Reducing the environmental impact of rice production in subtropical India by minimising reactive nitrogen loss.

The future of reactive nitrogen (N) for subtropical lowland rice to be characterised under diverse N-management to develop adequate sustainable practices. It is a challenge to increase the efficiency of N use in lowland rice, as N can be lost in various ways, e.g., through nitrous oxide (N2O) or dinitrogen (N2) emissions, ammonia (NH3) volatilization and nitrate (NO3-) leaching. A field study was carried out in the subsequent wet (2021) and dry (2022) seasons to assess the impacts of different N management strategies on yield, N use efficiency and different N losses in a double-cropped rice system. Seven different N-management practices including application of chemical fertilisers, liquid organic fertiliser, nitrification inhibitors, organic nutrient management and integrated nutrient management (INM) were studied. The application of soil test-based neem-coated urea (NCU) during the wet season resulted in the highest economic yield, while integrated nutrient management showed the highest economic yield during the dry season. Total N losses by volatilization of NH3, N2O loss and leaching were 0.06-4.73, 0.32-2.14 and 0.25-1.93 kg ha-1, corresponding to 0.06-5.84%, 0.11-2.20% and 0.09-1.81% of total applied N, respectively. The total N-uptake in grain and straw was highest in INM (87-89% over control) followed by the soil test-based NCU (77-82% over control). In comparison, recovery efficiency of N was maximum from application of NCU + dicyandiamide during both the seasons. The N footprint of paddy rice ranged 0.46-2.01 kg N-eq. t-1 during both seasons under various N management. Ammonia volatilization was the process responsible for the largest N loss, followed by N2O emissions, and NO3- leaching in these subtropical lowland rice fields. After ranking the different N management practices on a scale of 1-7, soil test-based NCU was considered the best N management approach in the wet year 2021, while INM scored the best in the dry year 2022.

High nitrous oxide fluxes from rice indicate the need to manage water for both long- and short-term climate impacts.

Global rice cultivation is estimated to account for 2.5% of current anthropogenic warming because of emissions of methane (CH4), a short-lived greenhouse gas. This estimate assumes a widespread prevalence of continuous flooding of most rice fields and hence does not include emissions of nitrous oxide (N2O), a long-lived greenhouse gas. Based on the belief that minimizing CH4 from rice cultivation is always climate beneficial, current mitigation policies promote increased use of intermittent flooding. However, results from five intermittently flooded rice farms across three agroecological regions in India indicate that N2O emissions per hectare can be three times higher (33 kg-N2O⋅ha-1⋅season-1) than the maximum previously reported. Correlations between N2O emissions and management parameters suggest that N2O emissions from rice across the Indian subcontinent might be 30-45 times higher under intensified use of intermittent flooding than under continuous flooding. Our data further indicate that comanagement of water with inorganic nitrogen and/or organic matter inputs can decrease climate impacts caused by greenhouse gas emissions up to 90% and nitrogen management might not be central to N2O reduction. An understanding of climate benefits/drawbacks over time of different flooding regimes because of differences in N2O and CH4 emissions can help select the most climate-friendly water management regimes for a given area. Region-specific studies of rice farming practices that map flooding regimes and measure effects of multiple comanaged variables on N2O and CH4 emissions are necessary to determine and minimize the climate impacts of rice cultivation over both the short term and long term.

Comparative Genomics of a Paddy Field Bacterial Isolate Ochrobactrum sp. CPD-03: Analysis of Chlorpyrifos Degradation Potential.

Ochrobactrum genus is known to catabolize aromatic compounds. This study reports a complete genome sequence of Ochrobactrum sp. CPD-03 (~ 4.6 Mb of chromosomal features) responsible for chlorpyrifos (CP) isolated form a paddy field (20.3588° N, 85.8333° E) in Bhubaneswar, India. A comparative genomics approach was performed between CPD-03 and eight closely related genomes of other Ochrobactrum strains in order to deepen our knowledge, to establish its phylogenetic and functional relationships. The involvement of CP degrading genes indicated a versatile role of CPD-03 in additional field trails. This research would provide the genetic information for its use in natural environment for the depletion of organophosphorus (OP) compounds.

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.

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).

Degradation of chlorpyrifos in tropical rice soils.

Chlorpyrifos [O,O-diethyl O-(3,5,6-trichloro-2-pyridinol) phosphorothioate] is used worldwide as an agricultural insecticide against a broad spectrum of insect pests of economically important crops including rice, and soil application to control termites. The insecticide mostly undergoes hydrolysis to diethyl thiophosphoric acid (DETP) and 3,5,6-trichloro-2-pyridinol (TCP), and negligible amounts of other intermediate products. In a laboratory-cum-greenhouse study, chlorpyrifos, applied at a rate of 10 mg kg(-1) soil to five tropical rice soils of wide physico-chemical variability, degraded with a half-life ranging from 27.07 to 3.82 days. TCP was the major metabolite under both non-flooded and flooded conditions. Chlorpyrifos degradation had significant negative relationship with electrical conductivity (EC), cation exchange capacity (CEC), clay and sand contents of the soils under non-flooded conditions. Results indicate that degradation of chlorpyrifos was accelerated with increase in its application frequency, across the representative rice soils. Management regimes including moisture content and presence or absence of rice plants also influenced the process. Biotic factors also play an important role in the degradation of chlorpyrifos as demonstrated by its convincing degradation in mineral salts medium inoculated with non-sterile soil suspension.

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)).

ACC deaminase and IAA producing growth promoting bacteria from the rhizosphere soil of tropical rice plants.

Beneficial plant-associated bacteria play a key role in supporting and/or promoting plant growth and health. Plant growth promoting bacteria present in the rhizosphere of crop plants can directly affect plant metabolism or modulate phytohormone production or degradation. We isolated 355 bacteria from the rhizosphere of rice plants grown in the farmers' fields in the coastal rice field soil from five different locations of the Ganjam district of Odisha, India. Six bacteria producing both ACC deaminase (ranging from 603.94 to 1350.02 nmol α-ketobutyrate mg(-1) h(-1) ) and indole acetic acid (IAA; ranging from 10.54 to 37.65 µM ml(-1) ) in pure cultures were further identified using polyphasic taxonomy including BIOLOG((R)) , FAME analysis and the 16S rRNA gene sequencing. Phylogenetic analyses of the isolates resulted into five major clusters to include members of the genera Bacillus, Microbacterium, Methylophaga, Agromyces, and Paenibacillus. Seed inoculation of rice (cv. Naveen) by the six individual PGPR isolates had a considerable impact on different growth parameters including root elongation that was positively correlated with ACC deaminase activity and IAA production. The cultures also had other plant growth attributes including ammonia production and at least two isolates produced siderophores. Study indicates that presence of diverse rhizobacteria with effective growth-promoting traits, in the rice rhizosphere, may be exploited for a sustainable crop management under field conditions.

Microbial Dynamics and Diversity of Bacillus thuringiensis in Textile Effluent Polluted and Non-polluted Rice Field Soils of Orissa, India.

Microbial diversity was assessed in the soils of non-polluted rice fields of Central Rice Research Institute and Choudwar, and textile effluent contaminated (about 30 years) rice fields of Choudwar about 4 years after cessation of pollution. The soils contained 0.62-1.01 % organic C and 0.07-0.12 % total N, and measured 6.18-8.24 pH and 0.6-2.68 mS/cm Eh which were more in the polluted Choudwar soil. The microbial populations (×10(6) cfu/g soil) in the soils were: heterotrophs 1.21-10.9, spore formers 0.9-2.43, Gram (-)ve bacteria 4.11-8.0, nitrifiers 0.72-1.5, denitrifiers 0.72-2.43, phosphate solubilizers 0.14-0.9, asymbiotic nitrogen fixers 0.34-0.59, actinomycetes 0.07-0.11, fungi 0-0.5 and Bacillus thuringiensis (Bt) 0.4-0.61 which predominated in the polluted soil of Choudwar. The fungi were scarce in the polluted rice fields. The Bt isolates belonged to three motile and one non-motile group. Two motile Bt isolates were phenotyped as Bt subsp. sotto and israelensis, whereas, the non-motile isolate was Bt subsp. wahuensis. All Bt isolates produced extracellular protease, lipase and amylase enzymes. The microbial guilds had positive correlation among themselves, as well as, with soil physico-chemical characters but the fungi had negative relation and the nitrogen fixers were unrelated with the biotic and abiotic components.

Escherichia coli, but Not Staphylococcus aureus, Functions as a Chelating Agent That Exhibits Antifungal Activity against the Pathogenic Yeast Candida albicans.

Humans are colonized by diverse populations of microbes. Infections by Candida albicans, an opportunistic fungal pathogen, are a result of imbalances in the gut microbial ecosystem and are due to the suppressed immunity of the host. Here, we explored the potential effects of the polymicrobial interactions of C. albicans with Staphylococcus aureus, a Gram-positive bacterium, and Escherichia coli, a Gram-negative bacterium, in dual and triple in vitro culture systems on their respective growth, morphology, and biofilms. We found that S. aureus promoted the fungal growth and hyphal transition of C. albicans through cell-to-cell contacts; contrarily, both the cell and cell-free culture filtrate of E. coli inhibited fungal growth. A yet to be identified secretory metabolite of E. coli functionally mimicked EDTA and EGTA to exhibit antifungal activity. These findings suggested that E. coli, but not S. aureus, functions as a chelating agent and that E. coli plays a dominant role in regulating excessive growth and, potentially, the commensalism of C. albicans. Using animal models of systemic candidiasis, we found that the E. coli cell-free filtrate suppressed the virulence of C. albicans. In general, this study unraveled a significant antimicrobial activity and a potential role in the nutritional immunity of E. coli, and further determining the underlying processes behind the E. coli-C. albicans interaction could provide critical information in understanding the pathogenicity of C. albicans.

Food and fruit waste valorisation for pectin recovery: Recent process technologies and future prospects.

Pectin possesses a dual property of resistance and flexibility and thus has diverse commercial value which has generated research interest on this versatile biopolymer. Formulated products using pectin could be useful in food, pharma, foam, plasticiser and paper substitute industries. Pectin is structurally tailor-made for greater bioactivity and diverse applications. Sustainable biorefinery leaves greener footprints while producing high-value bioproducts like pectin. The essential oils and polyphenols obtained as byproducts from a pectin-based biorefinery are useful in cosmetics, toiletries and fragrance industries. Pectin can be extracted from organic sources following eco-friendly strategies, and the extraction techniques, structural alterations and the applications are continually being upgraded and standardized. Pectin has great applications in diverse areas, and its green synthesis is a welcome development. In future, growing industrial application of pectin is anticipated as research orients on biopolymers, biotechnologies and renewable source-based processes. As the world is gradually adopting greener strategies in sync with the global sustainable development goal, active involvement of policy makers and public participation are prime. Governance and policy framing are essential in the transition of the world economy towards circularity since green circular bioeconomy is ill-understood among the public in general and within the administrative circles in particular. Concerted efforts by researchers, investors, innovators, and policy and decision makers to integrate biorefinery technologies as loops within loop of biological structures and bioprocesses is suggested. The review focusses on generation of the different nature of food wastes including fruits and vegetables with cauterization of their components. It discusses the innovative extraction and biotransformation approaches for these waste conversions into value-added products at cost-effective and eco-friendly way. This article compiles numerous effective and efficient and green way pectin extraction techniques with their advantages with varying success in an integrated manner.

Environmental remediation using metals and inorganic and organic materials: a review.

In recent times, environmental pollution has been an alarming concern. This is increasing day-in-and-day-out, especially in the Asia-Pacific region due to the increasing population, urbanization, industrialization and inappropriate waste management measures. Pollution abatement is the need of the hour to sustain the biosphere in general and the human life in particular. A range of physical, chemical and biological strategies are commonly employed to remove pollutants from the contained water, soil and air. Physical, chemical or physicochemical remediation processes are commonly employed owing to their high efficiency, stability, recyclable property and low procurement cost as compared to metals, inorganic and organic materials. Materials of the later type include biocomposites, thin films, modified (bio)polymers, nanoparticles, nanofilters, sorbent like activated charcoal, and carbon nanotubes and nanosensors. Remediation mechanism largely follows sorption, degradation, oxidation, reduction, catalytic conversion, detection and microbial toxicity principles. This review details the mechanisms of action by these various remediating entities, their successful applications in pollution abatement, drawbacks and future prospects.HighlightsEnvironmental remediation using metals, inorganic and organic materials are discussed extensively.Major remediating approaches, viz., physical, physicochemical and chemical are elaborated citing latest references.The significance of biocomposites, biopolymers, polymers, thin films, nanoparticles, nanofilters, nanosensors and sorbents in remediation are highlighted.Pollutant removal from water, air and soil has been precisely discussed.A note on drawbacks, improvement and future prospects of remediating agents is presented.

Combined biostimulation and bioaugmentation for chlorpyrifos degradation in laboratory microcosms.

Chlorpyrifos (CP) is a persistent organophosphorus pesticide (OP) used in soil ecosystem for insect control. Bioremediation process has been proven promising in degrading these toxic molecules and restoring the physio-chemical properties of soil. This work reports a laboratory microcosm study in both non-sterile & sterile conditions, conducted over a period of 56 days to examine the combined effect of additional supplements like biostimulants (BSs) such as N, P, and K in the presence of suitable carrier materials (compost, wheat straw, and corncob) along with bioaugmentation by a Ochrobactrum sp. CPD-03 on CP degradation from the contaminated soil. CP degradation was thoroughly monitored at an interval of 7 days over a period of 56 days. Results showed biostimulation and bioaugmentation along with compost as carrier material had shown higher CP degradation efficiency of 76 ± 2.8 and 74 ± 1.6% in non-sterile and sterile microcosms over a period of 56 days. Moreover, bacterial community profiling (16s rRNA and opd gene) demonstrated increased microbial counts, corroborating the efficiency of the bioremediation process. The survival of CPD-03 at the end of the assay validated its ability of colonizing modified soils. By this integrated method with compost as carrier material, bioremediation process could be enhanced for restoration CP-contaminated soils. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-021-02980-9.

The role of soils in delivering Nature's Contributions to People.

This theme issue provides an assessment of the contribution of soils to Nature's Contributions to People (NCP). The papers in this issue show that soils can contribute positively to the delivery of all NCP. These contributions can be maximized through careful soil management to provide healthy soils, but poorly managed, degraded or polluted soils may contribute negatively to the delivery of NCP. Soils are also shown to contribute positively to the UN Sustainable Development Goals. Papers in the theme issue emphasize the need for careful soil management. Priorities for soil management must include: (i) for healthy soils in natural ecosystems, protect them from conversion and degradation, (ii) for managed soils, manage in a way to protect and enhance soil biodiversity, health, productivity and sustainability and to prevent degradation, and (iii) for degraded soils, restore to full soil health. Our knowledge of what constitutes sustainable soil management is mature enough to implement best management practices, in order to maintain and improve soil health. The papers in this issue show the vast potential of soils to contribute to NCP. This is not only desirable, but essential to sustain a healthy planet and if we are to deliver sustainable development in the decades to come. This article is part of the theme issue 'The role of soils in delivering Nature's Contributions to People'.

Soil-derived Nature's Contributions to People and their contribution to the UN Sustainable Development Goals.

This special issue provides an assessment of the contribution of soils to Nature's Contributions to People (NCP). Here, we combine this assessment and previously published relationships between NCP and delivery on the UN Sustainable Development Goals (SDGs) to infer contributions of soils to the SDGs. We show that in addition to contributing positively to the delivery of all NCP, soils also have a role in underpinning all SDGs. While highlighting the great potential of soils to contribute to sustainable development, it is recognized that poorly managed, degraded or polluted soils may contribute negatively to both NCP and SDGs. The positive contribution, however, cannot be taken for granted, and soils must be managed carefully to keep them healthy and capable of playing this vital role. A priority for soil management must include: (i) for healthy soils in natural ecosystems, protect them from conversion and degradation; (ii) for managed soils, manage in a way to protect and enhance soil biodiversity, health and sustainability and to prevent degradation; and (iii) for degraded soils, restore to full soil health. We have enough knowledge now to move forward with the implementation of best management practices to maintain and improve soil health. This analysis shows that this is not just desirable, it is essential if we are to meet the SDG targets by 2030 and achieve sustainable development more broadly in the decades to come. This article is part of the theme issue 'The role of soils in delivering Nature's Contributions to People'.

Trading water: virtual water flows through interstate cereal trade in India.

Cereals are an important component of the Indian diet, providing 47% of the daily dietary energy intake. Dwindling groundwater reserves in India especially in major cereal-growing regions are an increasing challenge to national food supply. An improved understanding of interstate cereal trade can help to identify potential risks to national food security. Here, we quantify the trade between Indian states of five major cereals and the associated trade in virtual (or embedded) water. To do this, we modelled interstate trade of cereals using Indian government data on supply and demand; calculated virtual water use of domestic cereal production using state- and product-specific water footprints and state-level data on irrigation source; and incorporated virtual water used in the production of internationally-imported cereals using country-specific water footprints. We estimate that 40% (94 million tonnes) of total cereal food supply was traded between Indian states in 2011-12, corresponding to a trade of 54.0 km3 of embedded blue water, and 99.4 km3 of embedded green water. Of the cereals traded within India, 41% were produced in states with over-exploited groundwater reserves (defined according to the Central Ground Water Board) and a further 21% in states with critically depleting groundwater reserves. Our analysis indicates a high dependency of Indian cereal consumption on production in states with stressed groundwater reserves. Substantial changes in agricultural practices and land use may be required to secure future production, trade and availability of cereals in India. Diversifying production systems could increase the resilience of India's food system.

"More crop per drop": Exploring India's cereal water use since 2005.

India has the highest national freshwater demand globally and 91% of India's freshwater is used in the agriculture sector. Cereals account for over 50% of the dietary water footprint in India and represent a potential opportunity for reducing water use in Indian agriculture. This study combines governmental production and irrigation statistics with crop distribution maps to examine trends in annual water use for cereal production in India between 2005 and 2014. A new online water assessment tool, Cool Farm Tool Water (CFTW), was used to calculate water use and derive seasonal state-level blue and green water footprints for rice, wheat, sorghum, millet and maize. The analysis indicates that India achieved 26.4% increased total cereal production between 2005 and 2014 without additional water or land use. Cereal water footprints have declined due to higher yields for most crops and slightly lower rates of evapotranspiration. There has also been a shift in the area under production away from the Kharif (monsoon) towards the Rabi (dry) season in which total water footprints for all cereals except rice are substantially lower (-33.4% to -45.0% compared to Kharif), but show a significantly higher dependency on ground and surface water. The value of this study is two-fold. First, it provides a full assessment of production trends for the five major cereals in India for each year from 2005 to 2014 and links it to water use. Secondly, it uses updated seasonal water footprints, which demonstrate the potential for changes in cereal production practices to contribute to improved efficiency of water use in India. Future pressures on scarce water resources may encourage transition to cereals with lower irrigation dependency, in particular maize, but also sorghum and millet. In addition, increased emphasis on improving millet and sorghum yields would be of benefit to secure cereal production and reduce its overall water footprint.

Purification and characterization of an extracellular thermo-alkali stable, metal tolerant chitinase from Streptomyces chilikensis RC1830 isolated from a brackish water lake sediment.

An extracellular thermo-alkali stable chitinase was obtained from Streptomyces chilikensis RC1830, a novel actinobacterial strain isolated from the sediments of Chilika lake, India. Purification of the enzyme was carried out by concentrating the enzyme with centrifugal device followed by chromatographic separation by DEAE Sepharose ion exchange resin.The molecular weight of the enzyme was 10.5 kDa as determined by SDS-PAGE. The optimum pH and temperature for the partially purified chitinase was pH 7 and 60 °C. The chitinase showed 40% activity at pH 11 after 24 h exposure at room temperature. The chitinase exhibited Km and Vmax values are 0.02 mM and 3.184 mol/min/mg of enzyme respectively. The 6 residue N-terminal sequence of the enzyme was not found similar to any of the reported chitinase enzyme. Based on the SDS PAGE, zymogram analysis, activity assays and other characteristics, it is proposed that the purified enzyme from S.chilikensis RC1830 is a chitinase.