Flavobacterium aquicola sp. nov., isolated from river water

Hatayama, Kouta; Ushida, Ayako; Kuno, Teruaki

doi:10.1099/ijsem.0.001057

Cited by 15 publications

(7 citation statements)

References 36 publications

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“…The resource pool, including nitrogenous molecules like proteins, as well as carbohydrates such as cellulose and resistant starches, significantly changed from primary wastewater to activated sludge as larger molecules are degraded. This aligned with increases in 42% of putative soil and waterassociated species in activated sludge (11% being absent from primary wastewater), such as Uliginosibacterium gangwonense, Flavobacterium ardleyense, Leucobacter zeae, Ferruginibacter alkalilentus and Curvibacter fontana, characterized as extracellular proteases producers (Weon et al, 2008;Lim et al, 2009;Ding and Yokota, 2010;Kim et al, 2012;Lai et al, 2015;Hatayama et al, 2016;Zhou et al, 2017). Similarly, increases in starch utilizing Flavobacterium aquicola and Flavobacterium cheonanense Hatayama et al, 2016) and lipid-degrading Agitococcus lubricus (Franzmann and Skerman, 1981) were observed in activated sludge.…”

Section: Humans and Animalsmentioning

confidence: 64%

“…This aligned with increases in 42% of putative soil and water‐associated species in activated sludge (11% being absent from primary wastewater), such as Uliginosibacterium gangwonense , Flavobacterium ardleyense , Leucobacter zeae , Ferruginibacter alkalilentus and Curvibacter fontana , characterized as extracellular proteases producers (Weon et al ., 2008; Lim et al ., 2009; Ding and Yokota, 2010; Kim et al ., 2012; Lai et al ., 2015; Hatayama et al ., 2016; Zhou et al ., 2017). Similarly, increases in starch utilizing Flavobacterium aquicola and Flavobacterium cheonanense ( Lee et al ., 2011; Hatayama et al ., 2016) and lipid‐degrading Agitococcus lubricus (Franzmann and Skerman, 1981) were observed in activated sludge. This suggests that the microbial community change is associated with important compositional change of proteins, carbohydrates and lipids, commonly observed in gut microbiome studies (Sheflin et al ., 2017).…”

Section: Discussionmentioning

confidence: 99%

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Microbial community origin and fate through a rural wastewater treatment plant

Newton

González

Pitre

et al. 2022

Environmental Microbiology

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Summary Conventional wastewater treatment relies on a complex microbiota; however, much of this community is still to be characterized. To better understand the origin, dynamics and fate of bacteria within a wastewater treatment plant: untreated primary wastewater, activated sludge and post‐treatment effluent were characterized. From 3163 exact sequence variants (ESVs), 860 were annotated to species‐level. In primary wastewater, 28% of ESVs were putative bacterial species previously associated with humans, 14% with animals and 5% as common to the environment. Differential abundance analysis revealed significant relative reductions in ESVs from potentially human‐associated species from primary wastewater to activated sludge, and significant increases in ESVs from species associated with nutrient cycling. Between primary wastewater and effluent, 51% of ESVs from human‐associated species did not significantly differ, and species such as Bacteroides massiliensis and Bacteroides dorei increased. These findings illustrate that activated sludge increased extracellular protease and urease‐producing species, ammonia and nitrite oxidizers, denitrifiers and specific phosphorus accumulators. Although many human‐associated species declined, some persisted in effluent, including strains of potential health or environmental concern. Species‐level microbial assessment may be useful for understanding variation in wastewater treatment efficiency as well as for monitoring the release of microbes into surface water and the wider ecosystem.

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Section: Humans and Animalsmentioning

confidence: 64%

Section: Discussionmentioning

confidence: 99%

Microbial community origin and fate through a rural wastewater treatment plant

Newton

González

Pitre

et al. 2022

Environmental Microbiology

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“…The description is as before (Hatayama et al, 2016) with the following modification. The G+C content of the type-strain genome is 34.2%, its approximate size 5.12 Mbp, its IMG deposit 2739367662.…”

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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“…BH12.12 was positive for nirS amplification in a survey from estuary sediment in the United Kingdom ( Nogales et al, 2002 ). Other Flavobacterium species have been isolated as denitrifying microorganisms but their denitrifying genes have not been described so far, such is the case of Flavobacterium denitrificans ( Horn et al, 2005 ) and F. aquicola ( Hatayama et al, 2016 ). At the genome level, Flavobacterium columnare is the only one with identified nirK genes ( Tekedar et al, 2017 ).…”

Section: Discussionmentioning

confidence: 99%

“…Flavobacterium denitrificans (Horn et al, 2005) and F. aquicola (Hatayama et al, 2016). At the genome level, Flavobacterium columnare is the only one with identified nirK genes (Tekedar et al, 2017).…”

Section: Key Denitrifying Populations In Antarcticamentioning

confidence: 99%

Ubiquity and Diversity of Cold Adapted Denitrifying Bacteria Isolated From Diverse Antarctic Ecosystems

Cabezas¹,

Azziz²,

Bovio-Winkler

et al. 2022

Front. Microbiol.

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Nitrogen cycle has been poorly investigated in Antarctic ecosystems. In particular, how extreme conditions of low temperature, dryness, and high radiation select the microorganisms involved in the cycle is not yet understood. Denitrification is an important step in the nitrogen cycle in which nitrate is reduced stepwise to the gases NO, N2O, and N2. Denitrification is carried out by a wide group of microorganisms spread in the phylogenetic tree. The aim of this work was to isolate and characterize denitrifying bacteria present in different cold environments from Antarctica. Bacterial isolates were obtained from lake, meltwater, sea, glacier ice, ornithogenic soil, and penguin feces samples from King George Island, Fildes peninsula in the Antarctic. Samples were taken during the deicing season in five sampling campaigns. From all the samples we were able to isolate denitrifying strains. A total of 199 bacterial isolates with the capacity to grow in anaerobic mineral media reducing nitrate at 4°C were obtained. The characterization of the isolates by 16S rRNA gene sequence analysis showed a high predominance of the genus Pseudomonas, followed by Janthinobacterium, Flavobacterium, Psychrobacter, and Yersinia. Other minor genera detected were Cryobacterium, Iodobacter, Kaistella, and Carnobacterium. The capacity to denitrify was not previously described for most of the bacteria related to our isolates and in many of them denitrifying genes were not present suggesting the presence of new genes in this extreme environment. Our work demonstrates the ubiquity of denitrification in the Maritime Antarctica and gives important information linking denitrification at cold temperature with taxa in an unequivocal way.

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Flavobacterium aquicola sp. nov., isolated from river water

Abstract: A bacterial strain, designated TMd3a3T , was isolated from a freshwater sample collected from the Tamagawa River in Japan.

Cited by 15 publications

References 36 publications

Microbial community origin and fate through a rural wastewater treatment plant

Microbial community origin and fate through a rural wastewater treatment plant

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

Ubiquity and Diversity of Cold Adapted Denitrifying Bacteria Isolated From Diverse Antarctic Ecosystems

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