Denitrification dynamics in unsaturated soils with different porous structures and water saturation degrees: A focus on the shift in microbial community structures

Despite its environmental significance, little is known about denitrification in vadose zones owing to the complexity of such environments. Here, we investigated denitrification in unsaturated soils with different pore distributions. To this end, we performed batch-type denitrification experiments and analyzed microbial community shifts before and after possible reactions with nitrates to clarify the relevant denitrifying mechanism in the microcosms. For quantitative comparison, pore distribution in the test soil samples was characterized based on the uniformity coefficient (C_u) and water saturation degree (SD). Micro-CT analysis of the soil pore distribution confirmed that the proportion of bigger-sized pores increased with decreasing C_u. However, oxygen diffusion into the system was controlled by SD rather than C_u. Within a certain SD range (51-67%), the pore condition changed abruptly from an oxic to an anoxic state. Consequently, denitrification occurred even under unsaturated soil conditions when the SD increased beyond 51-67%. High throughput sequencing revealed that the same microbial species were potentially responsible for denitrification under both partially (SD 67%), and fully saturated (SD of 100%) conditions, implying that the mechanism of denitrification in a vadose zone, if it exists, might be possibly similar under varying conditions.

Whole Genome Sequencing of First Janibacter indicus Isolate in China Revealed Three Unique Genomic Islands Compared with Saprophytic Strains

Introduction

Janibacter caused bacteriemia is one of the rare infections.

Methods

In the present study, we report the first isolation of Janibacter, a rare bacterial infection, from a bacteremia patient in China. Its 16S rDNA was amplified and designated as Janibacter YFY001, which belongs to J. indicus. In addition, its genome was sequenced through combined second- and third-generation genome sequencing methods.

Results

Based on its genome, we identified many virulence factors, such as catalase, gelatinase, FbpABC systems, and resistant genes, among others. Interestingly, three genomic islands were found in YFY001 by comparing its genome to environmental Janibacter strains.

Discussion

Our study not only provides the necessary genomic information for in-depth study of Janibacter, but also provides a novel methodology for studying future cases of rare bacterial infection.

Performance and Application of 16S rRNA Gene Cycle Sequencing for Routine Identification of Bacteria in the Clinical Microbiology Laboratory

This review provides a state-of-the-art description of the performance of Sanger cycle sequencing of the 16S rRNA gene for routine identification of bacteria in the clinical microbiology laboratory. A detailed description of the technology and current methodology is outlined with a major focus on proper data analyses and interpretation of sequences. The remainder of the article is focused on a comprehensive evaluation of the application of this method for identification of bacterial pathogens based on analyses of 16S multialignment sequences. In particular, the existing limitations of similarity within 16S for genus- and species-level differentiation of clinically relevant pathogens and the lack of sequence data currently available in public databases is highlighted. A multiyear experience is described of a large regional clinical microbiology service with direct 16S broad-range PCR followed by cycle sequencing for direct detection of pathogens in appropriate clinical samples. The ability of proteomics (matrix-assisted desorption ionization-time of flight) versus 16S sequencing for bacterial identification and genotyping is compared. Finally, the potential for whole-genome analysis by next-generation sequencing (NGS) to replace 16S sequencing for routine diagnostic use is presented for several applications, including the barriers that must be overcome to fully implement newer genomic methods in clinical microbiology. A future challenge for large clinical, reference, and research laboratories, as well as for industry, will be the translation of vast amounts of accrued NGS microbial data into convenient algorithm testing schemes for various applications (i.e., microbial identification, genotyping, and metagenomics and microbiome analyses) so that clinically relevant information can be reported to physicians in a format that is understood and actionable. These challenges will not be faced by clinical microbiologists alone but by every scientist involved in a domain where natural diversity of genes and gene sequences plays a critical role in disease, health, pathogenicity, epidemiology, and other aspects of life-forms. Overcoming these challenges will require global multidisciplinary efforts across fields that do not normally interact with the clinical arena to make vast amounts of sequencing data clinically interpretable and actionable at the bedside.

Aerobic biodegradation of high explosive hexahydro-1,3,5- trinitro-1,3,5-triazine by Janibacter cremeus isolated from contaminated soil

OBJECTIVE

To evaluate the ability of Janibacter cremeus a soil bacterium isolated from explosive contaminated site in degradation of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) and to study enzyme responsible for degradation.

RESULTS

The isolate exhibited 88% degradation of RDX in 30 days of incubation. The biodegradation process followed the first order kinetics. The half- life of RDX was calculated to be 11.088 days. The RDX degradation process was complemented by concomitant release of nitrite ions with 0.78 mol of nitrite released per mole of RDX. The metabolites; Trinitroso- RDX, diamino-RDX, trimino-RDX, bis- (hydroxymethyl) nitramine and methylenedintramine derivative, viz, methylene- N- (hydroxy- methyl)- hydroxylamine- N-(hydroxymethyl) nitroamine corresponding to the molecular weights 174, 162, 132, 122 and 167 Da respectively were also detected. Nitroreductase enzyme was found to be responsible for RDX degradation.

CONCLUSION

J. cremeus could degrade RDX as sole source of nitrogen, via three different pathways wherein, Nitroreductase enzyme was found to play a major role. The efficient degradation of RDX makes J. cremeus suitable in treatment of contaminated water and soil at field scale levels.

Marine Rare Actinomycetes: A Promising Source of Structurally Diverse and Unique Novel Natural Products

Rare actinomycetes are prolific in the marine environment; however, knowledge about their diversity, distribution and biochemistry is limited. Marine rare actinomycetes represent a rather untapped source of chemically diverse secondary metabolites and novel bioactive compounds. In this review, we aim to summarize the present knowledge on the isolation, diversity, distribution and natural product discovery of marine rare actinomycetes reported from mid-2013 to 2017. A total of 97 new species, representing 9 novel genera and belonging to 27 families of marine rare actinomycetes have been reported, with the highest numbers of novel isolates from the families Pseudonocardiaceae, Demequinaceae, Micromonosporaceae and Nocardioidaceae. Additionally, this study reviewed 167 new bioactive compounds produced by 58 different rare actinomycete species representing 24 genera. Most of the compounds produced by the marine rare actinomycetes present antibacterial, antifungal, antiparasitic, anticancer or antimalarial activities. The highest numbers of natural products were derived from the genera Nocardiopsis, Micromonospora, Salinispora and Pseudonocardia. Members of the genus Micromonospora were revealed to be the richest source of chemically diverse and unique bioactive natural products.

Treatment of the liquid phase of digestate from a biogas plant for water reuse

Biogas plants struggle with managing nitrogen-rich digestate from manure co-digestion. In this study, the biologically treated liquid phase of digestate from an aerobic granular sludge batch reactor (GSBR) containing oxidized nitrogen forms (NO_x), phosphorus, COD and total suspended solids was post-denitrified (P-D), and then ultrafiltered. In P-D, various hydraulic retention times (from 10 to 60 h) and biomass concentrations (from 6 to 14 g MLSS/L) were tested. Then, waste glycerin (GL) was added to the P-D reactor at a COD_GL/NO_x ratio of 1.1, causing a large number of phosphate-accumulating and denitrifying Janibacter sp., and PHB-accumulating and denitrifying Paracoccus sp. and Thauera sp. to be present in granules, which improved nutrient removal. The effluent was ultrafiltered at 0.3 and 0.5 MPa. After biological treatment supported with GL and followed by ultrafiltration, the purified liquid phase of the digestate met FAO standards for water reuse for irrigation.

Description of Janibacter massiliensis sp. nov., cultured from the vaginal discharge of a patient with bacterial vaginosis

Strain Marseille-P4121^T was isolated from a vaginal sample of a 45-year-old French woman with bacterial vaginosis. It is a Gram-positive, asporogenous, non-motile and aerobic bacterium. Strain Marseille-P4121^T exhibits 98.2% 16S rRNA sequence similarity with Janibacter alkaliphilus strain SCSIO 10480^T, a phylogenetically closely related species with standing in nomenclature. Its major fatty acids were identified as C_18:1ω9 (34.4%), C_16:0 (30.1%), and C_18:0 (19%). The draft genome size of strain Marseille-P4121^T is 2,452,608 bp long with a 72.5% G+C content and contains 2351 protein-coding genes and 49 RNA genes including 3 rRNA genes. We propose that strain Marseille-P4121^T (= CECT 9671^T = CSUR P4121^T) is the type strain of the new species Janibacter massiliensis sp. nov.

Biodeterioration Risk Threatens the 3100 Year Old Staircase of Hallstatt (Austria): Possible Involvement of Halophilic Microorganisms

Background

The prosperity of Hallstatt (Salzkammergut region, Austria) is based on the richness of salt in the surrounding mountains and salt mining, which is documented as far back as 1500 years B.C. Substantial archaeological evidence of Bronze and Iron Age salt mining has been discovered, with a wooden staircase (1108 B.C.) being one of the most impressive and well preserved finds. However, after its discovery, fungal mycelia have been observed on the surface of the staircase, most probably due to airborne contamination after its find.

Objective

As a basis for the further preservation of this valuable object, the active micro-flora was examined to investigate the presence of potentially biodegradative microorganisms.

Results

Most of the strains isolated from the staircase showed to be halotolerant and halophilic microorganisms, due to the saline environment of the mine. Results derived from culture-dependent assays revealed a high fungal diversity, including both halotolerant and halophilic fungi, the most dominant strains being members of the genus Phialosimplex (synonym: Aspergillus). Additionally, some typical cellulose degraders, namely Stachybotrys sp. and Cladosporium sp. were detected. Numerous bacterial strains were isolated and identified as members of 12 different genera, most of them being moderately halophilic species. The most dominant isolates affiliated with species of the genera Halovibrio and Marinococcus. Halophilic archaea were also isolated and identified as species of the genera Halococcus and Halorubrum. Molecular analyses complemented the cultivation assays, enabling the identification of some uncultivable archaea of the genera Halolamina, Haloplanus and Halobacterium. Results derived from fungi and bacteria supported those obtained by cultivation methods, exhibiting the same dominant members in the communities.

Conclusion

The results clearly showed the presence of some cellulose degraders that may become active if the requirements for growth and the environmental conditions turn suitable; therefore, these microorganisms must be regarded as a threat to the wood.

Janibacter indicus sp. nov., isolated from hydrothermal sediment of the Indian Ocean

A Gram-staining-positive, aerobic and non-motile strain, 0704P10-1T, was isolated from hydrothermal sediment of the Indian Ocean. Phylogenetic, phenotypic and chemotaxonomic data for the organism supported that it belonged to the genus Janibacter . Strain 0704P10-1T showed 97.2–98.7 % 16S rRNA gene sequence similarities to the type strains of recognized members of the genus Janibacter . It contained meso-diaminopimelic acid as the diagnostic diamino acid in the cell wall. MK-8(H4) was the only menaquinone detected. The major fatty acids were iso-C16 : 0, C17 : 1ω8c and 10-methyl C17 : 0. Meanwhile, the results of DNA–DNA hybridization studies and other physiological and biochemical tests allowed the genotypic and phenotypic differentiation of strain 0704P10-1T from closely related species. Thus, strain 0704P10-1T represents a novel species of the genus Janibacter , for which the name Janibacter indicus sp. nov. is proposed. The type strain is 0704P10-1T ( = LMG 27493T = CGMCC 1.12511T).