Povalibacter uvarum gen. nov., sp. nov., a polyvinyl-alcohol-degrading bacterium isolated from grapes

Describing five new strains in the family Woeseiaceae and emended description of the order Woeseiales with genomic features related to environmental adaptation

The family Woeseiaceae, also known as the JTB255 bacterial group, are ubiquitous and abundant core members of microbial communities in marine surface sediments. However, to date, only one Woeseiaceae strain isolated from marine sediments has been described, and the phylogeny and environmental adaptation mechanisms of this group have been little explored. Here, we isolated five novel Woeseiaceae strains from the marine solar saltern in Weihai, China. Multiple genomic, physiological, and chemotaxonomic characteristics supported that these five isolates represent three novel species within a novel genus, for which Lentisalinibacter gen. nov. and three species Lentisalinibacter sediminis sp. nov., Lentisalinibacter salinarum sp. nov. and Lentisalinibacter orientalis sp. nov. are proposed. Moreover, phylogenetic analysis based on the 16S rRNA genes and genome sequences revealed that Woeseiaceae is most closely related to Steroidobacterales. Further comparative genomics analysis indicated the separate evolution of Woeseiaceae and Steroidobacterales, supporting the emended description of the order Woeseiales. Woeseiales representitives showed facultatively anaerobic characteristics and small genome sizes in contrast to their phylogenetic relatives. They primarily inhabit surface marine sediment environments using multiple metabolic and ecological strategies to adapt to the changing microenvironments. Our results demonstrate the novel representatives of Woeseiales and their environmental adaptation mechanisms in marine environments.

Performance and mechanism of pilot-scale carbon fibers enhanced ecological floating beds for urban tail water treatment in optimized ecological floating beds water surface coverage

A pilot-scale carbon fibers enhanced ecological floating beds (CF-EFBs) was constructed. Compared to EFBs without carbon fibers enhancement, CF-EFBs have the better removal of total inorganic nitrogen (TIN), total phosphorus (TP), and chemical oxygen demand (COD), the removal efficiencies were 3.19, 3.49, and 2.74 times higher than EFBs. Throughout the pilot test (under three different coverage rates), the concentrations of COD, TIN and TP of effluent were 18.11 ± 4.52 mgL-1, 1.95 ± 0.92 mgL-1 and 0.13 ± 0.08 mgL-1. Meanwhile, the average removal of TIN, TP and COD from tailwater was 0.96 gm-2d-1, 0.07 gm-2d-1 and 2.37 gm-2d-1 respectively. When the coverage was 30 %, the CF-EFBs had better nitrogen removal effectiveness (TIN purification ability of 1.49 gm-2d-1). The enrichment of denitrifying bacteria, such as Aridibacter, Nitrospira, Povalibacter, and Phaeodactylibacter increased denitrification efficiency. These results verified the feasibility of CF-EFBs in tailwater treatment at pilot-scale, which was of great significance for the practical application of CF-EFBs.

Diversity of bacterial community in the rhizosphere and bulk soil of Artemisia annua grown in highlands of Uganda

High land areas in Uganda are suitable for the farming of Artemisia annua. However, harvested A. annua from these areas contain varying concentrations of antimalarial components. This may be attributed to variation in soil properties which affect vegetative growth characters, yield and active compounds of A. annua. Thus, bacterial composition and physiochemical properties of soil from Kabale and Kabarole high land areas where A. annua is grown were studied. The study objective was to determine the diversity of bacterial community in the rhizosphere and bulk soil of A. annua grown in highlands of Uganda. Composition of bacterial community was analyzed by amplicon sequencing of 16S rRNA genes on an Illumina Miseq platform. A total of 1,420,688 read counts was obtained and clustered into 163,493 Operational Taxonomic Units ((OTU). Kabarole highland had more OTUs (87,229) than Kabale (76,264). The phylum Proteobacteria (34.2%) was the most prevalent followed by Acidobacteria (17.3%) and Actinobacteria (15.5%). The bacteria community in the two highlands significantly differed (p <0.05) among all phyla except Proteobacteria. The main genera in bulk soil were povalibacter, brevitalea, nocardioides, stenotrophobacter, gaiella and solirubrobacter. Sphingomonas, ramlibacter paludibaculum and pseudarthrobacter were the main genera in A. annua rhizospheric soil.

The effect of a polystyrene nanoplastic on the intestinal microbes and oxidative stress defense of the freshwater crayfish, Procambarus clarkii

The widespread generation and accumulation of plastic waste has become a globally recognized problem. However, there are limited reports on the adverse effects of nanomaterials on freshwater crustaceans. This study tested the acute effects of different concentrations (0, 5, 10, and 20 mg/L) after 48 h exposure of 75 nm polystyrene nanoplastic on intestinal microbes, and oxidative stress parameters of freshwater crayfish, Procambarus clarkii. High-throughput sequencing analysis revealed the richness, diversity, and composition of intestinal microbiota in P. clarkii exposed to polystyrene nanoplastic. At the genus level, abundances of Lactobacillus, Faecalibaculum, Niveibacterium, and Candidatus Bacilloplasma were significantly different. The reduced abundance of Lactobacillus could affect the balance of intestinal microbes through quantitative disadvantage, which may lead to reduced immunity of P. clarkii. Streptococcus salivarius, Clostridium butyricum and Lachnospiraceae bacterium10-1 in intestinal tract reached maximum abundance at a polystyrene concentration of 20 mg/L. The increase in the number of some pathogenic bacteria may upset the balance of intestinal microorganisms through the number of dominance, and the decrease in the relative abundance of lactic acid bacteria. Probiotics, such as Lactobacillus salivarius, Lactobacillus murinus, Lactobacillus gasseri, Lactobacillus reuteri, Lactobacillus iners AB-1, and Lactobacillus crispatus in the intestinal tract reached the lowest value at a concentration of 10 mg/L. The reduced abundance of Lactobacillus can affect the balance of intestinal microbes through quantitative disadvantage, which may lead to reduced immunity in P. clarkii. At nanoplastic 10 mg/L, the relative abundance of intestinal pathogens increased, while the relative abundance of lactic acid bacteria and other probiotics decreased. With increases in nanoplastic concentrations, the values of glutathione (GSH), superoxide dismutase (SOD), acid phosphatase (ACP), lysozyme (LZM), alkaline phosphatase (AKP), peroxidase (POD), glutathione peroxidase (GPX), and protein carbonylation were significantly changed. Our data suggested that Lactobacillus may play an adjunctive role in the treatment of oxidative stress in P. clarkii exposed to 75 nm polystyrene. This study represents an important step towards a better understanding of the toxic effects of nanoplastics on aquatic crustaceans.

Discovery of lignin-transforming bacteria and enzymes in thermophilic environments using stable isotope probing

Characterizing microorganisms and enzymes involved in lignin biodegradation in thermal ecosystems can identify thermostable biocatalysts. We integrated stable isotope probing (SIP), genome-resolved metagenomics, and enzyme characterization to investigate the degradation of high-molecular weight, ¹³C-ring-labeled synthetic lignin by microbial communities from moderately thermophilic hot spring sediment (52 °C) and a woody "hog fuel" pile (53 and 62 °C zones). ¹³C-Lignin degradation was monitored using IR-GCMS of ¹³CO₂, and isotopic enrichment of DNA was measured with UHLPC-MS/MS. Assembly of 42 metagenomic libraries (72 Gb) yielded 344 contig bins, from which 125 draft genomes were produced. Fourteen genomes were significantly enriched with ¹³C from lignin, including genomes of Actinomycetes (Thermoleophilaceae, Solirubrobacteraceae, Rubrobacter sp.), Firmicutes (Kyrpidia sp., Alicyclobacillus sp.) and Gammaproteobacteria (Steroidobacteraceae). We employed multiple approaches to screen genomes for genes encoding putative ligninases and pathways for aromatic compound degradation. Our analysis identified several novel laccase-like multi-copper oxidase (LMCO) genes in ¹³C-enriched genomes. One of these LMCOs was heterologously expressed and shown to oxidize lignin model compounds and minimally transformed lignin. This study elucidated bacterial lignin depolymerization and mineralization in thermal ecosystems, establishing new possibilities for the efficient valorization of lignin at elevated temperature.

Spatially Targeted Biological Control of Mile-a-Minute Weed Using Rhinoncomimus latipes (Coleoptera: Curculionidae) and an Unmanned Aircraft System

Rhinoncomimus latipes Korotyaev is a specialist biocontrol agent of mile-a-minute weed, Persicaria perfoliata (L.) H. Gross (Caryophyllales: Polygonaceae). Currently, R. latipes is released by hand where the presence of the weed is readily detected. However, the hand-release method is not applicable to weed patches spread in hard-to-access areas. This study was conducted to develop a spatially targeted biocontrol strategy by using an unmanned aircraft system (UAS, a.k.a. drone) for the detection of P. perfoliata and aerial release of R. latipes. A ground survey was performed to locate P. perfoliata patches and then a rotary-wing UAS was flown at 15 different altitudes to determine the detectability of P. perfoliata patches. We developed an insect-release system including a pod that housed R. latipes for aerial release. The pod was 3D printed with biodegradable polyvinyl alcohol (PVA), and field tests were conducted to determine the ability of R. latipes to escape the pod and assess their post-release mortality and feeding ability. The results of this study showed that P. perfoliata patches were readily detectable on the aerial images taken at ≤15 m above the ground. More than 98% of R. latipes (n = 118) successfully escaped from the pod within 24 h after aerial deployment. There were no significant (P > 0.05) effects of PVA exposure on the mortality and feeding ability of R. latipes. These results indicate that aerial detection of P. perfoliata and deployment of R. latipes for spatially targeted biological control in hard-to-access areas can be accomplished using a rotary-wing UAS.

Insight into functionally active bacteria in nitrification following Na+ and Mg2+ exposure based on 16S rDNA and 16S rRNA sequencing

Despite increasing interests in osmotic membrane bioreactors, the information regarding the bacterial toxicity effects of reversely transported draw solute (RTDS) is limited. In this study, two representative draw solutes (NaCl and MgCl₂) were used at different concentrations (0, 2.5, 5.0, 7.5 and 10.0 g/L) to evaluate their toxicity in a continuous nitrifying bioreactor. Notably, Mg²⁺ selectively inhibited the activity of ammonia-oxidizing bacteria (AOB), which decreased to 11.3% at 7.5 g-Mg²⁺/L. The rRNA-based analysis was more effective than the rDNA-based analysis to elucidate the relationship between active communities of nitrifying bacteria and the actual nitrifying performance. Nitrosomonas europaea, a representative AOB, was vulnerable to Mg²⁺ in comparison to Na⁺. In contrast, the dominant nitrite-oxidizing bacteria (NOB), Nitrobacter winogradskyi and Nitrolancea hollandica, maintained a relevant level of relative abundance for achieving nitrite oxidation after exposure to 10 g/L Na⁺ and Mg²⁺. This fundamental inhibition information of the draw solute can be applied to set the operational regime preventing the critical solute concentration in mixed liquor of nitrifying OMBRs.

Characterization and Distribution of Agar-degrading Steroidobacter agaridevorans sp. nov., Isolated from Rhizosphere Soils

The environment of plant rhizosphere soil differs from that of non-rhizosphere soil due to the secretion of mucilage polysaccharides from the roots. This environment is regarded as one of the preferential habitats for agar-degrading bacteria. In a previous study, agar-degrading Steroidobacter agariperforans KA5-BT was isolated from agar-enriched agricultural soil using diffusible metabolites from Rhizobiales bacteria. Based on the hypothesis that similar characteristic bacteria still exist in the rhizosphere, isolation was performed using rhizosphere soils. Agar-degrading SA29-BT and YU21-B were isolated from onion and soybean rhizosphere soils. The 16S rRNA genes of these strains showed ≥98.7% identities with the most closely related strain KA5-BT. However, differences were noted in polysaccharide utilization, and average nucleotide identities were <95-96% against strain KA5-BT, indicating that they are different species from S. agariperforans KA5-BT. To investigate the distribution of bacterial sequences affiliated with novel strains, a primer set was designed and a meta-analysis of the 16S rRNA gene was performed. Sequences were widely distributed in rhizospheres throughout Japan, but varied in plant- and region-dependent manners. Regarding phenotypic characterization, distinguishable features were observed in growth temperatures, pH, and dominant fatty acids. SA29-BT and YU21-B grew at 15-40°C and pH 6.0-12 and contained C16:0 as the dominant cell fatty acid, whereas KA5-BT showed no growth at 40°C and pH 12 and contained a moderate amount of C16:0. Based on these characteristics, SA29-BT (JCM 333368T=KCTC 72223T) and YU21-B (JCM 333367=KCTC 72222) represent novel species in the genus Steroidobacter, for which the name Steroidobacter agaridevorans sp. nov. is proposed.

Treatment of low-strength ammonia wastewater by single-stage partial nitritation and anammox using upflow dual-bed gel-carrier reactor (UDGR)

This study investigated the single-stage partial nitritation and anammox (S-PNA) treatment of low-strength ammonia wastewater (≤140 mg NH₄⁺-N/L). Upflow dual-bed gel-carrier reactor (UDGR) with polyvinyl alcohol cryogel biocarriers, developed in this study, was employed for the anammox biomass enrichment from conventional activated sludge and subsequent S-PNA experiments. Anammox biomass was successfully enriched from conventional activated sludge. The enriched anammox carriers were inoculated together with gel carriers containing nitrifying sludge into the S-PNA reactors. S-PNA activity developed rapidly, and the nitrogen removal efficiency and rate reached up to 90.1% (with complete ammonia removal) and 0.15 kg N/m³⋅d, respectively, under low nitrogen loading conditions (0.10-0.17 kg N/m³⋅d). The microbial community structure changed significantly while adapting to anammox and S-PNA conditions. Anammox was likely driven solely by a Candidatus Jettenia population accounting for ≤49.4% of bacterial 16S rRNA genes. The results demonstrate that the UDGR-based S-PNA is suitable for treating low-strength wastewater.

New insights of enhanced anaerobic degradation of refractory pollutants in coking wastewater: Role of zero-valent iron in metagenomic functions

Coking wastewater (CWW) has long been a serious challenge for anaerobic treatment due to its high concentrations of phenolics and nitrogen-containing heterocyclic compounds (NHCs). Herein, we proposed and validated a new strategy of using zero-valent iron (ZVI) to strengthen the anaerobic treatment of CWW. Results showed that COD removal efficiencies was increased by 9.5-13.7% with the assistance of ZVI. GC-MS analysis indicated that the removal of phenolics and NHCs was improved, and the intermediate 2(1H)-Quinolinone of quinoline degradation was further removed by ZVI addition. High-throughput sequencing showed that phenolics and NHCs degraders, such as Levilinea and Sedimentibacter were significantly enriched, and the predicted gene abundance of xenobiotic degradation and its downstream metabolic pathways was also increased by ZVI. Network and redundancy analysis indicated that the decreased oxidation-reduction potential (ORP) by ZVI was the main driver for microbial community succession. This study provided an alternative strategy for strengthening CWW anaerobic treatment.

The role of a newly isolated strain Corynebacterium pollutisoli SPH6 in waste activated sludge alkaline fermentation

Alkaline fermentation has been considered as one of the efficient methods for waste activated sludge (WAS) treatment, but usually limited by microbial fermentation activities under extreme pH condition. One newly isolated alkali-tolerant strain Corynebacterium pollutisoli SPH6 was used to assess its potential role and effect on WAS alkaline fermentation process. Results from response surface method showed that the optimal organic nitrogen degradation rate by SPH6 was obtained under temperature of 35 °C, initial pH of 10, shaking speed of 80 rpm, inoculation ratio of 6.5%. Batch-scale experiments demonstrated that, compared with the control group, the inoculation of SPH6 finally achieved higher productions with 13.4% of carbohydrates, 27.1% of protein and 25.4% of total volatile fatty acids (VFAs), and more predominant functional bacteria characterized by high-throughput sequencing, such as genera Acinetobacter in phylum Proteobacteria, Tissierella and Acetoanaerobium in phylum Firmicutes. The strain SPH6 might play a vital role in maintaining and facilitating the growth and diversity of functional bacteria in WAS alkaline fermentation process. It has implied promising practical application of the present strain in enhancing WAS reduction and utilization.

Diversity and metabolism of Woeseiales bacteria, global members of marine sediment communities

Surveys of 16S rRNA gene sequences derived from marine sediments have indicated that a widely distributed group of Gammaproteobacteria, named “JTB255-Marine Benthic Group” (now the candidate order Woeseiales), accounts for 1–22% of the retrieved sequences. Despite their ubiquity in seafloor communities, little is known about their distribution and specific ecological niches in the deep sea, which constitutes the largest biome globally. Here, we characterized the phylogeny, environmental distribution patterns, abundance, and metabolic potential of Woeseiales bacteria with a focus on representatives from the deep sea. From a phylogenetic analysis of publicly available 16S rRNA gene sequences (≥1400 bp, n = 994), we identified lineages of Woeseiales with greater prevalence in the deep sea than in coastal environments, a pattern corroborated by the distribution of 16S oligotypes recovered from 28 globally distributed sediment samples. Cell counts revealed that Woeseiales bacteria accounted for 5 ± 2% of all microbial cells in deep-sea surface sediments at 23 globally distributed sites. Comparative analyses of a genome, metagenome bins, and single-cell genomes suggested that members of the corresponding clades are likely to grow on proteinaceous matter, potentially derived from detrital cell membranes, cell walls, and other organic remnants in marine sediments.

Steroidobacter soli sp. nov., isolated from farmland soil

A Gram-stain-negative bacterial strain, designated JW-3^T, was isolated from a soil sample collected from farmland in Yantai, Shandong Province, PR China. Cells of strain JW-3^T are motile rods and strictly aerobic, showing catalase- and oxidase-positive reactions. Strain JW-3^T could grow at 16-37 °C (optimum, 30 °C), at pH 6.0-9.0 (pH 7.0) and in the presence of 0-1 % (w/v) NaCl (0.5 %, in Luria-Bertani broth). The major fatty acids were summed feature 3 (C_16 : 1 ω7c and/or C_16 : 1 ω6c; 35.5 %), iso-C_16 : 0 (16.7 %) and C_12 : 0 (10.8 %). The major respiratory quinone was ubiquinone-8 (Q8). The polar lipids of strain JW-3^T consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, four unidentified phospholipids, two unidentified lipids, two unidentified glycolipids and a partial unidentified aminophospholipid. Strain JW-3^T was most closely related to Steroidobacter agariperforans KA5-B^T with 97.67 % 16S rRNA gene sequence similarity. Results of phylogenetic analyses, based on 16S rRNA gene sequencing, showed that strain JW-3^T forms a distinct phylogenic lineage within the genus Steroidobacter of the family Sinobacteraceae. The DNA G+C content of strain JW-3^T was 62.57 mol%, based on its draft genome sequence. Average nucleotide identity values and digital DNA-DNA hybridization values for draft genomes, between strain JW-3^T and strain KA5-B^T, were 84.54 and 30.80 %, respectively. Based on its phenotypic, chemotaxonomic and molecular features, and DNA-DNA hybridization results, strain JW-3^T represents a novel species of the genus Steroidobacter, for which the name Steroidobactersoli sp. nov. is proposed. The type strain is JW-3^T (=CCTCC AB 2018184^T=KCTC 62820^T).

Polyvinyl alcohol degradation by Bacillus cereus RA23 from oil sludge sample

A novel polyvinyl alcohol (PVA)-degrading strain Bacillus cereus RA23 was isolated from an oil sludge sample and environmental factors affecting its PVA degradation efficiency were optimized in detail. Inorganic nitrogen source, ammonium chloride (NH4Cl), was found to be the best nitrogen source and enhanced the PVA degradation rate greatly. The optimal medium for PVA biodegradation consisted of (g/L) PVA 1, NH4Cl 1, K2HPO4 1.6, MgSO4·7H2O 0.05, FeSO4·6H2O 0.02, CaCl2 0.05, NaCl 0.02. The optimal temperature and pH for PVA biodegradation by strain RA23 was 28 °C and 7.0, respectively, and 85% of 0.1% PVA was degraded after 5 days under these conditions. FTIR studies showed that the carboxylic acids (possibly including aldehyde or ketone) could be the intermediate product of PVA biodegradation. The investigation of strain RA23 for PVA degradation will provide important information to facilitate the removal of wastewater pollution in industrial zones.

Stenotrophobium rhamnosiphilum gen. nov., sp. nov., isolated from a glacier, proposal of Steroidobacteraceae fam. nov. in Nevskiales and emended description of the family Nevskiaceae

A Gram-stain-negative strain, designated GT1R17^T, was isolated from an ervoconite sample collected from Gawalong glacier in the Tibet Autonomous Region, PR China. Strain GT1R17^T was catalase- and oxidase-positive, and grew optimally at 20-25°C and pH 7.0. The highest level of 16S rRNA gene sequence similarities were found to members of the genera Nevskia(92.27-93.15 %) and Hydrocarboniphaga(91.92-92.96 %). Phylogenetic analyses based on 16S rRNA gene sequences and genomic data revealed that the strain GT1R17^T belonged to the family Nevskiaceae, but could not be assigned to any known genera. The genomic DNA G+C content was 54.4 mol%. The major fatty acids were summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), summed feature 8 (C18 : 1 ω7c and/or C18 : 1ω6c), C16 : 0, iso-C16 : 0 and summed feature 2 (C14 : 0 3OH and/or iso-C16 : 1 I). The polar lipids were phosphatidylglycerol, phosphatidylethanolamine and one unidentified lipid. The ubiquinone was Q-8. On the basis of the phenotypic, chemotaxonomic, genotypic and phylogenetic data, a novel species of a new genus,Stenotrophobiumrhamnosiphilum gen. nov., sp. nov. within the family Nevskiaceae, is proposed, with GT1R17^T (=CGMCC 1.16137^T=NBRC 113346^T) as the type strain. In addition, phylogenetic analyses revealed that Steroidobacter and Povalibacter formed an independent clade in the order Nevskiales and were away from the families Nevskiaceae, Algiphilaceae and Salinisphaeraceae. Therefore, we propose to remove Steroidobacter and Povalibacter from the family Nevskiaceae and propose a new family Steroidobacteraceae in the order Nevskiales.

Molecular characterization of long-term impacts of macrophytes harvest management in constructed wetlands

There is little understanding of constructed wetlands (CWs) microbial community patterns in response to harvest management. Therefore, long-term impacts of harvesting Phragmites australis (Cav.) Trin. ex Steudel annually in November on the activity and community structure of microorganisms critical to the treatment efficiency of CW are elucidated. Findings show exponential increases in P. australis density and biomass with continuous harvesting, up to three times over unharvested CW. High-throughput pyrosequencing analysis demonstrates that plants harvesting improves the microbial community diversity and richness significantly, and more particularly, the relative abundance of Flavobacterium, Paenisporosarcina, and Povalibacter, which are extensively associated with CW performance. Consequently, increased plants biomass resulted in enhanced plants nutrients uptake in harvested (56.5 g N/m², 5.5 g P/m²) than unharvested CWs (17.5 g N/m², 1.8 g P/m²), whereas improved rhizosphere microclimates significantly enhanced nutrients removals in harvested CW (TN 109.9 g/m² vs 67.4 g/m², TP 18.0 g/m² vs 13.0 g/m²).

Characterization of odor emissions and microbial community structure during degradation of pig carcasses using the soil burial-composting method

A soil burial-composting method was proposed as a hybrid disposal method for infected carcasses. This is a modified soil burial technique that involves covering carcasses with compost to achieve a final compost bed of 1.0-1.2 m during the soil burial process. To evaluate the feasibility and applicability of the soil burial-composting method, a pilot-scale system was constructed to dispose of pig carcasses and monitored its performance for 346 days. Temperature around the pig carcasses in the compost bed increased gradually, and was in the range of 35-45 °C after 200 days. Mesophilic (Sporosarcina and Steroidobacter) and thermophilic (Truepera) bacteria were dominant in the compost bed. Based on odor gas profiling and the morphological properties of the carcasses excavated after 346 days, it was estimated that an advanced decay stage was reached after 243 days. Considering the results of previous studies, the carcass degradation rate achieved by soil burial-composting was faster than that of soil burial, but slower than that of the composting method. Sum of odor quotient (SOQ) in the upper soil bed was lower than the SOQ in the compost bed where the carcasses were buried. This result demonstrated that the upper soil bed functioned as a biofilter to mitigate odor gases emitted during degradation of the carcasses. The soil burial-composting disposal method is preferred over soil burial because the degradation of carcasses is faster, and over composting because odor complaints and compost usage can be minimized.

Ahniella affigens gen. nov., sp. nov., a gammaproteobacterium isolated from sandy soil near a stream

A bacterial strain, designated D13^T, was isolated from sandy soil near a stream in Sinan-gun, Republic of Korea. Cells were Gram-stain-negative, aerobic, non-motile and flexible rod-shaped. Growth occurred at 15-35 °C (optimum 30 °C) and pH 6.5-8.0 (pH 7.0). NaCl was not obligatory for growth but could be tolerated at up to 0.5 % (w/v) NaCl. The DNA G+C content of the genomic DNA of strain D13^T was 57.7 mol% and a phylogenetic analysis of the 16S rRNA gene sequence revealed that strain D13^T formed a distinct evolutionary lineage within the family Rhodanobacteraceae of the order Lysobacterales. Strain D13^T showed highest 16S rRNA sequence similarity to Lysobacter hankyongensis KTCe-2^T (92.7 %), followed by Luteimonas cucumeris Y4^T (92.7 %), Dyella japonica XD53^T (92.6 %) and Aquimonas voraii GPTSA 20^T (92.5 %). The major cellular fatty acids (>10 % of the total) were iso-C16 : 0, iso-C15 : 0 and summed feature 9 (iso-C17 : 1ω9с and/or C16 : 0 10-methyl). The respiratory quinone was ubiquinone-8 and the major polar lipids of the isolate consisted of phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylmonomethylethanolamine. Based on polyphasic analysis, strain D13^T could be differentiated from other genera in the family Rhodanobacteraceae, which suggests that strain D13^T represents a novel species of a new genus in the family Rhodanobacteraceae, for which the name Ahniella affigens gen. nov., sp. nov. is proposed. The type strain is D13^T (=KACC 19270^T=JCM 31634^T).

Text mining tools for extracting information about microbial biodiversity in food

Information on food microbial diversity is scattered across millions of scientific papers. Researchers need tools to assist their bibliographic search in such large collections. Text mining and knowledge engineering methods are useful to automatically and efficiently find relevant information in Life Science. This work describes how the Alvis text mining platform has been applied to a large collection of PubMed abstracts of scientific papers in the food microbiology domain. The information targeted by our work is microorganisms, their habitats and phenotypes. Two knowledge resources, the NCBI taxonomy and the OntoBiotope ontology were used to detect this information in texts. The result of the text mining process was indexed and is presented through the AlvisIR Food on-line semantic search engine. In this paper, we also show through two illustrative examples the great potential of this new tool to assist in studies on ecological diversity and the origin of microbial presence in food.

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We present new text-mining tools to extract information in food microbiology.

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The results of the extraction are available in an on-line semantic search engine.

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Taxa, habitats, phenotypes and links between them can be queried in PubMed abstracts.

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Text-mining tools could assist to browse past and recent scientific literature.

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Two use-cases are presented: fruit microbiota and spore-forming bacteria in food.

Enhanced nitrogen removal from piggery wastewater with high NH4+ and low COD/TN ratio in a novel upflow microaerobic biofilm reactor

To enhance nutrient removal more cost-efficiently in microaerobic process treating piggery wastewater characterized by high ammonium (NH₄⁺-N) and low chemical oxygen demand (COD) to total nitrogen (TN) ratio, a novel upflow microaerobic biofilm reactor (UMBR) was constructed and the efficiency in nutrient removal was evaluated with various influent COD/TN ratios and reflux ratios. The results showed that the biofilm on the carriers had increased the biomass in the UMBR and enhanced the enrichment of slow-growth-rate bacteria such as nitrifiers, denitrifiers and anammox bacteria. The packed bed allowed the microaerobic biofilm process perform well at a low reflux ratio of 35 with a NH₄⁺-N and TN removal as high as 93.1% and 89.9%, respectively. Compared with the previously developed upflow microaerobic sludge reactor, the UMBR had not changed the dominant anammox approach to nitrogen removal, but was more cost-efficiently in treating organic wastewater with high NH₄⁺-N and low COD/TN ratio.

Novel bacteria capable of degrading phenanthrene in activated sludge revealed by stable-isotope probing coupled with high-throughput sequencing

The indigenous microorganisms responsible for degrading phenanthrene (PHE) in activated biosludge were identified using DNA-based stable isotope probing. Besides the well-known PHE degraders Burkholderia, Ralstonia, Sinobacteraceae and Arthrobacter, we for the first time linked the taxa Paraburkholderia and Kaistobacter with in situ PHE biodegradation. Analysis of PAH-RHD_α gene detected in the heavy DNA fraction of ¹³C-PHE treatment suggested the mechanisms of horizontal gene transfer or inter-species hybridisation in PAH-RHD gene spread within the microbial community. Additionally, three cultivable PHE degraders, Microbacterium sp. PHE-1, Rhodanobacter sp. PHE-2 and Rhodococcus sp. PHE-3, were isolated from the same activated biosludge. Among them, Rhodanobacter sp. PHE-2 is the first identified strain in its genus with PHE-degrading ability. However, the involvement of these strains in PHE degradation in situ was questionable, due to their limited enrichment in the heavy DNA fraction of ¹³C-PHE treatment and lack of PAH-RHD_α gene found in these isolates. Collectively, our findings provide a deeper understanding of the diversity and functions of indigenous microbes in PHE degradation.

Poly(vinyl alcohol): review of its promising applications and insights into biodegradation

Poly(vinyl alcohol) is a promising class of synthetic polymer biodegradable under a two-step metabolism consisting of an oxidation and hydrolysis.