Chromium contamination accentuates changes in the microbiome and heavy metal resistome of a tropical agricultural soil

The impacts of hexavalent chromium (Cr) contamination on the microbiome, soil physicochemistry, and heavy metal resistome of a tropical agricultural soil were evaluated for 6 weeks in field-moist microcosms consisting of a Cr-inundated agricultural soil (SL9) and an untreated control (SL7). The physicochemistry of the two microcosms revealed a diminution in the total organic matter content and a significant dip in macronutrients phosphorus, potassium, and nitrogen concentration in the SL9 microcosm. Heavy metals analysis revealed the detection of seven heavy metals (Zn, Cu, Fe, Cd, Se, Pb, Cr) in the agricultural soil (SL7), whose concentrations drastically reduced in the SL9 microcosm. Illumina shotgun sequencing of the DNA extracted from the two microcosms showed the preponderance of the phyla, classes, genera, and species of Actinobacteria (33.11%), Actinobacteria_class (38.20%), Candidatus Saccharimonas (11.67%), and Candidatus Saccharimonas aalborgensis (19.70%) in SL7, and Proteobacteria (47.52%), Betaproteobacteria (22.88%), Staphylococcus (16.18%), Staphylococcus aureus (9.76%) in SL9, respectively. Functional annotation of the two metagenomes for heavy metal resistance genes revealed diverse heavy metal resistomes involved in the uptake, transport, efflux, and detoxification of various heavy metals. It also revealed the exclusive detection in SL9 metagenome of resistance genes for chromium (chrB, chrF, chrR, nfsA, yieF), cadmium (czcB/czrB, czcD), and iron (fbpB, yqjH, rcnA, fetB, bfrA, fecE) not annotated in SL7 metagenome. The findings from this study revealed that Cr contamination induces significant shifts in the soil microbiome and heavy metal resistome, alters the soil physicochemistry, and facilitates the loss of prominent members of the microbiome not adapted to Cr stress.

Accumulation of nylon microplastics and polybrominated diphenyl ethers and effects on gut microbial community of Chironomus sancticaroli

Microplastics (MP) are emerging contaminants with the capacity to bind and transport hydrophobic organic compounds of environmental concern, such as polybrominated diphenyl ethers (PBDEs). The aim of this study was to investigate the ingestion of nylon (polyamide) MP alone and when associated with PBDEs and their effects on Chironomus sancticaroli larvae survival and microbiome structure. Survival, PBDE uptake and microbial community composition were measured in fourth instar larvae exposed for 96 h to BDEs- 47, 99, 100 and 153 in the presence and absence of 1% w/w MP in sediment. Microbiome community structures were determined through high throughput sequencing of 16S small subunit ribosomal RNA gene (16S rRNA). Initial experiments showed that larvae ingested MP faster at 0.5% w/w MP, while depuration was more efficient at 1% w/w MP, although retention of MP was seen even after 168 h depuration. No mortality was observed as a result of PBDEs and MP exposure. MP had a negative effect on PBDE concentration within larvae (η² = 0.94) and a negative effect on sediment concentrations (η² = 0.48). In all samples, microbial communities were dominated by Alphaproteobacteria, Betaproteobacteria, Actinobacteria and Gammaproteobacteria. Bacterial alpha diversity was not significantly affected by PBDEs or MP exposure. However, the abundance of discrete bacterial taxa was more sensitive to MP (X² = 45.81, p = 0.02), and PBDE exposure. Our results highlight that C. sancticaroli showed no acute response to MPs and PBDEs, but that MPs influenced bacterial microbiome structure even after only short-term acute exposure.

Leucobacter chinensis sp. nov., with plant growth-promoting potential isolated from field soil after seven-years continuous maize cropping

A novel Gram-stain-positive, aerobic, non-motile and rod-shaped bacterium, designated strain NC76-1^T, was isolated from soil from a field that had undergone seven years continuous maize cropping from Liuba town located in Zhangye city, Gansu province, PR China. Colonies of strain NC76-1^T were white, opaque and circular with a convex shape. The isolate was found to be able to grow at 10-40 °C (optimum 30 °C), pH 6.0 to 12.0 (optimum 7.0-8.0) and with 0-5.0 % (w/v) NaCl (optimum 0%). On the basis of the results of 16S rRNA gene sequence analysis, the strain fell within the clade of the genus Leucobacter, showing the highest sequence similarities with Leucobacter iarius 40^T (97.4%), Leucobacter aridicollis CIP 108388^T (97.0%), Leucobacter chromiireducens subsp. solipictus TAN 31504^T (96.7%) and Leucobacter denitrificans M1T8B10^T (96.7%). The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between NC76-1^T and its closest relatives, L. iarius 40^T, L. aridicollis CIP 108388^T, L. chromiireducens subsp. solipictus TAN 31504^T and L. denitrificans M1T8B10^T were ≤73.5 % and 20.3%, respectively. The genomic DNA G+C content of NC76-1^T was 61.5 mol%. It presented MK-11 as the predominant menaquinone. The major cellular fatty acids were anteiso-C_15 : 0 (49.2 %) and iso-C_16 : 0 (35.7%). The major polar lipids were found to be diphosphatidyglycerol, phosphatidylglycerol, phosphatidylethanolamine, aminoglycolipid, five glycolipid and one unidentified lipids. The cell wall amino acids were 2,4-diaminobutyric acid, alanine, glutamic acid, glycine and threonine. On the basis of the phylogenetic, phenotypic and chemotaxonomic characteristics, strain NC76-1^T is concluded to represent a novel species within the genus Leucobacter, for which the name Leucobacter chinensis sp. nov. is proposed. The type strain is NC76-1^T (GDMCC 1.2286^T= JCM 34651^T).

The Chironomid Microbiome Plays a Role in Protecting Its Host From Toxicants

Organisms are assemblages of the host and their endogenous bacteria, which are defined as microbiomes. The host and its microbiome undergo a mutual evolutionary process to adapt to changes in the environment. Chironomids (Diptera; Chironomidae), are aquatic insects that grow and survive in polluted environments; however, the mechanisms that protect them under these conditions are not fully understood. Here we present evidence that the chironomids’ microbiome enables them to survival in polluted environments. It has been demonstrated that about 40% of the microbiota that inhabit Chironomus transvaalensis egg masses and larvae has the potential to detoxify different toxicants. Metagenomic analysis of Chironomus ramosus larvae demonstrated the presence of genes in the insects’ microbiome that can help the insects to survive in hostile environments. A set of experiments demonstrated that short exposure of C. transvaalensis larvae to metals significantly changed their microbiota composition in comparison to unexposed larvae. Another experiment, that followed Koch’s postulates, demonstrated that disinfected C. transvaalensis larvae can survive toxic lead and chromium exposure when they are recolonized with bacteria that can detoxify these toxic metals. This accumulating research, points to the conclusion that the chironomid microbiome plays a role in protecting its host from toxicants.

Leucobacter soli sp. nov., from soil amended with humic acid

A Gram-positive, non-spore-forming actinobacterium (IMT-300^T) was isolated from soil amended with humic acid in Malvern, AL, USA. This soil has been used for 50+years for the cultivation of earthworms for use as fish bait. Based on 16S rRNA gene sequence similarity studies, strain IMT-300^T was shown to belong to the genus Leucobacter and was closely related to the type strain of 'Leucobacter margaritiformis' L1^T (97.8%). Similarity to all other type strains of Leucobacter species was lower than 97.2 %. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the IMT-300^T genome assembly and those of the closest relative Leucobacter type strain were 81.4 and 23.3 % (Leucobacter chironomi), respectively. The peptidoglycan of strain IMT-300^T contained l-2,4-diaminobutyric acid as the diagnostic diamino acid. In addition, glycine, d- and l-alanine and d-glutamic acid were found. The peptidoglycan type represents a variant of B2δ (B11). The major quinones were menaquinones MK-10 and MK-11. The polar lipid profile consisted of the major lipids diphosphatidylglycerol, phosphatidylglycerol and moderate to minor amounts of two unidentified phospholipids, two unidentified glycolipids and an unidentified aminophospholipid. The polyamine pattern contained major amounts of spermidine and spermine. Strain IMT-300^T contained the major fatty acids C_15 : 0 anteiso, C_16 : 0 iso and C_17 : 0 anteiso, like other members of the genus Leucobacter. The results of ANI and dDDH analyses and physiological and biochemical tests allowed a genotypic and phenotypic differentiation of strain IMT-300^T from the most closely related Leucobacter species. Strain IMT-300^T represents a novel Leucobacter species, for which we propose the name Leucobacter soli sp. nov., with the type strain IMT-300^T (CIP 111803^T=DSM 110505^T=CCM 9020^T=LMG 31600^T).

Leucobacter muris sp. nov., isolated from the nose of a laboratory mouse

A Gram-stain-positive, rod-shaped, aerobic, non-motile, white, opaque bacterial isolate, designated 924/12^T, was isolated from the nose of a laboratory mouse in Düsseldorf, Germany. The 16S rRNA gene sequence analyses indicated the phylogenetic position of the strain within the genus Leucobacter. Similarity levels over 97 % were recorded between the 16S rRNA gene sequence of strain 924/12^T and the type strains of the species Leucobacter chironomi DSM 19883^T (99.5 %), followed by Leucobacter celersubsp. astrifaciens CBX151^T (97.6 %), Leucobacter celersubsp. celer NAL101^T (97.5 %), 'Leucobacter kyeonggiensis' F3-P9 (97.5 %), Leucobacter zeae CC-MF41^T (97.3 %), Leucobacter chromiiresistens JG31^T (97.1 %), Leucobacter triazinivorans JW-1^T (97.1 %), Leucobacter corticis 2 C-7^T (97.0 %) and Leucobacter aridicolis CIP108388^T (97.0 %). DNA-DNA hybridization and whole genomic comparison, mandatory to taxonomically separate strain 924/12^T from the type strain of L. chironomi, revealed similarity values of 40.4 and 30.8 %, respectively, thus below the threshold of 70 % recommended differentiating between species. The cell-wall amino acids of the novel isolate were diaminobutyric acid, alanine, glycine, threonine and glutamic acid. The major fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, glycolipid and one unknown lipid, whereas the predominant menaquinones were MK-11 and MK-10. The genomic DNA G+C content of strain 924/12^T was 70.6 mol%. Phylogenetic analyses based on the 16S rRNA gene sequences and the phenotypical differences between strain 924/12^T and the other closely related type strains of the genus Leucobacter indicated that strain 924/12^T represents a novel species within the genus Leucobacter, family Microbacteriaceae, for which the name Leucobacter muris sp. nov. is proposed. The type strain is 924/12^T (=DSM 101948^T=CCM 8761^T).

Chromate Resistance Mechanisms in Leucobacter chromiiresistens

Chromate is one of the major anthropogenic contaminants on Earth. Leucobacter chromiiresistens is a highly chromate-resistant strain, tolerating chromate concentrations in LB medium of up to 400 mM. In response to chromate stress, L. chromiiresistens forms biofilms, which are held together via extracellular DNA. Inhibition of biofilm formation leads to drastically decreased chromate tolerance. Moreover, chromate is reduced intracellularly to the less-toxic Cr(III). The oxidation status and localization of chromium in cell aggregates were analyzed by energy-dispersive X-ray spectroscopy coupled to scanning transmission electron microscopy and X-ray absorption spectroscopy measurements. Most of the heavy metal is localized as Cr(III) at the cytoplasmic membrane. As a new cellular response to chromate stress, we observed an increased production of the carotenoid lutein. Carotenoid production could increase membrane stability and reduce the concentration of reactive oxygen species. Bioinformatic analysis of the L. chromiiresistens genome revealed several gene clusters that could enable heavy-metal resistance. The extreme chromate tolerance and the unique set of resistance factors suggest the use of L. chromiiresistens as a new model organism to study microbial chromate resistance.IMPORTANCE Chromate is a highly toxic oxyanion. Extensive industrial use and inadequate waste management has caused the toxic pollution of several field sites. Understanding the chromate resistance mechanisms that enable organisms to thrive under these conditions is fundamental to develop (micro)biological strategies and applications aiming at bioremediation of contaminated soils or waters. Potential detoxifying microorganisms are often not sufficient in their resistance characteristics to effectively perform, e.g., chromate reduction or biosorption. In this study, we describe the manifold strategies of L. chromiiresistens to establish an extremely high level of chromate resistance. The multitude of mechanisms conferring it make this organism suitable for consideration as a new model organism to study chromate resistance.

Genome-Based Taxonomic Classification of the Phylum Actinobacteria

The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum Actinobacteria but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.

Defining microbial community composition and seasonal variation in a sewage treatment plant in India using a down-flow hanging sponge reactor

The characteristics of the microbial community in a practical-scale down-flow hanging sponge (DHS) reactor, high in organic matter and sulfate ion concentration, and the seasonal variation of the microbial community composition were investigated. Microorganisms related to sulfur oxidation and reduction (2-27%), as well as Leucobacter (7.50%), were abundant in the reactor. Anaerobic bacteria (27-38% in the first layer) were also in abundance and were found to contribute to the removal of organic matter from the sewage in the reactor. By comparing the Simpson index, the abundance-based coverage estimator (ACE) index, and the species composition of the microbial community across seasons (summer/dry, summer/rainy, autumn/dry, and winter/dry), the microbial community was found to change in composition only during the winter season. In addition to the estimation of seasonal variation, the difference in the microbial community composition along the axes of the DHS reactor was investigated for the first time. Although the abundance of each bacterial species differed along both axes of the reactor, the change of the community composition in the reactor was found to be greater along the vertical axis than the horizontal axis of the DHS reactor.

Genome sequence of "Leucobacter massiliensis" sp. nov. isolated from human pharynx after travel to the 2014 Hajj

"Leucobacter massiliensis" strain 122RC15T sp. nov. is a new species within the genus Leucobacter. The genome of this strain is described here. It was isolated from the pharynx of a 76-year-old Algerian female after travelling from the 2014 Hajj. "Leucobacter massiliensis" is a Gram-positive, aerobic bacillus. Here we describe the features including complete genome and annotation of this strain. The 3 136 406-bp long genome contains 2797 protein-coding genes and 49 RNA genes.

Leucobacter weissii sp. nov., an isolate from activated sludge once described as first representative of the peptidoglycan variation B2δ, and emended description of the genus Leucobacter

Strain S27^T is a Gram-stain-positive, regular rod-shaped, non-motile, non-spore-forming, yellow pigmented actinobacterium which was isolated from an aerated laboratory scale fermenter fed with wastes of a yeast factory. The strain was classified as Microbacterium sp. after the analysis of its peptidoglycan revealed a novel B-type structure established as variation B2δ by Hensel in 1984. As the combination of the peptidoglycan amino acids 2,4-diaminobutyric acid (Dab), threonine (Thr), glycine (Gly), alanine (Ala) and glutamic acid (Glu) is in disagreement with the current genus definition of Microbacterium but is typical of several Leucobacter species, the taxonomic status of strain S27^T was re-examined by a polyphasic study. Comparative analyses of 16S rRNA gene sequences and the occurrence of l-Dab, d-Ala, l-Ala, Gly, l-Thr, d-Glu and lower amounts of l-Glu in the peptidoglycan in combination with the predominating menaquinones MK-11, MK-10 and MK-9, phosphatidylglycerol, and one unknown glycolipid as the major polar lipids (and trace amounts of diphosphatidylglycerol and an unknown phospholipid), a profile with anteiso-C15 : 0, iso-C15 : 0, iso-C16 : 0, anteiso-C17 : 0 and iso-C17 : 0 as major fatty acids and the G+C value of 70.1 mol% confirmed the affiliation to the genus Leucobacter and revealed that S27^T (=DSM 20621^T =CCM 8762^T) is the type strain of a new species for which the name Leucobacter weissii sp. nov. is proposed. The availability of new data allows for an emended description of the genus Leucobacter.

Nesterenkonia pannonica sp. nov., a novel alkaliphilic and moderately halophilic actinobacterium

An alkaliphilic and moderately halophilic bacterial strain characterized by optimal growth at pH 9.0-10.0 and with 5-7 % (w/v) NaCl, designated BV-35^T, was isolated from water of a soda pan located in Kiskunság National Park, Hungary. Cells of the orange-pigmented colony were Gram-stain-positive, non-motile and non-endospore-forming coccoid rods. The isolate was strictly aerobic, catalase-positive and oxidase-negative. Strain BV-35^T displayed a peptidoglycan similar to type A4α, l-Lys-l-Glu (A11.54 according to www.peptidoglycan-types.info) but containing additionally 4-aminobutyric acid. Menaquinone-7 (MK-7) was the predominant isoprenoid quinone, and anteiso-C15 : 0 and anteiso-C17 : 0 were its major cellular fatty acids. The DNA G+C content of strain BV-35^T was 65.4 mol%. Based on 16S rRNA gene sequence similarities, the novel isolate showed the closest relationship to Nesterenkonia populi GP 10-3^T (97.9 %). The DNA-DNA relatedness between BV-35^T and N. populi was 46.7 %. The distinguishing phenotypic and genetic results of this polyphasic study revealed that strain BV-35^T represents a novel member of the genus Nesterenkonia, for which the name Nesterenkonia pannonica sp. nov. is proposed. The type strain is BV-35^T (=DSM 29786^T=NCAIM B 02606^T).

Bacterial fauna associating with chironomid larvae from lakes of Bengaluru city, India - A 16s rRNA gene based identification

Chironomid larvae that inhabit in aquatic sediments play an important role as vector for bacterial pathogens. Its life cycle consists of four stages i.e. eggs, larvae, pupae and adult. In the present study we identified bacterial species associated with whole larvae of chironomids from 11 lake sediments of Bangalore region using 16s rRNA gene Sanger sequencing. We found that larvae from all lake sediments associated with bacterial species which include key pathogens. Totally we identified 65 bacterial isolates and obtained GenBank accession numbers (KX980423 - KX980487). Phylogenetic tree constructed using MEGA 7 software and tree analysis highlight the predominant bacterial community associated with larvae which include Enterobacteriaceae (43.08%; 28 isolates) and Aeromonas (24.62%; 16 isolates), Shewanella, Delftia, Bacillus (6.15%; 4 isolates each), Pseudomonas (4.62%; 3 isolates) and Exiguobacterium (3.08%; 2 isolates). Current findings state that among bacterial population Aeromonas, Enterobacter and Escherichia with serotypes are commonly associated with larvae in maximum lake points. In other hand Vibrio, Pseudomonas, Klebsiella, Shigella, Bacillus, and other bacterial species were identified moderately in all lakes. Interestingly, we identified first time Shigella Gram negative, rod shaped pathogenic organism of Enterobacteriaceae and Rheinheimera Gram negative, rod shaped organism associating chironomid larvae.

Description of Leucobacter holotrichiae sp. nov., isolated from the gut of Holotrichia oblita larvae

A Gram-stain-positive bacterium, designated T14T, was isolated from the gut of Holotrichia oblita larvae and was subjected to a taxonomic study. The isolate was rod-shaped, aerobic, non-motile, non-spore-forming and yellow-pigmented. Phylogenetic analysis based on 16S rRNA gene sequence comparison indicated that the isolate is related to the genus Leucobacter. Its closest neighbours were the type strains 'Leucobacter kyeonggiensis' F3-P9 (96.8% 16S rRNA gene sequence similarity), Leucobacter celer NAL101T (96.2%) and Leucobacter chironomi DSM 19883T (95.5%). The DNA G+C content of strain T14T was 69.3 mol%, and DNA-DNA hybridization values with closely related strains were <32%. The predominant cellular fatty acids were anteiso-C15:0 (49.3%), iso-C16:0 (16.4%) and anteiso-C17:0 (16.8%). The major polar lipids were aminolipid, diphosphatidylglycerol, phosphatidylglycerol, phospholipid, phosphoglycolipid and unidentified glycolipids. The predominant respiratory quinone was MK-11. Based on these phylogenetic and phenotypic results, strain T14T can be clearly distinguished from all of the recognized species of the genus Leucobacter and is considered to represent a novel species of the genus Leucobacter. The name Leucobacter holotrichiae sp. nov. is proposed, with the type strain T14T (=DSM 28968T=JCM 30245T).

High-Quality Draft Genome Sequence of Leucobacter sp. Strain G161, a Distinct and Effective Chromium Reducer

Here, we report the genome sequence for Leucobacter sp. strain G161 due to its distinct and effective hexavalent chromium reduction under aerobic growth conditions, followed by facultative anaerobic incubation. The draft genome sequence of Leucobacter sp. G161 comprises 3,554,188 bp, with an average G+C content of 65.3%, exhibiting 3,341 protein-coding genes and 55 predicted RNA genes.

Leucobacter zeae sp. nov., isolated from the rhizosphere of maize (Zea mays L.)

A novel yellow-pigmented, aerobic, rod-shaped, non-motile bacterium, designated strain CC-MF41T, was isolated from rhizosphere soil of maize (Zea mays) collected in Wufeng District, Taichung, Taiwan. Strain CC-MF41T exhibited 16S rRNA gene sequence similarity of 97.5, 97.3, 97.2 and 97.1 % to Leucobacter chironomi MM2LBT (and ‘Leucobacter kyeonggiensis’ F3-P9 and ‘L. humi’ Re-6, the names of which have not been validly published), Leucobacter tardus K70/01T, L. komagatae IFO 15245T and ‘Leucobacter margaritiformis’ A23. However, CC-MF41T and ‘L. margaritiformis’ A23 formed a loosely bound phylogenetic lineage (with a low bootstrap value) associated with species of the genus Leucobacter. In DNA–DNA reassociation experiments, the relatedness of strain CC-MF41T to L. chironomi DSM 19883T was 57.1 % (reciprocal value 29.1 %). The DNA G+C content of strain CC-MF41T was 72.1 mol% and the cell-wall peptidoglycan contained 2,4-diaminobutyric acid, alanine, glycine, glutamic acid and threonine. The major menaquinone was MK-11 and the predominant fatty acids were iso-C16 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. The polar lipid profile of strain CC-MF41T contained major amounts of diphosphatidylglycerol followed by an unidentified glycolipid, phosphatidylglycerol and an unknown phospholipid. Based on its phylogenetic, phenotypic and chemotaxonomic distinctiveness, strain CC-MF41T represents a novel species of Leucobacter, for which the name Leucobacter zeae sp. nov. is proposed. The type strain is CC-MF41T ( = BCRC 80515T = LMG 27265T).

Leucobacter musarum subsp. musarum sp. nov., subsp. nov., Leucobacter musarum subsp. japonicus subsp. nov., and Leucobacter celer subsp. astrifaciens subsp. nov., three nematopathogenic bacteria isolated from Caenorhabditis, with an emended description of Leucobacter celer

Three Gram-stain-positive, irregular-rod-shaped, non-motile, non-spore-forming bacteria were isolated from nematodes collected from Santa Antao, Cabo Verde (CBX151^T, CBX152^T) and Kakegawa, Japan (CBX130^T). Based on 16S rRNA gene sequence similarity, strains CBX130^T, CBX151^T and CBX152^T were shown to belong to the genus Leucobacter. This affiliation was supported by chemotaxonomic data (2,4-diaminobutyric acid in the cell wall; major respiratory quinones MK-10 and MK-11; major polar lipids phosphatidylglycerol and diphosphatidylglycerol; major fatty acids anteiso-C_15 : 0, anteiso-C_17 : 0 and iso-C_16 : 0). Strains CBX130^T and CBX152^T were found to share salient characteristics. Based on morphological, physiological, chemotaxonomic and biochemical analysis, strain CBX152^T represents a novel species of the genus Leucobacter, for which the name Leucobacter musarum sp. nov. (type strain CBX152^T = DSM 27160^T = CIP 110721^T) is proposed. Two subspecies of Leucobacter musarum sp. nov. are proposed: Leucobacter musarum sp. nov. subsp. musarum subsp. nov. (type strain CBX152^T = DSM 27160^T = CIP 110721^T) and Leucobacter musarum sp. nov. subsp. japonicus subsp. nov. (type strain CBX130^T = DSM 27158^T = CIP 110719^T). The third novel strain, CBX151^T, showed genetic similarities with Leucobacter celer NAL101^T indicating that these strains belong to the same species. Based on morphological, physiological, chemotaxonomic and biochemical differences it is proposed to split the species Leucobacter celer into two novel subspecies, Leucobacter celer subsp. celer subsp. nov. (type strain NAL101^T = KACC 14220^T = JCM 16465^T) and Leucobacter celer subsp. astrifaciens subsp. nov. (type strain CBX151^T = DSM 27159^T = CIP 110720^T), and to emend the description of Leucobacter celerShin et al. 2011.

High quality draft genome sequence of Leucobacter chironomi strain MM2LB(T) (DSM 19883(T)) isolated from a Chironomus sp. egg mass

Leucobacter chironomi strain MM2LB^T (Halpern et al., Int J Syst Evol Microbiol 59:665-70 2009) is a Gram-positive, rod shaped, non-motile, aerobic, chemoorganotroph bacterium. L. chironomi belongs to the family Microbacteriaceae, a family within the class Actinobacteria. Strain MM2LB^T was isolated from a chironomid (Diptera; Chironomidae) egg mass that was sampled from a waste stabilization pond in northern Israel. In a phylogenetic tree based on 16S rRNA gene sequences, strain MM2LB^T formed a distinct branch within the radiation encompassing the genus Leucobacter. Here we describe the features of this organism, together with the complete genome sequence and annotation. The DNA GC content is 69.90%. The chromosome length is 2,964,712 bp. It encodes 2,690 proteins and 61 RNA genes. L. chironomi genome is part of the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG) project.

Chironomid microbiome

Chironomids are abundant insects in freshwater habitats. They undergo a complete metamorphosis of four life stages: eggs, larvae, and pupae in water, and a terrestrial adult stage. Chironomids are known to be pollution-tolerant, but little is known about their resistance mechanisms to toxic substances. Here we review current knowledge regarding the chironomid microbiome. Chironomids were found as natural reservoirs of Vibrio cholerae and Aeromonas spp. A stable bacterial community was found in the egg masses and the larvae when both culture-dependent and -independent methods were used. A large portion of the endogenous bacterial species was closely related to species known as toxicant degraders. Bioassays based on Koch's postulates demonstrated that the chironomid microbiome plays a role in protecting its host from toxic hexavalent chromium and lead. V. cholerae, a stable resident in chironomids, is present at low prevalence. It degrades the egg masses by secreting haemagglutinin/protease, prevents eggs from hatching, and exhibits host pathogen interactions with chironomids. However, the nutrients from the degraded egg masses may support the growth of the other microbiome members and consequently control V. cholerae numbers in the egg mass. V. cholerae, other chironomid endogenous bacteria, and their chironomid host exhibit complex mutualistic relationships.

Genome sequence of the chromate-resistant bacterium Leucobacter salsicius type strain M1-8(T.)

Leucobacter salsicius M1-8(T) is a member of the Microbacteriaceae family within the class Actinomycetales. This strain is a Gram-positive, rod-shaped bacterium and was previously isolated from a Korean fermented food. Most members of the genus Leucobacter are chromate-resistant and this feature could be exploited in biotechnological applications. However, the genus Leucobacter is poorly characterized at the genome level, despite its potential importance. Thus, the present study determined the features of Leucobacter salsicius M1-8(T), as well as its genome sequence and annotation. The genome comprised 3,185,418 bp with a G+C content of 64.5%, which included 2,865 protein-coding genes and 68 RNA genes. This strain possessed two predicted genes associated with chromate resistance, which might facilitate its growth in heavy metal-rich environments.

16S ribosomal DNA sequence-based identification of bacteria in laboratory rodents: a practical approach in laboratory animal bacteriology diagnostics

Correct identification of bacteria is crucial for the management of rodent colonies. Some bacteria are difficult to identify phenotypically outside reference laboratories. In this study, we evaluated the utility of 16S ribosomal DNA (rDNA) sequencing as a means of identifying a collection of 30 isolates of rodent origin which are conventionally difficult to identify. Sequence analysis of the first approximate 720 to 880 bp of the 5'- end of 16S rDNA identified 25 isolates (83.33%) with ≥ 99% similarity to a sequence of a type strain, whereas three isolates (10%) displayed a sequence similarity ≥ 97% but <99% to the type strain sequences. These similarity scores were used to define identification to species and genus levels, respectively. Two of the 30 isolates (6.67%) displayed a sequence similarity of ≥ 95 but <97% to the reference strains and were thus allocated to a family. This technique allowed us to document the association of mice with bacteria relevant for the colonies management such as Pasteurellaceae, Bordetella hinzii or Streptococcus danieliae. In addition, human potential pathogens such as Acinetobacter spp., Ochrobactrum anthropi and Paracoccus yeei or others not yet reported in mouse bacterial species such as Leucobacter chironomi, Neisseria perflava and Pantoea dispersa were observed. In conclusion, the sequence analysis of 16S rDNA proved to be a useful diagnostic tool, with higher performance characteristics than the classical phenotypic methods, for identification of laboratory animal bacteria. For the first time this method allowed us to document the association of certain bacterial species with the laboratory mouse.

Molecular mechanisms of Cr(VI) resistance in bacteria and fungi

Hexavalent chromium [Cr(VI)] contamination is one of the main problems of environmental protection because the Cr(VI) is a hazard to human health. The Cr(VI) form is highly toxic, mutagenic, and carcinogenic, and it spreads widely beyond the site of initial contamination because of its mobility. Cr(VI), crossing the cellular membrane via the sulfate uptake pathway, generates active intermediates Cr(V) and/or Cr(IV), free radicals, and Cr(III) as the final product. Cr(III) affects DNA replication, causes mutagenesis, and alters the structure and activity of enzymes, reacting with their carboxyl and thiol groups. To persist in Cr(VI)-contaminated environments, microorganisms must have efficient systems to neutralize the negative effects of this form of chromium. The systems involve detoxification or repair strategies such as Cr(VI) efflux pumps, Cr(VI) reduction to Cr(III), and activation of enzymes involved in the ROS detoxifying processes, repair of DNA lesions, sulfur metabolism, and iron homeostasis. This review provides an overview of the processes involved in bacterial and fungal Cr(VI) resistance that have been identified through 'omics' studies. A comparative analysis of the described molecular mechanisms is offered and compared with the cellular evidences obtained using classical microbiological approaches.

Draft Genome Sequence of Leucobacter sp. Strain UCD-THU (Phylum Actinobacteria)

Here we present the draft genome of Leucobacter sp. strain UCD-THU. The genome contains 3,317,267 bp in 11 scaffolds. This strain was isolated from a residential toilet as part of an undergraduate project to sequence reference genomes of microbes from the built environment.

The protective role of endogenous bacterial communities in chironomid egg masses and larvae

Insects of the family Chironomidae, also known as chironomids, are distributed worldwide in a variety of water habitats. These insects display a wide range of tolerance toward metals and organic pollutions. Bacterial species known for their ability to degrade toxicants were identified from chironomid egg masses, leading to the hypothesis that bacteria may contribute to the survival of chironomids in polluted environments. To gain a better understanding of the bacterial communities that inhabit chironomids, the endogenous bacteria of egg masses and larvae were studied by 454-pyrosequencing. The microbial community of the egg masses was distinct from that of the larval stage, most likely due to the presence of one dominant bacterial Firmicutes taxon, which consisted of 28% of the total sequence reads from the larvae. This taxon may be an insect symbiont. The bacterial communities of both the egg masses and the larvae were found to include operational taxonomic units, which were closely related to species known as toxicant degraders. Furthermore, various bacterial species with the ability to detoxify metals were isolated from egg masses and larvae. Koch-like postulates were applied to demonstrate that chironomid endogenous bacterial species protect the insect from toxic heavy metals. We conclude that chironomids, which are considered pollution tolerant, are inhabited by stable endogenous bacterial communities that have a role in protecting their hosts from toxicants. This phenomenon, in which bacteria enable the continued existence of their host in hostile environments, may not be restricted only to chironomids.

Diversity of marine bacteria producing beta-glucosidase inhibitors

BACKGROUND

Beta-glucosidase inhibitors are being extensively studied for use as anti-diabetics, anti-obesity and anti-tumour compounds. So far, these compounds have been reported in large numbers from plants, mushrooms, algae and fungi. There are very few reports of such inhibitors from bacteria in the open literature, particularly marine bacteria; although the best known inhibitor deoxynojirimycin was isolated from bacilli and actinomycete. Through this study, we tried to discover the diversity of microbial associates of marine sponge and sediment producing β-glucosidase inhibitors.

RESULTS

We found 41 (22.7%) out of 181 bacteria, produced such inhibitors. The inhibitors are abundant in bacterial associates of marine sponge Aka coralliphaga. When these bacteria were phylogenetically analyzed, it was found that marine bacteria producing glucosidase inhibitors belong to the phylum Firmicutes (23), Actinobacteria (9), Proteobacteria (7) and Bacteroidetes (1).

CONCLUSION

A significant number of marine bacteria belonging to a wide range of bacterial taxa were found to produce β-glucosidase inhibitors. These compounds are abundantly present in bacteria of the phylum Firmicutes followed by the phylum Actinobacteria. The results nurture a hope of finding new compounds, which can inhibit glucosidases, in the bacterial domain of marine organisms. Thus, marine microbial cells can be utilized as producers of pharmacologically essential enzyme inhibitors.

Bacterial community composition associated with chironomid egg masses

Chironomids (Diptera: Chironomidae) are the most widely distributed and often the most abundant insect in freshwater. They undergo a complete metamorphosis of four life stages, of which the egg, larva, and pupae are aquatic and the adult is terrestrial. Chironomid egg masses were found to be natural reservoirs of Vibrio cholerae and Aeromonas species. To expand the knowledge of the endogenous bacterial community associated with chironomid egg masses, denaturing gradient gel electrophoresis and clone analysis of 16S rRNA gene libraries were used in this study. Bacterial community composition associated with chironomid egg masses was found to be stable among different sampling periods. Cloned libraries of egg masses revealed that about 40% of the clones were related to bacteria known to degrade various toxicants. These findings were further supported when bacterial species that showed resistance to different toxic metals were isolated from egg masses and larval samples. Chironomids are found under a wide range of water conditions and are able to survive pollutants. However, little is known about their protective mechanisms under these conditions. Chironomid egg masses are inhabited by a stable endogenous bacterial community, which may potentially play a role in protecting chironomids from toxicants in polluted environments. Further study is needed to support this hypothesis.

Leucobacter celer sp. nov., isolated from Korean fermented seafood

A novel, Gram-reaction-positive, aerobic, rod-shaped, non-motile bacterial strain, designated NAL101T, was isolated from gajami-sikhae, a traditional Korean fermented seafood made of flatfish. Growth occurred at 4–45 °C, at pH 5–10 and in 0–12 % (w/v) NaCl. Optimum growth occurred at 30–37 °C, at pH 8 and in 0–1 % (w/v) NaCl. The cell-wall amino acids were 2,4-diaminobutyric acid, alanine, glycine, threonine and glutamic acid and the major fatty acids were anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. The predominant menaquinone was MK-11. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and an unknown glycolipid. The 16S rRNA gene sequence of strain NAL101T showed 97.7 % similarity to that of Leucobacter chironomi MM2LBT, its closest relative. The DNA G+C content was 68.8 mol% and DNA–DNA hybridization values with closely related strains were <22 %. Phylogenetic analyses based on 16S rRNA gene sequences as well as differences in its physiological and biochemical characteristics indicated that strain NAL101T represents a novel species of the genus Leucobacter in the family Microbacteriaceae, for which the name Leucobacter celer sp. nov. is proposed. The type strain is NAL101T ( = KACC 14220T  = JCM 16465T).

Leucobacter chromiiresistens sp. nov., a chromate-resistant strain

A Gram-positive, irregular rod-shaped, non-motile, yellow-pigmented bacterium, strain JG 31T, was isolated in the course of identifying chromium-resistant soil bacteria. 16S rRNA gene sequence analysis of the isolated bacterium indicated its phylogenetic position within the genus Leucobacter. Binary 16S rRNA gene sequence alignments of the isolated bacterium with the 11 species of the genus recognized at the time of writing revealed sequence similarities of more than 97 % with Leucobacter alluvii (GenBank accession no: AM072820; 99.4 %), Leucobacter iarius (AM040493; 98.2 %), Leucobacter aridicollis (AJ781047; 97.8 %), Leucobacter komagatae (AB007419; 97.4 %), Leucobacter chironomi (EU346911; 97.1 %) and Leucobacter luti (AM072819; 97.1 %). In contrast, DNA–DNA hybridization experiments showed similarity values below 28 % for DNA samples from the most closely related type strains of L. alluvii, L. aridicollis and L. iarius. Protein analysis by matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and automated RiboPrinting using the restriction enzyme PvuII differentiated strain JG 31T from all type strains of the genus Leucobacter. The dominant fatty acids of the novel isolate were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0, while the quinone system consisted of menaquinones MK-11, MK-10, MK-9 and MK-8. In a B-type cross-linked peptidoglycan, the cell-wall amino acids were alanine, glycine, threonine, glutamic acid and 2,4-diaminobutyric acid. Strain JG 31T was able to grow in a medium containing up to 300 mM K2CrO4 and showed cellular aggregation in response to chromate stress. From biochemical and genomic analyses, the new strain is considered to represent a novel species of the genus Leucobacter, for which the name Leucobacter chromiiresistens sp. nov. is proposed. The type strain is strain JG 31T ( = DSM 22788T  = CCOS 200T).

Leucobacter salsicius sp. nov., from a salt-fermented food

Strain M1-8T was isolated from jeotgal, a Korean salt-fermented food. Cells were aerobic, non-motile, Gram-reaction-positive and rod-shaped. Colonies were cream-coloured and circular with entire margins. Strain M1-8T exhibited optimal growth at 25–30 °C and pH 7.0–8.0 and in 0–4 % (w/v) NaCl. The strain tolerated up to 10.0 mM Cr(VI). Phylogenetic analyses of 16S rRNA gene sequences indicated that strain M1-8T represents a novel species in the genus Leucobacter. The 16S rRNA gene sequence of M1-8T exhibited 98.1 % similarity to that of Leucobacter chromiireducens subsp. chromiireducens L-1T. The new isolate was clustered with Leucobacter species on a 16S rRNA gene sequence-based phylogenetic tree. The chromosomal DNA G+C content of strain M1-8T was 62.8 mol%. Its cell-wall peptidoglycan contained 2,4-diaminobutyric acid, glutamic acid, alanine, glycine and γ-aminobutyric acid. The major menaquinone was MK-11 and the predominant fatty acids were anteiso-C15 : 0 (63.6 %), anteiso-C17 : 0 (16.7 %) and iso-C16 : 0 (14.2 %). The polar lipid profile of strain M1-8T contained diphosphatidylglycerol and one unknown glycolipid. Significant genotypic and phenotypic differences were found between strain M1-8T and other Leucobacter species. These differentiating characteristics indicate that strain M1-8T represents a novel species of the genus Leucobacter, for which the name Leucobacter salsicius sp. nov. is proposed. The type strain is M1-8T (=KACC 21127T =JCM 16362T).

Leucobacter aerolatus sp. nov., from the air of a duck barn

A Gram-positive, non-spore-forming actinobacterium (Sj 10T) was isolated on tryptone soy agar from the air of a duck barn after filter sampling. Based on 16S rRNA gene sequence similarity studies, strain Sj 10T was shown to belong to the genus Leucobacter and was closely related to Leucobacter chromiireducens subsp. chromiireducens L-1T (97.8 %), Leucobacter tardus DSM 19811T (97.3 %) and Leucobacter luti RF6T (97.3 %). The peptidoglycan of strain Sj 10T contained 2,4-diaminobutyric acid in combination with a lower amount of lysine as diagnostic diamino acids. In addition, threonine, glycine, alanine and glutamic acid were found. Menaquinone MK-11 was the major respiratory quinone; MK-12 and MK-10 were detected in minor amounts. The polar lipid pattern consisted of phosphatidylglycerol, diphosphatidylglycerol and one unknown component each of a phospholipid, glycolipid and aminoglycolipid. Strain Sj 10T contained the major fatty acids anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0, like other members of the genus Leucobacter. Results of DNA–DNA hybridization, physiological and biochemical tests enabled strain Sj 10T to be differentiated genotypically and phenotypically from the most closely related Leucobacter species. Strain Sj 10T represents a novel species of the genus Leucobacter, for which the name Leucobacter aerolatus sp. nov. is proposed, with Sj 10T (=DSM 22806T =CCM 7705T) as the type strain.