Distillers' grains organic fertilizer alters soil bacterial composition and co-occurrence patterns in a tobacco-growing field

In recent years, numerous studies have indicated that the combination of organic and inorganic fertilizers can effectively improve soil fertility and soil productivity. Distillers' grain (DG), the primary by-product of Chinese spirits production, has a high utilization value for producing organic fertilizer. We investigated the effects of distillers' grain organic fertilizer (DGOF) on soil chemical properties and microbial community composition, as well as the effects of chemical properties on the abundance of keystone species. The results indicated that the application of DGOF significantly increased tobacco yield by 14.8% and mainly affected the composition rather than the alpha diversity of the bacterial community. Ten amplicon sequence variants (ASVs) were identified as keystone species in the bacterial communities, and most of their relative abundance was influenced by the DGOF addition through affecting soil chemical properties. Our results elucidated the alterations in soil chemical properties and microbial community composition resulting from DGOF application, which is of great importance to better understand the relationship between DGOF and soil microorganisms in the flue-cured tobacco cultivation field.

Effects of fermented Andrographis paniculata on growth performance, carcass traits, immune function, and intestinal health in Muscovy ducks

The study aimed to examine the effects of unfermented and fermented Andrographis paniculata on growth performance, carcass traits, immune function, and intestinal health in Muscovy ducks. A total of 450 (16-day-old) Muscovy ducks weighing 271.44 ± 8.25 g were randomly assigned to 5 dietary treatments (6 replicate pens of 15 ducks per treatment), consisting of one control treatment (basal diet without A. paniculata), one unfermented A. paniculata treatment (basal diet plus 30 g/kg unfermented A. paniculata) and 3 fermented A. paniculata treatments (basal diet plus 10, 30, and 50 g/kg). 30 g/kg unfermented A. paniculata increased the ADG, thymus index, peripheral blood lymphocyte conversion rate, villi height, intestinal thickness, villi surface area, intraepithelial lymphocytes rate, while decreased the FCR. 10 g/kg fermented A. paniculata markedly boosted ADG, bursa of fabricius index, thymus index, serum lysozyme, lymphocyte conversion rate, villi height, vilii width, intestinal thickness, villi surface area, while decreased the FCR. 30 g/kg fermented A. paniculata clearly improved ADG, bursa of fabricius index, thymus index, serum lysozyme, lymphocyte conversion rate, villi height, vilii width, intestinal thickness, villi surface area, intraepithelial lymphocytes, while decreased FCR. 50 g/kg fermented A. paniculata significantly increased villi height, vilii width, and villi surface area, while clearly reduced BW. Additionally, compared to 30 g/kg unfermented A. paniculata, 30 g/kg fermented A. paniculata obviously increased bursa of fabricius indices, lymphocyte conversion rate, vilii width, villi surface area. On top of that, supplementation with unfermented and fermented A. paniculata (30 g/kg each) decreased the relative abundance of harmful bacteria (Succinivibrio, Succinatimonas, Sphaerochaeta, and Mucispirillum) and increase the abundance of beneficial bacteria (Rikenellaceae, Methanocorpusculum, Fournierella, Ruminococcaceae) in the ceca of the ducks. However, fermented A. paniculata had considerable better effects than unfermented A. paniculate on all above measured indices. Overall, these results revealed that supplementation with unfermented and fermented A. paniculata across different treatments improved growth, immune status, intestinal morphology, and intestinal microbiota composition and structure in Muscovy ducks, making it a potential alternative to antibiotics in poultry production.

Global Grassland Diazotrophic Communities Are Structured by Combined Abiotic, Biotic, and Spatial Distance Factors but Resilient to Fertilization

Grassland ecosystems cover around 37% of the ice-free land surface on Earth and have critical socioeconomic importance globally. As in many terrestrial ecosystems, biological dinitrogen (N₂) fixation represents an essential natural source of nitrogen (N). The ability to fix atmospheric N₂ is limited to diazotrophs, a diverse guild of bacteria and archaea. To elucidate the abiotic (climatic, edaphic), biotic (vegetation), and spatial factors that govern diazotrophic community composition in global grassland soils, amplicon sequencing of the dinitrogenase reductase gene—nifH—was performed on samples from a replicated standardized nutrient [N, phosphorus (P)] addition experiment in 23 grassland sites spanning four continents. Sites harbored distinct and diverse diazotrophic communities, with most of reads assigned to diazotrophic taxa within the Alphaproteobacteria (e.g., Rhizobiales), Cyanobacteria (e.g., Nostocales), and Deltaproteobacteria (e.g., Desulforomonadales) groups. Likely because of the wide range of climatic and edaphic conditions and spatial distance among sampling sites, only a few of the taxa were present at all sites. The best model describing the variation among soil diazotrophic communities at the OTU level combined climate seasonality (temperature in the wettest quarter and precipitation in the warmest quarter) with edaphic (C:N ratio, soil texture) and vegetation factors (various perennial plant covers). Additionally, spatial variables (geographic distance) correlated with diazotrophic community variation, suggesting an interplay of environmental variables and spatial distance. The diazotrophic communities appeared to be resilient to elevated nutrient levels, as 2–4 years of chronic N and P additions had little effect on the community composition. However, it remains to be seen, whether changes in the community composition occur after exposure to long-term, chronic fertilization regimes.

Arenibaculum pallidiluteum gen. nov., sp. nov., a novel bacterium in the family Azospirillaceae, isolated from desert soil, and reclassification of Skermanella xinjiangensis to a new genus Deserticella as Deserticella xinjiangensis comb. nov., and transfer of the genera Indioceanicola and Oleisolibacter from the family Rhodospirillaceae to the family Azospirillaceae

A novel pale orange-coloured bacterium, designated strain SYSU D00532^T, was isolated from sandy soil collected from the Gurbantunggut desert in Xinjiang, PR China. Cells of strain SYSU D00532^T were found to be aerobic, Gram-stain-negative, oxidase-positive, catalase-positive, motile and rod-shaped with a single polar or subpolar flagellum. Growth occurred at 15-45 °C (optimum, 28-37 °C, pH 5.0-8.0 (optimum, pH 6.0-7.0) and with 0-1.5% NaCl (w/v; optimum, 0.5 %). The major polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and phosphatidylglycerol. Unidentified aminolipids, unidentified polar lipids, an unidentified aminophospholipid and an unidentified phospholipid were also detected. The major respiratory quinone was ubiquinone-10 and the major fatty acids were summed feature 8 (C_18:1 ω7c and/or C_18:1 ω6c), C_16:0 and C_19:0 cyclo ω8c. The genomic DNA G+C content was 69.8 mol%. Results of phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SYSU D00532^T belonged to the family Azospirillaceae and showed 93.4% (Desertibacter roseus 2622^T), 93.2% (Skermanella xinjiangensis 10-1-101^T), 93.2% ('Skermanella rubra' YIM 93097^T) and 92.4% (Desertibacter xinjiangensis M71^T) similarities. Based on the phylogenetic, phenotypic and chemotaxonomic data, strain SYSU D00532^T is proposed to represent a new species of a new genus, named Arenibaculum pallidiluteum gen. nov., sp. nov., within the family Azospirillaceae. The type strain is SYSU D00532^T (=KCTC 82269^T=CGMCC 1.18631^T=MCCC 1K04984^T). We also propose the reclassification of Skermanella xinjiangensis to a new genus Deserticella as Deserticella xinjiangensis comb. nov., and the transfer of the genera Indioceanicola and Oleisolibacter from the family Rhodospirillaceae to the family Azospirillaceaewe based on the phylogenetic results.

Impact of heavy metals on water quality and indigenous Bacillus spp. prevalent in rat-hole coal mines

The present study reports pollution evaluation indices employed to assess the intensity of metal pollution in water systems affected by acid mine drainage from rat-hole coal mines prevalent in North-east India. The concentration of seven eco-toxic metals was evaluated from coal mine waters which showed concentration order of Iron (Fe) > Manganese (Mn) > Zinc (Zn) > Chromium (Cr) > Lead (Pb) > Copper (Cu) > Cadmium (Cd). The water samples were acidic with mean pH 2.67 and burdened with dissolved solids (924.8 mg/L). The heavy metal pollution index (HPI) and heavy metal evaluation index (HEI) displayed high and medium range of pollution level in majority of the water samples. Statistical correlation suggested strong positive correlation between metals such as Cr with Mn (r = 0.780), Mn with Fe (r = 0.576), Cr with Fe (r = 0.680), Pb with Mn (r = 0.579) and Cr with Pb (r = 0.606), indicating Mn, Pb, Fe and Cr to be major metal contaminants; an unequivocal affirmation of degradation in water quality. The sampled waters had lower heavy metal concentration during monsoon and post-monsoon seasons. The commonly occurring bacterial species Bacillus pseudomycoides and Bacillus siamensis were chosen to understand their behavioral responses toward metal contamination. Findings demonstrated that Bacillus spp. from control environment had low tolerance to metals stress as evident from their MTC, MIC and growth curve studies. The survival of the native isolates across varying pH, salinity and temperature in the coal mine areas suggest these isolates as promising candidates for reclamation of rat-hole coal mining sites.

Characterization and bioremediation potential of native heavy-metal tolerant bacteria isolated from rat-hole coal mine environment

Identification and characterization of endogenous and stress adapted bacterial species, from rat-hole coal mines in Meghalaya, amplify the ambit of bioremediation for eco-restoration. 52 native bacterial isolates, drawn from soil and water samples of these mines, were analysed for bioremediation potential, based on growth and metal tolerance parameters. 12 of these isolates were metal tolerant with Bacillus spp. being the most promising taxon. Three isolates, namely, Serratia marcescens KH-CC, Bacillus altitudinis KH-16F and Bacillus siamensis KH-12A, exhibited high Maximum Tolerable Concentration (MTC) against Fe (500 ppm), Mn (830 ppm) and Pb (1400 ppm). B. siamensis showed highest Fe remediation with 48.34% removal capacity, while maximum removal for Mn and Pb was exhibited by Serratia marcescens at 72.5 and 83%, respectively. The growth profile of the isolates indicated their ability to survive under pH, temperature and salt stress conditions. In vitro growth kinetics studies of the isolates revealed their ability to decrease the acidity of growth media and improve alkalinity from an initial of pH 4.8-5.2 to an alkaline level of pH 8.5-9. These native bacteria, extracted from the stressed coal mine habitat, are potential germane applicants for rehabilitation and eco-restoration of ecologically degraded mine sites.

Aerophototrophica crusticola gen. nov., sp. nov., isolated from desert biocrusts

A pink-pigmented, Gram-stain-negative, rod-shaped, strictly aerobic bacterial strain MIMtkB3^T, was isolated from moss crusts in Hunshandake desert of China. Cells grew at 15-45 °C (optimum of 28 °C), at pH of 6.0-8.5 (optimum of 7.0) and with 0-1.0 % (w/v) NaCl (optimum of 0 %). The strain could biosynthesize the green-coloured pigment bacteriochlorophyll a (BChl a). The respiratory quinone was ubiquinone Q-10, while C_18 : 1 ω7c and C_18 : 1 2OH were the major fatty acids. Phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified aminophospholipid, one unidentified phospholipid, three unidentified glycolipid and one unidentified lipid were the major polar lipids. Strain MIMtkB3^T was most closely related to Oleisolibacter albus NAU-10^T, Niveispirillum fermenti CC-LY736^T, and Rhodocista centenaria SW of the family Rhodospirillaceae with 16S rRNA gene similarities of 93.09, 92.02 and 91.73%, respectively. The genomic DNA G+C content calculated on complete genome sequencing was 69.3 mol%. The average nucleotide identity between strain MIMtkB3^T and its closely related type strains in Rhodospirillaceae was below 77.96 % and digital DNA-DNA hybridization lower than 24.70 %. Full light utilization pathway of aerobic anoxygenic phototrophic bacteria was identified in the genome. Based on phenotypic, chemotaxonomic and phylogenetic characteristics, strain MIMtkB3^T represents a novel genus of the family Rhodospirillaceae, for which the name Aerophototrophica crusticola gen. nov., sp. nov. is proposed. The type strain is MIMtkB3^T (=KCTC 42633^T=MCCC 1K00570^T).

Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria

The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.

Skermanella pratensis sp. nov., isolated from meadow soil, and emended description of the genus Skermanella

A novel Gram-stain-negative, light pink-coloured, short rod-shaped, designated strain W17T, was isolated from a meadow soil sample collected from Xinjiang, PR China. The 16S rRNA gene sequence analysis indicated that strain W17T was related most closely to Skermanella rosea M1T (98.72 %) and Skermanella mucosa 8-14-6T (98.44 %). However, strain W17T showed a low level of DNA–DNA relatedness to S. rosea M1T (32.4±2.6 %) and S. mucosa 8-14-6T (33.5±0.1 %). The genome size of the novel strain was 5.87 Mb and the genomic DNA G+C content was 67.27 mol%. The only respiratory quinone of strain W17T was Q-10. Diphosphatidylglycerol, phosphatidylglycerol. phosphatidylethanolamine and phosphatidylcholine were the major polar lipids. The predominant cellular fatty acids were C18 : 1ω6c and/or C18 : 1ω7c (48.53 %), C16 : 0 (20.88 %) and C18 : 0 (14.92 %). The phylogenetic, phenotypic and chemotaxonomic data showed that strain W17T represents a novel species of the genus Skermanella , for which the name Skermanella pratensis sp. nov. is proposed. The type strain is W17T (=GDMCC 1.1392T=KCTC 62434T).

Genetic diversity of diazotrophs and total bacteria in the phyllosphere of Pyrus serotina, Prunus armeniaca, Prunus avium, and Vitis vinifera

The phyllosphere, which supports a large number of microorganisms, represents the interface between the aboveground parts of plants and air. In this study, four nifH clone libraries were constructed from the phyllosphere of Pyrus serotina (L), Vitis vinifera (P), Prunus armeniaca (X), and Prunus avium (Y). Clones related to Skermanella (L, 12.1%; X, 15.6%; Y, 62.5%; P 70.8%), Bradyrhizobium (X, 2.1%; P, 15.1%; L, 63.7%), Erwinia (X, 68.8%), Pseudomonas (L, 3.3%; P, 7.6%), and Chroococcidiopsis (P, 0.9%; L, 4.4%, X; 5.2%, Y; 19.6%) were present at high percentages, highlighting their critical role in contributing nitrogen to the phyllosphere ecosystem. The 16S rDNA sequence analysis suggested that phyllosphere-associated bacteria were affiliated with a wide range of taxa, encompassing members from Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, Actinobacteria, Bacteroidetes, Firmicutes, Cyanobacteria, Tenericutes, and Deinococcus-Thermus. Additionally, the abundance of the nifH gene and 16S rDNA was assessed with quantitative PCR. The number of copies of nifH and 16S rDNA ranged from 1.14 × 10³ to 1.49 × 10⁴ and from 3.72 × 10⁶ to 7.02 × 10⁷ copies/g fresh leaf sample, respectively. In conclusion, our work sheds light on the microbial communities of the phyllosphere that are important for plant growth. Moreover, we observed a unique composition of nitrogen-fixing bacteria in each phyllosphere sample, suggesting the existence of specific interactions between these functional microorganism and plants, which may provide information or be a reference for the development of bacterial fertilizers.

Organic Farming Improves Soil Microbial Abundance and Diversity under Greenhouse Condition: A Case Study in Shanghai (Eastern China)

Agricultural practices have significant impacts on soil properties and microbial communities; however, little is known about their responses to open field and plastic tunnels under organic and conventional farming. We therefore investigated the responses of soil chemical variables and microbial communities to different agricultural management and cultivation types, including organic management in open field (OF), organic management in plastic tunnels (OP), conventional management in open field (CF) and conventional management in plastic tunnels (CP), by using a pyrosequencing approach of 16S rRNA gene amplicon. Both factors had significant influences on the soil properties and microbial communities. Organic farming increased the nutrient-related soil variables compared to conventional farming regardless of cultivation type, especially for the available N and P, which were increased by 137% and 711%, respectively, in OP compared to CP. Additionally, OP had the highest microbial abundance and diversity among treatments, whereas no difference was found between OF, CF and CP. Furthermore, OP possessed diverse differential bacteria which were mainly related to the organic material turnover (e.g., Roseiflexus, Planctomyces and Butyrivibrio) and plant growth promotion (e.g., Nostoc, Glycomyces and Bacillus). Redundancy analysis (RDA) showed that pH, electrical conductivity (EC), nutrient levels (e.g., available N and available P) and total Zn content were significantly correlated to the structure of the microbial community. Overall, our results showed that the long-term organic farming with high fertilizer input increased soil nutrient levels and microbial abundance and diversity under plastic-tunnel condition compared to other cultivation systems.

Larvicidal potential of Skermanella sp. against rice leaf folder (Cnaphalocrosis medinalis Guenee) and pink stem borer (Sesamia inferens Walker)

Insect pests in the rice agroecosystem, particularly the leaf folder, Cnaphalocrosis medinalis (Guenee) and stem borer, Sesamia inferens (Walker), cause significant yield losses. These pests are generally managed by farmers by application of insecticides and a few biocontrol agents. As a component of integrated pest management, biocontrol agents play a dynamic role in pest control. Although diverse microbial communities are available in the rice ecosystem, bacterial genera such as Bacillus and Pseudomonas spp. are broadly used as biocontrol agents. Therefore, an attempt was made to identify other effective entomopathogenic bacteria to manage the above mentioned pests. In this study, the two entomopathogenic bacteria isolated from diseased pink stem borer (S. inferens Walker) larvae collected from rice fields were identified as Skermanella sp. (KX611462) and Serratia sp. (KX761232). The larvicidal activity of these two bacteria was evaluated against third instar larvae of C. medinalis and S. inferens in in vitro assays and on potted rice plants (Oryza sativa var. TN1). The results of this study demonstrated 50% (LC₅₀) larval mortality of C. medinalis at 2.95 × 10³ and 5.88 × 10³ colony forming units (CFU) ml^-1 for Skermanella sp. and Serratia sp., respectively, under in vitro conditions, 2.57 × 10⁴ and 3.38 × 10⁴ CFU ml^-1, respectively, in whole plant assays. Similarly, the LC₅₀ value for Skermanella sp. was 3.80 × 10⁴ CFU ml^-1 and Serratia sp. was 2.29 × 10⁵ CFU ml^-1 for S. inferens larvae. Our study reports the larvicidal activity of Skermanella sp. against C. medinalis and S. inferens.

Microbial communities associated with the anthropogenic, highly alkaline environment of a saline soda lime, Poland

Soda lime is a by-product of the Solvay soda process for the production of sodium carbonate from limestone and sodium chloride. Due to a high salt concentration and alkaline pH, the lime is considered as a potential habitat of haloalkaliphilic and haloalkalitolerant microbial communities. This artificial and unique environment is nutrient-poor and devoid of vegetation, due in part to semi-arid, saline and alkaline conditions. Samples taken from the surface layer of the lime and from the depth of 2 m (both having pH ~11 and EC_e up to 423 dS m⁻¹) were investigated using culture-based (culturing on alkaline medium) and culture-independent microbiological approaches (microscopic analyses and pyrosequencing). A surprisingly diverse bacterial community was discovered in this highly saline, alkaline and nutrient-poor environment, with the bacterial phyla Proteobacteria (representing 52.8% of the total bacterial community) and Firmicutes (16.6%) showing dominance. Compared to the surface layer, higher bacterial abundance and diversity values were detected in the deep zone, where more stable environmental conditions may occur. The surface layer was dominated by members of the genera Phenylobacterium, Chelativorans and Skermanella, while in the interior layer the genus Fictibacillus was dominant. The culturable aerobic, haloalkaliphilic bacteria strains isolated in this study belonged mostly to the genus Bacillus and were closely related to the species Bacillus pseudofirmus, B. cereus, B. plakortidis, B. thuringensis and B. pumilus.

Diversity of Phototrophic Genes Suggests Multiple Bacteria May Be Able to Exploit Sunlight in Exposed Soils from the Sør Rondane Mountains, East Antarctica

Microbial life in exposed terrestrial surface layers in continental Antarctica is faced with extreme environmental conditions, including scarcity of organic matter. Bacteria in these exposed settings can therefore be expected to use alternative energy sources such as solar energy, abundant during the austral summer. Using Illumina MiSeq sequencing, we assessed the diversity and abundance of four conserved protein encoding genes involved in different key steps of light-harvesting pathways dependent on (bacterio)chlorophyll (pufM, bchL/chlL, and bchX genes) and rhodopsins (actinorhodopsin genes), in exposed soils from the Sør Rondane Mountains, East Antarctica. Analysis of pufM genes, encoding a subunit of the type 2 photochemical reaction center found in anoxygenic phototrophic bacteria, revealed a broad diversity, dominated by Roseobacter- and Loktanella-like sequences. The bchL and chlL, involved in (bacterio)chlorophyll synthesis, on the other hand, showed a high relative abundance of either cyanobacterial or green algal trebouxiophyceael chlL reads, depending on the sample, while most bchX sequences belonged mostly to previously unidentified phylotypes. Rhodopsin-containing phototrophic bacteria could not be detected in the samples. Our results, while suggesting that Cyanobacteria and green algae are the main phototrophic groups, show that light-harvesting bacteria are nevertheless very diverse in microbial communities in Antarctic soils.

Microbial Antimony Biogeochemistry: Enzymes, Regulation, and Related Metabolic Pathways

Antimony (Sb) is a toxic metalloid that occurs widely at trace concentrations in soil, aquatic systems, and the atmosphere. Nowadays, with the development of its new industrial applications and the corresponding expansion of antimony mining activities, the phenomenon of antimony pollution has become an increasingly serious concern. In recent years, research interest in Sb has been growing and reflects a fundamental scientific concern regarding Sb in the environment. In this review, we summarize the recent research on bacterial antimony transformations, especially those regarding antimony uptake, efflux, antimonite oxidation, and antimonate reduction. We conclude that our current understanding of antimony biochemistry and biogeochemistry is roughly equivalent to where that of arsenic was some 20 years ago. This portends the possibility of future discoveries with regard to the ability of microorganisms to conserve energy for their growth from antimony redox reactions and the isolation of new species of "antimonotrophs."

Nitrospirillum irinus sp. nov., a diazotrophic bacterium isolated from the rhizosphere soil of Iris and emended description of the genus Nitrospirillum

A polyphasic approach was used to characterize a novel nitrogen-fixing bacterial strain, designated YC6995(T), isolated from the rhizosphere soil of Iris ensata var. spontanea (Makino) Nakai inhabiting a wetland located at an altitude of 960 m on Jiri Mountain, Korea. Strain YC6995(T) cells were Gram-negative, and rod-shaped, with motility provided by a single polar flagellum. Optimal growth conditions were 30 °C and pH 7.0. The major fatty acids of strain YC6995(T) were C18:1 ω7c, C18:1 2-OH and C16:0 3-OH. The major respiratory quinone was ubiquinone-10 (Q-10). The polar lipids were phosphatidylethanolamine, phosphatidyldimethylethanolamine, phosphatidylcholine, phosphatidylglycerol and unidentified glycolipids. The genomic DNA G+C content was 64.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed strain YC6995(T) to form a phyletic lineage with Nitrospirillum amazonense DSM 2787(T) with a high sequence similarity (97.2 %), but it displayed low sequence similarity with other remotely related genera, including Azospirillum (<93 %), Rhodocista (93.1-93.4 %), and Skermanella (91.2-93.3 %) in the family Alphaproteobacteria. Based on the phenotypic, chemotaxonomic, and phylogenetic evidences, strain YC6995(T) represents a novel species within the genus Nitrospirillum, for which the name Nitrospirillum irinus sp. nov. is proposed. The type strain is YC6995(T) (= KACC 13777(T) = DSM 22198(T)). An emended description of the genus Nitrospirillum is also proposed.

Skermanella rubra sp. nov., a bacterium isolated from the desert of Xinjiang, China

A Gram-negative, pink-coloured, rod-shaped, motile bacterium, designated YIM 93097(T), was isolated from the desert soil collected from Xinjiang province of China. Strain YIM 93097(T) was found to grow at 20-45 °C (optimum 28-37 °C), pH 5.0-7.0 (optimum pH 7.0) and 0-8 % (w/v) NaCl (optimum 1 %, w/v). Based on 16S rRNA gene sequence similarity studies, it belongs to the genus Skermanella. The 16S rRNA gene sequence similarity was identified to be 98.7 % to Skermanella xinjiangensis CCTCC AB 207153(T) while the DNA-DNA hybridization value was found to be only 48.1 %. The predominant isoprenoid quinone was determined to be Q-10. The major fatty acids were identified to be C16:0, C18:1 ω7c and summed feature 4 (consisting of C17:1 anteiso B/iso I). The major polar lipids were identified as phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, two unidentified phospholipids and one unidentified aminolipid. The DNA G+C content was found to be 67.2 mol %. The analysis of the genotypic and phenotypic data indicated that strain YIM 93097(T) belongs to a novel species of the genus Skermanella, for which the name Skermanella rubra sp. nov. is proposed. The type strain is YIM 93097(T) (=DSM 21389(T)=CCTCC AB 2015161(T)).

Genomic analysis of Skermanella stibiiresistens type strain SB22 (T.)

Members of genus Skermanella were described as Gram-negative, motile, aerobic, rod-shaped, obligate-heterotrophic bacteria and unable to fix nitrogen. In this study, the genome sequence of Skermanella stibiiresistens SB22(T) is reported. Phylogenetic analysis using core proteins confirmed the phylogenetic assignment based on 16S rRNA gene sequences. Strain SB22(T) has all the proteins for complete glycolysis, tricarboxylic acid cycle and pentose phosphate pathway. The RuBisCO encoding genes cbbL1S1 and nitrogenase delta subunit gene anfG are absent, consistent with its inability to fix carbon and nitrogen, respectively. In addition, the genome possesses a series of flagellar assembly and chemotaxis genes to ensure its motility.

Lacibacterium aquatile gen. nov., sp. nov., a new member of the family Rhodospirillaceae isolated from a freshwater lake

A bacterial strain designated LTC-2T was isolated from a freshwater lake in Taiwan and characterized using a polyphasic taxonomic approach. Cells of strain LTC-2T were Gram-reaction-negative, facultatively anaerobic, poly-β-hydroxybutyrate-accumulating, motile by means of a monopolar flagellum, non-spore-forming, slightly curved rods surrounded by a thick capsule and formed creamy white colonies. Growth occurred at 10–37 °C (optimum, 20–30 °C), at pH 6.0–9.0 (optimum, pH 7.0–8.0) and with 0–1.0 % NaCl (optimum, 0 %). The predominant fatty acids were C18 : 1ω7c, summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The major isoprenoid quinone was Q-10 and the DNA G+C content was 58.5 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, two uncharacterized phospholipids and two uncharacterized aminophospholipids. The major polyamines were putrescine, homospermidine and spermidine. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain LTC-2T forms a distinct lineage with respect to closely related genera in the family Rhodospirillaceae , most closely related to the genera Elstera and Dongia , and the levels of 16S rRNA gene sequence similarity with respect to the type species of related genera were less than 94 %. On the basis of the genotypic and phenotypic data, strain LTC-2T represents a novel genus and species of the family Rhodospirillaceae , for which the name Lacibacterium aquatile gen. nov., sp. nov. is proposed. The type strain is LTC-2T ( = BCRC 80445T = LMG 26999T = KCTC 32017T).