Airborne and indigenous microbiomes co-drive the rebound of antibiotic resistome during compost storage

Composting is widely used to reduce the abundance of antibiotic resistance genes (ARGs) in solid waste. While ARG dynamics have been extensively investigated during composting, the fate and abundance of residual ARGs during the storage remain unexplored. Here, we tested experimentally how ARG and mobile genetic element (MGE) abundances change during compost storage using metagenomics, quantitative PCR and direct culturing. We found that 43.8% of ARGs and 39.9% of MGEs quickly recovered already during the first week of storage. This rebound effect was mainly driven by the regrowth of indigenous, antibiotic-resistant bacteria that survived the composting. Bacterial transmission from the surrounding air had a much smaller effect, being most evident as MGE rebound during the later stages of storage. While hyperthermophilic composting was more efficient at reducing the relative abundance of ARGs and MGEs, relatively greater ARG rebound was observed during the storage of hyperthermophilic compost, exceeding the initial levels of untreated sewage sludge. Our study reveals that residual ARGs and MGEs left in the treated compost can quickly rebound during the storage via airborne introduction and regrowth of surviving bacteria, highlighting the need to develop better storage strategies to prevent the rebound of ARGs and MGEs after composting.     

Diversity of archaea and niche preferences among putative ammonia-oxidizing Nitrososphaeria dominating across European arable soils

Archaeal communities in arable soils are dominated by Nitrososphaeria, a class within Thaumarchaeota comprising all known ammonia-oxidizing archaea (AOA). AOA are key players in the nitrogen cycle and defining their niche specialization can help predicting effects of environmental change on these communities. However, hierarchical effects of environmental filters on AOA and the delineation of niche preferences of nitrososphaerial lineages remain poorly understood. We used phylogenetic information at fine scale and machine learning approaches to identify climatic, edaphic and geomorphological drivers of Nitrososphaeria and other archaea along a 3000 km European gradient. Only limited insights into the ecology of the low-abundant archaeal classes could be inferred, but our analyses underlined the multifactorial nature of niche differentiation within Nitrososphaeria. Mean annual temperature, C:N ratio and pH were the best predictors of their diversity, evenness and distribution. Thresholds in the predictions could be defined for C:N ratio and cation exchange capacity. Furthermore, multiple, independent and recent specializations to soil pH were detected in the Nitrososphaeria phylogeny. The coexistence of widespread ecophysiological differences between closely related soil Nitrososphaeria highlights that their ecology is best studied at fine phylogenetic scale.     

Synthesis, crystal structures and magnetic studies of dicyanamide bridged two new 1D copper(II) complexes

Two new dicyanamide bridged 1D polynuclear copper(II) complexes [Cu(L¹){μ_1,5-N(CN)₂}]_n (1) [L¹H = C₆H₅C(O)NHNC(CH₃)C₅H₄N] and [Cu(L²){μ_1,5-N(CN)₂}]_n (2) [L²H=C₆H₅C(O)CHC(CH₃)NCH₂CH₂N(CH₃)₂] have been synthesised and structures of both the complexes and their crystal packing arrangements have been established by X-ray crystallography. For complex 1, a tridentate hydrazone ligand (L¹H) obtained by the condensation of benzhydrazide and 2-acetylpyridine is used, whereas a tridentate Schiff base (L²H) derived from benzoylacetone and 2-dimethylaminoethylamine is employed for the preparation of complex 2. Variable temperature magnetic susceptibility measurement studies indicate there are weak antiferromagnetic interactions with J values −0.10 and −1.41 cm⁻¹ for 1 and 2, respectively.     

Isolation of a singly oxo-bridged Fe(III) dinuclear complex: Synthesis, crystal structure, spectroscopic and magnetic studies

The μ-oxo dinuclear complex {Fe₂O(tptz)₂[N(CN)₂]₂(NO₃)₂} (1) (where tptz = 2,4,6-tris(2-pyridyl)-1,3,5-triazine) has been synthesised and characterised by elemental analysis, FT-IR, UV-vis, cyclic voltammetry, Mössbauer spectroscopy, and variable-temperature magnetic susceptibility measurements and single crystal X-ray diffraction. The iron centres have a pentagonal-bipyramidal geometry. The dimeric neutral complex exhibits typical Fe-μ-O bond lengths of 1.763(1) Å and a bridge angle of 180.00°. The Fe?Fe separation is 3.526(3) Å. The Mössbauer spectrum at room temperature consists of one quadrupole doublet with an isomer shift of 0.41 mm/s and a quadrupole splitting of 1.12 mm/s. Variable-temperature magnetic susceptibility measurements have been measured in the temperature range 300-2 K, revealing an intramolecular antiferromagnetic coupling (J = −211.6 cm⁻¹).     

Two new end-to-end single dicyanamide bridged Cu(II) complexes with Schiff base ligands: Structural, electrochemical and magnetic properties

The synthesis, crystal structures and magnetic properties of two different copper(II) complexes of formula [Cu(L¹)(dca)]_n · nClO₄ (1) and [Cu(L²)]₂(dca)(ClO₄) (2) [L¹ = N,N-dimethylethylene-N′-(pyridine-2-carbaldiiminato), HL² = N,N-dimethylethylene-N′-salicylaldiiminato, dca = dicyanamide anion] are described. Spectroscopic and electrochemical properties have also been discussed. A one-dimensional chain structure with single, symmetrical, μ_1,5-dca bridges is found in compound 1. The copper atom in 1 has a square pyramidal geometry. A tridentate Schiff base ligand, having NNN donor sites, and one nitrogen atom from dca occupy the basal plane. N(18) of a neighbouring unit occupies the apical site. The Schiff base used in compound 2 is a tridentate anion with NNO donor sites, which changes the structure in a dinuclear unit of copper atoms bridged by single end-to-end dicyanamide ion. The environment around copper in 2 is square planar. Magnetic susceptibility measurements for 1 and 2 reveal the occurrence of weak antiferromagnetic interaction through the dca ligand.     

A semiparametric modeling framework for potential biomarker discovery and the development of metabonomic profiles

Background  

The discovery of biomarkers is an important step towards the development of criteria for early diagnosis of disease status. Recently electrospray ionization (ESI) and matrix assisted laser desorption (MALDI) time-of-flight (TOF) mass spectrometry have been used to identify biomarkers both in proteomics and metabonomics studies. Data sets generated from such studies are generally very large in size and thus require the use of sophisticated statistical techniques to glean useful information. Most recent attempts to process these types of data model each compound's intensity either discretely by positional (mass to charge ratio) clustering or through each compounds' own intensity distribution. Traditionally data processing steps such as noise removal, background elimination and m/z alignment, are generally carried out separately resulting in unsatisfactory propagation of signals in the final model.     

Two new pseudohalide-bridged Cu(II) complexes with a hydrazone ligand: Syntheses,crystal structures and magnetic studies

Two new pseudohalide-bridged copper(II) complexes [{Cu(PBH)(μ_1,1-CNO)}₂] (1) and {Cu(PBH)(μ_1,5-NCNCN)}_n (2) (where HPBH = 2-pyridinecarboxaldehyde benzoyl hydrazone) have been synthesised and characterised by elemental analysis, CV, IR and UV–Vis spectral studies. The tridentate hydrazone pro-ligand (HPBH) was obtained by the condensation of benzhydrazide and pyridine-2-carboxaldehyde. Structures of both complexes have been established by X-ray crystallography which shows that 1 is a μ_1,1-CNO^?-bridged dimer whereas 2 is a μ_1,5-dca-bridged (dca = dicyanamide) linear polynuclear structure. Variable temperature magnetic susceptibility studies indicate weak antiferromagnetic interactions with J values ?0.50 cm^?1 and ?0.10 cm^?1 for 1 and 2, respectively.     

Enhanced production and partial characterization of an extracellular polysaccharide from newly isolated Azotobacter sp. SSB81

A strain was selected by its highest extracellular polysaccharide (EPS) production ability compare to other isolates from the same rhizospheric soil. The selected strain was identified by 16S rDNA sequencing and designated as SSB81. Phylogenetic analysis of the gene sequence showed its close relatedness with Azotobacter vinelandii and Azotobacter salinestris. Maximum EPS (2.52 g l⁻¹) was recovered when the basal medium was supplemented with glucose (2.0%), riboflavin (1 mg l⁻¹) and casamino acid (0.2%). The EPS showed a stable viscosity level at acidic pH (3.0–6.5) and the pyrolysis temperature was found to be at 116.73 °C with an enthalpy (ΔH) of 1330.72 Jg⁻¹. MALDI TOF mass spectrometric result suggests that polymer contained Hex₅Pent₃ as oligomeric building subunit. SEM studies revealed that the polymer had a porous structure with small pore size distribution indicating the compactness of the polymer. This novel EPS may find possible application as a polymer for environmental bioremediation and biotechnological processes.     

Erosion reduces soil microbial diversity,network complexity and multifunctionality

While soil erosion drives land degradation, the impact of erosion on soil microbial communities and multiple soil functions remains unclear. This hinders our ability to assess the true impact of erosion on soil ecosystem services and our ability to restore eroded environments. Here we examined the effect of erosion on microbial communities at two sites with contrasting soil texture and climates. Eroded plots had lower microbial network complexity, fewer microbial taxa, and fewer associations among microbial taxa, relative to non-eroded plots. Soil erosion also shifted microbial community composition, with decreased relative abundances of dominant phyla such as Proteobacteria, Bacteroidetes, and Gemmatimonadetes. In contrast, erosion led to an increase in the relative abundances of some bacterial families involved in N cycling, such as Acetobacteraceae and Beijerinckiaceae. Changes in microbiota characteristics were strongly related with erosion-induced changes in soil multifunctionality. Together, these results demonstrate that soil erosion has a significant negative impact on soil microbial diversity and functionality.Subject terms: Soil microbiology, Microbial ecology     

Effect of Arsenic on Nodulation and Nitrogen Fixation of Blackgram (<Emphasis Type="Italic">Vigna mungo</Emphasis>)

Rhizobium–legume symbiotic interaction is an efficient model system for soil remediation and reclamation. We earlier isolated an arsenic (As) (2.8 mM arsenate) tolerant and symbiotically effective Rhizobium strain, VMA301 from Vigna mungo and in this study we further characterized its efficacy for arsenic removal from the soil and its nitrogen fixation capacity. Although nodule formation is delayed in plants with As-treated composite when the inoculum was prepared without arsenic in culture medium, whereas it attains the significant number of nodules compare to plant grown in As-free soil when the inoculum was prepared with arsenic supplemented medium. Arsenic accumulation was higher in roots than root nodules. Nitrogenase activity is reduced to almost 2 fold in plants with As-treated soil but not abolished. These results suggest that this strain, VMA301, has been able to establish an effective symbiotic interaction in V. mungo in As-contaminated soil and can perform dual role of arsenic bioremediation as well as soil nitrogen improvement.