The plant endomicrobiome: Structure and strategies to produce stress resilient future crop.

Plants have a microbiome, a diverse community of microorganisms, including bacteria, fungi, and viruses, living inside and on their tissues. Versatile endophytic microorganisms inhabited in every plant part without causing disease and develop endophytic microbiome or endo-microbiome. Plant endo-microbiome are drawn by the nutrient rich micro-environment, and in turn some microbes mutualistically endorse and protect plant from adverse environmental stresses. Plant endo-microbiome interact within well-designed host equilibrium containing xylem, phloem, nutrients, phytohormones, metabolites and shift according to environmental and nutritional change. Plant endo-microbiome regulate and respond to environmental variations, pathogens, herbivores by producing stress regulators, organic acids, secondary metabolites, stress hormones as well as unknown substances and signalling molecules. Endomicrobiome efficiently synthesizes multiple bioactive compounds, stress phytohormones with high competence. The technological innovation as next generation genomics biology and high-throughput multiomics techniques stepping stones on the illumination of critical endo-microbiome communities and functional characterization that aid in improving plant physiology, biochemistry and immunity interplay for best crop productivity. This review article contains deeper insight in endomicrobiome related research work in last years, recruitment, niche development, nutrient dynamics, stress removal mechanisms, bioactive services in plant health development, community architecture and communication, and immunity interplay in producing stress resilient future crop.

Prospective of Indole-3-Acteic Acid (IAA) and Endophytic Microbe Bacillus subtilis Strain SSA4 in Paddy Seedlings Development and Ascorbate-Glutathione (AsA-GSH) Cycle Regulation to Mitigate NaCl Toxicity.

Plant growth promoting endophytes significantly affected plant health. The present study demonstrates effect of endophytic isolate Bacillus subtilis strain SSA4 and exogenous Indole-3-acetic acid (IAA) on paddy seedlings growth parameters, photosynthetic pigments, photosynthesis, leaf gas exchange parameters, respiration, oxidative stress biomarkers and Ascorbate-Glutathione (AsA-GSH) cycle under different NaCl (0-300 mM) stresses. The Bacillus subtilis SSA4 was identified by 16S r-RNA gene sequence analyses and NCBI BLASTn tools. The B. subtilis SSA4 tolerated 1100 mM NaCl and produced IAA (42.15 µg m/L) at 300 mM NaCl stress. The paddy genotype (HUR 917) treated with exogenous IAA (21 µg m/L) and B. subtilis strain SSA4 egg cell based bioformulation was significantly affected seedlings physiology and biochemistry at lower (150 mM) and higher (300 mM) NaCl doses. In conclusion, co-inoculation found as effective green tool to mitigating salinity stress in paddy seedlings.

Poly-ß-Hydroxybutyrate Production by the Cyanobacterium Scytonema geitleri Bharadwaja under Varying Environmental Conditions.

The production of poly-ß-hydroxybutyrate (PHB) under varying environmental conditions (pH, temperature and carbon sources) was examined in the cyanobacterium Scytonema geitleri Bharadwaja isolated from the roof-top of a building. The S. geitleri produced PHB and the production of PHB was linear with the growth of cyanobacterium. The maximum PHB production (7.12% of dry cell weight) was recorded when the cells of S. geitleri were at their stationary growth phase. The production of PHB was optimum at pH 8.5 and 30 °C, and acetate (30 mM) was the preferred carbon source.

Land use change: A key ecological disturbance declines soil microbial biomass in dry tropical uplands.

Land use changes such as transformation of natural landscapes, forest degradation and increase in croplands due to human activities are considered amongst the most influential ecological disturbances affecting soil, ecosystems and environmental sustainability. The previous works from India are limited to show that soil disturbances influence abiotic and biotic factors along a rural-urban gradient. However, variations in soil microbial biomass (SMB) -C, -N and -P quantity due to land use changes at different soil depths across different land use types remain poorly understood on comparative ground. We investigated the impact of land use types on soil properties and SMB -C, -N and -P levels across different soil depths (0-10, 10-20 and 20-30 cm) in dry tropical uplands. Four land use types/covers (natural forest, mixed forest, savanna and agriculture land) were selected. The present study is based on two hypotheses: i) different land use types affect SMB levels in top surface soil (0-10 cm), but have less effects in deeper soil profiles (20-30 cm); and ii) SMB levels in top surface soil are highest in natural forest, followed by mixed forest and then savanna and agriculture lands. ANOVA showed significant differences in SMB values due to land use covers (P < 0.001), soil depths (P < 0.001) and land use types × soil depths interaction (P < 0.001). Although, there had no effect of land use types on SMB levels in deeper soil profiles (20-30 cm) but soil parameters (soil pH, soil moisture, soil temperature, total-N, C/N ratio and organic-C) significantly affect SMB levels in top surface (0-10 cm) soil. The study suggests that SMB may be considered as a key indicator of soil fertility index, while land use practices are a major cause for loss of microbial community composition/biomass in dry tropical upland soil.

Microbial bio-fuels: a solution to carbon emissions and energy crisis.

Increasing energy demand, limited fossil fuel resources and climate change have prompted development of alternative sustainable and economical fuel resources such as crop-based bio-ethanol and bio-diesel. However, there is concern over use of arable land that is used for food agriculture for creation of biofuel. Thus, there is a renewed interest in the use of microbes particularly microalgae for bio-fuel production. Microbes such as micro-algae and cyanobacteria that are used for biofuel production also produce other bioactive compounds under stressed conditions. Microbial agents used for biofuel production also produce bioactive compounds with antimicrobial, antiviral, anticoagulant, antioxidant, antifungal, anti-inflammatory and anticancer activity. Because of importance of such high-value compounds in aquaculture and bioremediation, and the potential to reduce carbon emissions and energy security, the biofuels produced by microbial biotechnology might substitute the crop-based bio-ethanol and bio-diesel production.

Soil microbial biomass: A key soil driver in management of ecosystem functioning.

Although patterns of microbial diversity and biomass have been described and reviewed at local and regional scales, a unifying driver, or set of environmental drivers affecting soil microbial biomass (SMB) pattern at global level is still missing. Biomass of soil microbial community, known as SMB is considered widely as the index of soil fertility and ecosystem productivity. The escalating soil stresses due to land degradation and climatic variability are directly correlated with loss of microbial diversity and abundance or biomass dynamics. Therefore, alleviating soil stresses on microbial communities with ecological restoration could reduce the unpredictability and turnover rates of SMB. Thus, the key ecological factors which stabilize the SMB and minimize its turnover, are supposed to play an important role in the soil nutrient dynamics and productivity of the ecosystems. Because of the existing public concern about the deleterious impacts of ecosystem degradation, there is an increasing interest in improving the understanding of SMB, and the way, it contributes to restoration and functioning of ecosystems.

Biogenic synthesis and spatial distribution of silver nanoparticles in the legume mungbean plant (Vigna radiata L.).

The present investigation aimed to study the in vivo synthesis of silver nanoparticles (AgNPs) in the legume Vigna radiata. The level of plant metabolites such as total phenolics, lipid, terpenoids, alkaloids and amino acid increased by 65%, 133%, 19%, 67% and 35%, respectively, in AgNO3 (100 mg L-1) treated plants compared to control. Whereas protein and sugar contents in the treated plants were reduced by 38% and 27%, respectively. FTIR analysis of AgNO3 (20-100 mg L-1) treated plants exhibited changes in the IR regions between 3297 and 3363 cm-1, 1635-1619 cm-1, 1249-1266 cm-1 and that corresponded to alterations in OH groups of carbohydrates, OH and NH groups of amide I and II regions of protein, when compared with the control. Transmission electron micrographs showed the spatial distribution of AgNPs in the chloroplast, cytoplasmic spaces, vacuolar and nucleolar plant regions. Metal quantification in different tissues of plants exposed to 20-100 mg L-1 AgNO3 showed about a 22 fold accumulation of Ag in roots as compared to shoots. The phytotoxic parameters such as percent seed germination and shoot elongation remained almost unaltered at low AgNO3 doses (20-50 mg L-1). However, at higher levels of exposure (100 mg L-1), the percent seed germination as well as root and shoot elongation exhibited concentration dependent decline. In conclusion, synthesis of AgNPs in V. radiata particularly at lower doses of AgNO3, could be used as a sustainable and environmentally safe technology for large scale production of metal nanoparticles.

Degraded Land Restoration in Reinstating CH4 Sink.

Methane (CH4), a potent greenhouse gas, contributes about one third to the global green house gas emissions. CH4-assimilating microbes (mostly methanotrophs) in upland soils play very crucial role in mitigating the CH4 release into the atmosphere. Agricultural, environmental, and climatic shifts can alter CH4 sink profiles of soils, likely through shifts in CH4-assimilating microbial community structure and function. Landuse change, as forest and grassland ecosystems altered to agro-ecosystems, has already attenuated the soil CH4 sink potential, and are expected to be continued in the future. We hypothesized that variations in CH4 uptake rates in soils under different landuse practices could be an indicative of alterations in the abundance and/or type of methanotrophic communities in such soils. However, only a few studies have addressed to number and methanotrophs diversity and their correlation with the CH4 sink potential in soils of rehabilitated/restored lands. We focus on landuse practices that can potentially mitigate CH4 gas emissions, the most prominent of which are improved cropland, grazing land management, use of bio-fertilizers, and restoration of degraded lands. In this perspective paper, it is proposed that restoration of degraded lands can contribute considerably to improved soil CH4 sink strength by retrieving/conserving abundance and assortment of efficient methanotrophic communities. We believe that this report can assist in identifying future experimental directions to the relationships between landuse changes, methane-assimilating microbial communities and soil CH4 sinks. The exploitation of microbial communities other than methanotrophs can contribute significantly to the global CH4 sink potential and can add value in mitigating the CH4 problems.

Cyanobacteria: A Precious Bio-resource in Agriculture, Ecosystem, and Environmental Sustainability.

Keeping in view, the challenges concerning agro-ecosystem and environment, the recent developments in biotechnology offers a more reliable approach to address the food security for future generations and also resolve the complex environmental problems. Several unique features of cyanobacteria such as oxygenic photosynthesis, high biomass yield, growth on non-arable lands and a wide variety of water sources (contaminated and polluted waters), generation of useful by-products and bio-fuels, enhancing the soil fertility and reducing green house gas emissions, have collectively offered these bio-agents as the precious bio-resource for sustainable development. Cyanobacterial biomass is the effective bio-fertilizer source to improve soil physico-chemical characteristics such as water-holding capacity and mineral nutrient status of the degraded lands. The unique characteristics of cyanobacteria include their ubiquity presence, short generation time and capability to fix the atmospheric N2. Similar to other prokaryotic bacteria, the cyanobacteria are increasingly applied as bio-inoculants for improving soil fertility and environmental quality. Genetically engineered cyanobacteria have been devised with the novel genes for the production of a number of bio-fuels such as bio-diesel, bio-hydrogen, bio-methane, synga, and therefore, open new avenues for the generation of bio-fuels in the economically sustainable manner. This review is an effort to enlist the valuable information about the qualities of cyanobacteria and their potential role in solving the agricultural and environmental problems for the future welfare of the planet.

Biologically derived fertilizer: A multifaceted bio-tool in methane mitigation.

Methane emissions are affected by agricultural practices. Agriculture has increased in scale and intensity because of greater food, feed and energy demands. The application of chemical fertilizers in agriculture, particularly in paddy fields, has contributed to increased atmospheric methane emissions. Using organic fertilizers may improve crop yields and the methane sink potential within agricultural systems, which may be further improved when combined with beneficial microbes (i.e. biofertilizers) that improve the activity of methane oxidizing bacteria such as methanotrophs. Biofertilizers may be an effective tool for agriculture that is environmentally beneficial compared to conventional inorganic fertilizers. This review highlights and discusses the interplay between ammonia and methane oxidizing bacteria, the potential interactions of microbial communities with microbially-enriched organic amendments and the possible role of these biofertilizers in augmenting the methane sink potential of soils. It is suggested that biofertilizer applications should not only be investigated in terms of sustainable agriculture productivity and environmental management, but also in terms of their effects on methanogen and methanotroph populations.

Fly ash application in nutrient poor agriculture soils: impact on methanotrophs population dynamics and paddy yields.

There are reports that the application of fly ash, compost and press mud or a combination thereof, improves plant growth, soil microbial communities etc. Also, fly ash in combination with farmyard manure or other organic amendments improves soil physico-chemical characteristics, rice yield and microbial processes in paddy fields. However, the knowledge about the impact of fly ash inputs alone or in combination with other organic amendments on soil methanotrophs number in paddy soils is almost lacking. We hypothesized that fly ash application at lower doses in paddy agriculture soil could be a potential amendment to elevate the paddy yields and methanotrophs number. Here we demonstrate the impact of fly ash and press mud inputs on number of methanotrophs, antioxidants, antioxidative enzymatic activities and paddy yields at agriculture farm. The impact of amendments was significant for methanotrophs number, heavy metal concentration, antioxidant contents, antioxidant enzymatic activities and paddy yields. A negative correlation was existed between higher doses of fly ash-treatments and methanotrophs number (R(2)=0.833). The content of antioxidants and enzymatic activities in leaves of higher doses fly ash-treated rice plants increased in response to stresses due to heavy metal toxicity, which was negatively correlated with rice grain yield (R(2)=0.944) and paddy straw yield (R(2)=0.934). A positive correlation was noted between heavy metals concentrations and different antioxidant and enzymatic activities across different fly ash treated plots.The data of this study indicate that heavy metal toxicity of fly ash may cause oxidative stress in the paddy crop and the antioxidants and related enzymes could play a defensive role against phytotoxic damages. We concluded that fly ash at lower doses with press mud seems to offer the potential amendments to improving soil methanotrophs population and paddy crop yields for the nutrient poor agriculture soils.

Impact of PGPR inoculation on growth and antioxidant status of wheat under saline conditions.

Two plant growth-promoting rhizobacterial (PGPR) strains, Bacillus subtilis SU47 and Arthrobacter sp. SU18, were found to tolerate 8% NaCl. Wheat co-inoculated with these two PGPR strains, and grown under different salinity regimes (2-6 dS m(-1) ), showed an increase in dry biomass, total soluble sugars and proline content. Wheat sodium content was reduced under co-inoculated conditions but not after single inoculation with either strain or in the control. The activity of antioxidant enzymes in wheat leaves decreased under salinity stress after PGPR co-inoculation, suggesting these PGPR species could be used for amelioration of stress in wheat plants. Activity of three antioxidant enzymes in wheat grown with both PGPR strains was reduced, most notably that of catalase activity at a salinity of 6 dS m(-1) , when compared with the control. The results indicate that co-inoculation with B. subtilis and Arthrobacter sp. could alleviate the adverse effects of soil salinity on wheat growth.

Genetically engineered bacteria: an emerging tool for environmental remediation and future research perspectives.

This minireview explores the environmental bioremediation mediated by genetically engineered (GE) bacteria and it also highlights the limitations and challenges associated with the release of engineered bacteria in field conditions. Application of GE bacteria based remediation of various heavy metal pollutants is in the forefront due to eco-friendly and lesser health hazards compared to physico-chemical based strategies, which are less eco-friendly and hazardous to human health. A combination of microbiological and ecological knowledge, biochemical mechanisms and field engineering designs would be an essential element for successful in situ bioremediation of heavy metal contaminated sites using engineered bacteria. Critical research questions pertaining to the development and implementation of GE bacteria for enhanced bioremediation have been identified and poised for possible future research. Genetic engineering of indigenous microflora, well adapted to local environmental conditions, may offer more efficient bioremediation of contaminated sites and making the bioremediation more viable and eco-friendly technology. However, many challenges are to be addressed concerning the release of genetically engineered bacteria in field conditions. There are possible risks associated with the use of GE bacteria in field condition, with particular emphasis on ways in which molecular genetics could contribute to the risk mitigation. Both environmental as well as public health concerns need to be addressed by the molecular biologists. Although bioremediation of heavy metals by using the genetically engineered bacteria has been extensively reviewed in the past also, but the bio-safety assessment and factors of genetic pollution have been never the less ignored.