Undervalued Pseudo- nifH Sequences in Public Databases Distort Metagenomic Insights into Biological Nitrogen Fixers

Nitrogen-fixing microbes affect biogeochemical cycling, agricultural productivity, and microbial ecosystems, and their distributions have been investigated intensively using genomic and metagenomic sequencing. Currently, insights into nitrogen fixers in the environment have been acquired by homology searches against nitrogenase genes, particularly the nifH gene, in public databases.

Plant ecological genomics at the limits of life in the Atacama Desert

The Atacama Desert in Chile—hyperarid and with high–ultraviolet irradiance levels—is one of the harshest environments on Earth. Yet, dozens of species grow there, including Atacama-endemic plants. Herein, we establish the Talabre–Lejía transect (TLT) in the Atacama as an unparalleled natural laboratory to study plant adaptation to extreme environmental conditions. We characterized climate, soil, plant, and soil–microbe diversity at 22 sites (every 100 m of altitude) along the TLT over a 10-y period. We quantified drought, nutrient deficiencies, large diurnal temperature oscillations, and pH gradients that define three distinct vegetational belts along the altitudinal cline. We deep-sequenced transcriptomes of 32 dominant plant species spanning the major plant clades, and assessed soil microbes by metabarcoding sequencing. The top-expressed genes in the 32 Atacama species are enriched in stress responses, metabolism, and energy production. Moreover, their root-associated soils are enriched in growth-promoting bacteria, including nitrogen fixers. To identify genes associated with plant adaptation to harsh environments, we compared 32 Atacama species with the 32 closest sequenced species, comprising 70 taxa and 1,686,950 proteins. To perform phylogenomic reconstruction, we concatenated 15,972 ortholog groups into a supermatrix of 8,599,764 amino acids. Using two codon-based methods, we identified 265 candidate positively selected genes (PSGs) in the Atacama plants, 64% of which are located in Pfam domains, supporting their functional relevance. For 59/184 PSGs with an Arabidopsis ortholog, we uncovered functional evidence linking them to plant resilience. As some Atacama plants are closely related to staple crops, these candidate PSGs are a “genetic goldmine” to engineer crop resilience to face climate change.

Seasonal Variation in Microbial Communities in Rhizosphere and Non-Rhizosphere soil of Different Fruit Tree Species in Semiarid Irrigated Conditions of Haryana

The present study was undertaken to analyze seasonal variations in microbial communities in different fruit tree orchards (mango, guava, ber, bael, jamun, aonla and sweet orange) during summer, rainy and winter season of 2018-19 under semiarid irrigated ecosystem. In rhizosphere and non-rhizosphere, maximum TBC, PSB and nitrogen fixers were found in mango orchard during summer and rainy season while maximum fungal count in jamun orchard during all the seasons. Maximum actinomycete was counted in guava orchard during summer and winter while in mango during rainy season. In rhizosphere and non-rhizosphere, the total microbial count, phosphate solubilizing bacteria and nitrogen fixers were maximum in rainy season while fungal and actinomycetes count in summer season. The maximum increase in total microbial count, PSB and nitrogen fixers or diazotrophs were found in mango orchard during summer (11.61%, 7.88%, 7.67%) and rainy season (11.16%, 7.57%, 6.93%) respectively, over the control while lowest total bacterial count, phosphate solubilizing bacteria and nitrogen fixers count were observed in ber (20.03%), guava (10.25%) and sweet orange orchard (13.58%). However, maximum increase in fungal count over control was found in jamun orchard during summer (25.77%), rainy (21.83%) and winter season (33.44%). Maximum increase in actinomycetes count over control was found in guava orchard during summer (8.72%) and (9.37%) during winter season. Whereas in mango orchard during rainy (10.71%).

Purple Bacteria Fix Nitrogen in Proterozoic-Analogue Lake

A new study challenges the assumption that cyanobacteria were the only major nitrogen fixers in the Proterozoic eon.

Characterization of Terrihabitans soli gen. nov., sp. nov., a Novel 0.2 μm-Filterable Soil Bacterium Belonging to a Widely Distributed Lineage of Hyphomicrobiales (Rhizobiales)

We previously showed that novel filterable bacteria remain in “sterile” (<0.2 μm filtered) terrestrial environmental samples from Japan, China, and Arctic Norway. Here, we characterized the novel filterable strain IZ6T, a representative strain of a widely distributed lineage. Phylogenetic analysis showed that this strain was affiliated with the Rhizobiales (now proposed as Hyphomicrobiales) of Alphaproteobacteria, but distinct from any other type strains. Strain IZ6T shared the following chemotaxonomic features with the closest (but distantly) related type strain, Flaviflagellibacter deserti SYSU D60017T: ubiquinone-10 as the major quinone; phosphatidylethanolamine, phosphatidylcholine, and phosphatidylglycerol as major polar lipids; and slightly high G+C content of 62.2 mol%. However, the cellular fatty acid composition differed between them, and the unsaturated fatty acid (C18:1ω7c/C18:1ω6c) was predominantly found in our strain. Moreover, unlike methyrotrophs and nitrogen-fixers of the neighboring genera of Hyphomicrobiales (Rhizobiales), strain IZ6T cannot utilize a one-carbon compound (e.g., methanol) and fix atmospheric nitrogen gas. These findings were consistent with the genome-inferred physiological potential. Based on the phylogenetic, physiological, and chemotaxonomic traits, we propose that strain IZ6T represents a novel genus and species with the name Terrihabitans soli gen. nov., sp. nov. (=NBRC 106741T = NCIMB 15058T). The findings will provide deeper insight into the eco-physiology of filterable microorganisms.

A promiscuity locus confers Lotus burttii nodulation with rhizobia from five different genera

Legumes acquire access to atmospheric nitrogen through nitrogen fixation by rhizobia in root nodules. Rhizobia are soil dwelling organisms and there is a tremendous diversity of rhizobial species in different habitats. From the legume perspective, host range is a compromise between the ability to colonize new habitats, where the preferred symbiotic partner may be absent, and guarding against infection by suboptimal nitrogen fixers. Here, we investigate natural variation in rhizobial host range across Lotus species. We find that Lotus burttii is considerably more promiscuous than Lotus japonicus, represented by the Gifu accession, in its interactions with rhizobia. This promiscuity allows Lotus burttii to form nodules with Mesorhizobium, Rhizobium, Sinorhizobium, Bradyrhizobium, and Allorhizobium species that represent five distinct genera. Using recombinant inbred lines, we have mapped the Gifu/burttii promiscuity QTL to the same genetic locus regardless of rhizobial genus, suggesting a general genetic mechanism for host-range expansion. The Gifu/burttii QTL now provides an opportunity for genetic and mechanistic understanding of promiscuous legume-rhizobia interactions.

Jeevamrut and Panchagavya’s Consequences on Growth, Quality and Productivity of Organically Grown Crops: A Review

Organic farming and organically produced food products are gaining popularity very rapidly in India and world. To trounce the reliance on chemical fertilizers for crop production liquid organic bio-fertilizers and manures are very excellent and cheap sources on the earth because of easy availability and good source of nutrients. Among these Jeevamrut, Beejamrut and panchagavya are the one of the best, which contains almost essential plant nutrients (nitrogen, phosphorus, potassium, zinc, copper, manganese etc.), enzymes (acid phosphatise, alkaline phosphatise, dehydrogenase etc.) and microbes (bacteria, fungi, actinomycetes, free living nitrogen fixers and phosphorus solubilising organisms), which directly enhances plant metabolism resulting better growth and development. Jeevamrut is well thought-out to be a brilliant source of natural carbon, nitrogen, phosphorous, potassium and lot of other micro nutrients required for the crops and popularly used as means of organic farming. Panchagavya was used in conventional Hindu rituals which is prepared by mixing five ingredients viz., cow dung, urine, milk, curd and ghee. Jeevamrut and Panchagavya have potential to play the role of promoting growth and provide immunity in plant system. In this manuscript various effects of applications of Jeevamrut and Panchagavya on crops grown in organic farming and their consequences will be discussed.

Global distribution patterns of marine nitrogen-fixers by imaging and molecular methods

Nitrogen fixation has a critical role in marine primary production, yet our understanding of marine nitrogen-fixers (diazotrophs) is hindered by limited observations. Here, we report a quantitative image analysis pipeline combined with mapping of molecular markers for mining >2,000,000 images and >1300 metagenomes from surface, deep chlorophyll maximum and mesopelagic seawater samples across 6 size fractions (<0.2–2000 μm). We use this approach to characterise the diversity, abundance, biovolume and distribution of symbiotic, colony-forming and particle-associated diazotrophs at a global scale. We show that imaging and PCR-free molecular data are congruent. Sequence reads indicate diazotrophs are detected from the ultrasmall bacterioplankton (<0.2 μm) to mesoplankton (180–2000 μm) communities, while images predict numerous symbiotic and colony-forming diazotrophs (>20 µm). Using imaging and molecular data, we estimate that polyploidy can substantially affect gene abundances of symbiotic versus colony-forming diazotrophs. Our results support the canonical view that larger diazotrophs (>10 μm) dominate the tropical belts, while unicellular cyanobacterial and non-cyanobacterial diazotrophs are globally distributed in surface and mesopelagic layers. We describe co-occurring diazotrophic lineages of different lifestyles and identify high-density regions of diazotrophs in the global ocean. Overall, we provide an update of marine diazotroph biogeographical diversity and present a new bioimaging-bioinformatic workflow.

Transmitting silks of maize have a complex and dynamic microbiome

In corn/maize, silks emerging from cobs capture pollen, and transmit resident sperm nuclei to eggs. There are > 20 million silks per U.S. maize acre. Fungal pathogens invade developing grain using silk channels, including Fusarium graminearum (Fg, temperate environments) and devastating carcinogen-producers (Africa/tropics). Fg contaminates cereal grains with mycotoxins, in particular Deoxynivalenol (DON), known for adverse health effects on humans and livestock. Fitness selection should promote defensive/healthy silks. Here, we report that maize silks, known as styles in other plants, possess complex and dynamic microbiomes at the critical pollen-fungal transmission interval (henceforth: transmitting style microbiome, TSM). Diverse maize genotypes were field-grown in two trial years. MiSeq 16S rRNA gene sequencing of 328 open-pollinated silk samples (healthy/Fg-infected) revealed that the TSM contains > 5000 taxa spanning the prokaryotic tree of life (47 phyla/1300 genera), including nitrogen-fixers. The TSM of silk tip tissue displayed seasonal responsiveness, but possessed a reproducible core of 7–11 MiSeq-amplicon sequence variants (ASVs) dominated by a single Pantoea MiSeq-taxon (15–26% of sequence-counts). Fg-infection collapsed TSM diversity and disturbed predicted metabolic functionality, but doubled overall microbiome size/counts, primarily by elevating 7–25 MiSeq-ASVs, suggestive of a selective microbiome response against infection. This study establishes the maize silk as a model for fundamental/applied research of plant reproductive microbiomes.

Effect of bio-fertilizers on foliage and floral traits of chrysanthemum cv Little Pink

Chrysanthemum (Dendranthema grandiflora) is a leading commercial flower crop from asteraceae family grown for cut and loose flowers and also as a pot plant. It is preferred practically due to vast range of shapes and size of flowers, brilliance of colour tones, long lasting floret life, diversity of height and growth habit of the plant, especially hardy nature, relative ease to grow all the year round and versatility of use. Biofertilizers are the multiplied live cells of beneficial strains of micro-organism, are used as biological nitrogen fixers, Phosphate solubilizing, and also used for mineralization of nitrogen and transformation of several elements like sulphur and iron etc. into available forms. The present investigation was conducted at the Horticulture experimental field of Janta College, Bakewar in Complete Randomize Design with 4 treatments and 4 replications. Observations were recorded for vegetative and floral traits upon various biofertilizers treatments viz., T1: Control, T2: (FYM 50% + Soil 50% + 2gm PSB @Per pot), T3 : (FYM 50% + Soil 50% + 2gm Azotobacter @Per pot) and T4: (FYM 50% + Soil 50% + 1gm PSB + 1g Azotobacter@Per pot).