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Regular application of synthetic chemicals in rice ecosystem led to loss of nitrogen (N) and affected the native microbial communities. Controlled release fertilizers (CRFs), a solution to poor nitrogen use efficiency (NUE) of urea and associated environmental implications while diminished economic advantages by high CRF use, is major obstacle that still exists. Reviving the diazotrophic native bacteria from rice cultivated locations should be the alternate for bounciness of potential bioinoculants for better performance and yield enhancement. In the present investigation, two potential nitrogen fixing bacteria, Pseudomonas lini GHM32 and Brevundimonas nasdae GHM62 isolated from rice rhizosphere on Rennie medium. These two bacteria were evaluated for yield and NUE in field studies in a randomized block design with treatments, T1- 100% recommended dose of nitrogen through neem coated urea (RDN), T2- 50% RDN, T3- 50% RDN + P. lini GHM32, T4- 50% RDN + B. nasdae GHM62 and T5- co-application of both bacterial isolates during Rabi-2020-21 (dry season) and Kharif-2021 (wet season). Experimental results for plant height, chlorophyll, nitrogen content and yield in T3 were on par T1. Nitrogen use efficiency indices, such as partial factor productivity (PFP), nitrogen use efficiency (NUE) and nitrogen requirement (NR) of T3 were at par T1 throughout the experimental period. This is the first report with field trials on P. lini and B. nasdae as potential diazotrophic bacterial application by reduction in application of inorganic N fertilizer through neem coated urea with a focus on NUE indices and yield improvement of rice. [ABSTRACT FROM AUTHOR]

The Sustainable Development Goal 2 of the United Nations towards 2030 aimed to end hunger, achieve food security and improved nutrition, and promote sustainable agriculture. According to the 2023 report by the Food and Agriculture Organization, the world is not on track to end hunger or promote sustainable agriculture by that time. Climate change acts as a "crisis multiplier", resulting in lower food productivity and higher prices, contributing further to poverty, hunger, and instability. The number of undernourished people in drought-sensitive and low-income regions of the world has increased this decade. In this review, we analyze the potential of microalgae and cyanobacteria to aid conventional agriculture in providing critical services such as carbon capture, wastewater management, food/feed, biofuels, and other higher value bioproducts. Specifically, we focus on the use of filamentous N2-fixing cyanobacteria for providing those benefits, even in semidry regions of the world with limited access to affordable nitrogen fertilizers to boost crop productivity. We comprehensively consider the eco-physiological basis of this potential, and the available alternative technologies for large-scale biomass production. We analyze venues for filamentous N2-fixing cyanobacteria applications in standalone processes, or integrated into more complex industrial symbioses, towards increased crop productivity, and water and N-fertilizer use efficiency. Throughout the text, we highlight aspects which still require further optimization, or technological breakthroughs, for full realization of the potential of filamentous N2-fixing cyanobacteria for contributing to Sustainable Development Goals. [ABSTRACT FROM AUTHOR]

Microbes living inside or around sugarcane (Saccharum spp.) are crucial for their resistance to abiotic and biotic stress, growth, and development. Sequences of microbial genomes and genes are helpful to understand the function of these microbes. However, there is currently a lack of such knowledge in sugarcane. Here, we combined Nanopore and Illumina sequencing technologies to successfully construct the first high-quality metagenome-assembled genomes (MAGs) and gene catalogues of sugarcane culturable microbes (GCSCMs), which contained 175 species-level genome bins (SGBs), and 7,771,501 non-redundant genes. The SGBs included 79 novel culturable bacteria genomes, and 3 bacterial genomes with nitrogen-fixing gene clusters. Four single scaffold near-complete circular MAGs (cMAGs) with 0% contamination were obtained from Nanopore sequencing data. In conclusion, we have filled a research gap in the genomes and gene catalogues of culturable microbes of sugarcane, providing a vital data resource for further understanding the genetic basis and functions of these microbes. In addition, our methodology and results can provide guidance and reference for other plant microbial genome and gene catalogue studies. [ABSTRACT FROM AUTHOR]

Background and aims: Drought is one of the main causes of global crop decline. Plant growth-promoting rhizobacteria enhance plant tolerance to adverse environmental conditions. This study aimed to determine whether the rhizobacteria Microvirga vignae (BR 3296 and BR 3299) and Bradyrhizobium sp. (BR 3301) can maintain cowpea growth under drought stress. Methods: We analyzed biomass, nodulation, nitrogen accumulation, and physiological traits of the inoculated plants. Rhizobacterial strains were assessed for exopolysaccharide (EPS) and indole acetic acid (IAA) production, growth, and biofilm formation in a water-stress medium induced by polyethylene glycol (PEG)-6000. The expression of genes associated with abscisic acid (ABA) biosynthesis in root nodules was also investigated. Results: All evaluated strains were grown in a culture medium supplemented with PEG. M. vignae strains exhibited increased biofilm formation and EPS production, while Bradyrhizobium showed high IAA production. Cowpea plants inoculated with Bradyrhizobium exhibit higher levels of nodulation, biomass, and nitrogen accumulation. Conversely, M. vignae strains were more efficient at alleviating drought stress and maintaining nodulation, biomass, nitrogen accumulation, and stomatal conductance similar to well-watered plants. Drought-inducible genes were more strongly upregulated in the nodules of plants inoculated with Bradyrhizobium than in those inoculated with M. vignae. Conclusion: Our results suggest that M. vignae strains, isolated from a semi-arid region, help plants withstand water-stress, whereas the strain of Bradyrhizobium sp. isolated from a wet region did not effectively alleviate drought stress. However, Bradyrhizobium sp. conferred growth and nitrogen accumulation to cowpea superior to M. vignae and like plants supplied with nitrogen fertilizer. [ABSTRACT FROM AUTHOR]

The discovery of nitrogen fixation in unicellular cyanobacteria provided the first clues for the existence of a circadian clock in prokaryotes. However, recalcitrance to genetic manipulation barred their use as model systems for deciphering the clock function. Here, we explore the circadian clock in the now genetically amenable Cyanothece 51142, a unicellular, nitrogen-fixing cyanobacterium. Unlike non-diazotrophic clock models, Cyanothece 51142 exhibits conspicuous self-sustained rhythms in various discernable phenotypes, offering a platform to directly study the effects of the clock on the physiology of an organism. Deletion of kaiA, an essential clock component in the cyanobacterial system, impacted the regulation of oxygen cycling and hindered nitrogenase activity. Our findings imply a role for the KaiA component of the clock in regulating the intracellular oxygen dynamics in unicellular diazotrophic cyanobacteria and suggest that its addition to the KaiBC clock was likely an adaptive strategy that ensured optimal nitrogen fixation as microbes evolved from an anaerobic to an aerobic atmosphere under nitrogen constraints. The authors investigate the circadian clock in a unicellular diazotrophic cyanobacterium. They demonstrate the role of the clock in regulating intracellular oxygen dynamics, a necessity to accommodate nitrogen fixation in an oxygen-producing cell. [ABSTRACT FROM AUTHOR]

The increasing global demand for food, coupled with concerns about the environmental impact of synthetic fertilizers, underscores the urgency of developing sustainable agricultural practices. Nitrogen-fixing bacteria, known as diazotrophs, offer a potential solution by converting atmospheric nitrogen into bioavailable forms, reducing the reliance on synthetic fertilizers. However, a deeper understanding of their interactions with plants and other microbes is needed. In this study, we introduce a recently developed label-free 3D quantitative phase imaging technology called dynamic quantitative oblique back-illumination microscopy (DqOBM) to assess the functional dynamic activity of diazotrophs in vitro and in situ. Our experiments involved three different diazotrophs (Sinorhizobium meliloti, Azotobacter vinelandii, and Rahnella aquatilis) cultured on media with amendments of carbon and nitrogen sources. Over 5 days, we observed increased dynamics in nutrient-amended media. These results suggest that the observed bacterial dynamics correlate with their metabolic activity. Furthermore, we applied qOBM to visualize microbial dynamics within the root cap and elongation zone of Arabidopsis thaliana primary roots. This allowed us to identify distinct areas of microbial infiltration in plant roots without the need for fluorescent markers. Our findings demonstrate that DqOBM can effectively characterize microbial dynamics and provide insights into plant-microbe interactions in situ, offering a valuable tool for advancing our understanding of sustainable agriculture. [ABSTRACT FROM AUTHOR]

The effectiveness of Methylobacterium symbioticum in maize and strawberry plants was measured under different doses of nitrogen fertilisation. The biostimulant effect of the bacteria was observed in maize and strawberry plants treated with the biological inoculant under different doses of nitrogen fertiliser compared to untreated plants (control). It was found that bacteria allowed a 50 and 25% decrease in the amount of nitrogen applied in maize and strawberry crops, respectively, and the photosynthetic capacity increased compared with the control plant under all nutritional conditions. A decrease in nitrate reductase activity in inoculated maize plants indicated that the bacteria affects the metabolism of the plant. In addition, inoculated strawberry plants grown with a 25% reduction in nitrogen had a higher concentration of nitrogen in leaves than control plants under optimal nutritional conditions. Again, this indicates that Methylobacterium symbioticum provide an additional supply of nitrogen. [ABSTRACT FROM AUTHOR]

Coffea arabica L. and Coffea canephora L. are coffee species most consumed and marketed in the world. The coffee crop requires a large amount of nitrogen, which shows the importance of knowledge of the population of nitrogen-fixing bacteria (NFB) from the rhizosphere of these crops. These microorganisms may help the reduction of nitrogen fertilizing. However, there is no production of NFB inoculum in the coffee. Therefore, our objective was to evaluate the diversity of potential nitrogen-fixing bacteria (PNFB) in the rhizosphere of C. arabica and C. canephora. The microbial DNA of the soil was extracted, amplified through PCR, and sequenced at the Illumina Miseq. platform. The PNFB prediction was performed using the program PICRUSt2. Three hundred and thirty-seven amplicon sequence variants (ASVs) were identified as PNFB in two coffee species. Xanthobacteraceae, Rhizobium multhospitiium, Rhizobium mesosinicum, and Bradyrhizobium sp. were detected in all samples and main components of the core microbiota of the coffee plant rhizosphere. Some ASVs are exclusive from one of the coffee farms, showing that the coffee specie cultivated may influence the PNFB communities. However, edaphoclimatic factors and soil chemical attributes can also influence the distribution of ASVs in coffee soil. In the C. canephora, the PNFB diversity was influenced by the altitude and the soil chemical attributes, while the altitude and the phosphorus content influenced the PNFB population in C. arabica. Our results are important to the understanding of the PNFB dynamic in coffee soil and for the agricultural inputs bioprospecting to coffee. [ABSTRACT FROM AUTHOR]

Moss-associated abundant microorganisms may play an important role in manganese ore remediation. In this paper, we investigated the structure and diversity of moss rhizobial communities in manganese slag piles at Xiaoqiao Manganese Mine, Songtao County, Tongren City, Guizhou Province, and explored the response of moss rhizobial communities under different levels of soil heavy metal contamination. Inductively coupled plasma mass spectrometry (ICP-MS) was used to determine the heavy metal content in the soil. The structure and abundance of the moss rhizobia community were characterized by 16S rRNA high-throughput sequencing, and the relationship between the indicators was analyzed. The results showed that among the dominant bacteria in the moss rhizosphere of the manganese mine dumps, Actinomycetes, Proteus, Green algae and Cyanobacteria showed better tolerance to heavy metals. The results of the correlation analysis between bacterial abundance and heavy metal content showed that Mn was significantly positively correlated with Planctomycetes and positively correlated with Verrucomicrobia and Abditibacteriota. Cd was positively correlated with Planctomycetes and WPS-2. Pb was negatively correlated with Firmicutes and positively correlated with WS2. Analysis of the correlation between bacterial diversity and heavy metal content showed that Cu was significantly correlated with OTU, Ace, and Chao (p < 0.05). In summary, the diversity and community structure of moss rhizobia differed significantly under different levels of heavy metal contamination, and most moss rhizobia showed strong tolerance, and these bacteria may be a key factor in the remediation process of mine soils. [ABSTRACT FROM AUTHOR]

Legumes have the unique ability to form symbiosis with nitrogen-fixing bacteria of the genus Rhizobium by forming special symbiotic organs called nodules. The process of symbiosis initiation and development between legumes and rhizobia is tightly controlled by a complex network of transcription factors. Control of root nodule development and infection thread formation involves the recognition of rhizobial signal molecules through specific receptors, which trigger signal transduction cascades. IPD3 and NIN transcription factors begin to act early in this process. The IPD3 transcription factor has been previously shown to regulate infection processes associated with rhizobial invasion and activate several downstream components, including NIN transcription factor. NIN, in turn, plays an important role in the control of infection process as well as in nodule organogenesis. Nevertheless, their targets in developing nodules of legumes such as Pisum sativum and Medicago truncatula remain unclear. In our study, we used chromatin immunoprecipitation combined with the next-generation sequencing (ChIP-Seq) method to identify targets of PsIPD3 and PsNIN in the Pisum sativum genome. To do this, we generated transgenic plants carrying the p35S::PsIPD3~3XFLAG::t35S and p35S::PsNIN~3XFLAG::t35S constructs using the Agrobacterium rhizogenes-mediated transformation approach. Immunoprecipitation of chromatin bound to PsIPD3~3XFLAG and PsNIN~3XFLAG proteins was performed using anti-FLAG antibodies, and libraries generated from bound chromatin were sequenced on the Illumina NovaSeq 6000 platform. Here, the methodical approaches for preparation of IPD3-targets-enriched and NIN-targets-enriched samples in pea plants using ChiP-Seq are discussed. [ABSTRACT FROM AUTHOR]

Ustilago maydis is a pathogenic fungus in Basidiomycota causing corn smut disease. A strain of U. maydis YZZF202006 was isolated from the tumor of corn smut collected from Jingzhou city in China. The intracellular bacteria were confirmed inner hyphal of the strain YZZF202006 by PCR amplification and fluorescence in situ hybridization (FISH) and SYTO-9. An endohyphal bacterium YZUMF202001 was isolated from the protoplasts of the strain YZZF202006. It was gram-negative, short rod-shaped with smooth light yellow colony. The endohyphal bacterium was genomic evidenced as Klebsiella michiganensis on the basis of average nucleotide identity (ANI) analysis and the phylogram. Then K. michiganensis was GFP-Labeled and reintroduced into U. maydis, which confirmed the bacterium can live in hyphae of U.maydis. The bacterium can grow on N-free culture media. Its nitrogenase activity was reached av. 646.25 ± 38.61 nmol·mL− 1·h− 1 C2H4 by acetylene reduction assay. A cluster of nitrogen fixation genes (nifJHDKTXENXUSVWZMFLABQ) was found from its genome. The endohyphal K. michiganensis may play an important role to help nitrogen fixation for fungi in the future. Key points: A endohyphal bacterium Klebsiella sp. was found and isolated from Ustilago maydis. Endohyphal bacterium was identified and evaluated for nitrogen fixation. A GFP-Labeled K. michiganensis was reintroduced into U. maydis by a new method. [ABSTRACT FROM AUTHOR]

Aims: Our objective was to examine short-term responses of A.sinensis agronomic, soil productivity to agricultural management (i.e. amino acid (AAs) and nitrogen-fixing bacteria (NFB) as alone or co-applicationed exogenous nitrogen (N) after cover planting). Methods: A field experiment was established with four fertilization treatments, including NFB (Y1), NFB and AAs (Y2), AAs (Y3), and sterile water (CK). The plant yield, biomass, N and C content, photosynthesis and the soil chemical properties, microbial community and metabolite spectrum were evaluated. Results: Y2 improved the crop biomass by 32–66% than CK, Y1 and Y3. It also decreased soil C/N by 24.29% than CK. 16S rRNA and ITS genes revealed that Y2 markedly enhanced the growth of copiotrophic taxa (Alloprevotella, Bactriodies and Alistipes) while inhibiting the growth of oligotrophic taxa (Sphingomonas and Ellin6055), among the dominant bacteria. Y2 reduced the growth of pathogenic taxa (Thanatephorus and Fusarium) that are encouraged by AAs. Further, AAs and NFB addition directly affected the diversity of bacteria and fungi and indirectly affected fungal diversity by altering soil total organic carbon (TOC), total nitrogen (TN), C/N. Additionally, soil metabolomics analysis revealed that Y3 elevated the concentration of chemical compounds that impede microbial growth, while decreasing fructose, N-Acetylglutamic acid, and arginine involved in C and N metabolism. Y2 augmented the content of disease-resistant compounds and lysine in N metabolism. Conclusion: Inoculating AAs with NFB (Bacillus amyloliquefaciae and Pseudomonas fluorescence) is a strategy with immense benefits as a biofertilizer for sustainable A.sinensis production, which also renders soil ecological services. [ABSTRACT FROM AUTHOR]

Nodules are formed as a result of symbiosis with nitrogen-fixing bacteria on the roots of legume plants. Symbiotic nodule development shares common developmental processes with lateral roots, including cell proliferation of the pericycle and cortical cell layers leading to primordium formation, and both these organs are assumed to be evolutionarily related. The progression of their development is realized with the help of phytohormones, in particular auxin and cytokinin. Due to common evolutionary origin, the hormonal pathway and response may have similar functionality in cell fate specification during lateral root and nodule development. It is known that auxin and cytokinin both positively regulate nodule primordia development. However during lateral root development, auxin is a key positive regulator, while cytokinin suppresses lateral root development. Therefore, a comparative review of auxin and cytokinin action in the development of these two organs to elucidate how their identity is established should be of special interest. This review discusses the involvement of auxin and cytokinin in the development of symbiotic nodules and lateral roots, with a special focus on the similarity and differences of their action during lateral root and nodule developmental processes. The spatio-temporal peculiarities of auxin and cytokinin biosynthesis, transport and response during lateral root and symbiotic nodule formation are reviewed, which should help to clarify how the identity of these two root lateral organs depends on auxin-cytokinin interplay. [ABSTRACT FROM AUTHOR]

Agave lechuguilla is a widely distributed plant in arid ecosystems. It has been suggested that its microbiome is partially responsible for its great adaptability to the oligotrophic environments of the Chihuahuan Desert. To lead the recruitment of beneficial rhizobacteria, the root exudates are essential; however, the amino acids contained within these compounds had been largely overlooked. Thus, we investigated how the variations of amino acids in the rhizosphere at different growth stages of A. lechuguilla affect the rhizobacterial community composition, its functions, and activity of the beneficial bacteria. In this regard, it was found that arginine and tyrosine were related to the composition of the rhizobacterial community associated to A. lechuguilla, where the most abundant genera were from the phylum Proteobacteria and Bacteroidetes. Moreover, Firmicutes was largely represented by Bacillus in the phosphorus-mineralizing bacteria community, which may indicate its great distribution and versatility in the harsh environments of the Chihuahuan Desert. In contrast, we found a high proportion of Unknown taxa of nitrogen-fixing bacteria, reflecting the enormous diversity in the rhizosphere of these types of plants that remains to be explored. This work also reports the influence of micronutrients and the amino acids methionine and arginine over the increased activity of the nitrogen-fixing and phosphorus-mineralizing bacteria in the rhizosphere of lechuguillas. In addition, the results highlight the multiple beneficial functions present in the microbiome that could help the host to tolerate arid conditions and improve nutrient availability. [ABSTRACT FROM AUTHOR]

Aims: To understand the species composition, abundance and diversity of nitrogen-fixing bacteria in the Cenchrus fungigraminus rhizosphere and to screen nitrogen-fixing bacteria to study their potential role in plant growth promotion. Methods: Soil were collected from 4 depths (G1, G2, G3 and G4) of the C. fungigraminus rhizosphere, and their physical and chemical properties were determined. The diversity and abundance of nitrogen-fixing bacteria and the nifH gene was analysed. Nitrogen-fixing bacteria were screened and selected to promote growth of C. fungigraminus seedlings. Results: The highest diversity and abundance of nitrogen-fixing bacteria was observed in the G2 samples collected from the C. fungigraminus rhizosphere. These bacteria mainly included Proteobacteria (93.91%), Actinobacteria (0.42%), and Firmicutes (0.18%) and were significantly affected by total nitrogen, available nitrogen and soil depth. The nifH gene copy number was highest (1.56 ± 0.17 × 107copies/g) in G2. Rhizobium pusense No. 8 and No. 28 were isolated from G1 and G2, with nitrogenase activities of 145.06 ± 4.10 and 199.78 ± 7.50 U/L. The promotion experiment revealed that the plant height, root length, and leaf length of C. fungigraminus seedlings treated with both strains significantly increased by 56.79%, 76.99% and 55.71%, and the soil moisture and total nitrogen were significantly increased compared to the control (P < 0.05). The available nitrogen, organic matter and organic carbon in soil with strain No. 28 significantly increased compared to CK. Conclusion: Rhizobacteria in the C. fungigraminus rhizosphere play an important role as plant growth promoting rhizobacteria (PGPR). Two strains showed potential for the development of biological fertilizers. [ABSTRACT FROM AUTHOR]

Background: A 2-year field trial was conducted to test the effect of biochar addition (0, 15, 30, and 45 t hm−2) on soil properties, nutrients, diazotrophic community diversity, abundance, and structure, and soybean growth, yield, and quality. Furthermore, we aimed to explore the responses of diazotrophs, grain yield, and quality to nine soil environmental factors. Rhizosphere soil and plant samples were collected after harvest. Results: Biochar application resulted in a lower soil bulk density (γd) but higher total organic carbon (TOC), effective phosphorus (AP) and total nitrogen (TN). Compared with untreated soil, the diversity index of diazotrophic bacteria in biochar-amended soil decreased, but the abundance of diazotrophic bacteria increased. The microbial community remained stable when a small amount of biochar was applied but changed as biochar amount increased. Furthermore, biochar reduced the proportion of unique nitrogen-fixing bacteria, but did not affect that of common nitrogen-fixing bacteria between biochar-amended and untreated soils, and increased the relative abundance of Bradyrhizobium (B9 vs. B0) and Sinorhizobium (B18 or B21 vs. B0) involved in symbiotic nitrogen fixation. The main components and content of fatty acids (except for stearic acid) and the content of protein and soybean oil remained stable under biochar application. The low biochar treatment (15 t hm−2) promoted soybean growth and yield. Redundancy analysis suggested that TN greatly influenced the diazotrophic community structure at the phylum and genus levels, and that pH, TOC, and NO3−-N greatly influenced grain yield and quality. Conclusions: Soil diazotroph environment can be improved by targeted farmland implementation based on changes in soil physicochemical properties, which would benefit biological N fixation in agricultural soils and further increase economic benefit. [ABSTRACT FROM AUTHOR]

The potential nitrogen-fixing bacterial diversity in the rhizospheric soil of the native switchgrass (Panicum virgatum L.) from Tall Grass Prairies of Northern Oklahoma was studied using a partial region of nitrogenase structural gene—nifH. Eleven clone libraries constructed from nifH amplicons gave 407 good-quality sequences. More than 70% of sequences showed similarity of nifH with uncultured bacteria (< 98%). The dominance of sequences affiliated with Deltaproteobacterial nifH was observed, followed by Betaproteobacterial nifH sequences. The nifH gene library was dominated by the genera Geobacter, Rhizobacter, Paenibacillus, and Azoarcus. Sequences affiliated with rhizobia, such as Bradyrhizobium, Methylocystis, Ensifer, etc., were also in the rhizosphere in small numbers. From Deltaproteobacteria, five genera, namely Geobacter, Pelobacter, Geomonas, Desulfovibrio, and Anaeromyxobacter, contributed to 48% of the total sequences suggesting the dominance of group Deltaproteobacteria in the rhizosphere of native switchgrass. Considering the percent similarity of the nifH sequences with cultivated bacteria, this study demonstrated the presence of novel bacterial species in switchgrass rhizospheric soil from Tall Grass Prairie. [ABSTRACT FROM AUTHOR]

A new study reports synergistic inhibitory effects of ocean acidification and phosphate limitation on the nitrogen-fixing capacity of a globally important cyanobacterium species. Inspired by the report, this Comment presents the complexity of how ocean acidification and phosphate limitation affect phytoplankton physiologies and species beyond nitrogen fixation and cyanobacteria, and what future research is needed to address the remaining crucial questions. This Comment discusses the complexity of how ocean acidification and phosphate limitation affect phytoplankton physiologies, as well as what future research is needed to address remaining crucial questions. [ABSTRACT FROM AUTHOR]

This review evaluates oilseed crop soybean endophytic bacteria, their prospects, and challenges for sustainable agriculture. Soybean is one of the most important oilseed crops with about 20–25% protein content and 20% edible oil production. The ability of soybean root-associated microbes to restore soil nutrients enhances crop yield. Naturally, the soybean root endosphere harbors root nodule bacteria, and endophytic bacteria, which help increase the nitrogen pool and reclamation of another nutrient loss in the soil for plant nutrition. Endophytic bacteria can sustain plant growth and health by exhibiting antibiosis against phytopathogens, production of enzymes, phytohormone biosynthesis, organic acids, and secondary metabolite secretions. Considerable effort in the agricultural industry is focused on multifunctional concepts and bioprospecting on the use of bioinput from endophytic microbes to ensure a stable ecosystem. Bioprospecting in the case of this review is a systemic overview of the biorational approach to harness beneficial plant-associated microbes to ensure food security in the future. Progress in this endeavor is limited by available techniques. The use of molecular techniques in unraveling the functions of soybean endophytic bacteria can explore their use in integrated organic farming. Our review brings to light the endophytic microbial dynamics of soybeans and current status of plant microbiome research for sustainable agriculture. [ABSTRACT FROM AUTHOR]

This study is aimed at adding different types of mature compost and sulfur powder, as additives into food waste composting to investigate the effect on nitrogen loss and compost maturity. The composting experiment used the in-vessel composting method and was conducted continuously for 15 days. High-throughput sequencing was used to analyze the bacterial community during composting. Results showed that the secondary fermentation mature compost mixed with sulfur powder group had the most reduction of ammonia emission (56%) and the primary fermentation mature compost amendments were the most effective for nitrous oxide emission reduction (37%). The temperature, pH, and nitrogen forms of transformation of the pile significantly affect the nitrogen loss during composting. Firmicutes helped to promote the rapid warming of the pile, and Actinobacteria and Proteobacteria played an important role in decomposition of organic matter. Thermobifida and Ureibacillus had a main contribution to the rapid degradation of organic matter in the process of composting. The relative abundance of nitrogen-fixing bacteria was higher, and the relative abundance of predominantly ammonifying and denitrifying bacteria was lower than the control group, with the addition of different additives. [ABSTRACT FROM AUTHOR]

In the boreal forests, feather mosses such as Hylocomium splendens and Pleurozium schreberi are colonized by cyanobacteria, which provide large amounts of nitrogen to forest ecosystems through nitrogen fixation. Although these feather mosses are also ubiquitous in subalpine forests of East Asia, little is known regarding their associated cyanobacteria and their ability to fix nitrogen. In this study, we investigated (1) whether cyanobacteria co-exist and fix nitrogen in the two species of feather mosses that cover the ground surface in a subalpine forest of Mt. Fuji, (2) whether cyanobacteria belonging to a common cluster with boreal forests are found in feather mosses in Mt. Fuji, and (3) whether moss-associated nitrogen fixation rates differed among moss growing substrates, canopy openness, and moss nitrogen concentrations in the same forest area. Our results showed that cyanobacteria colonized feather mosses in the subalpine forests of Mt. Fuji and acetylene reduction rates as an index of nitrogen fixation tended to be higher in H. splendens than in P. schreberi. Based on analysis of the nifH gene, 43 bacterial operational taxonomic units (OTUs) were identified, 28 of which represented cyanobacteria. Among the five clusters of cyanobacteria classified based on their nifH gene and identified in northern Europe, four (Nostoc cluster I, Nostoc cluster II, Stigonema cluster, and nifH2 cluster) were also found at Mt. Fuji. The acetylene reduction rate differed depending on the moss growing substrate and the total nitrogen concentration of moss shoots, and a strong negative correlation was observed with the total nitrogen concentration. [ABSTRACT FROM AUTHOR]

Nitrogen is an important factor affecting crop yield, but excessive use of chemical nitrogen fertilizer has caused decline in nitrogen utilization and soil and water pollution. Reducing the utilization of chemical nitrogen fertilizers by biological nitrogen fixation (BNF) is feasible for green production of crops. However, there are few reports on how to have more ammonium produced by nitrogen-fixing bacteria (NFB) flow outside the cell. In the present study, the amtB gene encoding an ammonium transporter (AmtB) in the genome of NFB strain Kosakonia radicincitans GXGL-4A was deleted and the △amtB mutant was characterized. The results showed that deletion of the amtB gene had no influence on the growth of bacterial cells. The extracellular ammonium nitrogen (NH4+) content of the △amtB mutant under nitrogen-free culture conditions was significantly higher than that of the wild-type strain GXGL-4A (WT-GXGL-4A), suggesting disruption of NH4+ transport. Meanwhile, the plant growth-promoting effect in cucumber seedlings was visualized after fertilization using cells of the △amtB mutant. NFB fertilization continuously increased the cucumber rhizosphere soil pH. The nitrate nitrogen (NO3−) content in soil in the △amtB treatment group was significantly higher than that in the WT-GXGL-4A treatment group in the short term but there was no difference in soil NH4+ contents between groups. Soil enzymatic activities varied during a 45-day assessment period, indicating that △amtB fertilization influenced soil nitrogen cycling in the cucumber rhizosphere. The results will provide a solid foundation for developing the NFB GXGL-4A into an efficient biofertilizer agent. [ABSTRACT FROM AUTHOR]

Pot experiments were conducted to explore the effects of different rice straw returning soil on the community structure and function of bacteria in rice root, rhizosphere, leaf and phyllosphere under 7 conditions of rice straw combined with different fertilizers respectively. The results showed that: rice straw returning in different ways increased the content of soil pH and K, and reduced the accumulation of N, P and organic matter in soil, and different rice straw returning ways had different effects; rice straw returning reduced dry weight of rice grain, 2% of rice straw returning reduced rice grain greater than that of 1% rice straw returning; The reduction of NP combined fertilization is greater than that of NK combined fertilization and NPK combined fertilization. Except for the decrease of chao_1 index in rice root at maturity, rice straw returning significantly improved the abundance, diversity and evenness of bacteria in rice root, rhizosphere, leaf and phyllosphere. Rice straw returning increased the content of REEs in rice, and 2% of rice straw returning soil increased rare earth element (REE) content in rice grain greater than that of 1% rice straw returning soil. Different ways of rice straw returning soil reduced the abundance of Bacillus, while the abundance of Exiguobacterium in rice leaves was hundreds of times higher than that of the control group, and the genus in leaves was dozens of times higher than that of the control group, 2% of rice straw returning soil increased the abundance of harmful bacteria and pathogens of Acidovorax, Clostridium sensu stricto, Citrobacter, Curtobacterium, and 1% of rice straw returning soil promoted the abundance of nitrogen fixing bacteria, plant growth-promoting bacteria, stress resistant bacteria such as Lactobacillus, Azospira, Acinetobacter, Bradyrhizobium and Acidocella; Environmental factors such as available P, organic matter, total nitrogen, nitrate nitrogen, rare earth element content in rice roots, available K and soil moisture are important factors affecting the community structure of bacteria in rice roots, rhizosphere, leaf and phyllosphere at tillering stage of the rice. pH, REE content in rice roots, shoots, organic matter, total nitrogen, nitrate nitrogen and soil moisture content are the main environmental factors affecting the community structure of bacteria in rice roots, rhizosphere, leaf and phyllosphere at maturity stage of rice. 2% rice straw returning soil promoted the formation of harmful bacteria, which may be an important reason for its significant reduction in the dry weight of rice grains. [ABSTRACT FROM AUTHOR]

Background and aims: Straw amendment can increase nitrogen fixation in paddy field, however, the efficiency of carbon sources with different biochemical properties to enhance N2 fixation and nitrogen fixation activity is still unclear. Methods: A 15N2-labelling system was used in the field environment to determine biological nitrogen fixation (BNF) under the addition of three kinds of straw. The nifH gene (DNA) and nifH RNA gene (cDNA) of soil were amplified by real-time fluorescent quantitative PCR. The diversity and community composition of nitrogen fixing microorganisms were studied by high-throughput sequencing. The study is expected to reveal how different carbon sources impact biological nitrogen fixation and its mechanism in the paddy field system. Results: Results showed that the absolute abundance diazotrophs in the treatment of mature stage wheat straw (MWS) was 4.88 times as high as that in the CK treatment, but jointing stage wheat straw (JWS) and poplar branch (PB) did not induce any significant changes. Straw amendment had no impact on cyanobacteria abundance. The proportion of N2 fixation increased by MWS was 2.07 times, but which was much lower than the increase proportion of the heterotrophic diazotrophs, leading to a decrease of diazotrophic nitrogen fixation activity. Conclusions: Mature wheat straw addition increased biologically fixed nitrogen in paddy field by increasing the number of heterotrophic nitrogen fixing bacteria. The results indicated that to increase biological N2 fixation in paddy system, straws with low nitrogen content and high C/N ratio were recommended. [ABSTRACT FROM AUTHOR]

Biological nitrogen fixation is a major important source of nitrogen for low-nutrient surface oceanic waters. Nitrogen-fixing (diazotrophic) cyanobacteria are believed to be the primary contributors to this process, but the contribution of non-cyanobacterial diazotrophic organisms in oxygenated surface water, while hypothesized to be important, has yet to be demonstrated. In this study, we used simultaneous 15N-dinitrogen and 13C-bicarbonate incubations combined with nanoscale secondary ion mass spectrometry analysis to screen tens of thousands of mostly particle-associated, cell-like regions of interest collected from the North Pacific Subtropical Gyre. These dual isotope incubations allow us to distinguish between non-cyanobacterial and cyanobacterial nitrogen-fixing microorganisms and to measure putative cell-specific nitrogen fixation rates. With this approach, we detect nitrogen fixation by putative non-cyanobacterial diazotrophs in the oxygenated surface ocean, which are associated with organic-rich particles (<210 µm size fraction) at two out of seven locations sampled. When present, up to 4.1% of the analyzed particles contain at least one active putative non-cyanobacterial diazotroph. The putative non-cyanobacterial diazotroph nitrogen fixation rates (0.76 ± 1.60 fmol N cell−1 d−1) suggest that these organisms are capable of fixing dinitrogen in oxygenated surface water, at least when attached to particles, and may contribute to oceanic nitrogen fixation. Nitrogen-fixing (diazotrophic) cyanobacteria provide a critical nutrient input to the ocean. Non-cyanobacterial diazotrophs are also thought to contribute, but they have not been observed to fix nitrogen. Using dual isotope labeling combined with nanoscale secondary ion mass spectrometry, this study demonstrates that putative non-cyanobacterial diazotrophs attached to particles can fix nitrogen. [ABSTRACT FROM AUTHOR]

Island biogeography has classically focused on abiotic drivers of species distributions. However, recent work has highlighted the importance of mutualistic biotic interactions in structuring island floras. The limited occurrence of specialist pollinators and mycorrhizal fungi have been found to restrict plant colonization on oceanic islands. Another important mutualistic association occurs between nearly 15,000 plant species and nitrogen-fixing (N-fixing) bacteria. Here, we look for evidence that N-fixing bacteria limit establishment of plants that associate with them. Globally, we find that plants associating with N-fixing bacteria are disproportionately underrepresented on islands, with a 22% decline. Further, the probability of N-fixing plants occurring on islands decreases with island isolation and, where present, the proportion of N-fixing plant species decreases with distance for large, but not small islands. These findings suggest that N-fixing bacteria serve as a filter to plant establishment on islands, altering global plant biogeography, with implications for ecosystem development and introduction risks. Plants associated with nitrogen-fixing bacterial symbionts are disproportionately underrepresented on islands, suggesting that these bacteria might play a limiting role in island plant biogeography. [ABSTRACT FROM AUTHOR]

Many plants associate with arbuscular mycorrhizal fungi for nutrient acquisition, while legumes also associate with nitrogen-fixing rhizobial bacteria. Both associations rely on symbiosis signaling and here we show that cereals can perceive lipochitooligosaccharides (LCOs) for activation of symbiosis signaling, surprisingly including Nod factors produced by nitrogen-fixing bacteria. However, legumes show stringent perception of specifically decorated LCOs, that is absent in cereals. LCO perception in plants is activated by nutrient starvation, through transcriptional regulation of Nodulation Signaling Pathway (NSP)1 and NSP2. These transcription factors induce expression of an LCO receptor and act through the control of strigolactone biosynthesis and the karrikin-like receptor DWARF14-LIKE. We conclude that LCO production and perception is coordinately regulated by nutrient starvation to promote engagement with mycorrhizal fungi. Our work has implications for the use of both mycorrhizal and rhizobial associations for sustainable productivity in cereals. Lipochitooligosaccharide (LCO) perception by legumes is required to establish symbiotic relationships with nitrogen fixing bacteria. Here the authors show that nutrient starvation can activate LCO perception in cereals to promote symbiotic association with arbuscular mycorrhizal fungi. [ABSTRACT FROM AUTHOR]

Background: Straw return may affect the soil nitrogen (N) balance by changing soil carbon (C) and N components and contents. To understand how straw return affects the soil N fixation capacity, the relationship between biological N fixation and changes in soil C and N contents at different depths need to be examined. Methods: Soil samples were collected at 20-cm intervals from 0 to 100 cm after five years of a rice-rape rotation system with straw return (ST) and without (CK). Organic C and inorganic N contents, potential N fixation rate, and abundance and population composition of N-fixing bacteria were analyzed at different soil depths. Results: Compared with CK, ST increased soil organic C (SOC), particulate organic C (POC), mineral-associated organic C (MOC), and total N (TN) but decreased nitrate–N (NO3−-N). Straw return also increased the abundance of N-fixing bacteria from 2.9- to 18-fold at depths from 0 to 40 cm and increased the potential N fixation rate at 0–20 cm by 25%. The annual biological N fixation rates at 0–60 cm by soil N-fixing bacteria were estimated to be approximately 0.13–2.70 and 0.12–2.16 kg·ha−1 in ST and CK, respectively. Long-term ST significantly affected the composition of N-fixing bacteria at depths from 0 to 40 cm. Conclusions: Long-term straw return can increase the abundance of the N-fixing bacteria and effectively alter the structure of the N-fixing bacterial community. SOC, POC, TN, and NO3−-N were the main environmental factors driving changes in abundance, activity, and population composition of soil N-fixing bacteria under ST. [ABSTRACT FROM AUTHOR]

Nitrogen-fixing bacteria establish symbiosis with legumes for the biological nitrogen fixation process in specific root structures called nodules. Among these legumes, common bean and soybean are two of the most economically relevant crops relying on the process for efficient nitrogen acquisition. This review proposes to answer two problem questions: what are the already known epigenetic mechanisms involved in the regulation in common bean and soybean nodulation and how they act during the nodulation process. DNA methylation, histone modification, and small RNAs were the epigenetic mechanisms found. The adenine methylation pattern of the bacterial genome changes during the symbiosis, and rhizobial tRNA-derived small RNA fragments are transferred to plant cells to cleave mRNA-specific mRNA targets, increasing the nodule number. On the other side of the interaction, plant DNA methylation is essential during the nodule's life cycle, and histone lysine methyltransferases can also influence both bacterial colonization and nodule number. The microRNAs are the best-studied epigenetic modifiers that regulate legume nodulation. These epigenetic mechanisms can also be used for bacterial or plant autoregulation of nodulation since biological nitrogen fixation is a mandatory but energy-consuming process. This review article summarizes the state of the art of the epigenetic mechanisms involved in the regulatory network during common bean and soybean nodulation. Understanding of its mechanisms is essential to modulate and enhance nodulation in legume crops. [ABSTRACT FROM AUTHOR]

Annually, about, more than 7% of the Earth's land area becomes inappropriate for agriculture subsequently of salinization and desertification. Biofertilizers based on halophilic nitrogen-fixing bacteria can restore saline soils and stimulate plant growth, having a positive effect on germination, development of stems and roots, and fruiting. The aim of this work was to obtain osmo-resistant (Osm-r) nitrogen-fixing mutants isolated from saline soils of Armenia and selection of the best ones. To achieve this goal, we have obtained a collection of Osm-r strains based on soil nitrogen-fixing bacteria without the use of genetically modified technologies, which is an innovation in sphere of soil microbiology, and, especially, in nitrogen-fixing microorganisms. These mutants were obtained on the basis of Agrobacterium sp. Y-2 and Agrobacterium sp. M-1 nitrogen-fixing strains, both spontaneously and induced. Four strains with the higher nitrogen-fixing ability, which kept their vital activity in an environment with a high concentration of salts, were selected from collection of mutants. Selected strains in the future can become the basis for creating a new, effective, environmentally friendly biofertilizer for saline soils because they are plasmidless and have the highest priority for intensive use in agriculture. [ABSTRACT FROM AUTHOR]

A marine, facultatively anaerobic, nitrogen-fixing bacterium, designated strain DNF-1T, was isolated from the lagoon sediment of Dongsha Island, Taiwan. Cells grown in broth cultures were Gram-negative rods that were motile by means of monotrichous flagella. Cells grown on plate medium produced prosthecae and vesicle-like structures. NaCl was required and optimal growth occurred at about 2–3% NaCl, 25–30 °C and pH 7–8. The strain grew aerobically and was capable of anaerobic growth by fermenting D-glucose or other carbohydrates as substrate. Both the aerobic and anaerobic growth could be achieved with NH4Cl as a sole nitrogen source. When N2 served as the sole nitrogen source only anaerobic growth was observed. Major cellular fatty acids were C14:0, C16:0 and C16:1ω7c, while major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. The DNA G+C content was 42.2 mol% based on the genomic DNA data. Phylogenetic analyses based on 16S rRNA genes and the housekeeping genes, gapA, pyrH, recA and gyrB, revealed that the strain formed a distinct lineage at species level in the genus Vibrio of the family Vibrionaceae. These results and those from genomic, chemotaxonomic and physiological studies strongly support the assignment of a novel Vibrio species. The name Vibrio salinus sp. nov. is proposed for the novel species, with DNF-1T (= BCRC 81209T = JCM 33626T) as the type strain. This newly proposed species represents the second example of the genus Vibrio that has been demonstrated to be capable of anaerobic growth by fixing N2 as the sole nitrogen source. [ABSTRACT FROM AUTHOR]

Aims: Silicon (Si) uptake and accumulation improves plant resilience to environmental stresses, but most studies examining this functional role of Si have focussed on grasses (Poaceae) and neglected other important plant groups, such as legumes (Fabaceae). Legumes have evolved a symbiotic relationship with nitrogen-fixing bacteria (rhizobia) housed in root nodules. Our study determined the impacts of silicon (Si) supplementation on Medicago truncatula inoculated with Ensifer meliloti rhizobial strains that differed in their capacity for nitrogen fixation: Sm1021 ('low-efficiency') or Sm1022 ('high-efficiency'). Methods: We examined how Si and rhizobial efficacy influence nodule and plant functional traits, including their chemical aspects. These combinations were supplied with or without Si in a glasshouse experiment, where we quantified nodule flavonoids and foliar chemistry (free amino acids, soluble protein, elemental C, N and Si). Results: Si supply increased nodule number per plant, specific nodule flavonoid concentrations, contents of foliar nitrogenous compounds and foliar C, but not foliar Si. We also demonstrated that rhizobial efficacy altered the magnitude of Si effects on certain traits. For example, Si significantly promoted concentrations of foliar N and soluble protein in the plants associated with the 'low-efficiency' strain only, and this was not the case with the 'high-efficiency' one. Conclusions: Collectively, our study indicates that Si generates positive effects on M. truncatula, particularly when the association with rhizobia is relatively inefficient, and may play a more prominent role in rhizobial functionality than previously thought. [ABSTRACT FROM AUTHOR]

Symbiotic nitrogen fixing bacteria comprise of diverse species associated with the root nodules of leguminous plants. Using an appropriate taxonomic method to confirm the identity of superior and elite strains to fix nitrogen in legume crops can improve sustainable global food and nutrition security. The current review describes taxonomic methods preferred and commonly used to characterize symbiotic bacteria in the rhizosphere. Peer reviewed, published and unpublished articles on techniques used for detection, classification and identification of symbiotic bacteria were evaluated by exploring their advantages and limitations. The findings showed that phenotypic and cultural techniques are still affordable and remain the primary basis of species classification despite their challenges. Development of new, robust and informative taxonomic techniques has really improved characterization and identification of symbiotic bacteria and discovery of novel and new species that are effective in biological nitrogen fixation (BNF) in diverse conditions and environments. [ABSTRACT FROM AUTHOR]

This study investigated the distribution and genetic diversity of the indigenous Bradyrhizobium spp. in the Korean agricultural field. A total of 254 Bradyrhizobium strains were isolated from 97 soybean samples (9 cultivars) collected in 14 regions. B. elkanii dominated in the southern regions, while B. diazoefficiens dominated in most central and northern regions. Through non-parametric multidimensional scaling (NMDS) analysis, we confirmed the possibility that environmental factors such as annual average temperature and soybean cultivars might affect the distribution of Bradyrhizobium spp. in some regions. The DNA fingerprint using repetitive DNA sequences showed the genetic diversity among the Bradyrhizobium strains isolated from the different regions. Clustering the strains based on the genetic diversity indicated that Bradyrhizobium spp. grouped into different clusters depending on geographic location. This study suggests that the Korean indigenous Bradyrhizobium spp. distribute differently according to the geographical feature, and the high genetic diversity of each strain attribute to the geographic location. [ABSTRACT FROM AUTHOR]

Background and aims: Arbuscular mycorrhizal fungi (AMF) and nitrogen-fixing bacteria (NFB) can form symbiotic relationships with host plants, and this enhances nutrient uptake and plant performance of host plants. However, how AMF and NFB influence the complementarity and facilitation dynamics between grasses and legumes in grasslands is still not well understood.We conducted a greenhouse experiment to assess effects of different grass: legume ratios (GLRs) and microbial symbionts on plant production comprising two native C3 species from a semiarid steppe in northern China (grass (G): Leymus chinensis; legume (L): Medicago ruthenica). Different GLRs (G4L0: 4:0, G3L1: 3:1, G2L2: 2:2, G1L3: 1:3, G0L4: 0:4) were compared with or without AMF or NFB inoculation.Grass–legume mixtures, especially G1L3, produced significantly higher biomass than monocultures via altering the community structure of soil microorganisms. AMF inoculation increased the availability of nutrients (mainly soil available P (SAP) and/or NO3−–N), which increased plant community productivity due to increased biomass in both grass and legume. Co-occurrence networks revealed that keystone genera (e.g., Arenimonas, Dominikia, Claroideoglomus and Scutellospora) were the primary factors influencing plant community productivity among grass–legume mixtures. Structural equation model showed that GLRs and inoculation types consistently produced overyielding directly and indirectly via affecting SAP and NO3−–N concentrations.Our findings highlight that suitable grass: legume mixture ratios (e.g., 1:3) positively affect productivity, and soil microorganisms that improve soil resource acquisition (SAP and NO3−–N), especially AMF, play an important role in grass: legume mixtures in this process.Methods: Arbuscular mycorrhizal fungi (AMF) and nitrogen-fixing bacteria (NFB) can form symbiotic relationships with host plants, and this enhances nutrient uptake and plant performance of host plants. However, how AMF and NFB influence the complementarity and facilitation dynamics between grasses and legumes in grasslands is still not well understood.We conducted a greenhouse experiment to assess effects of different grass: legume ratios (GLRs) and microbial symbionts on plant production comprising two native C3 species from a semiarid steppe in northern China (grass (G): Leymus chinensis; legume (L): Medicago ruthenica). Different GLRs (G4L0: 4:0, G3L1: 3:1, G2L2: 2:2, G1L3: 1:3, G0L4: 0:4) were compared with or without AMF or NFB inoculation.Grass–legume mixtures, especially G1L3, produced significantly higher biomass than monocultures via altering the community structure of soil microorganisms. AMF inoculation increased the availability of nutrients (mainly soil available P (SAP) and/or NO3−–N), which increased plant community productivity due to increased biomass in both grass and legume. Co-occurrence networks revealed that keystone genera (e.g., Arenimonas, Dominikia, Claroideoglomus and Scutellospora) were the primary factors influencing plant community productivity among grass–legume mixtures. Structural equation model showed that GLRs and inoculation types consistently produced overyielding directly and indirectly via affecting SAP and NO3−–N concentrations.Our findings highlight that suitable grass: legume mixture ratios (e.g., 1:3) positively affect productivity, and soil microorganisms that improve soil resource acquisition (SAP and NO3−–N), especially AMF, play an important role in grass: legume mixtures in this process.Results: Arbuscular mycorrhizal fungi (AMF) and nitrogen-fixing bacteria (NFB) can form symbiotic relationships with host plants, and this enhances nutrient uptake and plant performance of host plants. However, how AMF and NFB influence the complementarity and facilitation dynamics between grasses and legumes in grasslands is still not well understood.We conducted a greenhouse experiment to assess effects of different grass: legume ratios (GLRs) and microbial symbionts on plant production comprising two native C3 species from a semiarid steppe in northern China (grass (G): Leymus chinensis; legume (L): Medicago ruthenica). Different GLRs (G4L0: 4:0, G3L1: 3:1, G2L2: 2:2, G1L3: 1:3, G0L4: 0:4) were compared with or without AMF or NFB inoculation.Grass–legume mixtures, especially G1L3, produced significantly higher biomass than monocultures via altering the community structure of soil microorganisms. AMF inoculation increased the availability of nutrients (mainly soil available P (SAP) and/or NO3−–N), which increased plant community productivity due to increased biomass in both grass and legume. Co-occurrence networks revealed that keystone genera (e.g., Arenimonas, Dominikia, Claroideoglomus and Scutellospora) were the primary factors influencing plant community productivity among grass–legume mixtures. Structural equation model showed that GLRs and inoculation types consistently produced overyielding directly and indirectly via affecting SAP and NO3−–N concentrations.Our findings highlight that suitable grass: legume mixture ratios (e.g., 1:3) positively affect productivity, and soil microorganisms that improve soil resource acquisition (SAP and NO3−–N), especially AMF, play an important role in grass: legume mixtures in this process.Conclusion: Arbuscular mycorrhizal fungi (AMF) and nitrogen-fixing bacteria (NFB) can form symbiotic relationships with host plants, and this enhances nutrient uptake and plant performance of host plants. However, how AMF and NFB influence the complementarity and facilitation dynamics between grasses and legumes in grasslands is still not well understood.We conducted a greenhouse experiment to assess effects of different grass: legume ratios (GLRs) and microbial symbionts on plant production comprising two native C3 species from a semiarid steppe in northern China (grass (G): Leymus chinensis; legume (L): Medicago ruthenica). Different GLRs (G4L0: 4:0, G3L1: 3:1, G2L2: 2:2, G1L3: 1:3, G0L4: 0:4) were compared with or without AMF or NFB inoculation.Grass–legume mixtures, especially G1L3, produced significantly higher biomass than monocultures via altering the community structure of soil microorganisms. AMF inoculation increased the availability of nutrients (mainly soil available P (SAP) and/or NO3−–N), which increased plant community productivity due to increased biomass in both grass and legume. Co-occurrence networks revealed that keystone genera (e.g., Arenimonas, Dominikia, Claroideoglomus and Scutellospora) were the primary factors influencing plant community productivity among grass–legume mixtures. Structural equation model showed that GLRs and inoculation types consistently produced overyielding directly and indirectly via affecting SAP and NO3−–N concentrations.Our findings highlight that suitable grass: legume mixture ratios (e.g., 1:3) positively affect productivity, and soil microorganisms that improve soil resource acquisition (SAP and NO3−–N), especially AMF, play an important role in grass: legume mixtures in this process. [ABSTRACT FROM AUTHOR]

Purpose: In cold climates, glyphosate residues may linger in soils, with effects on plant–microbe interactions and, consequently, plant performance. Here, we explore the influence of glyphosate residues on the endophytic microbiota (bacteria and fungi) and performance of the perennial nitrogen-fixing weed Lupinus polyphyllus. Methods: In a common garden, we grew plants from six populations of L. polyphyllus in glyphosate-treated or untreated control soils, with or without additional phosphorus. We sampled plant microbiota (leaves, roots, nodules) and assessed plant performance based on six traits: height, retrogression probability (i.e. shrinkage), biomass, root:shoot ratio, nodule number, and nodule viability. Results: The richness of plant endophytic microbial communities was determined by soil phosphorus level rather than by glyphosate treatment. However, for bacteria, the composition of these communities differed between glyphosate-treated and control soils across plant tissue types; no difference was observed for fungi. The plant bacterial communities in both soil types were dominated by potential nitrogen-fixing bacteria belonging to family Bradyrhizobiaceae, and particularly so in glyphosate-treated soils. Overall, though, these changes in plant bacterial communities had a minor effect on plant performance: the only difference we detected was that the probability of retrogression was occasionally higher in glyphosate-treated soils than in control soils. Conclusion: Our findings indicate that glyphosate-based herbicides, when applied at the recommended frequency and concentration, may not have critical effects on the growth of short-lived weeds after the safety period has passed; however, the endophytic microbiota of such weeds may experience longer-lasting shifts in community structure. [ABSTRACT FROM AUTHOR]

Two strains HN-1T and 39 were isolated from rhizospheres of different plants grown in different regions of PR China. The two strains exhibited high nitrogenase activities and possessed almost identical 16S rRNA gene sequences. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between the two strains were 99.9 and 99.8%, respectively, suggesting that they belong to one species. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strains HN-1T and 39 are the members of the genus Paenibacillus and both strains exhibited 99.5% similarity to Paenibacillus stellifer DSM 14472T and the both strains represented a separate lineage from all other Paenibacillus species. However, the ANI of type strain HN-1T with P. stellifer DSM 14472T was 90.69, which was below the recommended threshold value (< 95–96% ANI). The dDDH showed 42.1% relatedness between strain HN-1T and P. stellifer DSM 14472T, which was lower than the recommended threshold value (dDDH < 70%). The strain HN-1T contain anteiso-C15:0 as major fatty acids and MK-7 as predominant isoprenoid quinone. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, four aminophospholipids and an unidentified glycolipid. Unlike the most closely related P. stellifer DSM 14472T, strain HN-1T or 39 was positive for catalase reaction. Distinct phenotypic and genomic characterisations from previously described taxa support the classification of strains HN-1T or 39 as representatives of a novel species of the genus Paenibacillus, for which the name Paenibacillus sinensis is proposed, with type strains HN-1T (=CGMCC 1.18902, JCM 34,620), and reference strain 39 (=CGMCC 1.18879, JCM 34,616), respectively. [ABSTRACT FROM AUTHOR]

Seagrass ecosystems are among the most productive marine ecosystems, and diazotrophic communities play a crucial role in sustaining the productivity and stability of such ecosystems by introducing fixed nitrogen. However, information concerning both total and active diazotrophic groups existing in different compartments of seagrass is lacking. This study comprehensively investigated the diversity, structure, and abundance of diazotrophic communities in different parts of the seagrass Halophila ovalis at the DNA and RNA level from clone libraries and real-time quantitative PCR. Our results indicated that nearly one-third of existing nitrogen-fixing bacteria were active, and their abundance might be controlled by nitrogen to phosphorus ratio (N:P). Deltaproteobacteria and Gammaproteobacteria were dominant groups among the total and active diazotrophic communities in all samples. These two groups accounted for 82.21% and 70.96% at the DNA and RNA levels, respectively. The genus Pseudomonas and sulfate-reducing bacteria (genera: Desulfosarcina, Desulfobulbus, Desulfocapsa, and Desulfopila) constituted the significant fraction of nitrogen-fixing bacteria in the seagrass ecosystem, playing an additional role in denitrification and sulfate reduction, respectively. Moreover, the abundance of the nitrogenase gene, nifH, was highest in seawater and lowest in rhizosphere sediments from all samples. This study highlighted the role of diazotropic communities in the subtropical seagrass ecosystem. [ABSTRACT FROM AUTHOR]

Pesticide usage is becoming increasingly necessary to escalate agricultural productivity and meet food production needs. However, it harms in different degrees all living organisms, plants, and animals, whether terrestrial or aquatic. Soil microorganisms, are microbes belonging to microorganisms, are the first to be specifically affected by pesticides. This study aims to evaluate the impact of two herbicides, paraquat and glyphosate, on symbiotic nitrogen-fixing bacteria. Our study was carried out in the greenhouse. Bituminaria bituminosa plants were inoculated with four different nitrogen-fixing bacteria, Pantoea agglomerans, Rhizobium nepotum, Rhizobium radiobacter, and Rhizobium tibeticum, and then treated with varying herbicide concentrations were selected according to the doses recommended by the National Office of Food Safety (ONSSA) and according to a survey conducted among farmers in the Meknes region-Morocco, (0.05, 0.1, 5.4, 10.8 g/L glyphosate and 0.05, 0.1, 2, 4 g/L paraquat). After 6 months after sowing, the following parameters were evaluated: nodule number, nodule mass, nodule weight, nodule dry, and fresh weight, nitrogen content, and symbiotic efficiency. At higher doses (5.4, 10.8 g/L for glyphosate and 2, 4 g/L for paraquat), both herbicides decreased the number and the size of nodules, the weight of nodules, nitrogen content of Bituminaria bituminosa and symbiotic efficiency of the four different nitrogen-fixing bacteria studied. The effect of herbicides increased as the used concentration increased. The current research demonstrates that the decreased growth of herbicide-treated plants was caused by herbicides' direct effects on rhizobia rather than herbicides' indirect effects on Bituminaria bituminosa. [ABSTRACT FROM AUTHOR]

Ebinur Lake Wetland is an understudied desert wetland ecosystem, particularly regarding nitrogen cycling. This study aimed to ascertain the diversity and richness of nitrogen-fixing bacterial communities in the Ebinur Lake Wetland. The diversity of the nitrogen-fixing bacteria community of nifH genes from the rhizosphere and non-rhizosphere soils of four plants in different seasons were examined using Illumina HiSeq PE250 high-throughput sequencing technology. The correlation between soil environmental factors and diversity and richness of nitrogen-fixing bacteria was studied using the redundancy analysis (RDA). The results showed that the diversity of nitrogen-fixing bacteria in the rhizosphere soil of the constructive plants was higher than that in the non-rhizosphere soil; also, the diversity in July was higher than that in October and April. Geobacter, Pseudomonas and Bradyrhizobium were the dominant common bacteria in different samples of Ebinur Lake Wetland. The RDA showed that the total nitrogen, available potassium and available phosphoruswere significantly correlated with the diversity and richness of nitrogen-fixing bacteria. The diversity and community structure of nitrogen-fixing bacteria in soil samples also changed over time. The community structures of nitrogen-fixing bacteria in the rhizosphere and non-rhizosphere soils of the four plants were not the same during the same period. The correlation between soil environmental factors and the community structure and abundance of nitrogen-fixing bacteria can provide data basis and theoretical support for the degradation and restoration of Ebinur Lake Wetland. [ABSTRACT FROM AUTHOR]

Seagrass meadows are vital ecosystems with high productivity and biodiversity and often in the oligotrophic area. Nitrogen usually limits productivity in this ecosystem as the main nutrient factor. Biological nitrogen fixation by diazotrophs in the rhizosphere sediment can introduce "new" nitrogen into the ecosystem. Previous studies revealed that most sulfate-reducing bacteria (SRB) can also fix nitrogen like the nitrogen-fixing bacteria (NFB). Moreover, both sulfate reduction and nitrogen fixation were affected by the organic pollutant. However, rare information is available regarding the NFB and SRB community composition and their temporal response to the pollutant. The quantitative real-time polymerase chain reaction and polymerase chain reaction denaturing gradient gel electrophoresis have been used to analyze NFB and SRB communities' shifts under different PAHs concentrations. They both experienced a dramatic shift under PAHs stress but exhibited different patterns. SRB could use the low and high concentration PAHs at the early stage of the incubation, while only the low concentration of PAHs could stimulate the growth of NFB through the whole incubation period. The predominant species of NFB communities were Alphaproteobacteria, Gammaproteobacteria, and Deltaproteobacteria; while for SRB communities were class Epsilonproteobacteria. Redundancy analysis indicated the significant environmental factors for the two communities were both ammonium and pH (P < 0.05). There existed nifH sequences related to known nitrogen fixing SRB Desulfatibacillum alkenivorans, which confirmed that microbial N2 fixation and sulfate reduction were coupled in the seagrass ecosystem by molecular technique. Our investigation provides new insight into the NFB and SRB community in the seagrass meadow. [ABSTRACT FROM AUTHOR]

A nitrogen-fixing isolate of facultatively anaerobic, marine bacterium, designated strain NFV-1T, was recovered from the lagoon sediment of Dongsha Island, Taiwan. It was a Gram-negative rod which exhibited motility with monotrichous flagellation in broth cultures. The strain required NaCl for growth and grew optimally at about 25–35 °C, 3% NaCl and pH 7–8. It grew aerobically and could achieve anaerobic growth by fermenting d-glucose or other carbohydrates as substrates. NH4Cl could serve as a sole nitrogen source for growth aerobically and anaerobically, whereas growth with N2 as the sole nitrogen source was observed only under anaerobic conditions. Cellular fatty acids were predominated by C16:1ω7c, C16:0, and C18:1ω7c. The major polar lipids consisted of phosphatidylethanolamine and phosphatidylserine. Strain NFV-1T had a DNA G + C content of 42.5 mol%, as evaluated according to the chromosomal DNA sequencing data. Analyses of sequence similarities and phylogeny based on the 16S rRNA genes, together with the housekeeping genes, gyrB, ftsZ, mreB, topA and gapA, indicated that the strain formed a distinct species-level lineage in the genus Vibrio of the family Vibrionaceae. These phylogenetic data and those from genomic and phenotypic characterisations support the establishment of a novel Vibrio species, for which the name Vibrio nitrifigilis sp. nov. (type strain NFV-1T = BCRC 81211T = JCM 33628T) is proposed. [ABSTRACT FROM AUTHOR]

Previous studies have shown the sugarcane microbiome harbors diverse plant growth promoting microorganisms, including nitrogen-fixing bacteria (diazotrophs), which can serve as biofertilizers. The genomes of 22 diazotrophs from Colombian sugarcane fields were sequenced to investigate potential biofertilizers. A genome-enabled computational phenotyping approach was developed to prioritize sugarcane associated diazotrophs according to their potential as biofertilizers. This method selects isolates that have potential for nitrogen fixation and other plant growth promoting (PGP) phenotypes while showing low risk for virulence and antibiotic resistance. Intact nitrogenase (nif) genes and operons were found in 18 of the isolates. Isolates also encode phosphate solubilization and siderophore production operons, and other PGP genes. The majority of sugarcane isolates showed uniformly low predicted virulence and antibiotic resistance compared to clinical isolates. Six strains with the highest overall genotype scores were experimentally evaluated for nitrogen fixation, phosphate solubilization, and the production of siderophores, gibberellic acid, and indole acetic acid. Results from the biochemical assays were consistent and validated computational phenotype predictions. A genotypic and phenotypic threshold was observed that separated strains by their potential for PGP versus predicted pathogenicity. Our results indicate that computational phenotyping is a promising tool for the assessment of bacteria detected in agricultural ecosystems. [ABSTRACT FROM AUTHOR]

Spatiotemporal features of anthocyanin accumulation in a model legume Lotus japonicus (Regel) K.Larsen were elucidated to develop criteria for the genetic analysis of flavonoid biosynthesis. Artificial mutants and wild accessions, with lower anthocyanin accumulation in the stem than the standard wild type (B-129 'Gifu'), were obtained by ethyl methanesulfonate (EMS) mutagenesis and from a collection of wild-grown variants, respectively. The loci responsible for the green stem of the mutants were named as VIRIDICAULIS (VIC). Genetic and chemical analysis identified two loci, namely, VIC1 and VIC2, required for the production of both anthocyanins and proanthocyanidins (condensed tannins), and two loci, namely, VIC3 and VIC4, required for the steps specific to anthocyanin biosynthesis. A mutation in VIC5 significantly reduced the anthocyanin accumulation. These mutants will serve as a useful system for examining the effects of anthocyanins and proanthocyanidins on the interactions with herbivorous pests, pathogenic microorganisms and nitrogen-fixing symbiotic bacteria, Mesorhizobium loti. [ABSTRACT FROM AUTHOR]

AZC_2928 gene (GenBank accession no. BAF88926.1) of Azorhizobium caulinodans ORS571 has sequence homology to 2,3-aminomutases. However, its function is unknown. In this study, we are for the first time to knock out the gene completely in A. caulinodans ORS571 using the current advanced genome editing tool, CRISPR/Cas9. Our results show that the editing efficiency is 34% and AZC_2928 plays an extremely important role in regulating the formation of chemotaxis and biofilm. CRISPR/Cas9 knockout of AZC_2928 (△AZC_2928) significantly enhanced chemotaxis and biofilm formation. Both chemotaxis and biofilm formation play an important role in nitrogen-fixing bacteria and their interaction with their host plants. Interestingly, AZC_2928 did not affect the motility of A. caulinodans ORS571 and the nodulation formation in their natural host plant, Sesbania rostrata. Due to rhizobia needing to form bacteroids for symbiotic nitrogen fixation in mature nodules, AZC_2928 might have a direct influence on nitrogen fixation efficiency rather than the number of nodulations. [ABSTRACT FROM AUTHOR]

Saline area may tend to be a productive land; however, many of salt-affected soils have nitrogen limitation and depend on plant-associated diazotrophs as their source of 'new' nitrogen. Herein, a total of 316 salinity tolerant nitrogen-fixing endophytic bacteria were isolated from roots of the halophyte Suaeda sp. sampled from 22 different areas of Iran to prepare the collection of nitrogen-fixing bacterial endophytes and evaluate the plant growth–promoting effect of effective isolates on growth of the halophyte Suaeda maritima. All of the identified nitrogen-fixing endophytes were classified to Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes phylum while we did not detect common nitrogen-fixing endophyte of glycophytes like Azospirillum. The genera Pseudomonas and Microbacterium were both encountered in high abundance in all samples, indicating that they might play an advanced role in the micro-ecosystem of the halophyte Suaeda. In addition, the results also showed that not only soil salinity can affect halophyte endophytic composition but also other factors such as geographical location, plant species, and other soil properties may be involved. Interestingly, only Zhihengliuella halotolerans and Brachybacterium sp. belonging to Actinobacteria could grow in semi-solid N-free (NFb) medium supplemented with 6% NaCl and highly enhanced growth of S. maritima in vitro. Overall, this study offers useful new resources for nitrogen-fixing endophytic bacteria which may be utilized to improve approaches for providing bio-fertilizer useful in saline-based agriculture. [ABSTRACT FROM AUTHOR]

External loading reduction has been implemented to improve water quality in China since the 2000s. To evaluate the effects of nutrient reduction on phytoplankton, long-term monitoring data for Lake Wuli from 1998 to 2017 were analyzed. After the restoration since 2003, nitrogen decreased significantly from 8 to 2 mg/l until 2008 and then remained stable until 2017, while total phosphorus declined progressively from 0.2 mg/l to approximately 0.08 mg/l during 2003 and 2017. Biological data indicated that phytoplankton biovolume decreased after restoration until 2010 and then increased slightly from 2010 to 2017, mainly due to increasing of cyanobacterial biovolume. The dominant taxa shifted from cryptophyta to cyanobacteria since 2009. The results of both nonmetric multidimensional scaling and random forest regression showed that changes in nutrients, especially decreases in nitrogen, were the main drivers for phytoplankton community variation and increasing of cyanobacterial biovolume to the total phytoplankton biovolume ratio in summer and autumn. In addition to nutrients reduction, climatic variables such as wind speed decrease also played vital roles in increasing of cyanobacterial dominance in Lake Wuli. Our study confirmed that phytoplankton community respond strongly to nitrogen reduction in the subtropics and that climate change mediates the response. [ABSTRACT FROM AUTHOR]

The ammonia-secreting performance is one of the key factors for determining nitrogen-fixing capacity of the cell. Klebsiella variicola GN02 is an endophytic nitrogen-fixing bacterium isolated from the roots of mature Pennisetum giganteum z.x.lin. In order to reveal the key factor which influences the ammonia secretion in fermentation process of K. variicola, GC-TOF-MS metabolomics was used. The changes of OD600, ammonia nitrogen content and intracellular metabolites of bacteria were measured simultaneously during fermentation, and a total of 172 intracellular metabolites were detected. Then some methods were used to analysis these high-throughput data. Principal component analysis (PCA) showed that the substances with more contribution to major component exhibited an order as mannitol, glycerol, glucose-1-phosphate, 2‑hydroxypyridine, glutamic acid, fructose-6-phosphate, aniline, lyxose and norleucine. Orthogonal projection to latent structures (OPLS) results revealed that the most important substances for the secretion of ammonia from K. variicola GN02 were mannitol, Gly-Pro, fructose-6-phosphate, and other 12 substances including glycerol, Glu and diacylglycerol having a significant impact with variable importance plot (VIP) values higher than 1, which can be used as the key metabolites for the secretion of ammonia from bacteria. Heatmap clustering analysis showed that mannitol, Gly-Pro and fructose-6-phosphate were strongly expressed at different fermentation stages as the major metabolites. Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis showed that fructose-mannose metabolism and amino acid metabolism are both metabolic pathways with the greatest impact on the secretion of ammonia in bacteria. Mannitol, fructose-6-phosphate and Glu are at the core hub of the metabolic process in bacteria, and Gly-Pro is the major nitrogen-related metabolite synthesized. [ABSTRACT FROM AUTHOR]

Aims: Revealing genetic diversity in a root nodulation symbiosis under field conditions is critical to understand the formation of ecological communities of organisms associated with hosts and the nitrogen cycle in natural ecosystems. However, our knowledge of the genetic diversity of bacterial mutualists on a local scale is still poor because of the assumption that the genetic diversity of mutualistic bacteria is constrained by their hosts. Methods: We thoroughly investigated the genetic diversity of Frankia in a local forest stand. We collected root nodules from 213 Alnus hirsuta seedlings covering the spatial range of the continuous population, which means that Alnus individuals occurred in a relatively homogeneous distribution in a continuous forest. Then, a phylogenetic and diversity analysis was performed for the nifD-K IGS region, including global Frankia sequences from Alnus hosts. Results: The genetic diversity of Frankia detected even on a local scale measured as high as that shown by previous studies conducted on local and regional scales. Moreover, a genetic structure analysis revealed a spatially mosaic-like distribution of genetic variation in Frankia despite the small spatial scale. Conclusions: The genetic diversity and composition of bacterial mutualists are heterogeneous on a local scale. Our findings demonstrate that genetically different bacterial symbionts simultaneously interact with a single host population and interaction partnerships spatially vary. The standing variation could produce dynamic ecological and evolutionary outcomes in a heterogeneous forest ecosystem. [ABSTRACT FROM AUTHOR]

Rhizobia are nitrogen-fixing soil bacteria that can infect legume plants to establish root nodules symbiosis. To do that, a complex exchange of molecular signals occurs between plants and bacteria. Among them, rhizobial Nops (Nodulation outer proteins), secreted by a type III secretion system (T3SS) determine the host-specificity for efficient symbiosis with plant roots. Little is known about the molecular function of secreted Nops (also called effectors (T3E)) and their role in the symbiosis process. We performed the structure-function characterization of NopAA, a T3E from Sinorhizobium fredii by using a combination of X-ray crystallography, biochemical and biophysical approaches. This work displays for the first time a complete structural and biochemical characterization of a symbiotic T3E. Our results showed that NopAA has a catalytic domain with xyloglucanase activity extended by a N-terminal unfolded secretion domain that allows its secretion. We proposed that these original structural properties combined with the specificity of NopAA toward xyloglucan, a key component of root cell wall which is also secreted by roots in the soil, can give NopAA a strategic position to participate in recognition between bacteria and plant roots and to intervene in nodulation process. [ABSTRACT FROM AUTHOR]