Microbial and genetic ecology of tropical Vertisols under intensive chemical farming.

There are continued concerns on unscientific usage of chemical fertilizers and pesticides, particularly in many developing countries leading to adverse consequences for soil biological quality and agricultural sustainability. In farmers' fields in tropical Vertisols of peninsular India, "high" fertilizer and pesticide usage at about 2.3 times the recommended rates in black gram (Vigna mungo) did not have a deleterious effect on the abundance of culturable microorganisms, associative nitrogen fixers, nitrifiers, and 16S rRNA gene diversity compared to normal rates. However, "very high" application at about five times the fertilizers and 1.5 times pesticides in chilies (Capsicum annuum) adversely affected the populations of fungi, actinomycetes, and ammonifiers, along with a drastic change in the eubacterial community profile and diversity over normal rates. Actinobacteria were dominant in black gram normal (BG1) (47%), black gram high (BG2) (36%), and chili normal (CH1) (30%) and were least in chili very high (CH2) (14%). Geodermatophilus formed 20% of Actinobacteria in BG1 but disappeared in BG2, CH1, and CH2. Asticcacaulis dominated at "very high" input site (CH2). Diversity of nitrogen fixers was completely altered; Dechloromonas and Anaeromyxobacter were absent in BG1 but proliferated well in BG2. There was reduction in rhizobial nifH sequences in BG2 by 46%. Phylogenetic differences characterized by UniFrac and principal coordinate analysis showed that BG2 and CH2 clustered together depicting a common pattern of genetic shift, while BG1 and CH1 fell at different axis. Overall, there were adverse consequences of "very high" fertilizer and pesticide usage on soil microbial diversity and function in tropical Vertisols.

Comparative Study of Cytomorphological Robinson's Grading for Breast Carcinoma with Modified Bloom-Richardson Histopathological Grading.

Objective. To study the correlation of cytomorphological Robinson's grading for breast cancers with a modified Bloom-Richardson histopathological grading. Materials and Methods. One hundred sixteen cytologically malignant breast tumour cases were included in this study and correlated with paraffin embedded sections. Breast lumps were varied from less than 1 cm to 11 cm in greatest dimension. FNA was performed from different sites of the breast lump, and smears were stained with Giemsa and H&E stain and evaluated for cytological grading according to Robinson's grading system. Paraffin embedded tissue sections were stained with hematoxylin and eosin stain and graded according to modified Bloom-Richardson grading system. Comparison between these two grading systems was done. Results. Cytologically grade I, grade II, and grade III cases were 13.8%, 64.65%, and 21.55%, respectively. Histologically 25%, 54.31%, and 20.69% cases were grade I, grade II, and grade III, respectively. Concordance rate between cytology and histology of grade I, grade II, and grade III tumors was 75%, 70.67%, and 60% respectively. The absolute concordance rate was 68.97%. Conclusion. In the era of multiple treatment modalities and neoadjuvant therapy, cytological grading can be used as a prognostic factor for better management of patients.

Devosia lucknowensis sp. nov., a bacterium isolated from hexachlorocyclohexane (HCH) contaminated pond soil.

Strain L15(T), a Gram-negative, motile, orange colored bacterium was isolated from pond soil in the surrounding area of a hexachlorocyclohexane (HCH) dump site at Ummari village in Lucknow, India. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain L15(T) belongs to the family Hyphomicrobiaceae in the order Rhizobiales. Strain L15(T) showed highest 16S rRNA gene sequence similarity to Devosia chinhatensis IPL18(T) (98.0%). Chemotaxonomic data revealed that the major fatty acids were summed feature 8 (C18:1 ω7c and/or C18:1 ω6c), C18:1 ω7c 11-methyl, C16:0 and C18:0. The major polar lipids of strain L15(T) were diphosphatidylglycerol and phosphatidylglycerol. The genomic DNA G+C content of strain L15(T) was 59.8%. Polyamine profile showed the presence of sym-homospermidine with traces of putrescine. Ubiquinone Q-10 was the major respiratory quinone present. Based on these data, strain L15(T) (=CCM 7977(T) =DSM 25398(T)) was classified as a type strain of a novel species, for which the name Devosia lucknowensis sp. nov. is proposed.

Comparative metagenomic analysis of soil microbial communities across three hexachlorocyclohexane contamination levels.

This paper presents the characterization of the microbial community responsible for the in-situ bioremediation of hexachlorocyclohexane (HCH). Microbial community structure and function was analyzed using 16S rRNA amplicon and shotgun metagenomic sequencing methods for three sets of soil samples. The three samples were collected from a HCH-dumpsite (450 mg HCH/g soil) and comprised of a HCH/soil ratio of 0.45, 0.0007, and 0.00003, respectively. Certain bacterial; (Chromohalobacter, Marinimicrobium, Idiomarina, Salinosphaera, Halomonas, Sphingopyxis, Novosphingobium, Sphingomonas and Pseudomonas), archaeal; (Halobacterium, Haloarcula and Halorhabdus) and fungal (Fusarium) genera were found to be more abundant in the soil sample from the HCH-dumpsite. Consistent with the phylogenetic shift, the dumpsite also exhibited a relatively higher abundance of genes coding for chemotaxis/motility, chloroaromatic and HCH degradation (lin genes). Reassembly of a draft pangenome of Chromohalobacter salaxigenes sp. (∼8X coverage) and 3 plasmids (pISP3, pISP4 and pLB1; 13X coverage) containing lin genes/clusters also provides an evidence for the horizontal transfer of HCH catabolism genes.

Genome sequence of Acinetobacter sp. strain HA, isolated from the gut of the polyphagous insect pest Helicoverpa armigera.

In this study, Acinetobacter sp. strain HA was isolated from the midgut of a fifth-instar larva of Helicoverpa armigera. Here, we report the draft genome sequence (3,125,085 bp) of this strain that consists of 102 contigs, 2,911 predicted coding sequences, and a G+C content of 41%.

Acinetobacter indicus sp. nov., isolated from a hexachlorocyclohexane dump site.

The taxonomic position of a Gram-negative, non-motile, oxidase negative and catalase positive strain, A648(T), isolated from a hexachlorocyclohexane (HCH) dump site located in Lucknow, India, was ascertained by using a polyphasic approach. A comparative analysis of a partial sequence of the rpoB gene and the 16S rRNA gene sequence revealed that strain A648(T) belonged to the genus Acinetobacter. DNA-DNA relatedness values between strain A648(T) and other closely related members (16S rRNA gene sequence similarity greater than 97%), namely Acinetobacter radioresistens DSM 6976(T), A. venetianus ATCC 31012(T), A. baumannii LMG 1041(T), A. parvus LMG 21765(T) A. junii LMG 998(T) and A. soli JCM 15062(T), were found to be less than 8%. The major cellular fatty acids of strain A648(T) were 18:1ω9c (19.6%), summed feature 3 (15.9%), 16:0 (10.6%) and 12:0 (6.4%). The DNA G+C content was 40.4 mol%. The polar lipid profile of strain A648(T) indicated the presence of diphosphatidylglycerol, phosphatidylethanolamine, followed by phosphatidylglycerol and phosphatidylcholine. The predominant polyamine of strain A648(T) was 1,3-diaminopropane and moderate amounts of putrescine, spermidine and spermine were also detected. The respiratory quinone consisted of ubiquinone with nine isoprene units (Q-9). On the basis of DNA-DNA hybridization, phenotypic characteristics and chemotaxonomic and phylogenetic comparisons with other members of the genus Acinetobacter, strain A648(T) is found to be a novel species of the genus Acinetobacter, for which the name Acinetobacter indicus sp. nov. is proposed. The type strain is A648(T) ( = DSM 25388(T) = CCM 7832(T)).