Parafilimonas terrae gen. nov., sp. nov., isolated from greenhouse soil

Kim, Soojin; Park, Joo-Hyeon; Lim, Jun-Muk; Ahn, Jae-Hyung; Anandham, Rangasamy; Weon, Hang-Yeon; Kwon, Soon-Wo

doi:10.1099/ijs.0.061945-0

Cited by 21 publications

(7 citation statements)

References 24 publications

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“…Moreover, the genus Sphingomonas has been widely reported to possess diverse metabolic capabilities towards organic xenobiotics (Marchal et al ., ). In addition, the genera Parafilimonas and Arachidicoccus which belonged to family Chitinophagaceae, a member of phylum Bacteroidetes , were identified recently (Kim et al ., ; Madhaiyan et al ., ). Therefore, these results showed that bacterial community identified in the study is quite similar to the previous publications (Marchal et al ., ; Lv et al ., ; Madhaiyan et al ., ; Sun et al ., ).…”

Section: Resultsmentioning

confidence: 97%

Resuscitation of viable but non‐culturable bacteria to enhance the cellulose‐degrading capability of bacterial community in composting

Zhang

Mei

et al. 2018

Microbial Biotechnology

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SummaryNowadays, much of what we know regarding the isolated cellulolytic bacteria comes from the conventional plate separation techniques. However, the culturability of many bacterial species is controlled by resuscitation‐promoting factors (Rpfs) due to entering a viable but non‐culturable (VBNC) state. Therefore, in this study, Rpf from Micrococcus luteus was added in the culture medium to evaluate its role in bacterial isolation and enhanced effects on cellulose‐degrading capability of bacterial community in the compost. It was found that Proteobacteria and Actinobacteria were two main phyla in the compost sample. The introduction of Rpf could isolate some unique bacterial species. The cellulase activity of enrichment cultures with and without Rpf treatment revealed that Rpf treatment significantly enhanced cellulase activity. Ten isolates unique in Rpf addition displayed carboxymethyl‐cellulase (CMCase) activity, while six isolates possessed filter paper cellulase (FPCase) activity. This study provides new insights into broader cellulose degraders, which could be utilized for enhancing cellulosic waste treatment.

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Section: Resultsmentioning

confidence: 97%

Resuscitation of viable but non‐culturable bacteria to enhance the cellulose‐degrading capability of bacterial community in composting

Zhang

Mei

et al. 2018

Microbial Biotechnology

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“…The description is as before (Kim S.-J. et al, 2014) with the following modification. The G+C content of the type-strain genome is 39.6%, its approximate size 4.99 Mbp, its GenBank deposit SAMN05444277.…”

Section: Discussionmentioning

confidence: 99%

Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes

et al. 2019

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Although considerable progress has been made in recent years regarding the classification of bacteria assigned to the phylum Bacteroidetes, there remains a need to further clarify taxonomic relationships within a diverse assemblage that includes organisms of clinical, piscicultural, and ecological importance. Bacteroidetes classification has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees and a limited number of phenotypic features. Here, draft genome sequences of a greatly enlarged collection of genomes of more than 1,000 Bacteroidetes and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa proposed long ago such as Bacteroides, Cytophaga, and Flavobacterium but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which can be considered valuable taxonomic markers. We detected many incongruities when comparing the results of the present study with existing classifications, which appear to be caused by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. The few significant incongruities found between 16S rRNA gene and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences and the impediment in using ordinary bootstrapping in phylogenomic studies, particularly when combined with too narrow gene selections. While a significant degree of phylogenetic conservation was detected in all phenotypic characters investigated, the overall fit to the tree varied considerably, which is one of the probable causes of misclassifications in the past, much like the use of plesiomorphic character states as diagnostic features.

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“…14, which was identified to be a significantly (p<0.05) changed OTU and had the biggest contribution to the whole community change (Fig. 5a) compared to other OTUs, was 82% similar to Parafilimonas terrae, who has the ability to utilize propionic acid (Kim et al, 2014).…”

Section: A C C E P T E D Accepted Manuscriptmentioning

confidence: 97%

Bioaugmentation strategy for overcoming ammonia inhibition during biomethanation of a protein-rich substrate

et al. 2019

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High ammonia levels inhibit anaerobic digestion (AD) process and bioaugmentation with ammonia tolerant methanogenic culture is proposed to alleviate ammonia inhibition. In the current study, hydrogenotrophic Methanoculleus bourgensis was bioaugmented in an ammonia-inhibited continuous reactor fed mainly with microalgae (a protein-rich biomass), at extreme ammonia levels (i.e. 11 g NH 4 + -N L -1 ). The results showed 28% increase in methane production immediately after bioaugmentation.Moreover, volatile fatty acids decreased rapidly from more than 5 g L -1 to around 1 g L -1 , with a fast reduction in propionate concentration. High throughput 16s rRNA gene sequencing demonstrated that the bioaugmented M. bourgensis doubled its relative abundance after bioaugmentation. "Microbiological domino effect", triggered by the bioaugmented M. bourgensis establishing a newly efficient community, was proposed as the working mechanism of the successful bioaugmentation. Additionally, a strong aceticlastic methanogenesis was found at the end of the experiment evidenced by the dominant presence of Methanosarcina soligelidi and the low abundance of syntrophic acetate oxidising bacteria at the final period. Overall, for the first time, this study proved the positive effect of bioaugmentation on ammonia inhibition alleviation of the microalgae-dominating fed reactor, paving the way of efficient utilization of other protein-rich substrates in the future.

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Parafilimonas terrae gen. nov., sp. nov., isolated from greenhouse soil

Cited by 21 publications

References 24 publications

Resuscitation of viable but non‐culturable bacteria to enhance the cellulose‐degrading capability of bacterial community in composting

Resuscitation of viable but non‐culturable bacteria to enhance the cellulose‐degrading capability of bacterial community in composting

Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes

Bioaugmentation strategy for overcoming ammonia inhibition during biomethanation of a protein-rich substrate

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