Antonie van Leeuwenhoek

Mesorhizobium carboni s sp. nov., isolated from coal bed water Abstract A Gram-stain negative, aerobic, motile, short rod-shaped bacterium, designated as B2.3T, was isolated from coal bed water collected from Jincheng, Shanxi Province, China. The strain was able to grow at 10–40 °C (optimum 28–30 °C), pH 4.0–10.0 (optimum 7.0), and in the presence of 0–5.0% NaCl (optimum 3.0%, w/v). Phylogenetic analysis based on the 16S rRNA and concatenated housekeeping gene recA, atpD and glnA sequences showed strain B2.3Tbelongs to the genus Mesorhizobium, with Mesorhizobium oceanicum B7T as the closely related type strain. Strain B2.3T exhibited ANI value of 77.5% and GGDC value of 21.5% to M. oceanicum B7T. The major fatty acids were identified as summed feature 8 (C18:1ω7c and/or C18:1ω6c) and 11-methyl C18:1ω7c. The major polar lipids were found to consist of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and an unidentified aminophospholipid. The predominant ubiquinone was identified as Quinone 10. Phenotypic and biochemical analysis results indicated that strain B2.3T can be distinguished from closely related type strains. On the basis of phenotypic, genotypic and chemotaxonomic characteristics, strain B2.3T is concluded to represent a novel species in the genus Mesorhizobium, for which the name Mesorhizobium carbonis sp. nov. is proposed. The type strain is B2.3T (=CGMCC 1.15730T = KCTC 52461T).

Antibiotic susceptibility of marine Planctomycetes Abstract Antimicrobials are naturally produced by microbes and therefore have always been present in their environment, as well as accompanying resistance mechanisms. The antibiotic resistance profile of environmental species is particularly relevant since genetic determinants of resistance can spread through horizontal gene transfer and reach clinically important species. The phylum Planctomycetes comprises Gram-negative bacteria characterised by unusual features and appear to be ubiquitously distributed. Members of this group have recently been characterised as producers of bioactive compounds, namely antimicrobials, but their antibiotic susceptibility profile has been scarcely studied. In this study, the antibiotic susceptibility profile of six phylogenetically distinct strains of Planctomycetes was assessed. All strains showed resistance to beta-lactams, aminoglycosides and glycopeptides. Our results showed that antibiotics which target protein synthesis or DNA replication, with the exception of aminoglycosides, were the most effective against the tested strains. The highest efficacy was observed for chloramphenicol, clindamycin and ciprofloxacin. The highest level of antimicrobial resistance was observed in the uncharacterised novel taxon Planctomyces sp. strain FF15 which was only susceptible to erythromycin and ciprofloxacin.

Population structure and genetic diversity of Vibrio parahaemolyticus from a coastal area of China based on a multi-locus sequence typing (MLST) scheme Abstract The Gram-negative marine bacterium Vibrio parahaemolyticus has been identified as a major cause of bacterial food poisoning in China. Here, the population structure and genetic diversity of V. parahaemolyticus from Weihai, a coastal city in China, was studied by the multi-locus sequence typing (MLST) method. In this survey, we isolated 40 strains including environmental and clinical samples of patients with acute gastroenteritis or diarrhea; isolates from other countries were also included for comparison. DnaSP Version5, START V2, eBURST version3 and Mega 6 were used to analyse the data. We found that ST3 and ST332 were the most prevalent clones and that they were closely associated with acute diarrhoeal diseases. These STs showed a low dN/dS ratio and significant linkage disequilibrium. All isolates were divided into four clonal complexes, six groups and nine singletons, showing a high degree of genetic diversity. 18 STs, mostly from environmental isolates, were recognised by the MLST analysis for the first time. In conclusion, ST3 and ST332 were the epidemic STs in the coastal area. ST332 might be a region-specific ST, which needs to be confirmed by further analysis. Thus, the long-term monitoring of V. parahaemolyticus plays an important role in preventing and controlling the transmission between environment and people in Weihai.

Bacterial community pattern along the sediment seafloor of the Arctic fjorden (Kongsfjorden, Svalbard) Abstract The Arctic region has been the focus of increasing attention as an ecosystem that is highly sensitive to changes associated with global warming. Although it was assumed to be vulnerable to changes in climate, a limited number of studies have been conducted on the surface sediment bacteria of Arctic fjorden. This study assessed the diversity and distribution pattern of bacterial communities in eight marine sediments along the seafloor in a high Arctic fjorden (Kongsfjorden, Svalbard). A total of 822 operational taxonomic units (OTUs) were identified by Illumina MiSeq sequencing, targeting the V3–V4 hypervariable regions of the 16S rRNA gene. In these surface marine sediments, more than half of the sequences belonged to the phylum Proteobacteria, followed by Bacteroidetes, Verrucomicrobia, Actinobacteria, Chloroflexi and Lentisphaerae. The bacterial genera Marinicella, Desulfobulbus, Lutimonas, Sulfurovumand clade SEEP-SRB4 were dominant in all samples. Analysis of similarity indicated that bacterial communities were significantly different among the inner, central and outer basins (r2 = 0.5, P = 0.03 < 0.05). Canonical correspondence analysis and permutation tests revealed that location depth (r2 = 0.87, P < 0.01), temperature (r2 = 0.88, P < 0.01) and salinity (r2 = 0.88, P < 0.05) were the most significant factors that correlated with the bacterial communities in the sediments. 28 differentially abundant taxonomic clades in the inner and outer basin with an LDA score higher than 2.0 were found by the LEfSe method. The Spearman correlation heat map revealed different degrees of correlation between most major OTUs and environmental factors, while some clades have an inverse correlation with environmental factors. The spatial patterns of bacterial communities along the Kongsfjorden may offer insight into the ecological responses of prokaryotes to climate change in the Arctic ecosystem, which makes it necessary to continue with monitoring.

Runella soli sp. nov., isolated from garden soil Abstract A Gram-stain negative, aerobic, salmon-pink, non-motile and rod-shaped bacterium, designated strain 15J11-1T, was isolated from a soil sample collected from the university garden in Nowongu, South Korea. The 16S rRNA gene sequence analysis showed that strain 15J11-1T is phylogenetically related to Runella slithyformis DSM 19594T and Runella palustris HMF3829T (96.9% and 95.4% sequence similarity, respectively). The major fatty acids of strain 15J11-1T were identified as iso-C15:0, iso-C17:0 3-OH, C16:1ω5c and summed feature 3 (C16:1ω7c and/or C16:1ω6c). The predominant respiratory quinone was identified as MK-7. The polar lipids were found to comprise of phosphatidylethanolamine, three unidentified aminolipids, five unidentified glycolipids, two unidentified aminoglycolipids, an unidentified phospholipid and an unidentified polar lipid. The G + C content in the genomic DNA of the strain 15J11-1T was determined to be 49.9 mol%. Based on the results of genotypic, phenotypic and chemotaxonomic analyses, strain 15J11-1T is concluded to represent a novel species of the genus Runella, for which the name Runella soli sp. nov. (type strain 15J11-1T = KCTC 52021T = NBRC 112817T) is proposed.

Lysinibacillus capsici sp. nov, isolated from the rhizosphere of a pepper plant Abstract A strain of a Gram-positive, strictly aerobic, motile, rod-shaped, endospore forming bacterium was originally isolated from rhizospheric soil of a pepper plant when screening and bioprospecting for plant beneficial microorganisms. Phylogenetic analysis of the 16S rRNA gene sequences indicated that this strain, PB300T, is closely related to Lysinibacillus macroides DMS 54T (99.6%) and Lysinibacillus xylanilyticus DSM 23493T (99.4%). In phenotypic characterisation, the novel strain was found to grow between 15 and 40 °C and tolerate up to 10% (w/v) NaCl. Furthermore, the strain was found to grow in media with pH 5 to 10 (optimal growth at pH 7.0). The predominant cellular fatty acids were observed to be iso-C15 : 0 (56.6 %), anteiso-C15 : 0 (14.6%), C16 :1ω7C alcohol (9.3%) and C16 : 0 (7.1%). The cell wall peptidoglycan contains lysine-aspartic acid, as in its close relatives. A draft genome was completed and the DNA G + C content was determined to be 37.5% (mol content). A phylogenomic analysis of the core genome of the new strain and 5 closely related type strains of the genus Lysinibacillus revealed that this strain formed a distinct monophyletic clade with the nearest neighbour being Lysinibacillus boronitolerans. DNA–DNA relatedness studies using in silico DNA–DNA hybridizations (DDH) showed relationships for the new strain were below the species threshold of 70%. Based upon the consensus of phylogenetic and phenotypic analyses, we conclude that this strain represents a novel species within the genus Lysinibacillus, for which the name Lysinibacillus capsici sp. nov. is proposed, with type strain PB300T (= NRRL B-65515T, = CCUG 72241T).

Sugarcane must fed-batch fermentation by Saccharomyces cerevisiae: impact of sterilized and non-sterilized sugarcane must Abstract The presence of microbial contaminants is common in the sugarcane ethanol industry and can decrease process yield, reduce yeast cell viability and induce yeast cell flocculation. To evaluate the effect of microbial contamination on the fermentation process, we compared the use of sterilized and non-sterilized sugarcane must in the performance of Saccharomyces cerevisiae with similar fermentation conditions to those used in Brazilian mills. Non-sterilized sugarcane must had values of 103 and 108 CFU mL−1 of wild yeast and bacterial contamination, respectively; decreased total reducing sugar (TRS); and increased lactic and acetic acids, glycerol and ethanol concentrations during storage. During fermentation cycles with sterilized and non-sterilized sugarcane must, S. cerevisiae viability did not change, whereas ethanol yield varied from 74.1 to 80.2%, but it did not seem to be related to must microbial contamination. Ethanol productivity decreased throughout the fermentation cycles and was more pronounced in the last two fermentation cycles with non-sterilized must, but that may be related to the decrease in must TRS. High values of the ratio of total acid production per ethanol were reported at the end of the last two fermentation cycles conducted with non-sterilized must. Additionally, the values of wild yeast contamination increased from 102 to 103 CFU mL−1 and bacterial contamination increased from 104 to 106 CFU mL−1 when comparing the first and last fermentation cycles with non-sterilized must. In addition to the increase in microbial contamination and acid concentration, ethanol yield and yeast viability rates were not directly affected by the microbial contamination present in the non-sterilized sugarcane must.

Assessment of Rhodopirellula rubra as a supplementary and nutritional food source to the microcrustacean Daphnia magna Abstract The daily use of the planctomycete Rhodopirellula rubra as an alternative or supplementary food source for Daphnia magna and its feasibility in the nutrition of transgenerational populations were studied. The life history parameters, fatty acids (saturated, mono- and polyunsaturated; SFAs, MUFAs and PUFAs), glycogen and protein contents of organisms during feeding assays and of the first generation were analysed. An increase in the yields of D. magna with the increase of the cell concentration of R. rubra was evident, but overall, bacteria supplied as the only food source was nutritionally insufficient as observed for all the parameters analysed. However, when R. rubra was added as supplement to the microalgae Raphidocelis subcapitata a significant improvement in the life history parameters was observed namely in the reproductive output and the somatic growth rate. The identified SFAs, MUFAs and PUFAs were the fatty acids more abundant in daphniids, and the feed regimens influenced daphniids fatty acid profiles. Additionally, the mixed diet resulted in a larger number and size of offspring in the different F1 broods as also observed with the results of F0 generation. The pink colouration present in D. magna body and eggs confirmed that bacteria were absorbed, the pigment(s) retained and passed on to the next generation. Our results showed that R. rubra can play an essential role in D. magna diet as a nutritional supplement showing potential biotechnological applications.

Microbispora tritici sp. nov., a novel actinomycete isolated from a root of wheat ( Triticum aestivum L.) Abstract A novel actinomycete, designated strain NEAU-HRGS1-13T, was isolated from a root of wheat (Triticum aestivum L.) and characterised using a polyphasic approach. Morphological and chemotaxonomic characteristics were consistent with those of members of the genus Microbispora. The major menaquinones were identified as MK-9(H2) and MK-9(H4) and the whole cell hydrolysates found to contain meso-diaminopimelic acid and madurose. The phospholipid profile was found to consist of diphosphatidylglycerol, a ninhydrin-positive glycophospholipid, phosphatidylinositol mannosides, phosphatidylmonomethylethanolamine, an unidentified glycolipid and an unidentified lipid. The major fatty acids were identified as iso-C16:0, C16:0, 10-methyl C17:0, C18:0 and C17:0. The 16S rRNA gene sequence analysis showed that the isolate is closely related to Microbispora triticiradicis NEAU-HRDPA2-9T (99.4%), Microbispora bryophytorum NEAU-TX2-2T (99.0%), Microbispora camponoti 2C-HV3T (98.8%), Microbispora hainanensis DSM 45428T (98.8%), Microbispora amethystogenes JCM 3021T (98.6%), Microbispora siamensis NBRC 104113T (98.5%), Microbispora corallina JCM 10267T (98.3%) and Microbispora rosea subsp. rosea JCM 3006T (98.2%). However, DNA–DNA relatedness and cultural, physiological and biochemical data showed that strain NEAU-HRGS1-13T can be distinguished from its close relatives. Therefore, it is concluded that strain NEAU-HRGS1-13T represents a novel species of the genus Microbispora, for which the name Microbispora tritici sp. nov. is proposed. The type stain is NEAU-HRGS1-13T (= CGMCC 4.7402T = DSM 104650T).

Pseudoxanthomonas composti sp. nov., isolated from compost Abstract A Gram-staining negative bacterium, designated as GSS15T, was isolated from compost in Guangzhou, China. Cells of strain GSS15T were rod-shaped and non-motile. The isolate was able to grow at 15–42 °C (optimum 30 °C) and pH 6.0–11.0 (optimum pH 8.0), and tolerate up to 6.0% NaCl (w/v). When the 16S rRNA gene sequence of the isolate was compared with those of other bacteria, the highest similarity was observed with Pseudoxanthomonas helianthiroo10T (96.9%). Furthermore, strain GSS15T showed low ANI (75.7–79.5%) and DDH (24.2–18.3%) values to the closely related species. Q-8 was the predominant respiratory quinone. The major cellular fatty acids ( > 5%) were iso-C15:0 (18.7%), C16:1ω7c (18.6%), anteiso-C15:0 (13.2%), C16:0 (9.8%), and iso-C16:0 (8.8%). The polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol. Based on its phenotypic, chemotaxonomic and genotypic data, strain GSS15T (= KCTC 52974T = MCCC 1K03334T) is designated as the type strain of a novel species of the genus Pseudoxanthomonas, for which the name Pseudoxanthomonas composti sp. nov. is proposed.