Marivirga atlantica sp. nov., isolated from seawater and emended description of the genus 
               Marivirga

Lin, Chaoyi; Zhang, Xiying; Liu, Ang; Liu, Chang; Song, Xin; Su, Hai-Nan; Qin, Qi‐Long; Xie, Bin-Bin; Zhang, Yuzhong

doi:10.1099/ijs.0.000126

Cited by 20 publications

(16 citation statements)

References 14 publications

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“…A similar set of strains was investigated in the description of the two other Marivirga species, M. lumbricoides (Xu et al, 2015) and M. atlantica (Lin C.-Y. et al, 2015). Thus, the strain samplings in those earlier studies did not allow for detecting a closer affiliation of Marivirga to another family, which might explain the conflicting result obtained here.…”

Section: Resultsmentioning

confidence: 99%

Genome-Based Taxonomic Classification of Bacteroidetes

et al. 2016

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The bacterial phylum Bacteroidetes, characterized by a distinct gliding motility, occurs in a broad variety of ecosystems, habitats, life styles, and physiologies. Accordingly, taxonomic classification of the phylum, based on a limited number of features, proved difficult and controversial in the past, for example, when decisions were based on unresolved phylogenetic trees of the 16S rRNA gene sequence. Here we use a large collection of type-strain genomes from Bacteroidetes and closely related phyla for assessing their taxonomy based on the principles of phylogenetic classification and trees inferred from genome-scale data. No significant conflict between 16S rRNA gene and whole-genome phylogenetic analysis is found, whereas many but not all of the involved taxa are supported as monophyletic groups, particularly in the genome-scale trees. Phenotypic and phylogenomic features support the separation of Balneolaceae as new phylum Balneolaeota from Rhodothermaeota and of Saprospiraceae as new class Saprospiria from Chitinophagia. Epilithonimonas is nested within the older genus Chryseobacterium and without significant phenotypic differences; thus merging the two genera is proposed. Similarly, Vitellibacter is proposed to be included in Aequorivita. Flexibacter is confirmed as being heterogeneous and dissected, yielding six distinct genera. Hallella seregens is a later heterotypic synonym of Prevotella dentalis. Compared to values directly calculated from genome sequences, the G+C content mentioned in many species descriptions is too imprecise; moreover, corrected G+C content values have a significantly better fit to the phylogeny. Corresponding emendations of species descriptions are provided where necessary. Whereas most observed conflict with the current classification of Bacteroidetes is already visible in 16S rRNA gene trees, as expected whole-genome phylogenies are much better resolved.

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Section: Resultsmentioning

confidence: 99%

Genome-Based Taxonomic Classification of Bacteroidetes

et al. 2016

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“…Marivirga (Nedashkovskaya et al, 2010c; Lin et al, 2015) formed the sister group of Cyclobacteriaceae with strong support but was phylogenetically distant from this family and thus may best also be placed into a family of its own, a solution neither contradicted by analyses of rRNA genes (Supplementary Data Sheet 1) nor by the phenotype (Supplementary Table 1). To obtain well-supported families, the only alternative to splitting Flammeovirgaceae into that many families is to place most of its genera in Cyclobacteriaceae thus create a family covering the genera from Nafulsella to Algoriphagus in Figure 3.…”

Section: Resultsmentioning

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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“…were: Leadbetterella, Filomicrobium, Algoriphagus, Sphingopyxis, Gelidibacter, Cellulophaga, Hyphomicrobium, Planctomyces, Marivirga, Rhodococcus, Pseudomonas y Arenibacter. Members of these genera commonly exist in marine environments (Johansen et al, 1999;Kim et al, 2008;Lin et al, 2015;Martineau et al, 2013;Nedashkovskaya et al, 2004;Santina et al, 2015;Zhang et al, 2015). Halotolerant genera are presented in Table S2.…”

Section: Relative Abundance Of Bacterial Phylotypesmentioning

confidence: 99%

The role of salinity on the changes of the biomass characteristics and on the performance of an OMBR treating tannery wastewater

et al. 2018

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Tannery wastewaters are difficult to treat biologically due to the high salinity and organic matter concentration. Conventional treatments, like sequential batch reactors (SBR) and membrane bioreactors (MBR), have showed settling problems, in the case of SBR, and ultrafiltration (UF) membrane fouling in the case of MBR, slowing their industrial application. In this work, the treatment of tannery wastewater with an osmotic membrane bioreactor (OMBR) is assessed. Forward osmosis (FO) membranes are characterized by a much lower fouling degree than UF membranes. The permeate passes through the membrane pores (practically only water by the high membrane rejection) from the feed solution to the draw solution, which is also an industrial wastewater (ammonia absorption effluent) in this work. Experiments were carried out at laboratory scale with a FO CTA-NW membrane from Hydration Technology Innovations (HTI). Tannery wastewater was treated by means of an OMBR using as DS an actual industrial wastewater mainly consisting of ammonium sulphate. The monitoring of the biological process was carried out with biological indicators like microbial hydrolytic enzymatic activities, dissolved and total adenosine triphosphate (ATP) in the mixed liquor and microbial population. Results indicated a limiting conductivity in the reactor of 35 mS cm (on the 43th operation day), from which process was deteriorated. This process performance diminution was associated by a high decrease of the dehydrogenase activity and a sudden increase of the protease and lipase activities. The increase of the bacterial stress index also described appropriately the process performance. Regarding the relative abundance of bacterial phylotypes, 37 phyla were identified in the biomass. Proteobacteria were the most abundant (varying the relative abundance between 50.29% and 34.78%) during the first 34 days of operation. From this day on, Bacteroidetes were detected in a greater extent varying the relative abundance of this phylum between 27.20% and 40.45%.

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Marivirga atlantica sp. nov., isolated from seawater and emended description of the genus Marivirga

Cited by 20 publications

References 14 publications

Genome-Based Taxonomic Classification of Bacteroidetes

Genome-Based Taxonomic Classification of Bacteroidetes

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

The role of salinity on the changes of the biomass characteristics and on the performance of an OMBR treating tannery wastewater

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