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The Gram-positive strain R79T, isolated from the rhizosphere of young M26 apple rootstocks, was investigated by a polyphasic taxonomic approach. Phylogenetic identification based on the full-length 16S rRNA gene sequence revealed highest 16S rRNA gene sequence similarity to the type strains of Rhodococcus wratislaviensis (99.6%) and Rhodococcus opacus (99.2%) followed by Rhodococcus imtechensis (98.9%). All other 16S rRNA gene sequence similarities were below 98.65%. A phylogenomic tree calculated based on a whole-genome sequence also showed a distinct clustering with the type strain of Rhodococcus koreensis. Average nucleotide identity (ANI) values between whole-genome sequences of R79T and the closest related type strains were below 95% supported the novel species status. The DNA G + C content of R79T was 67.24% mol. Predominant fatty acids were C16:0, C15:0 and C17:1ω8c. The strain contained MK8-H2 as the major respiratory quinone. The polar lipid profile consists of diphosphatidylglycerol and phosphatidylethanolamine, as well as of some unidentified lipids. The peptidoglycan type of the strain is A1γ meso-diaminopimelic acid. Based on the obtained genotypic and phenotypic, including chemotaxonomic data, we conclude that R79T represents a novel species of the genus Rhodococcus, for which the name Rhodococcus pseudokoreensis sp. nov. is proposed. The type strain is R79T (= DSM 113102T = LMG 32444T = CCM 9183T). [ABSTRACT FROM AUTHOR]

Large baleen and toothed whales play crucial ecological roles in oceans; nonetheless, very little is known about their intestinal microbiomes. Based on striking differences in natural history and thus in feeding behaviours, it can be expected that intestinal microbiomes of large baleen whales and toothed whales are different. To test this hypothesis, the phylogenetic composition of faecal microbiomes was investigated by a 16S rRNA gene amplicon sequence–based approach for Bacteria and Archaea. Faecal samples from free-ranging large whales collected off the Azores Archipelago (Portugal) were used, comprising 13 individual baleen whales (one sei, two blue and ten fin whales) and four sperm whales. The phylogenetic composition of the Bacteria faecal microbiomes of baleen and toothed whales showed no significant differences at the phylum level. However, significant differences were detected at the family and genus levels. Most abundant phyla were Firmicutes, Bacteroidetes, Proteobacteria, Tenericutes and Spirochaeta. Few highly abundant bacterial genera were identified as key taxa with a high contribution to differences among baleen and toothed whales microbiomes. Only few archaeal sequences were detected, primarily Methanomassiliicoccales representing potential methanogenic Archaea. This is the first study that directly compares the faecal bacterial and archaeal microbiomes of free-ranging baleen and toothed whales which represent the two parvorders of Cetacea which members are fully aquatic large mammals which were evolutionary split millions of years ago. [ABSTRACT FROM AUTHOR]

Atopic dermatitis is one of the most common skin diseases in dogs. Pathogenesis is complex and incompletely understood. Skin colonizing bacteria likely play an important role in the severity of this disease. Studying the canine skin microbiota using traditional microbiological methods has many limitations which can be overcome by molecular procedures. The aim of this study was to describe the bacterial microbiota of the skin and ear canals of healthy non-allergic and allergic German shepherd dogs (GSDs) without acute flare or concurrent skin infection and to compare both. Bacterial 16S rRNA gene amplicon sequence data revealed no differences of bacterial community patterns between the different body sites (axilla, front dorsal interdigital skin, groin, and ear canals) in non-allergic dogs. The microbiota at the different body sites of non-allergic GSDs showed no significant differences. Only for the samples obtained from the axilla the bacterial microbiota of allergic dogs was characterized by a lower species richness compared to that of non-allergic dogs and the bacterial community composition of the skin and ear canals of allergic dogs showed body site specific differences compared to non-allergic dogs. Actinobacteria was the most abundant phylum identified from the non-allergic dogs and Proteobacteria from allergic dogs. Macrococcus spp. were more abundant on non-allergic skin while Sphingomonas spp. were more abundant on the allergic skin. Forward step redundancy analysis of metadata indicated that the household the dogs came from had the strongest impact on the composition of the skin microbiome followed by sex, host health status and body site. [ABSTRACT FROM AUTHOR]

Background: Wastewater from sewage treatment plants contains high levels of nutrients, which can be used for plant nutrition. Classical wastewater treatment plants use complex microbial consortia of autotrophic and heterotrophic microorganisms for biological wastewater treatment. Certain autotrophic microalgae (e.g., species of the genera Chlorella, Scenedesmus, and Pediastrum) accumulate nutrients from wastewater very effectively. Aims: We investigated the potential of microalgae biomass obtained from a prototype wastewater treatment plant as a source of nutrients for crops, focusing on nitrogen. Methods: We provided wheat plants with different levels of algae biomass equivalent to 60, 120, and 180 kg N per hectare or with mineral fertilizer (N, P, and K) equivalent to the amounts contained in the algal biomass. Physiological and phenotypic traits were measured during growth, including vegetation indices, photosynthetic performance, growth, and nitrogen use efficiency (NUE). In addition, the adundances of Bacteria, Archaea and fungi and genes of ammonium oxidizing Bacteria and Archaea were determined in the rhizosphere of differently fertilized plants. Results: Microalgal application at fertilizer levels of 120 and 180 kg N ha–1 showed significantly improved physiological performance, growth, yield and nutrient uptake compared to the unfertilized control. Nevertheless, their yields and NUE were lower than with the application of equal amounts of mineral fertilization, while the adundance of rhizosphere microbes and ammonia‐oxidizing microorganisms were not significantly affected. Conclusions: Microalgae from wastewater treatments form a suitable source of organic fertilizer for wheat plants with only moderate reductions in N use efficiency compared to mineral fertilizer. [ABSTRACT FROM AUTHOR]

Background: Trueperella pyogenes is a worldwide known bacterium causing mastitis, abortion and various other pyogenic infections in domestic animals like ruminants and pigs. In this study we represent the first case report of three unusual fatal infections of Grey Slender Lorises caused by Trueperella pyogenes. Meanwhile, this study represents the first in-depth description of the multilocus sequence analysis (MLSA) on T. pyogenes species. Case presentation: Three Trueperella pyogenes were isolated from three different Grey Slender Lorises, which died within a period of two years at Frankfurt Zoo (Frankfurt am Main - Germany). The three Grey Slender Loris cases were suffering from severe sepsis and died from its complication. During the bacteriological investigation of the three cases, the T. pyogenes were isolated from different organisms in each case. The epidemiological relationship between the three isolates could be shown by four genomic DNA fingerprint methods (ERIC-PCR, BOX-PCR, (GTG)5- PCR, and RAPD-PCR) and by multilocus sequence analysis (MLSA) investigating four different housekeeping genes (fusA-tuf-metG-gyrA). Conclusion: In this study, we clearly showed by means of using three different rep-PCRs, by RAPD-PCR and by MLSA that the genomic fingerprinting of the investigated three T. pyogenes have the same clonal origin and are genetically identical. These results suggest that the same isolate contaminated the animal's facility and subsequently caused cross infection between the three different Grey Slender Lorises. To the best of our knowledge, this is the first epidemiological approach concentrating on T. pyogenes using MLSA. [ABSTRACT FROM AUTHOR]

Vancomycin-resistant enterococci (VRE) and methicillin-resistant staphylococci (MRS) were detected in two mesophilic German biogas plants (BGPs) using selective pre-enrichment methods combined with cultivation on CHROMagar media and antibiotic resistance gene screening. Genetic fingerprinting and 16S rRNA gene sequencing showed the presence of enterococci isolated by the VRE selective cultivation (67 isolates) in input and output samples of BGPs. In contrast, MRS (44 isolates) were detected in input, but in none of the output samples. Enterococcus isolates showed highest 16S rRNA gene sequence similarity (>99.8%) to E. lemanii, E. casseliflavus/E. gallinarium or E. devriesei/E. pseudoavium/E. viikkiensis and carried vanA, vanB and/or vanC1 genes. Enterococcus faecium and E. faecalis VRE were not detected, but isolates closely related to those species (>99.9% 16S rRNA gene sequence similarity) were detected by the MRS selective cultivation methods. Staphylococcus isolates shared highest 16S rRNA gene sequence similarity (>99.9%) with S. haemolyticus, S. lentus and S. sciuri and carried mecA genes. Methicillin-resistant S. aureus (MRSA) were not detected. In summary, manure from livestock husbandry contained both, VRE and MRS. VRE were also detected in output samples, indicating that enterococci with vancomycin resistance genes could be release into the environment by the application of BGP output material as biofertilizers. [ABSTRACT FROM AUTHOR]

The presence of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli was investigated in input (manure from livestock husbandry) and output samples of six German biogas plants in 2012 (one sampling per biogas plant) and two German biogas plants investigated in an annual cycle four times in 2013/2014. ESBL-producing Escherichia coli were cultured by direct plating on CHROMagar ESBL from input samples in the range of 100 to 104 colony forming units (CFU) per g dry weight but not from output sample. This initially indicated a complete elimination of ESBL-producing E. coli by the biogas plant process. Detected non target bacteria were assigned to the genera Acinetobacter, Pseudomonas, Bordetella, Achromobacter, Castellaniella, and Ochrobactrum. A selective pre-enrichment procedure increased the detection efficiency of ESBL-producing E. coli in input samples and enabled the detection in five of eight analyzed output samples. In total 119 ESBL-producing E. coli were isolated from input and 46 from output samples. Most of the E. coli isolates carried CTX-M-type and/or TEM-type beta lactamases (94%), few SHV-type beta lactamase (6%). Sixty-four blaCTX-M genes were characterized more detailed and assigned mainly to CTX-M-groups 1 (85%) and 9 (13%), and one to group 2. Phylogenetic grouping of 80 E. coli isolates showed that most were assigned to group A (71%) and B1 (27%), only one to group D (2%). Genomic fingerprinting and multilocus sequence typing (MLST) showed a high clonal diversity with 41 BOX-types and 19 ST-types. The two most common ST-types were ST410 and ST1210. Antimicrobial susceptibility testing of 46 selected ESBL-producing E. coli revealed that several isolates were additionally resistant to other veterinary relevant antibiotics and some grew on CHROMagar STEC but shiga-like toxine (SLT) genes were not detected. Resistance to carbapenems was not detected. In summary the study showed for the first time the presence of ESBL-producing E. coli in output samples of German biogas plants. [ABSTRACT FROM AUTHOR]

Light excitation of humic matter generates reactive oxygen species (ROS) in surface waters of aquatic ecosystems. Abundant ROS generated in humic matter rich lakes include singlet oxygen (1O2) and hydrogen peroxide (H2O2). Because these ROS differ in half-life time and toxicity, we compared their effects on microbial activity (14C-Leucine incorporation) and bacterial community composition (BCC) in surface waters of humic Lake Grosse Fuchskuhle (North-eastern Germany). For this purpose, experiments with water samples collected from the lake were conducted in July 2006, September 2008 and August 2009. Artificially increased 1O2 and H2O2 concentrations inhibited microbial activity in water samples to a similar extent, but the effect of the respective ROS on BCC varied strongly. BCC analysis by 16S rRNA gene clone libraries and RT-PCR DGGE revealed ROS specific changes in relative abundance and activity of major bacterial groups and composition of dominating phylotypes. These changes were consistent in the three experiments performed in different years. The relative abundance of Polynucleobacter necessarius, Limnohabitans-related phylotypes (Betaproteobacteria), and Novosphingobium acidiphilum (Alphaproteobacteria) increased or was not affected by photo-sensitized 1O2 exposure, but decreased after H2O2 exposure. The opposite pattern was found for Actinobacteria of the freshwater AcI-B cluster which were highly sensitive to 1O2 but not to H2O2 exposure. Furthermore, group-specific RT-PCR DGGE analysis revealed that particle-attached P. necessarius and Limnohabitans-related phylotypes exhibit higher resistance to 1O2 exposure compared to free-living populations. These results imply that 1O2 acts as a factor in niche separation of closely affiliated Polynucleobacter and Limnohabitans-related phylotypes. Consequently, oxidative stress caused by photochemical ROS generation should be regarded as an environmental variable determining abundance, activity, and phylotype composition of environmentally relevant bacterial groups, in particular in illuminated and humic matter rich waters. [ABSTRACT FROM AUTHOR]

Summary The ultimate goal of taxonomy is to establish a system that mirrors the 'order in nature'. In prokaryote microbiology, almost all taxonomic concepts try to mirror the whole evolutionary order back to the origin of life with the cell as basic unit. The introduction of the 16S rRNA gene as molecular marker allowed for the first time the creation of a hierarchical taxonomic system based on one practical molecular marker. With the development of new and rapid sequencing technologies a wealth of new data can and will be used for critical evaluation of the taxonomic system. Comprehensive analyses of other molecular markers as well as total or partial genome comparisons confirmed the 16S rRNA based hierarchical system as 'backbone of prokaryote taxonomy' at least at the genus level and above. A tendency is visible to classify novel taxa more and more based on the genotype, i.e. comparative analyses of 16S rRNA and/or other gene sequence data (in multilocus sequence analysis, MLSA) at the genus and the species level, sometimes contrary to the indications of other (often phenotypic) data. The understanding of all the information behind these data is lagging far behind their accumulation. Genes and genomes do not function on its own and can only display their potential within the cell as the basic unit of evolution (and hence taxonomy). It is the phenotype and the natural selection that 'drive' evolution in a given environment. In this context, the 'polyphasic taxonomic approach' should be revisited again, taking into account the novel insights into genomes and other 'omic' sciences in a more strict and detailed context with the phenotype. This approach allows a more holistic view and provides a sound basis for describing the diversity of prokaryotes and has the potential to become the foundation of a more stable, in-depth taxonomy of the prokaryotes. [ABSTRACT FROM AUTHOR]

Photolysis of dissolved organic matter (DOM) leads to contrasting effects on bacterioplankton dynamics, i.e. stimulation and inhibition of bacterial activity. In particular, the role of short-lived reactive oxygen species (ROS), e.g. singlet oxygen (O), in altering microbial activity and species composition has scarcely been investigated. Therefore, we have artificially increased the natural rate of O formation in short-term (∼4 h) in situ and long-term (72 h) laboratory incubations of surface water samples from a humic acid-rich lake. Denaturing gradient gel electrophoresis (DGGE) patterns revealed significant changes in occurrence of abundant bacterioplankton phylotypes upon O exposure. Cluster analysis of DGGE patterns showed that a moderate increase in O exposure leads to similar changes in different years indicating the establishment of bacterial communities adapted to O exposure. Bacterioplankton phylotypes favoured under these conditions belonged to Betaproteobacteria of the beta II cluster (e.g. Polynucleobacter necessarius) and the beta I cluster related to Limnohabitans (R-BT subcluster) as well as Alphaproteobacteria affiliated to Novosphingobium acidiphilum. In contrast, Actinobacteria of the freshwater acI-B cluster were sensitive even against moderate O exposure. We conclude that O exposure due to DOM photolysis represents an important natural selective factor affecting bacterial species dynamics in aquatic ecosystems in many ways. [ABSTRACT FROM AUTHOR]

Quaternary alkylammonium compounds (QAACs) are a group of cationic surfactants which are disinfectants with numerous industrial and agricultural applications and frequently released into the environment. One recent hypothesis is that bacteria present in soil will be protected from acute toxic effects of QAACs in the presence of expandable layer silicates due to interlayer sorption. We therefore studied bacterial growth kinetics with high temporal resolution and determined minimal inhibitory concentrations (MICs) of two QAACs, benzyldimethyldodecylammonium chloride (BAC-C12) and didecyldimethylammonium chlorid (DADMAC-C10), for eight strains of different bacterial taxa (Escherichia coli, Acinetobacter, Enterococcus faecium, Enterococcus faecalis, and Pseudomonas fluorescens) in relation to QAAC sorption to smectite and kaolinite. The MICs of BAC-C12 and DADMAC-C10 were in the absence of smectite and kaolinite in the order of 10 to 30 µg mL−1 and 1.0 to 3.5 µg mL−1 for all strains except the more sensitive Acinetobacter strain. For all tested strains and both tested QAACs, the presence of smectite increased apparent MIC values while kaolinite had no effect on MICs. Sorption curves without bacteria showed that smectite sorbed larger amounts of QAACs than kaolinite. Correcting nominal QAAC concentrations employed in toxicity tests for QAAC sorption using the sorption curves explained well the observed shifts in apparent MICs. Transmission electron microscopy (TEM) demonstrated that the interlayer space of smectite expanded from 13.7 ± 1 Å to 19.9 ± 1.5 Å after addition of BAC-C12. This study provides first evidence that low charge 2:1 expandable layer silicates can play an important role for buffering QAAC toxicity in soils. [ABSTRACT FROM AUTHOR]

Associations of endophytic bacterial community composition of oilseed rape (Brassica napus L.) with quantitative resistance against the soil-borne fungal pathogen Verticillium longisporum was assessed by 16S rRNA gene amplicon sequencing in roots and hypocotyls of four plant lines with contrasting genetic composition in regard to quantitative resistance reactions. The plant compartment was found to be the dominating driving factor for the specificity of bacterial communities in healthy plants. Furthermore, V. longisporum infection triggered a stabilization of phylogenetic group abundance in replicated samples suggesting a host genotype-specific selection. Genotype-specific associations with bacterial phylogenetic group abundance were identified by comparison of plant genotype groups (resistant versus susceptible) and treatment groups (healthy versus V. longisporum -infected) allowing dissection into constitutive and induced directional association patterns. Relative abundance of Flavobacteria , Pseudomonas , Rhizobium and Cellvibrio was associated with resistance/susceptibility. Relative abundance of Flavobacteria and Cellvibrio was increased in resistant genotypes according to their known ecological functions. In contrast, a higher relative abundance of Pseudomonas and Rhizobium , which are known to harbor many species with antagonistic properties to fungal pathogens, was found to be associated with susceptibility, indicating that these groups do not play a major role in genetically controlled resistance of oilseed rape against V. longisporum. [ABSTRACT FROM AUTHOR]

Endophytic fungi, particularly from higher plants have proven to be a rich source of antimicrobial secondary metabolites. The purpose of this study is to examine the antimicrobial potential of three endophytic fungi Aspergillus sp. SA1, Aspergillus sp. SA2, and Aspergillus sp. SA3, cultivated from Nigella sativa seeds against Staphylococcus aureus (ATCC 9144), Escherichia coli (ATCC 25922), Pseudomonas aeruginosa (ATCC 27853), Klebsiella pneumoniae (ATCC 13883), MRSA (ATCC 33591), and human pathogen Candida albicans (ATCC 10231). Furthermore, the most active cultivated endophytic fungi were molecularly identified via internal transcribed spacer (ITS) sequencing. HR-ESIMS guided approach has been used successfully in chemical profiling of 26 known bioactive secondary metabolites (1–26), which belongs to different classes of natural compounds such as polyketides, benzenoids, quinones, alcohols, phenols or alkaloids. Finally, in-silico interactions within active site of fungal Cyp51 and bacterial DNA gyrase revealed possibility of being a hit-target for such metabolites as antimicrobials. [ABSTRACT FROM AUTHOR]

• There is an urgent need to work towards the invention of safer antimicrobial agents which are expected to be renewable, non-petrochemical, naturally eco-friendly and easily obtainable. • Efforts are being made to re-explore the potential of natural products as sources of novel drugs. • Endophytes are an endosymbiotic group of microorganisms that colonize in plants, while plant sources are being extensively explored for new chemical entities for therapeutic purposes; endophytic microbes also constitute an important source for drug discovery. • The choice of medium is virtually as important to the success of an industrial fermentation as the selection of organism to carry out the fermentation. Influence of particular nutrients on the antibiotic biosynthesis is determined by the chemical structures of antibiotic substances. • Evaluation of the antimicrobial activity of endophytic fungi from Ziziphus spina-christi (Nabq), in addition, the effect of different culture media on production of bioactive metabolites and the optimization of cultural conditions were performed. Twenty fungal endophytes were isolated from Nabq, and plug diffusion screening revealed four of those isolates to be promising. These isolates were identified molecularly as Aspergillus sp. of Sect. Flavi (ZSEFL2) and Sec. Niger (ZSEFL14), and Penicillium spp. closest related to Penicillum crustosum (ZSEFL15, 19). Investigations were conducted to determine the effects of culture parameters, such as the type of culture medium, incubation temperature, initial pH and agitation, on the production of antimicrobial metabolites in a culture filtrate extract. Using the disk diffusion technique, antimicrobial metabolite synthesis was evaluated. In comparison to the other three distinct culture media (PDB-y, rice, and Cz), PDB demonstrated to be the best culture medium for the four tested fungal endophytes, exhibiting high levels of the Antimicrobial Index (AI). Also, a restricted range of incubation temperatures resulted in the formation of bioactive metabolites, but raising the incubation temperatures from 25 to 30 °C increased the amount of bioactive metabolites produced. Moreover, the best initial hydrogen concentration typically ranged from pH 5 to 6. Finally, when the conditions changed from stationary to shaking, the bioactive secondary metabolite's antimicrobial efficacy reduced. The behavior of the four examined fungal isolates was consistent, and they all required the same conditions to produce the most bioactive metabolites. Moreover, ethyl acetate extract's MIC values against the investigated bacterial and fungal human pathogens ranged from 0.19 to 6.25 mg/mL. [ABSTRACT FROM AUTHOR]

A Gram-positive staining, aerobic, endospore-forming bacterial strain, isolated from the rhizosphere of Zea mays was studied for its detailed taxonomic allocation. Based on the 16S rRNA gene sequence similarity comparisons, strain JJ-42 T was shown to be a member of the genus Paenibacillus, most closely related to the type strain of Paenibacillus pectinilyticus (98.8%). The 16S rRNA gene sequence similarity to all other Paenibacillus species was below 98.5%. The pairwise average nucleotide identity (ANI) and digital DNA−DNA hybridization (dDDH) values of the JJ-42 T genome assembly against publicly available Paenibacillus type strain genomes were below 92% and 47%, respectively. The quinone system of strain JJ-42 T consisted exclusively of menaquinone MK-7. The polar lipid profile consisted of the major components diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, three aminophospholipids (APL), and one unidentified lipid. The major fatty acids were iso- and anteiso-branched with the major compound anteiso C15:0. Physiological and biochemical characteristics allowed a further phenotypic differentiation of strain JJ-42 T from the most closely related species. Thus, JJ-42 T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus allorhizoplanae sp. nov. is proposed, with JJ-42 T (= LMG 32089 T = CCM 9085 T = DSM 111786 T = CIP 111891 T) as the type strain. [ABSTRACT FROM AUTHOR]

Soils present a limited resource for agricultural production and bear a vast diversity of organisms crucial for crop health and the provision of ecosystem services. There is growing evidence that agricultural practices affect soil microbial community structure and function but currently, there is a knowledge gap when it comes to tropical arable farming systems. In this study, we investigated the long-term impact of organic and conventional production systems on bacterial communities in two field trial located on a rhodic and humic nitisol in the Central Highlands of Kenya. The field sites operate on a full factorial design, testing farming systems (organic vs conventional) and input levels (high vs low). Including four field replication we assessed soil bacterial community structure via amplicon sequencing of the 16S rRNA gene and soils capacity for nitrification and nitrous oxide reduction via qPCR of functional genes (bacterial and archaeal amoA , nosZ) after 12 years of distinct management and before the start of the 5th three-year crop rotation period in 2019. The abundances of amoA bearing nitrifiers and nosZ bearing nitrous oxide reducers were enhanced in the high input organic production system on humic but not in rhodic nitisols. For both soil types, high input organic production system resulted in distinct bacterial community structure with enhanced bacterial richness compared to conventional and low input production systems. In rhodic and humic nitisols 160 and 84 OTUs were found to be indicative for organic production system at high input levels organic. Taxa associated with this system were identified as potential primary decomposers or symbionts related to plant nitrogen fixation, suggesting organic fertilization strategies such as manure composting as major driver for changes in soil bacterial community structure. This study reveals that organic production systems at high input levels on tropical nitisols translates to distinct soil bacterial communities with increased capacity for soil processes that are crucial for crop nutrient supply. • Distinct soil bacterial communities in organic systems in humic and rhodic nitisols • Increased bacterial richness in high input organic systems in humic nitisols • High-input organic farming raises nitrification capacity in humic nitisols. • Lifestyle of indicative taxa mainly linked with organic matter decomposition [ABSTRACT FROM AUTHOR]

Studies considering environmental multidrug-resistant Acinetobacter spp. are scarce. The application of manure on agricultural fields is one source of multidrug-resistant bacteria from livestock into the environment. Here, Acinetobacter spp. were quantified by quantitative polymerase chain reaction in manure applied to biogas plants and in the output of the anaerobic digestion, and Acinetobacter spp. isolated from those samples were comprehensively characterized. The concentration of Acinetobacter 16S ribosomal ribonucleic acid (rRNA) gene copies per g fresh weight was in range of 106–108 in manure and decreased (partially significantly) to a still high concentration (105–106) in digestates. 16S rRNA, gyrB-rpoB and bla OXA51-like gene sequencing identified 17 different Acinetobacter spp. including six A. baumannii strains. Multilocus sequence typing showed no close relation of the six strains with globally relevant clonal complexes; however, they represented five novel sequence types. Comparative genomics and physiological tests gave an explanation how Acinetobacter could survive the anaerobic biogas process and indicated copper resistance and the presence of intrinsic beta-lactamases, efflux-pump and virulence genes. However, the A. baumannii strains lacked acquired resistance against carbapenems, colistin and quinolones. This study provided a detailed characterization of Acinetobacter spp. including A. baumannii released via manure through mesophilic or thermophilic biogas plants into the environment. [ABSTRACT FROM AUTHOR]

The leaf-colonizing bacterial microbiota was studied in a long-term warming experiment on a permanent grassland, which had been continuously exposed to increased surface temperature (+2°C) for more than six years. Two abundant plant species, Arrhenatherum elatius and Galium album , were studied. Surface warming reduced stomata opening and changed leaf metabolite profiles. Leaf surface colonization and the concentration of leaf-associated bacterial cells were not affected. However, bacterial 16S ribosomal RNA (rRNA) gene amplicon Illumina sequencing showed significant temperature effects on the plant species-specific phyllosphere microbiota. Warming partially affected the concentrations of cultured bacteria and had a significant effect on the composition of most abundant cultured plant species-specific bacteria. The abundance of Sphingomonas was significantly reduced. Sphingomonas isolates from warmed plots represented different phylotypes, had different physiological traits and were better adapted to higher temperatures. Among Methylobacterium isolates, a novel phylotype with a specific mxaF type was cultured from plants of warmed plots while the most abundant phylotype cultured from control plots was strongly reduced. This study clearly showed a correlation of long-term surface warming with changes in the plant physiology and the development of a physiologically and genetically adapted phyllosphere microbiota. [ABSTRACT FROM AUTHOR]

Background and Aims: Soil phosphorus (P) deficiency occurs in many developing and transition countries. One method of resolving soil P deficiency is a strong application of mineral and organic fertilizers in order to saturate the P binding capacity of soil. Another promising method is the implementation of crop-endophyte symbioses in combination with the application of smaller amount of P fertilizer. This study comparatively examined the effect of the fungal endophytes Trametes versicolor and Piriformospora indica in P-deprived and P-rich conditions on P uptake and yield in wheat (Triticum aestivum L., cv. Bobwhite).Methods: Three-day-old wheat seedlings were dip-inoculated with mycelia of (a) T. versicolor WC16GW axenically isolated from Galium album, a dicotyledonous plant obtained from grassland in Linden near Giessen, Germany, and (b) axenic cultures of P. indica DSM 11827 freshly re-isolated from surface-sterilized barley roots. Seedlings were subsequently grown in 6 l Mitscherlich pots (eight seedlings per pot) in soil containing mono-calcium phosphate [CP, Ca (H2PO4)2] with 100 mg P kg−1 soil and control (CO) with 6.3 mg CAL-P kg−1 soil P in an open-air pot experiment station for three months.Results: Colonization of wheat roots by T. versicolor and P. indica increased plant biomass, yield and P content. T. versicolor-colonized plants exhibited a significant increase in grain yield of 37% (CO treatment) and 8.5% (CP treatment), as well as straw yield of 27% (CO treatment) as compared to non-colonized plants. P. indica-colonized plants showed a significant increase in grain yield of 10% under high P (CP treatment) and straw yield of 22% (CO treatment). Moreover, P. indica improved grain P content by 30% (CO treatment), 16% (CP treatment) and straw P content by 33% (CO treatment), while T. versicolor increased grain P content by 16% (CP treatment) and straw by 35% (CP treatment).Conclusions: Both T. versicolor and P. indica improved wheat P uptake in both P-deprived and P-rich conditions. T. versicolor supported a high grain yield under the CO and CP treatments, suggesting this fungus has a promising potential for P management in cereal crops. [ABSTRACT FROM AUTHOR]

Streptococcus ( S .) agalactiae represents a significant pathogen for humans and animals. However, there are only a few elderly reports on S . agalactiae infections in wild and zoo elephants even though this pathogen has been isolated comparatively frequently in these endangered animal species. Consequently, between 2004 and 2015, we collected S. agalactiae isolates from African and Asian elephants (n = 23) living in four different zoos in Germany. These isolates were characterised and compared with isolates from other animal species (n = 20 isolates) and humans (n = 3). We found that the isolates from elephants can be readily identified by classical biochemistry and MALDI-TOF mass spectrometry. Further characterisations for epidemiological issues were achieved using Fourier transform-infrared spectroscopy, capsule typing and molecular fingerprinting (PFGE, RAPD PCR). We could demonstrate that our elephant isolate collection contained at least six different lineages that were representative for their source of origin. Despite generally broad antimicrobial susceptibility of S. agalactiae , many showed tetracycline resistance in vitro . S. agalactiae plays an important role in bacterial infections not only in cattle and humans, but also in elephants. Comparative studies were able to differentiate S. agalactiae isolates from elephants into different infectious clusters based on their epidemiological background. [ABSTRACT FROM AUTHOR]

Microbiome disruptions triggering disease outbreaks are increasingly threatening corals worldwide. In the Tropical Eastern Pacific, a necrotic-patch disease affecting gorgonian corals (sea fans, Pacifigorgia spp.) has been observed in recent years. However, the composition of the microbiome and its disease-related disruptions remain unknown in these gorgonian corals. Therefore, we analysed 16S rRNA gene amplicons from tissues of healthy colonies (n = 19) and from symptomatic-asymptomatic tissues of diseased colonies (n = 19) of Pacifigorgia cairnsi (Gorgoniidae: Octocorallia) in order to test for disease-related changes in the bacterial microbiome. We found that potential endosymbionts (mostly Endozoicomonas spp.) dominate the core microbiome in healthy colonies. Moreover, healthy tissues differed in community composition and functional profile from those of the symptomatic tissues but did not show differences to asymptomatic tissues of the diseased colonies. A more diverse set of bacteria was observed in symptomatic tissues, together with the decline in abundance of the potential endosymbionts from the healthy core microbiome. Furthermore, according to a comparative taxonomy-based functional profiling, these symptomatic tissues were characterized by the increase in heterotrophic, ammonia oxidizer and dehalogenating bacteria and by the depletion of nitrite and sulphate reducers. Overall, our results suggest that the bacterial microbiome associated with the disease behaves opportunistically and is likely in a state of microbial dysbiosis. We also conclude that the confinement of the disease-related consortium to symptomatic tissues may facilitate colony recovery. [ABSTRACT FROM AUTHOR]