Tapan Kumar Adhya

Global change pressures on soils from land use and management

Soils are subject to varying degrees of direct or indirect human disturbance, constituting a major global change driver. Factoring out natural from direct and indirect human influence is not always straightforward, but some human activities have clear impacts. These include land-use change, land management and land degradation (erosion, compaction, sealing and salinization). The intensity of land use also exerts a great impact on soils, and soils are also subject to indirect impacts arising from human activity, such as acid deposition (sulphur and nitrogen) and heavy metal pollution. In this critical review, we report the state-of-the-art understanding of these global change pressures on soils, identify knowledge gaps and research challenges and highlight actions and policies to minimize adverse environmental impacts arising from these global change drivers. Soils are central to considerations of what constitutes sustainable intensification. Therefore, ensuring that vulnerable and high environmental value soils are considered when protecting important habitats and ecosystems, will help to reduce the pressure on land from global change drivers. To ensure that soils are protected as part of wider environmental efforts, a global soil resilience programme should be considered, to monitor, recover or sustain soil fertility and function, and to enhance the ecosystem services provided by soils. Soils cannot, and should not, be considered in isolation of the ecosystems that they underpin and vice versa. The role of soils in supporting ecosystems and natural capital needs greater recognition. The lasting legacy of the International Year of Soils in 2015 should be to put soils at the centre of policy supporting environmental protection and sustainable development.

Isolation of ACC deaminase producing PGPR from rice rhizosphere and evaluating their plant growth promoting activity under salt stress

AimsBacteria possessing ACC deaminase activity reduce the level of stress ethylene conferring resistance and stimulating growth of plants under various biotic and abiotic stresses. The present study aims at isolating efficient ACC deaminase producing PGPR strains from the rhizosphere of rice plants grown in coastal saline soils and quantifying the effect of potent PGPR isolates on rice seed germination and seedling growth under salinity stress and ethylene production from rice seedlings inoculated with ACC deaminase containing PGPR.MethodsSoils from root region of rice growing in coastal soils of varying salinity were used for isolating ACC deaminase producing bacteria and three bacterial isolates were identified following polyphasic taxonomy. Seed germination, root growth and stress ethylene production in rice seedlings following inoculation with selected PGPR under salt stress were quantified.ResultsInoculation with selected PGPR isolates had considerable positive impacts on different growth parameters of rice including germination percentage, shoot and root growth and chlorophyll content as compared to uninoculated control. Inoculation with the ACC deaminase producing strains reduced ethylene production under salinity stress.ConclusionsThis study demonstrates the effectiveness of rhizobacteria containing ACC deaminase for enhancing salt tolerance and consequently improving the growth of rice plants under salt-stress conditions.

Engineering bacteria for bioremediation of persistent organochlorine pesticide lindane (γ-hexachlorocyclohexane).

Strategies were designed for bioremediation of the highly persistent toxic pesticide γ-hexachlorocyclohexane (γ-HCH) or lindane from the environment. Lindane caused the loss of stress-protective chaperone GroEL, and inhibited photosynthesis, respiration and nitrogen-fixation in Anabaena, resulting in growth arrest. To alleviate lindane toxicity, the linA2 gene, encoding HCH dehydrochlorinase from Sphingomonas paucimobilis B90, was knocked-in at an innocuous locus in Anabaena genome and over-expressed from an eco-friendly light-inducible PpsbA1 promoter. The recombinant Anabaena degraded >98% of 10 ppm lindane within 6-10 days. A LinA2 overexpressing Escherichia coli strain could degrade 10 ppm of all the isomers of lindane within 1h and displayed a visual degradation zone on a newly designed histochemical plate containing 50mg lindane within 12h. The study demonstrates (a) bioremediation of traces of lindane prevalent in paddy fields, using bioengineered photoautotrophic Anabaena, and, (b) biodegradation of huge stockpiles of lindane, by employing recombinant live/dead E. coli.

Streptomyces barkulensis sp. nov., isolated from an estuarine lake

The taxonomic position of a novel actinomycete, strain RC 1831(T), isolated from the sediment of a fish dumping yard at Barkul village near Chilika Lake, Odisha, India, was determined by a polyphasic approach. Based on morphological and chemotaxonomic characteristics the isolate was determined to belong to the genus Streptomyces. The phylogenetic tree based on its nearly complete 16S rRNA gene sequence (1428 nt) with representative strains showed that the strain consistently falls into a distinct phyletic line together with Streptomyces glaucosporus DSM 41689(T) (98.22% similarity) and a subclade consisting of Streptomyces atacamensis DSM 42065(T) (98.40%), Streptomyces radiopugnans R97 DSM 41901(T) (98.27%), Streptomyces fenghuangensis GIMN4.003(T) (98.33 %), Streptomyces nanhaiensis DSM 41926(T) (98.13%), Streptomyces megasporus NBRC 14749(T) (97.37%) and Streptomyces macrosporus NBRC 14748(T) (98.22%). However, the levels of DNA-DNA relatedness between strain RC 1831(T) and phylogenetically related strains Streptomyces atacamensis DSM 42065(T) (28.75 ± 3.25%) and Streptomyces glaucosporus DSM 41689(T) (15 ± 2.40%) were significantly lower than the 70% threshold value for delineation of genomic species. Furthermore, the isolate could be distinguished phenotypically on the basis of physiological, morphological and biochemical differences from its closest phylogenetic neighbours and other related reference strains. Strain RC 1831(T) is therefore considered to represent a novel species of the genus Streptomyces, for which the name Streptomyces barkulensis sp. nov. is proposed. The type strain is RC 1831(T) ( = JCM 18754(T) = DSM 42082(T)).

Molecular ecological perspective of methanogenic archaeal community in rice agroecosystem

Methane leads to global warming owing to its warming potential higher than carbon dioxide (CO2). Rice fields represent the major source of methane (CH4) emission as the recent estimates range from 34 to 112 Tg CH4 per year. Biogenic methane is produced by anaerobic methanogenic archaea. Advances in high-throughput sequencing technologies and isolation methodologies enabled investigators to decipher methanogens to be unexpectedly diverse in phylogeny and ecology. Exploring the link between biogeochemical methane cycling and methanogen community dynamics can, therefore, provide a more effective mechanistic understanding of CH4 emission from rice fields. In this review, we summarize the current knowledge on the diversity and activity of methanogens, factors controlling their ecology, possible interactions between rice plants and methanogens, and their potential involvement in the source relationship of greenhouse gas emissions from rice fields.

Salinity and macrophyte drive the biogeography of the sedimentary bacterial communities in a brackish water tropical coastal lagoon

Brackish water coastal lagoons are least understood with respect to the seasonal and temporal variability in their sedimentary bacterial communities. These coastal lagoons are characterized by the steep environmental gradient and provide an excellent model system to decipher the biotic and abiotic factors that determine the bacterial community structure over time and space. Using Illumina sequencing of the 16S rRNA genes from a total of 100 bulk surface sediments, we investigated the sedimentary bacterial communities, their spatiotemporal distribution, and compared them with the rhizosphere sediment communities of a common reed; Phragmites karka and a native seagrass species; Halodule uninervis in Chilika Lagoon. Spatiotemporal patterns in bacterial communities were linked to specific biotic factors (e.g., presence and type of macrophyte) and abiotic factors (e.g., salinity) that drove the community composition. Comparative assessment of communities highlighted bacterial lineages that were responsible for segregating the sediment communities over distinct salinity regimes, seasons, locations, and presence and type of macrophytes. Several bacterial taxa were specific to one of these ecological factors suggesting that species-sorting processes drive specific biogeographical patterns in the bacterial populations. Modeling of proteobacterial lineages against salinity gradient revealed that α- and γ-Proteobacteria increased with salinity, whereas β-Proteobacteria displayed the opposite trend. The wide variety of biogeochemical functions performed by the rhizosphere microbiota of P. karka must be taken into consideration while formulating the management and conservation plan for this reed. Overall, this study provides a comprehensive understanding of the spatiotemporal dynamics and functionality of sedimentary bacterial communities and highlighted the role of biotic and abiotic factors in generating the biogeographical patterns in the bacterial communities of a tropical brackish water coastal lagoon.

Draft Genome Sequence of Pseudomonas sp. Strain BMS12, a Plant Growth-Promoting and Protease-Producing Bacterium, Isolated from the Rhizosphere Sediment of Phragmites karka of Chilika Lake, India

ABSTRACT We report the 4.51 Mb draft genome of Pseudomonas sp. strain BMS12, a Gram-negative bacterium in the class of Gammaproteobacteria, isolated from the rhizospheric sediment of Phragmites karka, an invasive weed in Chilika Lake, Odisha, India. The Pseudomonas sp. strain BMS12 is capable of producing proteases and is also an efficient plant growth promoter that can be useful for various phytoremedial and industrial applications.

Draft Genome Sequence of Halobacillus sp. Strain KGW1, a Moderately Halophilic and Alkaline Protease-Producing Bacterium Isolated from the Rhizospheric Region of Phragmites karka from Chilika Lake, Odisha, India

ABSTRACT Halobacillus sp. strain KGW1 is a moderately halophilic, rod shaped, Gram-positive, yellow pigmented, alkaline protease-producing bacterium isolated from a water sample from Chilika Lake, Odisha, India. Sequencing of bacterial DNA assembled a 3.68-Mb draft genome. The genome annotation analysis showed various gene clusters for tolerance to stress, such as elevated pH, salt concentration, and toxic metals.

Taxonomic description and genome sequence of Halobacillus marinus sp. nov., a novel strain isolated from Chilika Lake, India

Abstractmoderately halophilic spore forming, motile, Gram-positive, rod-shaped bacterial strain designated as KGW1T was isolated from water sample of Chilika Lake and characterized taxonomically using polyphasic approach. The strain grew in the presence of 0–25% (w/v) NaCl in marine salt agar media, hydrolyzes casein, and gelatin and shows presence of alkaline proteases. The major cell wall menaquinone was MK7 and major cellular fatty acids were anteiso-C15:0 (44.89%), anteiso-C17:0 (6.18%), isoC15:0 (19.38%), and iso-C16:0 (7.39%). Several chemotaxonomic features conform the isolate be a member of genus Halobacillus. The isolate KGW1T contained A1γ meso-Dpm-direct type of peptidoglycan which is different from its phylogenetically closest neighbours. The 16S rRNA gene sequence based phylogenetic analysis also revealed the strain KGW1T was affiliated to the genus Halobacillus and sequence similarity between the isolated strain and the type strains of Halobacillus species were found closest to, H. dabanensis D-8 DSM 18199T (99.08%) and H. faecis IGA7-4 DSM 21559T (99.01%), H. trueperi SL-5 DSM 10404T (98.94%). The in silico DDH showed that the values in a range of 14.2–17.5% with the most closest strain H. dabanensis D-8 DSM 18199T and other type strains of the genus Halobacillus for which whole genome sequence is reported. DNA-DNA relatedness between strain KGW1T and the closest type strain Halobacillus trueperi DSM 10404T was 11.75% (± 1.15). The draft genome sequence includes 3,683,819 bases and comprises of 3898 predicted coding sequences with a G + C content of 46.98%. Thus, the significant distinctiveness supported by phenotypic and genotypic data with its closest neighbors and other closely related species confirm the strain KGW1T to be classified as a novel species within the genus Halobacillus, for which the name Halobacillus marinus sp. nov. is proposed. The type strain is KGW1T (= DSM 29522 = JCM 30443).

Streptomyces chitinivorans sp. nov., a chitinolytic strain isolated from estuarine lake sediment.

A novel actinobacterial strain RC1832T was isolated from the sediment of a fish dumping yard at Balugaon near Chilika Lake. The strain is halotolerant (15 % NaCl, w/v), alkali-tolerant (pH 7-10) and hydrolyzes chitin, starch, gelatin, cellulose, carboxymethyl cellulose, Tween 80, tributyrin, lecithin and casein. Apart from showing typical genus-specific morphological and chemotaxonomic features, the comparision and analysis of the near complete 16S rRNA gene sequence clearly revealed that the strain RC1832T represented a member of the genus Streptomyces. It exhibited the highest sequence similarities with the strains Streptomyces fenghuangensis GIMN4.003T (99.78 %), Streptomyces nanhaiensis DSM 41926T (99.07 %), Streptomyces radiopugnans R97T(98.71 %), Streptomyces atacamensis DSM 42065T (98.65 %) and Streptomyces barkulensis DSM 42082T (98.25 %). The DNA-DNA relatedness of strain RC 1832T with the closest phylogenetic neighbours S. fenghuangensis GIMN4.003T and S. nanhaiensis DSM 41926T were 20±2 % and 21±2 %, respectively. Thus, based on a range of phenotypic and genotypic properties, strain RC1832T was suggested to represent a novel species of the genus Streptomyces for which the name Streptomyces chitinivorans sp. nov. is proposed. The type strain is RC1832T (=JCM 30611=KCTC 29696).