Geofilum rhodophaeum sp. nov., isolated from coastal sediment

Mu, Xin; Xu, Zhenxing; Mu, Da-Shuai; Chen, Guanjun; Du, Zong‐Jun

doi:10.1099/ijsem.0.002223

Cited by 8 publications

(2 citation statements)

References 23 publications

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“…The description is as before (Mu et al, 2017) with the following restriction. The G+C content of the type-strain genome is 48.9%, its approximate size 4.15 Mbp, its GenBank deposit SAMN06473345.…”

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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Section: Discussionmentioning

confidence: 99%

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

et al. 2019

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“…However, the abundance of Pseudomonas increased to 36% at 5 g Na + /L, while it decreased to 4% at 7 g Na + /L, probably due to exceeding the maximum sodium concentration for its growth (Xiao et al, 2009 ). At 7 g Na + /L, the abundance of Geofilum and Marinobacterium was increased to 7 and 10% and are known to grow at a wide sodium concentration range of 2–20 g Na + /L (González et al, 1997 ; Mu et al, 2017 ). Other species detected in the stored PS were Treponema zuelzerae, Tissierella praeacuta, Clostridium saudiense , and Proteiniphilum acetatigenes , whose abundance was slightly changed.…”

Section: Resultsmentioning

confidence: 99%

Use of reverse osmosis concentrate for mitigating greenhouse gas emissions from pig slurry

Kang

Jang

et al. 2023

Front. Microbiol.

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Due to the high global warming potential (GWP) in a short time scale (GWP100 = 28 vs. GWP20 = 86), mitigating CH4 emissions could have an early impact on reducing current global warming effects. The manure storage tank emits a significant amount of CH4, which can diminish the environmental benefit resulting from the anaerobic digestion of manure that can generate renewable energy. In the present study, we added the reverse osmosis concentrate (ROC) rich in salt to the pig slurry (PS) storage tank to reduce CH4 emissions. Simultaneously, pure NaCl was tested at the same concentration to compare and verify the performance of ROC addition. During 40 days of storage, 1.83 kg CH4/ton PS was emitted, which was reduced by 7–75% by the addition of ROC at 1–9 g Na+/L. This decrease was found to be more intensive than that found upon adding pure sodium, which was caused by the presence of sulfate rich in ROC, resulting in synergistic inhibition. The results of the microbial community and activity test showed that sodium directly inhibited methanogenic activity rather than acidogenic activity. In the subsequent biogas production from the stored PS, more CH4 was obtained by ROC addition due to the preservation of organic matter during storage. Overall, 51.2 kg CO2 eq./ton PS was emitted during the storage, while 8 kg CO2 eq./ton PS was reduced by biogas production in the case of control, resulting in a total of 43.2 kg CO2 eq./ton PS. This amount of greenhouse gas emissions was reduced by ROC addition at 5 g Na+/L by 22 and 65 kg CO2 eq./ton PS, considering GWP100 and GWP20 of CH4, respectively, where most of the reduction was achieved during the storage process. To the best of our knowledge, this was the first report using salty waste to reduce GHG emissions in a proper place, e.g., a manure storage tank.

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Labilibacter

Lü

2021

Bergey's Manual of Systematics of Archaea and Bacteria

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La.bi.li.bac'ter. L. masc. adj. labilis , gliding; N.L. masc. n. bacter , rod; N.L. masc. n. Labilibacter , gliding rod. Bacteroidetes / Bacteroidia / Bacteroidales / Marinilabiliaceae / Labilibacter Labilibacter is a genus within the family Marinilabiliaceae , order Bacteroidales , class Bacteroidia , and phylum Bacteroidetes . It currently includes three species – Labilibacter sediminis , Labilibacter aurantiacus , and Labilibacter marinus – isolated from marine sediment or sea squirts ( Styela clava ). Colonies of Labilibacter are circular and yellow or orange. The three species of the genus show different features, including the ability to hydrolyze gelatin, starch and produce indole and valine arylamidase. The major fatty acids are iso‐C 15:0 and anteiso‐C 15:0 . The major respiratory quinone is MK‐7. The polar lipid profile of the genus contains unidentified lipid, phospholipid, aminophospholipid, phosphatidylethanolamine, and aminolipid. The size of the genome is between 5.88 and 6.37 Mb. 16S rRNA gene sequence analysis indicated that the closest phylogenetic relatives of the genus Labilibacter are members of the genera Saccharicinis and Carboxylicivirga . DNA G + C content (mol%) : 35.1–35.9 (genome), 35.1–36.1 (HPLC). Type species : Labilibacter aurantiacus Lu et al. 2017 VP .

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Geofilum rhodophaeum sp. nov., isolated from coastal sediment

Cited by 8 publications

References 23 publications

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

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

Use of reverse osmosis concentrate for mitigating greenhouse gas emissions from pig slurry

Labilibacter

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