Response of the bacterial metagenome in port environments to changing environmental conditions

Port environments are highly dynamic and hotspots for marine bioinvasion. This study investigated the bacterial diversity at two geographically distant ports (Mangalore-marine port; and Haldia-riverine port) using next-generation sequencing during southwest monsoon and non-monsoon (Pre-monsoon) seasons. During southwest monsoon, at both marine and riverine ports, operational taxonomic units (OTUs) affiliated to bacteria reported to have hydrocarbon degrading ability were observed. Whereas during pre-monsoon, a significant increase in benthic bacterial OTUs was evident at the marine port, and the riverine port was characterized by oceanic species OTUs. Results suggest that the dynamics of prevalent environmental conditions, driven by seasons, led to emergence of ecologically relevant bacteria, many of which have been observed for the first time in Indian coastal waters. Their presence could be used as indicators of prevailing environmental conditions and nature of anthropogenic influence in port ecosystems. Unravelling functional roles of such ecologically relevant species is a way forward.

Combined phyto-microbial-electrochemical system enhanced the removal of petroleum hydrocarbons from soil: A profundity remediation strategy

The soil contaminated by petroleum hydrocarbons has been a global environmental problem and its remediation is urgent. A combined phyto-microbial-electrochemical system (PMES) was constructed to repair the oil-contaminated soil in this study. During the 42-day operation time, a total petroleum hydrocarbons (TPHs) of 18.0 ± 3.0% were removed from PMES, which increased by 414% compared with the control group (CK1). The supervision of physicochemical properties of pore water in soil exhibited an enhanced microbial consumption of the total organic carbon (TOC) and N source under the applied potential with the generation of bio-current. The microbial succession indicated that the Dietzia, Georgenia and Malbranchea possibly participated in the degradation and current output in PMES. And a collaborative network of potential degrading microorganisms including unclassified norank_f__JG30-KF-CM45 (in Chloroflexi), Dietzia and Malbranchea was discovered in PMES. While the functional communities of microorganism were re-enriched with the reconstructed interactions in the system which was started with the sterilized soil (S+MEC). The superiority of TPHs degradation in S+MEC compared to P + CK2 (removing the electrochemical effect relative to CK1) revealed the key role of external potential in regulating the degradation microflora. The study provided a strategy of the potential regulated phyto-microbial interaction for the removal of TPHs.

Titanium Dioxide Nanoparticles Induce Inhibitory Effects against Planktonic Cells and Biofilms of Human Oral Cavity Isolates of Rothia mucilaginosa, Georgenia sp. and Staphylococcus saprophyticus

Multi-drug resistant (MDR) bacterial cells embedded in biofilm matrices can lead to the development of chronic cariogenesis. Here, we isolated and identified three Gram-positive MDR oral cocci, (1) SJM-04, (2) SJM-38, and (3) SJM-65, and characterized them morphologically, biochemically, and by 16S rRNA gene-based phylogenetic analysis as Georgenia sp., Staphylococcus saprophyticus, and Rothia mucilaginosa, respectively. These three oral isolates exhibited antibiotic-resistance against nalidixic acid, tetracycline, cefuroxime, methicillin, and ceftazidime. Furthermore, these Gram positive MDR oral cocci showed significant (p < 0.05) variations in their biofilm forming ability under different physicochemical conditions, that is, at temperatures of 28, 30, and 42 °C, pH of 6.4, 7.4, and 8.4, and NaCl concentrations from 200 to 1000 µg/mL. Exposure of oral isolates to TiO2NPs (14.7 nm) significantly (p < 0.05) reduced planktonic cell viability and biofilm formation in a concentration-dependent manner, which was confirmed by observing biofilm architecture by scanning electron microscopy (SEM) and optical microscopy. Overall, these results have important implications for the use of tetragonal anatase phase TiO2NPs (size range 5-25 nm, crystalline size 13.7 nm, and spherical shape) as an oral antibiofilm agent against Gram positive cocci infections. We suggest that TiO2NPs pave the way for further applications in oral mouthwash formulations and antibiofilm dental coatings.

Sugarcane monoculture drives microbial community composition, activity and abundance of agricultural-related microorganisms

Sugarcane monoculture (SM) often leads to soil problems, like soil acidification, degradation, and soil-borne diseases, which ultimately pose a negative impact on agricultural productivity and sustainability. Understanding the change in microbial communities' composition, activities, and functional microbial taxa associated with the plant and soil under SM is unclear. Using multidisciplinary approaches such as Illumina sequencing, measurements of soil properties, and enzyme activities, we analyzed soil samples from three sugarcane fields with different monoculture histories (1-, 2-, and 4-year cultivation times, respectively). We observed that SM induced soil acidity and had adverse effects on soil fertility, i.e., soil organic matter (OM), total nitrogen (TN), total carbon (TC), and available potassium (AK), as well as enzyme activities indicative for carbon, phosphorus, and nitrogen cycles. Non-metric multidimensional scaling (NMDS) analysis showed that SM time greatly affected soil attribute patterns. We observed strong correlation among soil enzymes activities and soil physiochemical properties (soil pH, OM, and TC). Alpha diversity analysis showed a varying response of the microbes to SM time. Bacterial diversity increased with increasing oligotrophs (e.g., Acidobacteria and Chloroflexi), while fungal diversity decreased with reducing copiotrophs (e.g., Ascomycota). β-Diversity analysis showed that SM time had a great influence on soil microbial structure and soil properties, which led to the changes in major components of microbial structure (soil pH, OM, TC, bacteria and soil pH; TC, fungi). Additionally, SM time significantly stimulated (four bacterial and ten fungal) and depleted (12 bacterial and three fungal) agriculturally and ecologically important microbial genera that were strongly and considerably correlated with soil characteristics (soil pH, OM, TC, and AK). In conclusion, SM induces soil acidity, reduces soil fertility, shifts microbial structure, and reduces its activity. Furthermore, most beneficial bacterial genera decreased significantly due to SM, while beneficial fungal genera showed a reverse trend. Therefore, mitigating soil acidity, improving soil fertility, and soil enzymatic activities, including improved microbial structure with beneficial service to plants and soil, can be an effective measure to develop a sustainable sugarcane cropping system.

Variation in Sodic Soil Bacterial Communities Associated with Different Alkali Vegetation Types

In this study, we examined the effect of salinity and alkalinity on the metabolic potential and taxonomic composition of microbiota inhabiting the sodic soils in different plant communities. The soil samples were collected in the Pannonian steppe (Hungary, Central Europe) under extreme dry and wet weather conditions. The metabolic profiles of microorganisms were analyzed using the MicroResp method, the bacterial diversity was assessed by cultivation and next-generation amplicon sequencing based on the 16S rRNA gene. Catabolic profiles of microbial communities varied primarily according to the alkali vegetation types. Most members of the strain collection were identified as plant associated and halophilic/alkaliphilic species of Micrococcus, Nesterenkonia, Nocardiopsis, Streptomyces (Actinobacteria) and Bacillus, Paenibacillus (Firmicutes) genera. Based on the pyrosequencing data, the relative abundance of the phyla Proteobacteria, Actinobacteria, Acidobacteria, Gemmatimonadetes and Bacteroidetes also changed mainly with the sample types, indicating distinctions within the compositions of bacterial communities according to the sodic soil alkalinity-salinity gradient. The effect of weather extremes was the most pronounced in the relative abundance of the phyla Actinobacteria and Acidobacteria. The type of alkali vegetation caused greater shifts in both the diversity and activity of sodic soil microbial communities than the extreme aridity and moisture.

Bacterial Community Composition in Produced Water of Diyarbakır Oil Fields in Turkey : Bacterial communities in produced waters of south-eastern Turkey reported in detail for the first time

Oil fields harbour a wide variety of microorganisms with different metabolic capabilities. To examine the microbial ecology of petroleum reservoirs, a molecular-based approach was used to assess the composition of bacterial communities in produced water of Diyarbakır oil fields in Turkey. Denaturing gradient gel electrophoresis (DGGE) of polymerase chain reaction (PCR)-amplified 16S rRNA gene fragments was performed to characterise the bacterial community structure of produced water samples and to identify predominant community members after sequencing of separated DGGE bands. The majority of bacterial sequences retrieved from DGGE analysis of produced water samples belonged to unclassified bacteria (50%). Among the classified bacteria, Proteobacteria (29.2%), Firmicutes (8.3%), Bacteroidetes (8.3%) and Actinobacteria (4.2%) groups were identified. Pseudomonas was the dominant genus detected in the produced water samples. The results of this research provide, for the first time, insight into the complexity of microbial communities in the Diyarbakır oil reservoirs and their dominant constituents.

Georgenia faecalis sp. nov. isolated from the faeces of Tibetan antelope

Two aerobic, Gram-stain-positive, non-motile, non-sporulating coccoid strains, designated ZLJ0423^T and ZLJ0321, were isolated from the faeces of Tibetan antelope (Pantholops hodgsonii). Their optimal temperature, NaCl concentration and pH for growth were 28°C, 0.5% (w/v) NaCl and pH 7.5, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains ZLJ0423^T and ZLJ0321 were very similar to each other (99.8%) and had a sequence similarity of 97.0% with Georgenia satyanarayanai NBRC 107612^T and Georgenia subflava CGMCC 1.12782^T. Phylogenomic analysis based on 688 core genes indicated that these strains formed a clade with G. satyanarayanai NBRC 107612^T and Georgenia wutianyii Z294. The predominant cellular fatty acids were anteiso-C_15:0, anteiso-C_15:1A and C_16:0. The major menaquinone was MK-8(H₄). The cell-wall amino acids consisted of alanine, lysine, glycine and aspartic acid, with lysine as the diagnostic diamino acid. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides and two unidentified lipids formed the polar lipid profile. The DNA G + C content of both isolates was 73.9 mol%. The digital DNA-DNA hybridization value between strains ZLJ0423^T and ZLJ0321 was 91.2%, but their values with closely related species and other available type strains of the genus Georgenia were lower than the 70% threshold. On the basis of polyphasic taxonomic data, strains ZLJ0423^T and ZLJ0321 represent a novel species within the genus Georgenia, for which the name Georgenia faecalis sp. nov. is proposed. The type strain is ZLJ0423^T (= CGMCC 1.13681^T = JCM 33470^T).

Georgenia wutianyii sp. nov. and Georgenia yuyongxinii sp. nov. isolated from plateau pika (Ochotona curzoniae) on the Qinghai-Tibet plateau of China

Four novel bacterial strains, designated Z294^T, Z311, Z443^T and Z446, were isolated from the intestinal contents of plateau pika (Ochotona curzoniae) on the Qinghai-Tibet Plateau of China. Cells were Gram-stain-positive, catalase-positive, oxidase-negative, aerobic, non-motile and short-rod shaped. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the four isolates belong to the genus Georgenia, but clearly separate from the currently recognized species. Both type strains (Z294^T and Z443^T) shared low 16S rRNA gene sequence similarity, digital DNA-DNA hybridization relatedness and average nucleotide identity values with Georginia satyanarayanai NBRC 107612^T, G. subflava JCM 19765^T, G. ruanii JCM 15130^T and G. thermotolerans DSM 21501^T and against each other. The genomic DNA G+C contents of strains Z294^T and Z443^T were 73.3 and 70 %, respectively. The major cellular fatty acids of strain Z294^T were anteiso-C_15 : 0, anteiso-C_15 : 1 A and C_16 : 0, in contrast to anteiso-C_15 : 0 and anteiso-C_15 : 1 A for strain Z443^T. Both type strains (Z294^T and Z443^T) shared the following common features: glucose, rhamnose and ribose as cell-wall sugars; MK-8(H₄) as major menaquinone; alanine, glutamic acid and lysine as cell-wall amino acids; and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside and one unidentified phosphoglycolipid as polar lipids. Comparing the phenotypic and phylogenetic features among the four strains and their related organisms, strains Z294^T and Z443^T represent two novel species within the genus Georgenia, for which the names Georgenia wutianyii sp. nov. (type strain Z294^T=CGMCC 1.16428^T=DSM 106344^T) and Georgenia yuyongxinii sp. nov. (type strain Z443^T=CGMCC 1.16435^T=DSM 106174^T) are proposed.

Effects of biogenic nanopalladium precipitation on the performance and microbial community structure of anaerobic granular sludge

Biogenic nanopalladium (BioPd) catalysts have drawn increasing attentions recently as a combination of metal catalyst over the support of biomass. Anaerobic granular sludge (AGS), as a special microbial granule, demonstrates a strong potential to reduce Pd(II) and precipitate Bio-Pd in the sludge body. The problem how the Bio-Pd precipitates would influence the function and microbial community of the Pd hosting AGS (Pd-AGS) remains unknown. In this study, Pd-AGS with different Bio-Pd loadings (1.7, 3.0, 4.4 and 8.0 wt% of Pd) was obtained through bio-reduction at different Na₂PdCl₄ concentrations. Effects of Bio-Pd precipitates on acidogenesis and methanogenesis of AGS were assayed. Response of bacterial and archaeal community of AGS towards Bio-Pd precipitation were also revealed based on high-throughput sequencing data on Illumina Miseq platform. Results showed that Bio-Pd precipitates affected the acidogenesis and methanogenesis process of the Pd-AGS, as the produced total volatile fatty acids (VFA) and methane were reduced by 25.8-53.0% and 33.9-87.7%, respectively, comparing to the native AGS. Bio-Pd precipitation resulted in microbial community shift and a decrease in the microbial diversity. The bacterial community suffered more influence than the archaeal community. Hydrogenotrophic methanogens were more sensitive to the toxicity of Pd(II)/Bio-Pd than acetotrophic methanogens. Overall, when the heterogeneous Pd-AGS catalyst is designed to possess both the function of microbial metabolism and Pd catalysis, it is necessary to control a suitable Pd(II) concentration during reduction process and the final Bio-Pd loading in AGS (<4.4 wt% of Pd).

Georgenia alba sp. nov., a novel halotolerant actinobacterium isolated from a desert sand sample

Strain SYSU D8008^T was isolated from a desert sand sample collected from Saudi Arabia. The strain was observed to be Gram-stain positive, non-motile and aerobic. It can grow at 15-37 °C, pH 6.0-10.0 and can tolerant up to 7% (w/v) NaCl. Pairwise comparison of the 16S rRNA gene sequence indicated that strain SYSU D8008^T shares high sequence similarities with Georgenia deserti SYSU D8004^T (96.8%) and Georgenia halophila YIM 93316^T (96.8%). Menaquinone MK-8(H₄) was detected as the respiratory isoprenologue. The polar lipid profile of strain SYSU D8008^T was found to consist of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, two phosphatidylinositol mannosides, an unidentified glycolipid and an unidentified phospholipid. Strain SYSU D8008^T was found to contain anteiso-C_15:0 and iso-C_15:0 as the predominant fatty acids. Galactose, glucose and rhamnose were detected as the whole cell sugars. Based on the phenotypic, genotypic and phylogenetic characteristics, strain SYSU D8008^T can be differentiated from other closely related members of the genus Georgenia. The strain SYSU D8008^T, therefore, is concluded to represent a novel species of the genus Georgenia, for which the name Georgenia alba sp. nov. is proposed. The type strain is SYSU D8008^T (= CGMCC 1.15800^T = KCTC 39988^T).

Georgenia deserti sp. nov., a halotolerant actinobacterium isolated from a desert sample

Strain SYSU D8004^T was isolated from a sample collected from an arid area in Saudi Arabia. The isolate was Gram-stain-positive, non-motile, aerobic and non-spore-forming. It could grow at 4-45 °C, at pH 6.0-10.0 and in the presence of up to 17 % (w/v) NaCl. Pairwise comparison of the 16S rRNA gene sequences indicated that strain SYSU D8004^T shared highest sequence similarity with Georgenia halophila YIM 93316^T (96.5 %). Menaquinone MK-8(H4) was detected as the respiratory quinone. The polar lipid profile of strain SYSU D8004^T consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, two phosphatidylinositol mannosides, two unidentified phospholipids and an unidentified glycolipid. Strain SYSU D8004^T contained anteiso-C15 : 0, iso-C15 : 0 and C14 : 0 as the predominant fatty acids (>10 %). Galactose, glucose and rhamnose were detected as whole-cell sugars. Based on analyses of the phenotypic, genotypic and phylogenetic characteristics, it was determined that strain SYSU D8004^T could be differentiated from other closely related members of the genus Georgenia. Strain SYSU D8004^T is therefore considered to represent a novel species of the genus Georgenia, for which the name Georgenia deserti sp. nov. is proposed. The type strain is SYSU D8004^T (=CGMCC 1.15793^T=KCTC 39987^T).

Oceanitalea nanhaiensis Fu et al. 2012 is a later heterotypic synonym of Georgenia satyanarayanai Srinivas et al. 2012

Oceanitalea nanhaiensis JLT1488T was compared with Georgenia satyanarayanai KCTC 19802T to clarify the taxonomic relationship of both species because they are phylogenetically highly related. 16S rRNA gene sequence comparisons demonstrated that these species share 99.6 % sequence similarity. Investigation of fatty acid patterns and substrate utilization profiles displayed no striking differences of the type strains of both species. DNA-DNA hybridizations between both strains showed a 100 % similarity clearly demonstrating that both strains are members of a single species. Due to priority Oceanitalea nanhaiensis is reclassified as Georgenia satyanarayanai, based on the estimated phylogenetic position derived from 16S rRNA gene sequence data, fatty acid, polar lipid and biochemical data, and DNA-DNA hybridization results.

Georgenia subflava sp. nov., isolated from a deep-sea sediment

A Gram-stain-positive, aerobic, motile and non-spore-forming actinobacterium, strain Y32T, was isolated from a deep-sea sediment of the western Pacific Ocean. Phylogenetic and phenotypic properties of the organism supported that it belonged to the genus Georgenia. Strain Y32T shared highest 16S rRNA gene sequence similarity of 97.8 % with Georgenia muralis 1A-CT, followed by Georgenia thermotolerans TT02-04T (97.4 %), Georgenia daeguensis 2C6-43T (97.2 %), Oceanitalea nanhaiensis JLT1488T (97.2 %), Georgenia ruanii YIM 004T (97.0 %) and Georgenia soli CC-NMPT-T3T (97.0 %). The organism grew in the presence of 0–10 % (w/v) NaCl, at 4–40 °C and at pH 6–11, with optimal growth occurring at 30–35 °C, at pH 7 and in the presence of 3.5 % (w/v) NaCl. The polar lipid profile of strain Y32T consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and two phosphatidylinositol mannosides. Strain Y32T contained MK-8(H4) and MK-7(H4) as the major components of the menaquinone system, and anteiso-C15 : 0, iso-C15 : 0 and iso-C14 : 0 as the predominant fatty acids. Galactose was detected as the cell-wall sugar. The G+C content of the DNA was 71.2 mol%. Based on the results of phenotypic, genotypic and phylogenetic analyses, it is considered that strain Y32T represents a novel species of the genus Georgenia, for which the name Georgenia subflava sp. nov. is proposed. The type strain is Y32T ( = LMG 28101T = CGMCC 1.12782T = JCM 19765T = MCCC 1A09955T).

Genomic analysis of novel phytopathogenic Georgenia sp. strain SUB25

A Gram positive bacterium, Georgenia sp. SUB25 was isolated from infected leaves of Solanum lycopersicum L. in Rajkot (22.30°N, 70.78°E), Gujarat, India. We sequenced and analyzed Georgenia sp. SUB25 that is novel plant pathogen using next generation sequencing platform and assembly yielded contigs representing a size of 4.84 Mb with 81 tRNAs and 88 rRNAs. The whole genome sequencing has been deposited in DDBJ/EMBL/GenBank under the accession number JNFL00000000. This genome sequence contains Type II secretion system genes, which involved in pathogenicity mechanism that may help to understand plant microbial interaction.

Thermophilic and alkaliphilic Actinobacteria: biology and potential applications

Microbes belonging to the phylum Actinobacteria are prolific sources of antibiotics, clinically useful bioactive compounds and industrially important enzymes. The focus of the current review is on the diversity and potential applications of thermophilic and alkaliphilic actinobacteria, which are highly diverse in their taxonomy and morphology with a variety of adaptations for surviving and thriving in hostile environments. The specific metabolic pathways in these actinobacteria are activated for elaborating pharmaceutically, agriculturally, and biotechnologically relevant biomolecules/bioactive compounds, which find multifarious applications.

Georgenia sediminis sp. nov., a moderately thermophilic actinobacterium isolated from sediment

A Gram-stain-positive actinobacterium, designated strain SCSIO 15020T, was isolated from sediment of the South China Sea, and characterized by using a polyphasic approach. The temperature range for growth was 24–60 °C, with optimal growth occurring at 50 °C. The pH range for growth was 6–10 (optimum pH 8–9). The NaCl concentration range for growth was 0–5 % (w/v). The peptidoglycan type was A4α. Polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside and an unknown polar lipid. The major menaquinone was MK-8(H4); MK-7(H4) was present as a minor component. The major fatty acids (>5 %) were anteiso-C15 : 0, iso-C15 : 0 and iso-C16 : 0. The DNA G+C content of strain SCSIO 15020T was 73.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain SCSIO 15020T belonged to the genus Georgenia , with the closest neighbours being Georgenia muralis 1A-CT (96.3 % similarity), Georgenia thermotolerans TT02-04T (95.7 %) and Georgenia ruanii YIM 004T (95.6 %). Based on evidence from the present polyphasic study, strain SCSIO 15020T is considered to represent a novel species of the genus Georgenia , for which the name Georgenia sediminis sp. nov. is proposed. The type strain is SCSIO 15020T ( = DSM 25884T = NBRC 108941T).

Georgenia satyanarayanai sp. nov., an alkaliphilic and thermotolerant amylase-producing actinobacterium isolated from a soda lake

A Gram-stain-positive, oxidase-negative, starch-hydrolysing, actinobacterium (strain JC82T) was isolated from a soda lake in Lonar, India. Based on 16S rRNA gene sequence similarity studies, strain JC82T belonged to the genus Georgenia and was most closely related to Georgenia muralis 1A-CT (96.8 %) and other members of the genus Georgenia (<96.5 %). The DNA G+C content of strain JC82T was 73.4 mol%. The cell-wall amino acids were alanine, glutamic acid and lysine with peptidoglycan type A4α. Polar lipids included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides, an unidentified lipid (L1) and an unidentified glycolipid (GL3). The predominant isoprenoid quinone was menaquinone MK-8(H4). Anteiso-C15 : 0 was the predominant fatty acid and significant proportions of iso-C14 : 0, C14 : 0, C16 : 0, iso-C15 : 0 and iso-C16 : 0 were also detected. Strain JC82T produced thermostable alkaline amylase. The results of physiological and biochemical tests allowed a clear phenotypic differentiation of strain JC82T from all other members of the genus Georgenia . Based on these data, strain JC82T represents a novel species of the genus Georgenia , for which the name Georgenia satyanarayanai sp. nov. is proposed. The type strain is JC82T ( = KCTC 19802T = NBRC 107612T).