Xenophilus arseniciresistens sp. nov., an arsenite-resistant bacterium isolated from soil

Co-composting of dewatered sludge and wheat straw with newly isolated Xenophilus azovorans: Carbon dynamics, humification, and driving pathways

Composting is a biological reaction caused by microorganisms. Composting efficiency can be adequately increased by adding biochar and/or by inoculating with exogenous microorganisms. In this study, we looked at four methods for dewatered sludge waste (DSW) and wheat straw (WS) aerobic co-composting: T1 (no additive), T2 (5% biochar), T3 (5% of a newly isolated strain, Xenophilus azovorans (XPA)), and T4 (5% of biochar-immobilized XPA (BCI-XPA)). Throughout the course of the 42-day composting period, we looked into the carbon dynamics, humification, microbial community succession, and modifications to the driving pathways. Compared to T1 and T2, the addition of XPA (T3) and BCI-XPA (T4) extended the thermophilic phase of composting without negatively affecting compost maturation. Notably, T4 exhibited a higher seed germination index (132.14%). Different from T1 and T2 treatments, T3 and T4 treatments increased CO2 and CH4 emissions in the composting process, in which the cumulative CO2 emissions increased by 18.61-47.16%, and T3 and T4 treatments also promoted the formation of humic acid. Moreover, T4 treatment with BCI-XPA addition showed relatively higher activities of urease, polyphenol oxidase, and laccase, as well as a higher diversity of microorganisms compared to other processes. The Functional Annotation of Prokaryotic Taxa (FAPROTAX) analysis showed that microorganisms involved in the carbon cycle dominated the entire composting process in all treatments, with chemoheterotrophy and aerobic chemoheterotrophy being the main pathways of organic materials degradation. Moreover, the presence of XPA accelerated the breakdown of organic materials by catabolism of aromatic compounds and intracellular parasite pathways. On the other hand, the xylanolysis pathway was aided in the conversion of organic materials to dissolved organics by the addition of BCI-XPA. These findings indicate that XPA and BCI-XPA have potential as additives to improve the efficiency of dewatered sludge and wheat straw co-composting.

Dynamics of Methane-Consuming Biomes from Wieliczka Formation: Environmental and Enrichment Studies

The rocks surrounding Wieliczka salt deposits are an extreme, deep subsurface ecosystem that as we studied previously harbors many microorganisms, including methanotrophs. In the presented research bacterial community structure of the Wieliczka Salt Mine was determined as well as the methanotrophic activity of the natural microbiome. Finally, an enrichment culture of methane-consuming methanotrophs was obtained. The research material used in this study consisted of rocks surrounding salt deposits in the Wieliczka Salt Mine. DNA was extracted directly from the pristine rock material, as well as from rocks incubated in an atmosphere containing methane and mineral medium, and from a methanotrophic enrichment culture from this ecosystem. As a result, the study describes the composition of the microbiome in the rocks surrounding the salt deposits, while also explaining how biodiversity changes during the enrichment culture of the methanotrophic bacterial community. The contribution of methanotrophic bacteria ranged from 2.614% in the environmental sample to 64.696% in the bacterial culture. The methanotrophic enrichment culture was predominantly composed of methanotrophs from the genera Methylomonas (48.848%) and Methylomicrobium (15.636%) with methane oxidation rates from 3.353 ± 0.105 to 4.200 ± 0.505 µmol CH4 mL-1 day-1.

Xylophilus rhododendri sp. nov., Isolated from Flower of Royal Azalea, Rhododendron schlippenbachii

A bacterial strain, designated CJ1-R5^T, was isolated from the flower of the royal azalea plant (Rhododendron schlippenbachii) collected in Jeju Island, Republic of Korea. The strain was a Gram-negative, strictly aerobic, motile, rod-shaped bacterium, growing at a temperature range of 4-33 °C (optimum 28-30 °C), pH 5.0-9.0 (optimum pH 7.0-8.0), and 0-1% NaCl (optimum 0%). The 16S rRNA sequence analysis of strain CJ1-R5^T revealed the highest sequence similarity (97.9%) with Xylophilus ampelinus ATCC 33914^T, and sequence similarities of less than 97.2% with other validly named species. Phylogenetic tree analysis based on the 16S rRNA gene sequences showed that strain CJ1-R5^T clustered with Xylophilus ampelinus ATCC 33914^T and two uncultured bacterial clones. The only quinone observed in strain CJ1-R5^T was ubiquinone-8. The polar lipids observed were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminophospholipid and two unidentified lipids. The major fatty acids were C_16:0, C_17:0 cyclo, and summed feature 8 (C_18:1 ω7c and/or C_18:1 ω6c). The genome size of strain CJ1-R5^T was 5.85 Mbp. The genomic G + C content was 68.4 mol%. ANI and dDDH values between strain CJ1-R5^T and Xylophilus ampelinus ATCC 33914^T were 79.0% and 22.5%, respectively. Based on the polyphasic taxonomic data, strain CJ1-R5^T is considered to represent a novel species, for which the name Xylophilus rhododendri sp. nov. is proposed. The type strain is CJ1-R5^T (= KACC 21265^T = CCTCC AB2020030^T).

Shifts in the Skin-Associated Microbiota of Hatchery-Reared Common Snook Centropomus undecimalis During Acclimation to the Wild

The skin-associated microbiota of fish competes against pathogens for space and nutrients, preventing colonization by harmful bacteria encountered during environmental transitions such as those faced during stock enhancement. Thus, alterations in bacterial community structure during release of cultured fish have important implications for health of these individuals. This study investigated microbiota structure during acclimation of juvenile hatchery-reared common snook Centropomus undecimalis to the wild by comparing skin-associated microflora among snook in captivity, after 48 h of acclimation at release sites, and from the wild. After two days of acclimation, the microbiota of hatchery-reared snook mirrored that observed on wild snook. Relative abundances of potential pathogens were higher in captive fish, whereas acclimated and wild fish harbored bacterial taxa influenced by geographical factors and water quality at release sites. Predicted microbiota function of acclimated and wild fish showed higher production of protective amino acids and antimicrobials, identifying a mechanism for microbial supplementation of the immune defense of these fish. The two-day transition to wild-type microbiota suggests a temporal scale of hours associated with bacterial succession indicating that the microbiota, whose structure is vital to fish health, aids in acclimation of fish to new environments during stock enhancement efforts.

Draft genome sequence of Xenophilus sp. E41 isolated from an activated sludge reactor treating wastewater with high cephalexin concentration

OBJECTIVES

This study reports the draft genome sequence of Xenophilus sp. E41, a strain resistant to multiple antimicrobials isolated from an activated sludge reactor treating wastewater with a high cephalexin concentration.

METHODS

Genomic DNA of Xenophilus sp. E41 was extracted and sequenced using an Illumina NovaSeq 6000 system. The generated sequence reads were assembled using MEGAHIT in combination with SOAPdenovo. Mauve and CompareM were used to align the Xenophilus sp. E41 genome to other draft genomes of the genus Xenophilus in order to determine their evolutionary relationships. The draft genome was annotated using the Rapid Annotation using Subsystem Technology (RAST) server and the nr database, whilst antimicrobial resistance genes (ARGs) were identified using the SARG 2.0 database, RAST server and nr database.

RESULTS

Xenophilus sp. E41, with a genome length of 5919552bp, harbours seven types of ARGs involving resistance to β-lactams, tetracycline, aminoglycosides, sulfonamides, chloramphenicol, teicoplanin and bleomycin. No virulence factors or plasmids were identified.

CONCLUSION

The genome sequence reported here will provide useful information for a better understanding of antimicrobial resistance profiles in this strain and the genus Xenophilus.

Description of Variovorax humicola sp. nov., isolated from a forest topsoil

Employing a modified cultivation method, we studied two bacterial strains, UC10 and UC38^T, found on the Kyonggi University campus, Suwon in Gyeonggi-Do province, South Korea. These strains were non-spore-forming, Gram-stain-negative, motile and rod-shaped. Growth occurred in the presence of 0-2 % (w/v) NaCl, at pH 4-9 and a temperature range of 4-35 °C. On an R2A agar plate incubated for 5 days at 28 °C, irregular, raised and pale-yellowish colonies were observed. Comparative analysis of nearly full-length 16S rRNA gene sequences indicated that these strains were closely related to Variovorax guangxiensis GXGD002^T, with 98.6 % similarity. Strains UC10 and UC38^T were 98.0 % similar to V.ariovorax soli GH9-3^T; 97.8 % to V.ariovorax dokdonensis DS-43^T; 97.3-97.7 % to V.ariovorax ginsengisoli Gsoil 3165^T; 97.7-98.0 % to V.ariovorax paradoxus IAM 12373^T; 97.4-97.6 % to V.ariovorax defluvii 2C1-b^T; and 97.3-97.4 % to V.ariovorax boronicumulans BAM-48^T. The predominant ubiquinone was Q-8. The primary polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major fatty acids were C16 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C17 : 0 cyclo. DNA-DNA hybridization assays indicated 89.2-91.4 % genomic DNA similarity between strains UC10 and UC38^T. Moreover, genomic DNA similarity between these novel strains and reference strains of the genus Variovoraxwas less than the 70 %. Based on these results, strain UC38^T was designated a representative of a novel species of the genus Variovorax, with the proposed name Variovorax humicola sp. nov. The type strain is UC38^T (=KACC 18501^T=NBRC 111520^T).

Corticibacter populi gen. nov., sp. nov., a new member of the family Comamonadaceae, from the bark of Populus euramericana

Three novel endophytic strains, designated 17B10-2-12T, 26C10-4-4 and D13-10-4-9, were isolated from the bark of Populus euramericana in Heze, Shandong Province, China. They were Gram-reaction-negative, aerobic, non-motile, short-rod-shaped, oxidase-positive and catalase-negative. A phylogenetic analysis of the 16S rRNA gene showed that the three novel strains clustered with members of the family Comamonadaceae and formed a distinct branch. The isolates shared 100 % similarities among themselves and had the highest sequence similarity with Xenophilus azovorans DSM 13620T (95.2 %) and Xenophilus arseniciresistens YW8T (95.0 %), and less than 95.0 % sequence similarities with members of other species. Their major fatty acids were C16 : 0, C17 : 0 cyclo, C18 : 1ω7c and C16 : 1ω7c/C16 : 1ω6c. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and three unknown aminophospholipids. The predominant quinone was ubiquinone-8 (Q-8). The DNA G+C content was 69.5–70.0 mol%. Based on data from a polyphasic taxonomy study, the three strains represent a novel species of a novel genus of the family Comamonadaceae, for which the name Corticibacter populi gen. nov., sp. nov. is proposed. The type strain is 17B10-2-12T ( = CFCC 12099T = KCTC 42091T).