Description of Acidovorax wautersii sp. nov. to accommodate clinical isolates and an environmental isolate, most closely related to Acidovorax avenae

Different responses of mesophilic and thermophilic anaerobic digestion of waste activated sludge to PVC microplastics

The effect of microplastics (MPs) retained in waste activated sludge (WAS) on anaerobic digestion (AD) performance has attracted more and more attention. However, their effect on thermophilic AD remains unclear. Here, the influence of polyvinyl chloride (PVC) MPs on methanogenesis and active microbial communities in mesophilic (37 °C) and thermophilic (55 °C) AD was investigated. The results showed that 1, 5, and 10 mg/L PVC MPs significantly promoted the cumulative methane yield in mesophilic AD by 5.62%, 7.36%, and 8.87%, respectively, while PVC MPs reduced that in thermophilic AD by 13.30%, 18.82%, and 19.99%, respectively. Moreover, propionate accumulation was only detected at the end of thermophilic AD with PVC MPs. Microbial community analysis indicated that PVC MPs in mesophilic AD enriched hydrolytic and acidifying bacteria (Candidatus Competibacter, Lentimicrobium, Romboutsia, etc.) together with acetoclastic methanogens (Methanosarcina, Methanosaeta). By contrast, most carbohydrate-hydrolyzing bacteria, propionate-oxidizing bacterium (Pelotomaculum), and Methanosarcina were inhibited by PVC MPs in thermophilic AD. Network analysis further suggested that PVC MPs significantly changed the relationship of key microorganisms in the AD process. A stronger correlation among the above genera occurred in mesophilic AD, which may promote the methanogenic performance. These results suggested that PVC MPs affected mesophilic and thermophilic AD of WAS via changing microbial activities and interaction.

Microbial consortia degrade several widely used organic UV filters, but a number of hydrophobic filters remain recalcitrant to biodegradation

Organic UV filters are important ingredients in many personal care products, including sunscreens. Evaluating the biodegradability of organic UV filters is key to estimate their recalcitrance and environmental fate and thus central to their overall environmental risk assessment. In order to further understand the degradation process, the aim was to investigate whether specific consortia could degrade certain UV filters. Several bacterial strains were isolated from enrichment cultures actively degrading octocrylene (OC), butyl methoxydibenzoylmethane (BM), homosalate (HS), and 2-ethylhexyl salicylate (ES) and were utilized to construct an in-house consortium. This synthetic consortium contained 27 bacterial strains and degraded OC, BM, HS, and ES 60-80% after 12 days, but not benzophenone-3 (BP3), methoxyphenyl triazine (BEMT), methylene bis-benzotriazolyl tetramethylbutylphenol (MBBT), diethylhexyl butamido triazone (DBT), ethylhexyl triazone (EHT), or diethylamino hydroxybenzoyl hexyl benzoate (DHHB). Furthermore, several commercial microbial mixtures from Greencell were tested to assess their degradation activity toward the same organic UV filters. ES and HS were degraded by some of the commercial consortia, but to a lesser extent. The rest of the tested UV filters were not degraded by any of the commercial bacterial mixes. These results confirm that some organic UV filters are recalcitrant to biodegradation, while others are degraded by a specific set of microorganisms.

Characterisation of Mid-Gestation Amniotic Fluid Cytokine and Bacterial DNA Profiles in Relation to Pregnancy Outcome in a Small Australian Cohort

A well-established association exists between intrauterine bacteria and preterm birth. This study aimed to explore this further through documenting bacterial and cytokine profiles in Australian mid-gestation amniotic fluid samples from preterm and term births. Samples were collected during amniocenteses. DNA was extracted and the full-length 16S rRNA gene was amplified and sequenced. Levels of the cytokines IL-1β, IL-6, IL-10, TNF-α and MCP-1 were determined using the Milliplex MAGPIX system. Bacterial DNA profiles were low in diversity and richness, with no significant differences observed between term and preterm samples. No differences in the relative abundance of individual OTUs between samples were identified. IL-1β and TNF-α levels were significantly higher in samples containing reads mapping to Sphingomonas sp.; however, this result should be interpreted with caution as similar reads were also identified in extraction controls. IL-6 levels were significantly increased in samples with reads that mapped to Pelomonas sp., whilst TNF-α levels were elevated in fluid samples from pregnancies that subsequently delivered preterm. Bacterial DNA unlikely to have originated from extraction controls was identified in 20/31 (64.5%) mid-gestation amniotic fluid samples. Bacterial DNA profiles, however, were not predictive of preterm birth, and although cytokine levels were elevated in the presence of certain genera, the biological relevance of this remains unknown.

Genome-based analyses of the genus Acidovorax: proposal of the two novel genera Paracidovorax gen. nov., Paenacidovorax gen. nov. and the reclassification of Acidovorax antarcticus as Comamonas antarctica comb. nov. and emended description of the genus Acidovorax

The genus Acidovorax is a genetically heterogeneous species clustering that comprises many environmental and plant-pathogenic taxa. To better understand the evolutionary relationships among the Acidovorax species, 22 available genome sequences of type strains including the genera Acidovorax and Comamonas were used to conduct the genome-based analyses. Three well-supported monophyletic clusters of the Acidovorax species were determined based on the phylogenomic tree reconstructed using core genes, while they were not grouped in the 16S rRNA gene-based phylogenetic tree. The species arrangements of the genus Acidovorax were further confirmed by the comparisons of the digital DNA-DNA hybridization and average nucleotide identity (ANI) values. The ANI, average amino acid identity, and the percentage of conserved proteins values among the inter-clusters were approximately 83, 81, and 61%, respectively, and thus were proposed as practical thresholds for genus delineation. Besides, Acidovorax antarcticus was much closer to members of the genus Comamonas rather than those of the genus Acidovorax based on the genome-based analysis. Taken together, we propose the division of the current genus Acidovorax into the emended genus Acidovorax and the two novel genera Paracidovorax gen. nov., Paenacidovorax gen. nov. and the transfer of Acidovorax antarcticus into the genus Comamonas as Comamonas antarctica comb. nov.

Draft Genome of Acidovorax kalamii Strain JM16, Isolated from Skin Mucus of Zebrafish (Danio rerio)

Acidovorax kalamii strain JM16 was isolated from the skin mucus of the zebrafish, Danio rerio. Its genome is 5.3 Mb with a 65.6% GC content and encodes quorum sensing capabilities, which could contribute to ecosystem functioning within the fish host skin bacterial community.

Culturomics revealed the bacterial constituents of the microbiota of a 10-year-old laboratory culture of planarian species S. mediterranea

The planarian species Schmidtea mediterranea is a flatworm living in freshwater that is used in the research laboratory as a model to study developmental and regeneration mechanisms, as well as antibacterial mechanisms. However, the cultivable microbial repertoire of the microbes comprising its microbiota remains unknown. Here, we characterized the bacterial constituents of a 10-year-old laboratory culture of planarian species S. mediterranea via culturomics analysis. We isolated 40 cultivable bacterial species, including 1 unidentifiable species. The predominant phylum is Proteobacteria, and the most common genus is Pseudomonas. We discovered that parts of the bacterial flora of the planarian S. mediterranea can be classified as fish pathogens and opportunistic human pathogens.

Acidovorax antarcticus sp. nov., isolated from a soil sample of Collins Glacier front, Antarctica

A Gram-stain-negative, rod-shaped, and aerobic bacterium, strain 16-35-5^T, was isolated from Collins Glacier front soil from the Fildes Peninsula, Antarctica. The bacterium grew optimally at 28 °C, pH 7.0 and in the presence of 0-4.0 % (w/v) NaCl. On the basis of the results of 16S rRNA gene sequence phylogenetic analyses, it was concluded that 16-35-5^T represented a member of the genus Acidovorax and had the highest sequence similarities with Acidovorax anthurii CFBP 3232^T (96.48 %). The genome of 16-35-5^T is 4.2 Mb long with a DNA G+C content of 66.3 mol%. Average nucleotide identity (ANI) value between the genomes of 16-35-5^T and Acidovorax wautersii DSM 27981^T, was 85.29 %. Strain 16-35-5^T had ubiquinone-8 (Q-8) as the respiratory ubiquinone. The polar lipids of 16-35-5^T were consisted of phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The main fatty acids were summed feature 3 (C_16 : 1ω7c and/or C_16 : 1ω6c, 25.2 %), summed feature 8 (C_18 : 1ω7c and/or C_18 : 1ω6c, 12.9 %), C_16 : 0 (35.2 %), and C_17 : 0 cyclo (19.0 %). On the basis of the evidence presented in this study, 16-35-5^T should be classified as representing a novel species of the genus Acidovorax, for which the name Acidovorax antarcticus sp. nov., is proposed, with the type strain 16-35-5^T (=CCTCC AB 2019325^T=KCTC 72915^T).

Isolation and characterization of a novel bacterial strain from a Tris-Acetate-Phosphate agar medium plate of the green micro-alga Chlamydomonas reinhardtii that can utilize common environmental pollutants as a carbon source

Background:Chlamydomonas reinhardtii, a green micro-alga can be grown at the lab heterotrophically or photo-heterotrophically in Tris-Phosphate-Acetate (TAP) medium which contains acetate as the sole carbon source. When grown in TAP medium, Chlamydomonas can utilize the exogenous acetate in the medium for gluconeogenesis using the glyoxylate cycle, which is also present in many bacteria and higher plants. A novel bacterial strain, LMJ, was isolated from a contaminated TAP medium plate of Chlamydomonas. We present our work on the isolation and physiological and biochemical characterizations of LMJ.

Methods: Several microbiological tests were conducted to characterize LMJ, including its sensitivity to four antibiotics. We amplified and sequenced partially the 16S rRNA gene of LMJ. We tested if LMJ can utilize cyclic alkanes, aromatic hydrocarbons, poly-hydroxyalkanoates, and fresh and combusted car motor oil as the sole carbon source on Tris-Phosphate (TP) agar medium plates for growth.

Results: LMJ is a gram-negative rod, oxidase-positive, mesophilic, non-enteric, pigmented, salt-sensitive bacterium. LMJ can ferment glucose, is starch hydrolysis-negative, and is very sensitive to penicillin and chloramphenicol. Preliminary spectrophotometric analyses indicate LMJ produces pyomelanin. NCBI-BLAST analyses of the partial 16S rRNA gene sequence of LMJ showed that it matched to that of an uncultured bacterium clone LIB091_C05_1243. The nearest genus relative of LMJ is an Acidovorax sp. strain. LMJ was able to use alkane hydrocarbons, fresh and combusted car motor oil, poly-hydroxybutyrate, phenanthrene, naphthalene, benzoic acid and phenyl acetate as the sole carbon source for growth on TP-agar medium plates.

Conclusions: LMJ has 99.14% sequence identity with the Acidovorax sp. strain A16OP12 whose genome has not been sequenced yet. LMJ’s ability to use chemicals that are common environmental pollutants makes it a promising candidate for further investigation for its use in bioremediation and, provides us with an incentive to sequence its genome.

Draft Genome Sequence of Acidovorax sp. Strain NB1, Isolated from a Nitrite-Oxidizing Enrichment Culture

Here, we report the draft genome sequence of Acidovorax sp. strain NB1, isolated from an enrichment culture of nitrite-oxidizing bacteria (NOB). Genes involved in denitrification were found in the draft genome of NB1. The closest strain to NB1 based on genomic relatedness is Acidovorax sp. strain GW101-3H11, with 91.5% average nucleotide identity.

Here, we report the draft genome sequence of Acidovorax sp. strain NB1, isolated from an enrichment culture of nitrite-oxidizing bacteria (NOB). Genes involved in denitrification were found in the draft genome of NB1. The closest strain to NB1 based on genomic relatedness is Acidovorax sp. strain GW101-3H11, with 91.5% average nucleotide identity.

Polyphasic characterization of four soil-derived phenanthrene-degrading Acidovorax strains and proposal of Acidovorax carolinensis sp. nov

Four bacterial strains identified as members of the Acidovorax genus were isolated from two geographically distinct but similarly contaminated soils in North Carolina, USA, characterized, and their genomes sequenced. Their 16S rRNA genes were highly similar to those previously recovered during stable-isotope probing (SIP) of one of the soils with the polycyclic aromatic hydrocarbon (PAH) phenanthrene. Heterotrophic growth of all strains occurred with a number of organic acids, as well as phenanthrene, but no other tested PAHs. Optimal growth occurred aerobically under mesophilic temperature, neutral pH, and low salinity conditions. Predominant fatty acids were C_16:1ω7c/C_16:1ω6c, C_16:0, and C_18:1ω7c, and were consistent with the genus. Genomic G+C contents ranged from 63.6 to 64.2%. A combination of whole genome comparisons and physiological analyses indicated that these four strains likely represent a single species within the Acidovorax genus. Chromosomal genes for phenanthrene degradation to phthalate were nearly identical to highly conserved regions in phenanthrene-degrading Delftia, Burkholderia, Alcaligenes, and Massilia species in regions flanked by transposable or extrachromosomal elements. The lower degradation pathway for phenanthrene metabolism was inferred by comparisons to described genes and proteins. The novel species Acidovorax carolinensis sp. nov. is proposed, comprising the four strains described in this study with strain NA3^T as the type strain (=LMG 30136, =DSM 105008).

What's in a Name? New Bacterial Species and Changes to Taxonomic Status from 2012 through 2015

Technological advancements in fields such as molecular genetics and the human microbiome have resulted in an unprecedented recognition of new bacterial genus/species designations by the International Journal of Systematic and Evolutionary Microbiology Knowledge of designations involving clinically significant bacterial species would benefit clinical microbiologists in the context of emerging pathogens, performance of accurate organism identification, and antimicrobial susceptibility testing. In anticipation of subsequent taxonomic changes being compiled by the Journal of Clinical Microbiology on a biannual basis, this compendium summarizes novel species and taxonomic revisions specific to bacteria derived from human clinical specimens from the calendar years 2012 through 2015.

First Draft Genome Sequence of the Acidovorax caeni sp. nov. Type Strain R-24608 (DSM 19327)

We report the draft genome sequence of the Acidovorax caeni type strain R-24608 that was isolated from activated sludge of an aerobic-anaerobic wastewater treatment plant. The closest strain to Acidovorax caeni strain R-24608 is Acidovorax sp. strain MR-S7 with a 55.4% (amino-acid sequence) open reading frames (ORFs) average similarity.

A novel molecular microbiologic technique for the rapid diagnosis of microbial invasion of the amniotic cavity and intra-amniotic infection in preterm labor with intact membranes

PROBLEM

The diagnosis of microbial invasion of the amniotic cavity (MIAC) has been traditionally performed using traditional cultivation techniques, which require growth of microorganisms in the laboratory. Shortcomings of culture methods include the time required (days) for identification of microorganisms, and that many microbes involved in the genesis of human diseases are difficult to culture. A novel technique combines broad-range real-time polymerase chain reaction with electrospray ionization time-of-flight mass spectrometry (PCR/ESI-MS) to identify and quantify genomic material from bacteria and viruses.

METHOD OF STUDY

AF samples obtained by transabdominal amniocentesis from 142 women with preterm labor and intact membranes (PTL) were analyzed using cultivation techniques (aerobic, anaerobic, and genital mycoplasmas) as well as PCR/ESI-MS. The prevalence and relative magnitude of intra-amniotic inflammation [AF interleukin 6 (IL-6) concentration ≥ 2.6 ng/mL], acute histologic chorioamnionitis, spontaneous preterm delivery, and perinatal mortality were examined.

RESULTS

(i) The prevalence of MIAC in patients with PTL was 7% using standard cultivation techniques and 12% using PCR/ESI-MS; (ii) seven of ten patients with positive AF culture also had positive PCR/ESI-MS [≥17 genome equivalents per PCR reaction well (GE/well)]; (iii) patients with positive PCR/ESI-MS (≥17 GE/well) and negative AF cultures had significantly higher rates of intra-amniotic inflammation and acute histologic chorioamnionitis, a shorter interval to delivery [median (interquartile range-IQR)], and offspring at higher risk of perinatal mortality, than women with both tests negative [90% (9/10) versus 32% (39/122) OR: 5.6; 95% CI: 1.4-22; (P < 0.001); 70% (7/10) versus 35% (39/112); (P = 0.04); 1 (IQR: <1-2) days versus 25 (IQR: 5-51) days; (P = 0.002), respectively]; (iv) there were no significant differences in these outcomes between patients with positive PCR/ESI-MS (≥17 GE/well) who had negative AF cultures and those with positive AF cultures; and (v) PCR/ESI-MS detected genomic material from viruses in two patients (1.4%).

CONCLUSION

(i) Rapid diagnosis of intra-amniotic infection is possible using PCR/ESI-MS; (ii) the combined use of biomarkers of inflammation and PCR/ESI-MS allows for the identification of specific bacteria and viruses in women with preterm labor and intra-amniotic infection; and (iii) this approach may allow for administration of timely and specific interventions to reduce morbidity attributed to infection-induced preterm birth.