatment plants

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