Sphingomonas gei sp. nov., isolated from roots of Geum aleppicum

Zhu, Lingfang; Si, Meiru; Li, Changfu; Xin, Kaiyun; Chen, Chaoqiong; Xu, Shichao; Huang, Ruijun; Zhao, Liang; Shen, Xihui; Zhang, Lei

doi:10.1099/ijs.0.000074

Cited by 31 publications

(12 citation statements)

References 36 publications

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“…16S rRNA gene amplicon sequencing revealed that Sphingomonas was the most frequently detected genus in the air samples. This genus has been found in various environments such as soil, water, clinical specimens, air, and other locations [30][31][32], indicating the opportunity for the bacteria to be released into the air. Pseudomonas and Achromobacter were signi cantly more abundant in air samples from bathrooms and other indoor sites, respectively.…”

Section: Discussionmentioning

confidence: 99%

Detection of Legionella Species and the Influence of Precipitation on the Amount of Legionella DNA Present in Aerosols from Outdoor Sites Near Asphalt Roads in Toyama Prefecture, Japan, with Microbiome Analysis

Kanatani

Watahiki

Kimata

et al. 2020

Preprint

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Background: Legionellosis can be caused by the inhalation of aerosolized water contaminated with Legionella. In this study, we investigated the prevalence of Legionella species in aerosols collected from outdoor sites near asphalt roads, bathrooms in public bath facilities, and other indoor sites such as buildings and private homes using culture methods, quantitative PCR with ethidium monoazide treatment (EMA-qPCR), and 16S rRNA gene amplicon sequencing. Results: Legionella species were not detected in culture. However, Legionella DNA was detected in 114/151 (75.5%) air samples collected near roads (geometric mean ± standard deviation was 1.80 ± 0.52 log10 copies/m3); these numbers were comparable to those obtained from bathrooms [15/21 (71.4%), 1.82 ± 0.50] and higher than those obtained from other indoor sites [11/30 (36.7%), 0.88 ± 0.56] (P < 0.05). By EMA-qPCR, Legionella DNA was detected in 20/30 (66.7%) samples collected near roads, indicating the presence of membrane-intact Legionella cells in the air. The amount of Legionella DNA correlated with the monthly total precipitation (r = 0.25, P < 0.01). It was also directly and inversely correlated with the daily total precipitation for seven days (r = 0.21, P = 0.01) and one day (r = −0.29, P < 0.01) before the sampling day, respectively. In addition, 16S rRNA gene amplicon sequencing revealed that the three most abundant bacterial genera in the samples collected near roads were Sphingomonas (21.1%), Streptococcus (14.6%), and Methylobacterium (1.6%); Legionella species were detected in 9/30 samples (30%) collected near roads (mean proportion of reads, 0.11%). At the species level, L. pneumophila was detected in 2/30 samples collected near roads (mean proportion of reads, 0.11% and 0.09% in the detected samples).Conclusions: DNA from Legionella species, including Legionella pneumophila, were widely detected in aerosols collected from outdoor sites near asphalt roads, especially during the rainy season. Our findings suggest that there may be a risk of exposure to Legionella species in the areas surrounding asphalt roads.

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Section: Discussionmentioning

confidence: 99%

Detection of Legionella Species and the Influence of Precipitation on the Amount of Legionella DNA Present in Aerosols from Outdoor Sites Near Asphalt Roads in Toyama Prefecture, Japan, with Microbiome Analysis

Kanatani

Watahiki

Kimata

et al. 2020

Preprint

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“…S4). The pH range for growth was determined in R2A medium at pH 4.0-10.0 at intervals of 1 pH unit by using the buffers 0.1 M citric acid/0.1 M sodium citrate (pH 4.0-5.0), 0.2 M Na 2 HPO 4 /0.2 M NaH 2 PO 4 (pH 6.0-8.0) and 0.1 M NaHCO 3 /0.1 M Na 2 CO 3 (pH 9.0-10.0) [34]. Growth on different media [nutrient agar, tryptic soy agar (15 g casein peptone, 5 g soy peptone, 5 g sodium chloride, 15 g agar per litre of laboratory quality water, pH 7), PTYG agar (0.25 g peptone, 0.25 g tryptone, 0.5 g yeast extract, 0.5 g glucose, 0.6 g MgSO 4 ·7H 2 O, 70 mg CaCl 2 ·2H 2 O and 15 g agar per litre of laboratory quality water, pH 7), PY agar (10 g peptone, 2 g yeast extract, 1 g MgSO 4 ·7H 2 O and 15 g agar per litre of laboratory quality water, pH 7)] was assessed on agar plates under 15 °C.…”

Section: Physiology and Chemotaxonomymentioning

confidence: 99%

Sphingomonas profundi sp. nov., isolated from deep-sea sediment of the Mariana Trench

Yang

Xiao

et al. 2020

International Journal of Systematic and Evolutionary Microbiology

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A Gram-stain-negative, short rod-shaped, yellow bacterium (strain LMO-1T) was isolated from deep-sea sediment of the Mariana Trench, Challenger Deep. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain LMO-1T belonged to genus Sphingomonas , with the highest sequence similarity to Sphingomonas formosensis CC-Nfb-2T (96.3 %), followed by Sphingomonas prati W18RDT (96.1 %), Sphingomonas arantia 6PT (96.0 %) and Sphingomonas montana W16RDT (95.9 %). The predominant polar lipids were phosphatidylethanolamine, sphingoglycolipid, phosphatidylglycerol and phosphatidylcholine. The main cellular fatty acids were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), C16 : 0 and C14 : 0 2-OH. The major polyamine was sym-homospermidine and the predominant isoprenoid quinone was ubiquinone-10. The genome DNA G+C content of strain LMO-1T was 69.2 mol%. The average nucleotide identity and DNA–DNA hybridization values between strain LMO-1T and CC-Nfb-2T were 75.9 and 20.5 %, respectively. Based on these data, LMO-1T should be classified as representing a novel species of the genus Sphingomonas , for which the name Sphingomonas profundi sp. nov. is proposed. The type strain is LMO-1T (=MCCC 1K04066T=JCM 33666T).

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“…These data suggest that the strongly labeled cellulolytic strain is degrading 13 C-cellulose extracellularly and the weakly 13 C-enriched strain can access degradation products as well as other sources of unlabeled carbon present in soil. The capacity of Sphingomonas species to degrade cellulose through the activity of extracellular enzymes is known [65,66].…”

Section: Mutualists Opportunists and Parasitesmentioning

confidence: 99%

Competitive exclusion and metabolic dependency among microorganisms structure the cellulose economy of agricultural soil

Wilhelm

Pepe-Ranney

Weisenhorn

et al. 2020

Preprint

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Background Microorganisms that degrade cellulose utilize extracellular processes that yield free intermediates which promote interactions with non-cellulolytic organisms. We hypothesized that these interactions determine the ecological and physiological traits governing the fate of cellulosic carbon (C) in soil. We used data from a metagenomic-SIP experiment to perform comparative genomics and characterize the attributes of cellulolytic and non-cellulolytic taxa accessing 13C from cellulose. We hypothesized that cellulolytic taxa would exhibit competitive traits to limit access, while non-cellulolytic taxa would display metabolic dependency, such as signatures of adaptive gene loss. We tested our hypotheses by evaluating genomic traits indicative of competitive exclusion or metabolic dependency, such as antibiotic production, growth rate, surface attachment, biomass degrading potential and auxotrophy.Results The most 13C-enriched taxa were cellulolytic Cellvibrio (Gammaproteobacteria) and Chaetomium (Ascomycota), which exhibited a strategy of self-sufficiency (prototrophy), rapid growth, and competitive exclusion via antibiotic production. Auxotrophy was more prevalent in cellulolytic Actinobacteria than in cellulolytic Proteobacteria, demonstrating differences in dependency among cellulose degraders. Non-cellulolytic taxa that accessed 13C from cellulose (Planctomycetales, Verrucomicrobia and Vampirovibrionales) were highly dependent, as indicated by patterns of auxotrophy and 13C-labeling (i.e. partial labelling or labeling at later-stages). Major 13C-labeled cellulolytic microbes (e.g. Sorangium, Actinomycetales, Rhizobiales and Caulobacteraceae) possessed adaptations for surface colonization (e.g. gliding motility, hyphae, attachment structures) signifying the importance of surface ecology in decomposition. Conclusions Our results demonstrate that access to cellulose was accompanied by ecological trade-offs characterized by differing degrees of metabolic dependency and competitive exclusion. These trade-offs influence microbial growth dynamics on particulate organic carbon and reveal that the fate of carbon is governed by a complex economy within the microbial community. We propose three ecological groups to describe participants in this economy: (i) independent primary degraders, (ii) integrated primary degraders and (iii) mutualists, opportunists and parasites. The relative importance and taxonomic composition of these groups reported here should be considered context dependent, likely reflecting disturbance and management practices common to agricultural soils.

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Sphingomonas gei sp. nov., isolated from roots of Geum aleppicum

Cited by 31 publications

References 36 publications

Detection of Legionella Species and the Influence of Precipitation on the Amount of Legionella DNA Present in Aerosols from Outdoor Sites Near Asphalt Roads in Toyama Prefecture, Japan, with Microbiome Analysis

Detection of Legionella Species and the Influence of Precipitation on the Amount of Legionella DNA Present in Aerosols from Outdoor Sites Near Asphalt Roads in Toyama Prefecture, Japan, with Microbiome Analysis

Sphingomonas profundi sp. nov., isolated from deep-sea sediment of the Mariana Trench

Competitive exclusion and metabolic dependency among microorganisms structure the cellulose economy of agricultural soil

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