Mercury remediation potential of mercury-resistant strain Rheinheimera metallidurans sp. nov. isolated from a municipal waste dumping site

A novel mercury-resistant bacterium, designated strain DCL_24^T, was isolated from the legacy waste at the Daddu Majra dumping site in Chandigarh, India. It showed resistance up to 300 µM of inorganic mercury (mercuric chloride). The isolate was found to be a Gram-negative, facultative anaerobic, motile, and rod-shaped bacterium that can grow at 4 - 30 °C (optimum 25 °C), pH 6.0 - 12.0 (optimum 7.0), and 0 - 4.0 % (w/v) NaCl (optimum 0.5 - 2.0 %). The 16 S rRNA gene-based phylogenetic analysis showed that DCL_ 24 ^T shared a 97.53 % similarity with itsºlosest type strain Rheinheimera muenzenbergensis E-49^T. Insilico DNA-DNA hybridization and average nucleotide identity values were found to be 18.60 % and 73.77 %, respectively, between the genomes of DCL_24^T and R. muenzenbergensis E-49^T. The strain DCL_24^T has 44.33 DNA G+C content (mol %). Based on the phenotypic, chemotaxonomic, and genotypic data, the strain DCL_24^T represents a novel species within the genus Rheinheimera, for which the name Rheinheimera metallidurans sp. nov is proposed. The type strain is DCL_24^T (MTCC13203^T = NBRC115780^T = JCM 35551 ^T). The isolate was found to volatilize and remove mercury efficiently, as demonstrated by X-ray film and dithizone-based colorimetric methods. Around 92 % of mercury removal was observed within 48 h. The mercury-resistant determinant mer operon consisting of merA, encoding the mercuric reductase enzyme, and transport and regulatory genes (merT, merP, merD, and merR) were found in the isolate. Relative expression analysis of merA at increasing concentrations of HgCl₂ was confirmed by quantitative real-time PCR. These data indicate the merA-mediated reduction of toxic Hg²⁺ into a non-toxic volatile Hg⁰. The phytotoxicity assay performed using Arabidopsis thaliana seeds further demonstrated the mercury toxicity reduction potential of DCL_24^T. The study shows that this novel isolate, DCL_24^T, is an interesting candidate for mercury bioremediation. However, further studies are required to assess the bioremediation efficacy of the strain under the harsh environmental conditions prevailing in polluted sites.

Arsukibacterium indicum sp. nov., isolated from deep-sea sediment, and transfer of Rheinheimera tuosuensis and Rheinheimera perlucida to the genus Arsukibacterium as Arsukibacterium tuosuense comb. nov. and Arsukibacterium perlucidum comb. nov

A Gram-stain-negative, aerobic, flagellated and rod-shaped bacterium, designated strain SM2107T, was isolated from a deep-sea sediment sample collected from the Southwest Indian Ocean. Strain SM2107T grew at 4–40 °C and with 0–10.0 % (w/v) NaCl. It reduced nitrate to nitrite and hydrolysed casein, gelatin, chitin and DNA. The phylogenetic trees based on the 16S rRNA genes and single-copy orthologous clusters showed that strain SM2107T, together with Rheinheimera tuosuensis , Rheinheimera perlucida and Arsukibacterium ikkense , formed a separate clade, having the highest similarity to the type strain of Rheinheimera tuosuensis (98.3%). The major polar lipids were phosphatidylethanolamine and phosphatidylglycerol and the major cellular fatty acids were summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c), C16 : 0, C17 : 1 ω8с and summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c). The only respiratory quinone was Q-8. The genomic DNA G+C content of strain SM2107T was 48.8 %. The digital DNA–DNA hybridization values between strain SM2107T and type strains of Rheinheimera tuosuensis , Rheinheimera perlucida and Arsukibacterium ikkense were 41.16, 37.70 and 31.80 %, while the average amino acid identity values between them were 87.59, 86.76 and 83.64 %, respectively. Based on the polyphasic evidence presented in this study, strain SM2107T was considered to represent a novel species within the genus Arsukibacterium , for which the name Arsukibacterium indicum was proposed. The type strain is SM2107T (=MCCC M24986T=KCTC 82921T). Moreover, the transfer of Rheinheimera tuosuensis and Rheinheimera perlucida to the genus Arsukibacterium as Arsukibacterium tuosuense comb. nov. (type strain TS-T4T=CGMCC 1.12461T=JCM 19264T) and Arsukibacterium perlucidum comb. nov. (type strain BA131T=LMG 23581T=CIP 109200T) is also proposed.

Rheinheimera maricola sp. nov., isolated from seawater of the Yellow Sea

A Gram-negative and facultative aerobic strain, designated as strain MA-13T, was isolated from seawater in the Yellow Sea Republic of Korea. Cells were oxidase- and catalase-positive and non-motile short rods. Growth of strain MA-13T was observed over a range of 10–37 °C (optimum, 30 °C), pH 6.0–11.0 (optimum, pH 7.0) and in the presence of 0–5.5 % (w/v) sodium chloride (optimum, 1.0–2.0 %). Strain MA-13T contained ubiquinone-8 as the respiratory quinone, phosphatidylethanolamine, an unidentified aminolipid, an unidentified phospholipid and four unidentified lipids as major polar lipids and C16 : 0, C12 : 0 3-OH and summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c) as major cellular fatty acids. The G+C content of the genomic DNA was 48.3 mol%. Phylogenetic analyses based on the 16S rRNA gene and whole-genome sequences revealed that strain MA-13T formed a distinct phyletic lineage in the genus Rheinheimera . Strain MA-13T was most closely related to Rheinheimera lutimaris YQF-2T, Rheinheimera aquimaris SW-353T, Rheinheimera pacifica KMM 1406T and Rheinheimera baltica DSM 14885T with 98.10, 98.08, 98.07 and 97.94 % 16S rRNA gene sequence similarities. Average nucleotide identity and DNA–DNA hybridization values between strain MA-13T and R. aquimaris KCTC 12840T, R. pacifica DSM 17616T and R. baltica DSM 14885T were 76.3, 78.6 and 76.9 % and 19.5, 21.3 and 20.5 %, respectively. Based on the phenotypic, chemotaxonomic and molecular features, strain MA-13T represents a novel species of the genus Rheinheimera , for which the name Rheinheimera maricola sp. nov. is proposed. The type strain is MA-13T (=KACC 22113T=JCM 34600T).

Bacterial Communities in Concrete Reflect Its Composite Nature and Change with Weathering

Concrete is an extreme but common environment and is home to microbial communities adapted to alkaline, saline, and oligotrophic conditions. Microbes inside the concrete that makes up buildings or roads have received little attention despite their ubiquity and capacity to interact with the concrete. Because concrete is a composite of materials which have their own microbial communities, we hypothesized that the microbial communities of concrete reflect those of the concrete components and that these communities change as the concrete ages. Here, we used a 16S amplicon study to show how microbial communities change over 2 years of outdoor weathering in two sets of concrete cylinders, one prone to the concrete-degrading alkali-silica reaction (ASR) and the other having the risk of the ASR mitigated. After identifying and removing taxa that were likely laboratory or reagent contaminants, we found that precursor materials, particularly the large aggregate (gravel), were the probable source of ∼50 to 60% of the bacteria observed in the first cylinders from each series. Overall, community diversity decreased over 2 years, with temporarily increased diversity in warmer summer months. We found that most of the concrete microbiome was composed of Proteobacteria, Firmicutes, and Actinobacteria, although community composition changed seasonally and over multiyear time scales and was likely influenced by environmental deposition. Although the community composition between the two series was not significantly different overall, several taxa, including Arcobacter, Modestobacter, Salinicoccus, Rheinheimera, Lawsonella, and Bryobacter, appear to be associated with ASR.

IMPORTANCE Concrete is the most-used building material in the world and a biologically extreme environment, with a microbiome composed of bacteria that likely come from concrete precursor materials, aerosols, and environmental deposition. These microbes, though seeded from a variety of materials, are all subject to desiccation, heating, starvation, high salinity, and very high pH. Microbes that survive and even thrive under these conditions can potentially either degrade concrete or contribute to its repair. Thus, understanding which microbes survive in concrete, under what conditions, and for how long has potential implications for biorepair of concrete. Further, methodological pipelines for analyzing concrete microbial communities can be applied to concrete from a variety of structures or with different types of damage to identify bioindicator species that can be used for structural health monitoring and service life prediction.

Influence of stormwater infiltration systems on the structure and the activities of groundwater biofilms: Are the effects restricted to rainy periods?

Stormwater infiltration systems (SIS) have been set up to collect and infiltrate urban stormwater runoff in order to reduce flooding and to artificially recharge aquifers. Such practices produce environmental changes in shallow groundwater ecosystems like an increase in organic matter concentrations that could drive changes in structure and functions of groundwater microbial communities. Previous works suggested that SIS influence groundwater physico-chemistry during either rainy and dry period but no study has examined the impact of SIS on groundwater microorganisms during both periods. This study aimed to fill this gap by assessing SIS impacts on groundwater quality parameters in three SIS with vadose zone thickness < 3 m during two contrasting meteorological conditions (rainy/dry periods). Physicochemical (dissolved organic carbon and nutrient concentrations) and microbial variables (biomass, dehydrogenase and hydrolytic activities, and bacterial community structure) were assessed on SIS-impacted and non-SIS-impacted zones of the aquifers for the three SIS. Using clay beads incubated in the aquifer to collect microbial biofilm, we show that SIS increased microbial activities, bacterial richness and diversity in groundwater biofilms during the rainy period but not during the dry period. In contrast, the significant differences in dissolved organic carbon and nutrient concentrations, biofilm biomass and bacterial community structures (Bray-Curtis distances, relative abundances of main bacterial orders) measured between SIS-impacted and non-SIS-impacted zones of the aquifer were comparable during the two periods. These results suggest that structural indicators of biofilm like biomass were probably controlled by long-term effects of SIS on concentrations of dissolved organic matter and nutrients whereas biofilm activities and bacterial richness were temporally stimulated by stormwater runoff infiltrations during the rainy period. This decoupling between the structural and functional responses of groundwater biofilms to stormwater infiltration practices suggests that biofilms functions were highly reactive to fluxes associated with aquifer recharge events.

Interactions between immune system and the microbiome of skin, blood and gut in pathogenesis of rosacea

The increasingly wide use of next-generation sequencing technologies has revolutionised our knowledge of microbial environments associated with human skin, gastrointestinal tract and blood. The collective set of microorganisms influences metabolic processes, affects immune responses, and so directly or indirectly modulates disease. Rosacea is a skin condition of abnormal inflammation and vascular dysfunction, and its progression is affected by Demodex mites on the skin surface. When looking into the effects influencing development of rosacea, it is not only the skin microbiome change that needs to be considered. Changes in the intestinal microbiome and their circulating metabolites, as well as changes in the blood microbiome also affect the progression of rosacea. Recent research has confirmed the increased presence of bacterial genera like Acidaminococcus and Megasphera in the intestinal microbiome and Rheinheimera and Sphingobium in the blood microbiome of rosacea patients. In this review we discuss our current knowledge of the interactions between the immune system and the skin, gut and blood microbiome, with particular attention to rosacea diagnostic opportunities.

A Novel Mobile Element ICERspD18B in Rheinheimera sp. D18 Contributes to Antibiotic and Arsenic Resistance

Antibiotics and organoarsenical compounds are frequently used as feed additives in many countries. However, these compounds can cause serious antibiotic and arsenic (As) pollution in the environment, and the spread of antibiotic and As resistance genes from the environment. In this report, we characterized the 28.5 kb genomic island (GI), named as ICERspD18B, as a novel chromosomal integrative and conjugative element (ICE) in multidrug-resistant Rheinheimera sp. D18. Notably, ICERspD18B contains six antibiotic resistance genes (ARGs) and an arsenic tolerance operon, as well as genes encoding conjugative transfer proteins of a type IV secretion system, relaxase, site-specific integrase, and DNA replication or partitioning proteins. The transconjugant strain 25D18-B4 was generated using Escherichia coli 25DN as the recipient strain. ICERspD18B was inserted into 3'-end of the guaA gene in 25D18-B4. In addition, 25D18-B4 had markedly higher minimum inhibitory concentrations for arsenic compounds and antibiotics when compared to the parental E. coli strain. These findings demonstrated that the integrative and conjugative element ICERspD18B could mediate both antibiotic and arsenic resistance in Rheinheimera sp. D18 and the transconjugant 25D18-B4.

Novel Mobilizable Genomic Island GEI-D18A Mediates Conjugational Transfer of Antibiotic Resistance Genes in the Multidrug-Resistant Strain Rheinheimera sp. D18

Aquatic environments act as reservoirs of antimicrobial-resistant bacteria and antimicrobial resistance (AMR) genes, and the dissemination of antibiotic resistance from these environments is of increasing concern. In this study, a multidrug-resistant bacterial strain, identified as Rheinheimera sp. D18, was isolated from the sea water of an industrial maricultural system in the Yellow Sea, China. Whole-genome sequencing of D18 revealed the presence of a novel 25.8 kb antibiotic resistance island, designated GEI-D18A, which carries several antibiotic resistance genes (ARGs), including aadA1, aacA3, tetR, tet(B), catA, dfrA37, and three sul1 genes. Besides, integrase, transposase, resolvase, and recombinase encoding genes were also identified in GEI-D18A. The transferability of GEI-D18A was confirmed by mating experiments between Rheinheimera sp. D18 and Escherichia coli 25DN, and efflux pump inhibitor assays also suggested that tet(B) in GEI-D18A was responsible for tetracycline resistance in both D18 and the transconjugant. This study represents the first characterization of a mobilizable antibiotic resistance island in a species of Rheinheimera and provides evidence that Rheinheimera spp. could be important reservoirs and vehicles for ARGs in the Yellow Sea area.

Rheinheimera sediminis sp. nov., a marine bacterium isolated from coastal sediment

A Gram-stain-negative, aerobic, rod-shaped bacterium, designated strain YQF-1^T, was isolated from coastal sediment in Jiangsu Province (PR China) and characterized phylogenetically and phenotypically. Bacterial optimal growth occurred at 28 °C (range 4-40 °C) and pH 7 (range pH 6-11). Phylogenetic analysis based on 16S rRNA gene sequence indicated that YQF-1^T was related to members of the genus Rheinheimera and shared the highest sequence identities with Rheinheimera mesophila DSM 29723^T (98.5 %), followed by Rheinheimera tangshanensis DSM 19460^T (98.4 %), Rheinheimera tilapiae Ruye-90^T (97.9 %), Rheinheimera soli BD-d46^T (97.9 %), Rheinheimera aquatica GR5^T (97.4 %), Rheinheimera coerulea TAPG2^T (97.3 %) and Rheinheimera texasensis A62-14B^T (97.1 %). The 16S rRNA gene sequence identities between YQF-1^T and other members of the genus Rheinheimera were below 97.0 %. The digital DNA-DNA hybridization value between YQF-1^T and Rheinheimera mesophila DSM 29723^T was 25.1±2.3 %. The average nucleotide identity (ANI) value between YQF-1^T and Rheinheimera mesophila DSM 29723^T was 81.4 %. The major respiratory quinone was Q-8. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phospholipid, two unidentified aminolipids and three unidentified lipids. The strain had summed feature 8 (C_18 : 1  ω7c and/or C_18 : 1  ω6c), C_16 : 0, summed feature 3 (C_16 : 1  ω7c and/or C_16 : 1  ω6c), iso-C_15 : 0, and anteiso-C_17 : 1  ω9c as the major fatty acids. The G+C content of the genomic DNA was 46.2 mol%. On the basis of phenotypic, genotypic and phylogenetic evidence, strain YQF-1^T represents a novel species of the genus Rheinheimera, for which the name Rheinheimera sediminis sp. nov. is proposed, with the type strain YQF-1^T (=KCTC 72183^T=MCCC 1K03646^T).

Rheinheimera riviphila sp. nov., isolated from a freshwater stream

Strain KYPC3^T, isolated from a freshwater stream in Taiwan, was characterized using a polyphasic taxonomy approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain KYPC3^T belonged to the genus Rheinheimera. Strain KYPC3^T exhibited 16S rRNA gene sequence similarity values of 94.8-97.9% to the type strains of species of the genus Rheinheimera. Strain KYPC3^T was most closely related to Rheinheimera chironomi K19414^T with 16S rRNA gene sequence similarity of 97.9%. Cells of strain KYPC3^T were Gram-stain negative, aerobic, motile by means of a single-polar flagellum, non-spore forming, coccoid or short rods surrounded by a thick capsule and forming off-white coloured colonies. Growth occurred at 15-30 °C (optimum, 20-25 °C), at pH 6-8 (optimum, pH 7) and with 0-0.5% NaCl (optimum, 0%). The major fatty acids (> 10%) of strain KYPC3^T were C_12:0 3-OH, summed feature 3 (C_16:1ω7c and/or C_16:1ω6c) and C_16:0. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, an uncharacterized aminophospholipid, an uncharacterized phospholipid and an uncharacterized lipid. The major isoprenoid quinone was Q-8. The draft genome was approximately 4.75 Mb in size with a G + C content of 49.8 mol%. The DNA-DNA relatedness of strain KYPC3^T with respect to recognized species of the genus Rheinheimera was significantly less than 70%. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain KYPC3^T should be classified as a novel species of the genus Rheinheimera, for which the name Rheinheimera riviphila sp. nov. is presented. The type strain is KYPC3^T (= BCRC 81008^T = LMG 29729^T = KCTC 52440^T).

PER extended-spectrum β-lactamases originate from Pararheinheimera spp

To investigate the origin of PER extended-spectrum β-lactamases, publicly available sequence databases were searched for bla_PER-like genes. Three genomes from Pararheinheimera, a genus associated with water and soil environments, were found to carry bla_PER-like genes but lacked the ISCR1/ISPa12/ISPa13 insertion sequences commonly associated with bla_PER in clinical isolates. Sequence analysis revealed 78-96% nucleotide identity and conserved synteny between the clinical mobile genetic elements (MGEs) encoding bla_PER-1 and the bla_PER locus in the Pararheinheimera genomes. Notably, bla_PER genes were only identified in 3 of 21 Pararheinheimera and Rheinheimera genomes, whereas the genetic environment of bla_PER genes as found in clinical MGEs was conserved in all Pararheinheimera and Rheinheimera genomes. These findings indicate that bla_PER genes were likely acquired by a branch of the Pararheinheimera genus long before the antibiotic era. Later, bla_PER genes were mobilised, likely through the involvement of insertion sequences, from one or several Pararheinheimera species, allowing their dissemination into human pathogens.

Rheinheimera coerulea sp. nov., isolated from a freshwater creek, and emended description of genus Rheinheimera Brettar et al. 2002

A bacterial strain designated TAPG2^T was isolated from a freshwater creek in Taiwan and characterized using the polyphasic taxonomic approach. Cells of TAPG2^T were Gram-stain negative, aerobic, motile, non-spore forming, short rods surrounded by a thick capsules and forming cream to dark-green colonies. Growth occurred at 15-37 °C (optimum, 25-30 °C), at pH 6.5-8 (optimum, pH 7) and with 0-1 % NaCl (optimum, 0.5 %). The major fatty acids (>10 %) of TAPG2^T were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C18 : 1ω7c. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, an uncharacterized aminophospholipid, an uncharacterized phospholipid, an uncharacterized aminolipid and an uncharacterized lipid. The polyamine profile was composed of the major compound putrescine and moderate amounts of spermidine. The only isoprenoid quinone was Q-8. The DNA G+C content was 53.6 mol%. Phylogenetic analyses based on 16S rRNA gene sequences indicated that TAPG2^T represented a member of the genus Rheinheimera and was most closely related to Rheinheimera aquatica GR5^T and Rheinheimera texasensis A62-14B^T with 98.6 and 98.2 % 16S rRNA gene sequence identities, respectively. However, DNA-DNA hybridization values of TAPG2^T with type strains of the species with validly published names were lower than 30 %. Differential phenotypic properties, together with the phylogenetic inference, demonstrate that TAPG2^T should be classified as representing a novel species of the genus Rheinheimera, for which the name Rheinheimera coerulea sp. nov. is presented. The type strain is TAPG2^T (=BCRC 81054^T=LMG 30056^T=KCTC 52815^T).

Microbial composition of biofilm treating wastewater rich in bisphenol A

Although microbial degradation plays a major role in the removal of bisphenol A (BPA) from water environments, there is little information on the effect of BPA on microorganisms in wastewater treatment systems. The aim of this study was to determine the dynamics of the microbial communities in biofilm growing on porous ceramic supports in a column up-flow reactor during exposure to BPA at increasing concentrations from 0 to 10 mg L^-1. Independent of BPA load, the efficiency of BPA removal was about 90%. Groups of microorganisms that differ in their sensitivity to the presence of BPA in wastewater were identified. The core microbial genera in the biofilm were Acidovorax, Pseudoxanthomonas and Acinetobacter. Arenimonas sp., Thauera sp. and Acidobacterium sp. were the main components of the biofilm in the absence of BPA in wastewater. Increased abundances of Pseudomonas sp., Acidovorax sp. and Luteimonas sp. in BPA-exposed biofilm indicate that these genera may have played important roles in BPA biodegradation. A correlation between Pseudomonas sp. abundance and BPA removal efficiency indicates that BPA was used directly as a source of carbon and energy for growth. This study indicates that the use of the biofilm reactor enables effective BPA removal from wastewater and expands knowledge about the microbial structure of communities responsible for BPA degradation.

Rheinheimera salexigens sp. nov., isolated from a fishing hook, and emended description of the genus Rheinheimera

A Gram-negative, rod-shaped bacterium, designated KH87^T, was isolated from a fishing hook that had been baited and suspended in seawater off O'ahu, Hawai'i. Based on a comparison of 1524 nt of the 16S rRNA gene sequence of strain KH87^T, its nearest neighbours were the GammaproteobacteriaRheinheimera nanhaiensis E407-8^T (96.2 % identity), Rheinheimera chironomi K19414^T (96.0 %), Rheinheimera pacifica KMM 1406^T (95.8 %), Rheinheimera muenzenbergensis E49^T (95.7 %), Alishewanella solinquinati KMK6^T (94.9 %) and Arsukibacterium ikkense GCM72^T (94.6 %). Cells of KH87^T were motile by a single polar flagellum, strictly aerobic, and catalase- and oxidase-positive. Growth occurred between 4 and 39 °C, and in a circumneutral pH range. Major fatty acids in whole cells of strain KH87^T were cis-9-hexadecenoic acid, hexadecanoic acid and cis-11-octadecenoic acid. The quinone system contained mostly menaquinone MK-7, and a minor amount of ubiquinone Q-8. The polar lipid profile contained the major lipids phosphatidylglycerol, phosphatidylserine, phosphatidylethanolamine, an unidentified aminolipid, and a lipid not containing phosphate, an amino group or a sugar moiety. Putrescine was the major polyamine. Physiological, biochemical and genomic data, including obligate halophily, absence of amylolytic activity, a quinone system dominated by MK-7 and DNA G+C content (42.0 mol%) distinguished KH87^T from extant Rheinheimera species; strain KH87^T was also distinguished by a multi-locus sequence analysis of aligned and concatenated 16S rRNA, gyrB, rpoB and rpoD gene sequences. Based on phenotypic and genotypic differences, the species Rheinheimera salexigens sp. nov. is proposed to accommodate KH87^T as the type strain (=ATCC BAA-2715^T=CIP 111115^T). An emended description of the genus Rheinheimera is also proposed.

Lactic acid bacteria isolated from yak milk show probiotic potential

Probiotic industries strive for new, efficient and promising probiotic strains that impart a positive impact on consumer health. Challenges are persisting in isolation, screening, and selection of the new indigenous probiotic strains. In the present research, we explored the probiotic potential of 17 lactic acid bacteria isolated from Yak milk in a series of in vitro tests. We also demonstrated their health benefits, i.e., cholesterol degradation, lactose digestion, antimicrobial activity, antioxidant, and anticancer activities. Principal component analysis revealed that more than 50% of the strains fulfilled the examined criteria, e.g., survival in acidic pH, bile concentrations, and adherent property. Approximately all the strains produced antimicrobial substances against the maximum number of tested strains including clinical strains. Most strains degraded cholesterol in comparison to the reference probiotic strain whereas strain Yc showed 1.5 times higher the degradation efficiency of the control strain. Lan4 strain exhibited remarkable anticancer activity and induced the maximum apoptosis (87%) in the Hela cells and was non-toxic to the non-cancerous HEK293 cells. Around ten strains showed positive lactose digestion. Overall, this can be concluded that selected lactic acid bacteria revealed excellent probiotic properties along with desirable health benefits. These strains need to be further investigated in details for their application in the development of novel probiotic preparations for the improvement of public health.

Microbial taxonomy in the era of OMICS: application of DNA sequences, computational tools and techniques

The current prokaryotic taxonomy classifies phenotypically and genotypically diverse microorganisms using a polyphasic approach. With advances in the next-generation sequencing technologies and computational tools for analysis of genomes, the traditional polyphasic method is complemented with genomic data to delineate and classify bacterial genera and species as an alternative to cumbersome and error-prone laboratory tests. This review discusses the applications of sequence-based tools and techniques for bacterial classification and provides a scheme for more robust and reproducible bacterial classification based on genomic data. The present review highlights promising tools and techniques such as ortho-Average Nucleotide Identity, Genome to Genome Distance Calculator and Multi Locus Sequence Analysis, which can be validly employed for characterizing novel microorganisms and assessing phylogenetic relationships. In addition, the review discusses the possibility of employing metagenomic data to assess the phylogenetic associations of uncultured microorganisms. Through this article, we present a review of genomic approaches that can be included in the scheme of taxonomy of bacteria and archaea based on computational and in silico advances to boost the credibility of taxonomic classification in this genomic era.

Emended description of the family Chromatiaceae, phylogenetic analyses of the genera Alishewanella, Rheinheimera and Arsukibacterium, transfer of Rheinheimera longhuensis LH2-2T to the genus Alishewanella and description of Alishewanella alkalitolerans sp. nov. from Lonar Lake, India

Phylogenetic analyses were performed for members of the family Chromatiaceae, signature nucleotides deduced and the genus Alishewanella transferred to Chromatiaceae. Phylogenetic analyses were executed for the genera Alishewanella, Arsukibacterium and Rheinheimera and the genus Rheinheimera is proposed to be split, with the creation of the Pararheinheimera gen. nov. Furthermore, the species Rheinheimera longhuensis, is transferred to the genus Alishewanella as Alishewanella longhuensis comb. nov. Besides, the genera Alishewanella and Rheinheimera are also emended. Strain LNK-7.1^T was isolated from a water sample from the Lonar Lake, India. Cells were Gram-negative, motile rods, positive for catalase, oxidase, phosphatase, contained C_16:0, C_17:1ω8c, summed feature3 (C_16:1ω6c and/or C_16:1ω7c) and summed feature 8 (C_18:1ω7c) as major fatty acids, PE and PG as the major lipids and Q-8 as the sole respiratory quinone. Phylogenetic analyses using NJ, ME, ML and Maximum parsimony, based on 16S rRNA gene sequences, identified Alishewanella tabrizica RCRI4^T as the closely related species of strain LNK-7.1^T with a 16S rRNA gene sequence similarity of 98.13%. The DNA-DNA similarity between LNK-7.1^T and the closely related species (A. tabrizica) was only 12.0% and, therefore, strain LNK-7.1^T was identified as a novel species of the genus Alishewanella with the proposed name Alishewanella alkalitolerans sp. nov. In addition phenotypic characteristics confirmed the species status to strain LNK-7.1^T. The type strain of A. alkalitolerans is LNK-7.1^T (LMG 29592^T = KCTC 52279^T), isolated from a water sample collected from the Lonar lake, India.

Isolation and characterization of a novel Gram-negative bacterium Chromobacterium alkanivorans sp. nov., strain IITR-71T degrading halogenated alkanes

The taxonomic position of a Gram-stain negative, non-violaceinpigmented bacterium isolated from an insecticide-contaminated site was characterized by a polyphasic approach. The bacterium was able to grow on three different halogenated compounds namely 1-hlorobutane, 1-hloropropane and 1,2-ichloroethane. As a critical step in the degradation of these haloalkanes, stoichiometric amounts of dechlorination were estimated. Based on selective enrichment method for three months, using a highly contaminated mixed chemical soil, a bacterium was obtained and designated as IITR-71T. Its versatility and novelty led us to further characterize it by polyphasic taxonomy. The 16S rRNA gene sequence (1446 bases) comparison showed highest similarity with those of members of the genus Chromobacterium with the most closely related species to strain IITR-71T being Chromobacterium aquaticum (99.3 %) followed by Chromobacterium haemolyticum (98.6 %) and Chromobacterium piscinae (97.1 %). The major ubiquinone was Q-8. Predominant polar lipids are phosphatidylethanolamine (PE), phosphatidylglycerol (PG) and diphosphatidylglycerol (DPG). The DNA G+C content of IITR-71T was estimated to be 61.2 mol%. The genotypic and phenotypic distinctiveness of IITR-71T and its phylogenetic relationships indicate that IITR-71T represents a novel species, for which the name Chromobacterium alkanivorans sp. nov. is proposed. The type strain is IITR-71T (=MTCC 11059T=JCM 30068T=KCTC 52433T).