Complete Genome Sequence of Rhodococcus opacus Strain MoAcy1 (DSM 44186), an Aerobic Acetylenotroph Isolated from Soil

We report the genome of Rhodococcus opacus strain MoAcy1 ( DSM 44186 ), an aerobic soil isolate capable of using acetylene as its primary carbon and energy source (acetylenotrophy). The genome is composed of a single circular chromosome of ∼8 Mbp and two closed plasmids, with a G+C content of 67.3%.

Genomes of novel Myxococcota reveal severely curtailed machineries for predation and cellular differentiation

Cultured Myxococcota are predominantly aerobic soil inhabitants, characterized by their highly coordinated predation and cellular differentiation capacities. Little is currently known regarding yet-uncultured Myxococcota from anaerobic, non-soil habitats. We analyzed genomes representing one novel order (o__JAFGXQ01) and one novel family (f__JAFGIB01) in the Myxococcota from an anoxic freshwater spring (Zodletone spring) in Oklahoma, USA. Compared to their soil counterparts, anaerobic Myxococcota possess smaller genomes, and a smaller number of genes encoding biosynthetic gene clusters (BGCs), peptidases, one- and two-component signal transduction systems, and transcriptional regulators. Detailed analysis of thirteen distinct pathways/processes crucial to predation and cellular differentiation revealed severely curtailed machineries, with the notable absence of homologs for key transcription factors (e.g. FruA and MrpC), outer membrane exchange receptor (TraA), and the majority of sporulation-specific and A-motility-specific genes. Further, machine-learning approaches based on a set of 634 genes informative of social lifestyle predicted a non-social behavior for Zodletone Myxococcota. Metabolically, Zodletone Myxococcota genomes lacked aerobic respiratory capacities, but encoded genes suggestive of fermentation, dissimilatory nitrite reduction, and dissimilatory sulfate-reduction (in f_JAFGIB01) for energy acquisition. We propose that predation and cellular differentiation represent a niche adaptation strategy that evolved circa 500 Mya in response to the rise of soil as a distinct habitat on earth. Importance The Myxococcota is a phylogenetically coherent bacterial lineage that exhibits unique social traits. Cultured Myxococcota are predominantly aerobic soil-dwelling microorganisms that are capable of predation and fruiting body formation. However, multiple yet-uncultured lineages within the Myxococcota have been encountered in a wide range of non-soil, predominantly anaerobic habitats; and the metabolic capabilities, physiological preferences, and capacity of social behavior of such lineages remain unclear. Here, we analyzed genomes recovered from a metagenomic analysis of an anoxic freshwater spring in Oklahoma, USA that represent novel, yet-uncultured, orders and families in the Myxococcota. The genomes appear to lack the characteristic hallmarks for social behavior encountered in Myxococcota genomes, and displayed a significantly smaller genome size and a smaller number of genes encoding biosynthetic gene clusters, peptidases, signal transduction systems, and transcriptional regulators. Such perceived lack of social capacity was confirmed through detailed comparative genomic analysis of thirteen pathways associated with Myxococcota social behavior, as well as the implementation of machine learning approaches to predict social behavior based on genome composition. Metabolically, these novel Myxococcota are predicted to be strict anaerobes, utilizing fermentation, nitrate reduction, and dissimilarity sulfate reduction for energy acquisition. Our results highlight the broad patterns of metabolic diversity within the yet-uncultured Myxococcota and suggest that the evolution of predation and fruiting body formation in the Myxococcota has occurred in response to soil formation as a distinct habitat on earth.

Impact of Azotobacter in Different Doses of Dichlorvos

Azotobacter is free living, non–symbiotic, heterotrophic bacteria capable of fixing an average of 20kg N / hector year. Azotobacter species are Gram negative, free–living, aerobic soil dwelling, oval or spherical bacteria that form thick–walled cysts (means of asexual reproduction under favorable condition). Out of six species of Azotobacter, some of them are motile by means of peritrichous flagella while others are not. They are typically polymorphic and their size ranges from 2–10µm long and 1–2µm wide. A. chroococcum is the first aerobic free– living nitrogen fixer. These bacteria utilize atmospheric nitrogen gas for their cell protein synthesis. Dichlorvos is an organophosphate widely used as an insecticide to control household pests, in public health, and protecting stored products from insects. In present study of dichlorvos in Azotobacter through different doses are effected of seed germination and observed the toxicity and harmful effect of dichlorvos solution.

Genomes of novel Myxococcota reveal severely curtailed machineries for predation and cellular differentiation

Cultured Myxococcota are predominantly aerobic soil inhabitants, characterized by their highly coordinated predation and cellular differentiation capacities. Little is currently known regarding yet-uncultured Myxococcota from anaerobic, non-soil habitats. We analyzed genomes representing one novel order (o__JAFGXQ01) and one novel family (f__JAFGIB01) in the Myxococcota from an anoxic freshwater spring in Oklahoma, USA. Compared to their soil counterparts, anaerobic Myxococcota possess smaller genomes, and a smaller number of genes encoding biosynthetic gene clusters (BGCs), peptidases, one- and two-component signal transduction systems, and transcriptional regulators. Detailed analysis of thirteen distinct pathways/processes crucial to predation and cellular differentiation revealed severely curtailed machineries, with the notable absence of homologs for key transcription factors (e.g. FruA and MrpC), outer membrane exchange receptor (TraA), and the majority of sporulation-specific and A-motility-specific genes. Further, machine-learning approaches based on a set of 634 genes informative of social lifestyle predicted a non-social behavior for Zodletone Myxococcota. Metabolically, Zodletone Myxococcota genomes lacked aerobic respiratory capacities, but encoded genes suggestive of fermentation, dissimilatory nitrite reduction, and dissimilatory sulfate-reduction (in f_JAFGIB01) for energy acquisition. We propose that predation and cellular differentiation represent a niche adaptation strategy that evolved circa 500 Mya in response to the rise of soil as a distinct habitat on earth.

Biodegradable Polymeric Foams Based on Modified Castor Oil, Styrene, and Isobornyl Methacrylate

The environmental issues of petroleum-derived polymeric foams have necessitated seeking renewable alternatives. This work aims to prepare renewable free-radically polymerized polymeric foams with the ability to biodegrade. Furthermore, this work attempted to incorporate a bio-based reactive diluent, which has not been reported in the literature. The synthesis of maleated castor oil glycerides was performed with products analyzed by Fourier transform infrared spectrometry using attenuated total reflection (ATR-FTIR) and 1H nuclear magnetic resonance (1H NMR) spectroscopy. Polymeric foams were prepared using maleated castor oil glycerides via free radical copolymerization with styrene and isobornyl methacrylate as reactive diluents. Scanning electron microscopy (SEM) was used to determine anisotropic macrocellular morphology, with log-normal cell diameter distributions. The compressive mechanical and energy absorption properties were investigated; the polymeric foams displayed Young’s modulus up to 26.85 ± 1.07 MPa and strength up to 1.11 ± 0.021 MPa using styrene as the reactive diluent, and Young’s modulus up to 1.38 ± 0.055 MPa and strength up to 0.088 MPa when incorporating isobornyl methacrylate. Furthermore, a thorough analysis of the cellular structure–property relationships was performed, indicating relationships to cell diameter, cell wall thickness and apparent density. The polymeric foams displayed rapid mass loss in an aerobic soil environment with multiple erosion sites revealed by SEM. In conclusion, renewable polymeric foams with excellent compressive properties were achieved using styrene as reactive diluent, but the incorporation of isobornyl methacrylate decreased strength-related properties.

Proofing Direct-Seeded Rice with Better Root Plasticity and Architecture

The underground reserve (root) has been an uncharted research territory with its untapped genetic variation yet to be exploited. Identifying ideal traits and breeding new rice varieties with efficient root system architecture (RSA) has great potential to increase resource-use efficiency and grain yield, especially under direct-seeded rice, by adapting to aerobic soil conditions. In this review, we tried to mine the available research information on the direct-seeded rice (DSR) root system to highlight the requirements of different root traits such as root architecture, length, number, density, thickness, diameter, and angle that play a pivotal role in determining the uptake of nutrients and moisture at different stages of plant growth. RSA also faces several stresses, due to excess or deficiency of moisture and nutrients, low or high temperature, or saline conditions. To counteract these hindrances, adaptation in response to stress becomes essential. Candidate genes such as early root growth enhancer PSTOL1, surface rooting QTL qSOR1, deep rooting gene DRO1, and numerous transporters for their respective nutrients and stress-responsive factors have been identified and validated under different circumstances. Identifying the desired QTLs and transporters underlying these traits and then designing an ideal root architecture can help in developing a suitable DSR cultivar and aid in further advancement in this direction.

Seasonal and interannual variations in the surface energy fluxes of a rice–wheat rotation in Eastern China

Quantitative knowledge of the water and energy exchanges in agroecosystems is vital for irrigation management and modeling crop production. In this study, the seasonal and annual variabilities of evapotranspiration (ET) and energy exchanges were investigated under two different crop environments – flooded and aerobic soil conditions – using three years (June 2014 to May 2017) of eddy covariance observations over a rice–wheat rotation in eastern China. Across the whole rice-wheat rotation, the average daily ET rate in the rice paddies and wheat fields was 3.6 mm d–1 and 2.4 mm d–1, respectively. The average seasonal ET was 473 and 387 mm for rice and wheat fields, indicating a higher water consumption for rice than for wheat. Averaging for the three cropping seasons, rice paddies had 52% more latent heat flux than wheat fields, whereas wheat had 73% more sensible heat flux than rice paddies. This resulted in a lower Bowen ratio in the rice paddies (0.14) than in the wheat fields (0.4). As eddy covariance observations of turbulent heat fluxes are typically less than the available energy (Rn − G, i.e., net radiation minus soil heat flux), energy balance closure (EBC) therefore does not occur. For rice, EBC was greatest at the vegetative growth stages (mean: 0.90) after considering the water heat storage, whereas wheat had its best EBC at the ripening stages (mean: 0.86).

Carbon sequestration and its impact on rice farming economic value: The quasi-experiment

The increasing level of the number of carbon dioxide will raise temperature on the earth and causes global climate changes. Paris agreement has responded global warming by doing mitigation, and Indonesian Government has ratified the suggestion. This research aims to determine the rice cultivation technology system which effectively could absorb the carbon dioxide into the form of biomass and C-organic in the earth. Applying the quasi-experiment by three types of technological systems – and it was conducted in farming area of Sukakarya District, Bekasi Regency, Indonesia – the research proved the T2 (IPAT-TS planting system) – in which it applies a minimum spacing of 30 cm × 30 cm and a maximum of 50 cm × 50 cm, in aerobic soil conditions – yields the highest number of biomass straw, C-Organic, and harvest dry grain and economically gives the highest profit margin. Therefore, the research recommends the adoption of T2 as mass common farming practice especially in entisolic soil types.

Contingent Effects of Liming on N2O-Emissions Driven by Autotrophic Nitrification

Liming acidic soils is often found to reduce their N2O emission due to lowered N2O/(N2O + N2) product ratio of denitrification. Some field experiments have shown the opposite effect, however, and the reason for this could be that liming stimulates nitrification-driven N2O production by enhancing nitrification rates, and by favoring ammonia oxidizing bacteria (AOB) over ammonia oxidizing archaea (AOA). AOB produce more N2O than AOA, and high nitrification rates induce transient/local hypoxia, thereby stimulating heterotrophic denitrification. To study these phenomena, we investigated nitrification and denitrification kinetics and the abundance of AOB and AOA in soils sampled from a field experiment 2–3 years after liming. The field trial compared traditional liming (carbonates) with powdered siliceous rocks. As expected, the N2O/(N2O + N2) product ratio of heterotrophic denitrification declined with increasing pH, and the potential nitrification rate and its N2O yield (YN2O: N2O-N/NO3–-N), as measured in fully oxic soil slurries, increased with pH, and both correlated strongly with the AOB/AOA gene abundance ratio. Soil microcosm experiments were monitored for nitrification, its O2-consumption and N2O emissions, as induced by ammonium fertilization. Here we observed a conspicuous dependency on water filled pore space (WFPS): at 60 and 70% WFPS, YN2O was 0.03-0.06% and 0.06–0.15%, respectively, increasing with increasing pH, as in the aerobic soil slurries. At 85% WFPS, however, YN2O was more than two orders of magnitude higher, and decreased with increasing pH. A plausible interpretation is that O2 consumption by fertilizer-induced nitrification cause hypoxia in wet soils, hence induce heterotrophic nitrification, whose YN2O decline with increasing pH. We conclude that while low emissions from nitrification in well-drained soils may be enhanced by liming, the spikes of high N2O emission induced by ammonium fertilization at high soil moisture may be reduced by liming, because the heterotrophic N2O reduction is enhanced by high pH.

Unexpected diversity of CPR bacteria and nanoarchaea in the rare biosphere of rhizosphere-associated grassland soil

Candidate Phyla Radiation (CPR) bacteria and nanoarchaea populate most ecosystems, but are rarely detected in soil. We concentrated particles less than 0.2 μm from grassland soil, enabling targeted metagenomic analysis of these organisms, which are almost totally unexplored in soil. We recovered a diversity of CPR bacteria and some nanoarchaea sequences, but no sequences from other cellular organisms. The sampled sequences include Doudnabacteria (SM2F11) and Pacearchaeota, organisms not previously reported in soil, as well as Saccharibacteria, Parcubacteria and Microgenomates. CPR and DPANN (an acronym of the names of the first included archaea phyla) enrichments of 100-1000-fold were achieved compared to bulk soil, in which we estimate these organisms comprise about 1 to 100 cells per gram of soil. Like most CPR and DPANN sequenced to date, we predict these microorganisms live symbiotic, anaerobic lifestyles. However, Saccharibacteria, Parcubacteria, and Doudnabacteria genomes sampled here also encode ubiquinol oxidase operons that may have been acquired from other bacteria, likely during adaptation to aerobic soil environments. We posit that although present at low abundance, CPR bacteria and DPANN archaea could impact overall soil microbial community function by modulating host organism abundances and activity.