Unexpected nondenitrifier nitrous oxide reductase gene diversity and abundance in soils.

Agricultural and industrial practices more than doubled the intrinsic rate of terrestrial N fixation over the past century with drastic consequences, including increased atmospheric nitrous oxide (N(2)O) concentrations. N(2)O is a potent greenhouse gas and contributor to ozone layer destruction, and its release from fixed N is almost entirely controlled by microbial activities. Mitigation of N(2)O emissions to the atmosphere has been attributed exclusively to denitrifiers possessing NosZ, the enzyme system catalyzing N(2)O to N(2) reduction. We demonstrate that diverse microbial taxa possess divergent nos clusters with genes that are related yet evolutionarily distinct from the typical nos genes of denitirifers. nos clusters with atypical nosZ occur in Bacteria and Archaea that denitrify (44% of genomes), do not possess other denitrification genes (56%), or perform dissimilatory nitrate reduction to ammonium (DNRA; (31%). Experiments with the DNRA soil bacterium Anaeromyxobacter dehalogenans demonstrated that the atypical NosZ is an effective N(2)O reductase, and PCR-based surveys suggested that atypical nosZ are abundant in terrestrial environments. Bioinformatic analyses revealed that atypical nos clusters possess distinctive regulatory and functional components (e.g., Sec vs. Tat secretion pathway in typical nos), and that previous nosZ-targeted PCR primers do not capture the atypical nosZ diversity. Collectively, our results suggest that nondenitrifying populations with a broad range of metabolisms and habitats are potentially significant contributors to N(2)O consumption. Apparently, a large, previously unrecognized group of environmental nosZ has not been accounted for, and characterizing their contributions to N(2)O consumption will advance understanding of the ecological controls on N(2)O emissions and lead to refined greenhouse gas flux models.

Metals Bioaccumulation Mechanism in Neem Bark.

The aim of this work was to define the bioaccumulation mechanism of metals onto the non-living biomaterial prepared from an extensively available plant bark biomass of neem (Azadirachta indica). Based on maximum ultimate fixation capacities (mmol/g) of the product, metals ions could be arranged as Hg(2+) < Cd(2+) < Pb(2+) ≅ Cu(2+). Surface properties of the biomaterial were characterized by X-ray photoelectron spectroscopy and X-ray diffraction techniques for their sorption mechanism. Whewellite (C2CaO4 · H2O) was identified in the biomaterial, which indicated that calcium ions are electrovalently bonded with carboxylate ions facilitating the ion exchange mechanism with metal ions. Bioaccumulation of metal ions was also studied by Fourier transform infrared spectroscopy, which indicated the presence of functional groups implicated in adsorbing metal ions. Biomaterial did not adsorb anionic As(III), As(V) and Cr(VI), because of their electrostatic repulsion with carboxylic functional groups. Neem bark can be used as bioindicators, bioaccumulators and biomonitors while determining environmental pressures. Metal bioaccumulative properties and structural investigation of plant bark has potential in providing quantitative information on the metal contamination in the surrounding environment.

Wide substrate range for a candidate bioremediation enzyme isolated from Nocardioides sp. strain SG-4 G.

Narrow substrate ranges can impact heavily on the range of applications and hence commercial viability of candidate bioremediation enzymes. Here we show that an ester hydrolase from Nocardioides strain SG-4 G has potential as a bioremediation agent against various pollutants that can be detoxified by hydrolytic cleavage of some carboxylester, carbamate, or amide linkages. Previously we showed that a radiation-killed, freeze-dried preparation (ZimA) of this strain can rapidly degrade the benzimidazole fungicide carbendazim due to the activity of a specific ester hydrolase, MheI. Here, we report that ZimA also has substantial hydrolytic activity against phthalate diesters (dimethyl, dibutyl, and dioctyl phthalate), anilide (propanil and monalide), and carbamate ester (chlorpropham) herbicides under laboratory conditions. The reaction products are substantially less toxic, or inactive as herbicides, than the parent compounds. Tests of strain SG-4 G and Escherichia coli expressing MheI found they were also able to hydrolyse dimethyl phthalate, propanil, and chlorpropham, indicating that MheI is principally responsible for the above activities.

Muscle Transcriptome Sequencing Revealed Thermal Stress-Responsive Regulatory Genes in Farmed Rohu, Labeo rohita (Hamilton, 1822).

Rohu, Labeo rohita, is one of the most important aquaculture species in the Indian subcontinent. Understanding the molecular-level physiological responses to thermal stress or climate change is essential. In the present work, transcriptome sequencing was carried out in the muscle tissue of the rohu in response to heat stress (35 °C) in comparison with the control (28 °C). A total of 125 Gb of sequence data was generated, and the raw-reads were filtered and trimmed, which resulted in 484 million quality reads. Reference-based assembly of reads was performed using L. rohita genome, and a total of 90.17% of reads were successfully mapped. A total of 37,462 contigs were assembled with an N50 value of 1854. The differential expression analysis revealed a total of 107 differentially expressed genes (DEGs) (15 up-, 37 down-, and 55 neutrally regulated) as compared to the control group (Log2FC > 2, P < 0.05). Gene enrichment analysis of DEGs indicates that transcripts were associated with molecular, biological, and cellular activities. The randomly selected differentially expressed transcripts were validated by RT-qPCR and found consistent expression patterns in line with the RNA-seq data. Several transcripts such as SERPINE1(HSP47), HSP70, HSP90alpha, Rano class II histocompatibility A beta, PGC-1 and ERR-induced regulator, proto-oncogene c-Fos, myozenin2, alpha-crystallin B chain-like protein, angiopoietin-like protein 8, and acetyl-CoA carboxylases have been identified in muscle tissue of rohu that are associated with stress/immunity. This study identified the key biomarker SERPINE1 (HSP47), which showed significant upregulation (~ 2- to threefold) in muscle tissue of rohu exposed to high temperature. This study can pave a path for the identification of stress-responsive biomarkers linked with thermal adaptations in the farmed carps.

Biosorption mechanism of nine different heavy metals onto biomatrix from rice husk.

A biomatrix was prepared from rice husk, a lignocellulosic waste from agro-industry, for the removal of several heavy metals as a function of pH and metal concentrations in single and mixed solutions. The biomatrix was characterized using scanning electron microscope and Fourier transform infrared spectroscopy, which indicated the presence of several functional groups for binding metal ions. Different experimental approaches were applied to show mechanistic aspects, especially the role of calcium and magnesium present in the biomatrix in ion exchange mechanism. The ultimate maximum adsorption capacity obtained from the Langmuir isotherm increases in the order (mmol/g): Ni (0.094), Zn (0.124), Cd (0.149), Mn (0.151), Co (0.162), Cu (0.172), Hg (0.18) and Pb (0.28). The sorption of Cr(III) onto biomatrix at pH 2 was 1.0 mmol/g. Speciation of chromium, cadmium and mercury loaded on the biomatrix was determined by X-ray photoelectron spectroscopy. The biomatrix has adsorption capacity comparable or greater to other reported sorbents.

Bagasse-assisted bioremediation of ammonia from shrimp farm wastewater.

Development of new economically feasible ecofriendly products from agricultural wastes or byproducts for shrimp farm wastewater treatment is the objective of our continued research. Ammonia is a nitrogenous toxicant, which is commonly found in wastewater from shrimp farms. In the present study, we explored the possibility of the use of simply and inexpensively prepared bagasse products so that this abundant crop byproduct could be used to remove ammonia from shrimp farm wastewater. Bagasse, a natural highly fibrous lignocellulosic byproduct of sugarcane, was converted into five different products. Experimental results have shown that ammonia is efficiently removed from wastewater by four bagasse products with a dose of 1 to 6 g/L within 24 hours. The effect of bagasse products on other water quality parameters and growth kinetics of biofilm bacteria onto bagasse fiber have also been studied. Efficacies of products were compared by using statistical analysis. Products developed from bagasse are useful and economical.

Bactericidal activity of elastin-like polypeptide biopolymer with polyhistidine domain and silver.

In the present study, elastin-like biopolymer (ELP) composed of a polyhistidine domain has been investigated as a silver binding agent for antibacterial activity against Escherichia coli, a model test strain for Gram-negative bacteria for antibacterial assays of nanoparticles, and Vibrio harveyi, an opportunistic pathogen which cause mass mortality in shrimp Penaeus monodon reared in coastal aquaculture. The concentration dependent antimicrobial activity of ELPH-Ag on E. coli and V. harveyi was examined by agar well diffusion method and further confirmed through growth curves using spectrophotometer assisted absorption observations. The increased concentrations of ELP-Ag effectively checked the bacterial growth and increased the diameter of inhibition zone. The results showed a minimum inhibitory concentration of 37 µg/ml. This study has an application in formulating artificial protein based antibacterial in diverse fields of healthcare and management of disease in coastal aquaculture.