Isolation and Identification of Salinity-Tolerant Rhizobia and Nodulation Phenotype Analysis in Different Soybean Germplasms.

Increasing the soybean-planting area and increasing the soybean yield per unit area are two effective solutions to improve the overall soybean yield. Northeast China has a large saline soil area, and if soybeans could be grown there with the help of isolated saline-tolerant rhizobia, the soybean cultivation area in China could be effectively expanded. In this study, soybeans were planted in soils at different latitudes in China, and four strains of rhizobia were isolated and identified from the soybean nodules. According to the latitudes of the soil-sampling sites from high to low, the four isolated strains were identified as HLNEAU1, HLNEAU2, HLNEAU3, and HLNEAU4. In this study, the isolated strains were identified for their resistances, and their acid and saline tolerances and nitrogen fixation capacities were preliminarily identified. Ten representative soybean germplasm resources in Northeast China were inoculated with these four strains, and the compatibilities of these four rhizobium strains with the soybean germplasm resources were analyzed. All four isolates were able to establish different extents of compatibility with 10 soybean resources. Hefeng 50 had good compatibility with the four isolated strains, while Suinong 14 showed the best compatibility with HLNEAU2. The isolated rhizobacteria could successfully establish symbiosis with the soybeans, but host specificity was also present. This study was a preliminary exploration of the use of salinity-tolerant rhizobacteria to help the soybean nitrogen fixation in saline soils in order to increase the soybean acreage, and it provides a valuable theoretical basis for the application of saline-tolerant rhizobia.

Integrated metabolomic and transcriptomic study unveils the gene regulatory mechanisms of sugarcane growth promotion during interaction with an endophytic nitrogen-fixing bacteria.

BACKGROUND: Sugarcane growth and yield are complex biological processes influenced by endophytic nitrogen-fixing bacteria, for which the molecular mechanisms involved are largely unknown. In this study, integrated metabolomic and RNA-seq were conducted to investigate the interaction between an endophytic bacterial strain, Burkholderia GXS16, and sugarcane tissue culture seedlings. RESULTS: During treatment, the colonization of GXS16 in sugarcane roots were determined, along with the enhanced activities of various antioxidant enzymes. Accordingly, 161, 113, and 37 differentially accumulated metabolites (DAMs) were found in the pairwise comparisons of adjacent stages. In addition, transcriptomic analyses obtained 1,371 (IN-vs-CN), 1,457 (KN-vs-IN), and 365 (LN-vs-KN) differentially expressed genes (DEGs), which were mainly involved in the pathways of glutathione metabolism and carbon metabolism. We then assessed the pattern of metabolite accumulation and gene expression in sugarcane during GXS16 colonization. The results showed that both DAMs and DGEs in the upregulated expression profiles were involved in the flavonoid biosynthesis pathway. Overall, p-coumaroyl-CoA in sugarcane roots transferred into homoeriodictyol chalcone and 5-deoxyleucopelargonidin due to the upregulation of the expression of genes shikimate O-hydroxycinnamoyltransferase (HCT), chalcone synthase (CHS), and phlorizin synthase (PGT1). CONCLUSIONS: This study provides insights into the gene regulatory mechanisms involved in the interaction between GXS16 and sugarcane roots, which will facilitate future applications of endophytic nitrogen-fixing bacteria to promote crop growth.

Regulation of an endophytic nitrogen-fixing bacteria GXS16 promoting drought tolerance in sugarcane.

BACKGROUND: Drought limits crop growth and is an important issue in commercial sugarcane (Saccharum officinarum) production. Drought tolerance in sugarcane induced by endophytic nitrogen-fixing bacteria is a complex biological process that ranges from altered gene expression and cellular metabolism to changes in growth and productivity. RESULTS: In this study, changes in physiological features and transcriptome related to drought tolerance in sugarcane conferred by the Burkholderia endophytic nitrogen-fixing bacterial strain GXS16 were investigated. Sugarcane samples inoculated with GXS16 exhibited significantly higher leaf relative water content than those without GXS16 inoculation during the drought stages. Sugarcane treated with GXS16 had lower levels of H2O2 and higher levels of abscisic acid than sugarcane not treated with GXS16 in the non-watering groups. Transcriptomic analysis of sugarcane roots identified multiple differentially expressed genes between adjacent stages under different treatments. Moreover, both trend and weighted correlation network analyses revealed that carotenoid biosynthesis, terpenoid backbone biosynthesis, starch and sucrose metabolism, and plant hormone signal transduction strongly contributed to the drought-tolerant phenotype of sugarcane induced by GXS16 treatment. Accordingly, a gene regulatory network including four differentially regulated genes from carotenoid biosynthesis (crtB, crtZ, ZEP and CYP707A) and three genes from terpenoid backbone biosynthesis (dxs, dxr, and PCME) was constructed. CONCLUSIONS: This study provides insights into the molecular mechanisms underlying the application of GXS16 treatment to enhance drought tolerance in sugarcane, which will lay the foundation for crop development and improve productivity.

Amino Acids in the Root Exudates of Agave lechuguilla Torr. Favor the Recruitment and Enzymatic Activity of Nutrient-Improvement Rhizobacteria.

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.

Bioprospecting and Challenges of Plant Microbiome Research for Sustainable Agriculture, a Review on Soybean Endophytic Bacteria.

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.

Rhizobium mayense sp. Nov., an efficient plant growth-promoting nitrogen-fixing bacteria isolated from rhizosphere soil.

The nitrogen-fixing bacterium has great prospects in replacing synthetic fertilizers with biofertilizers for plant growth. It would be a useful tool in eradicating chemical fertilizers from use. Five nitrogen-fixing bacteria were isolated from the Tea and Groundnut rhizosphere soil out of which RSKVG 02 proved to be the best. The optimized condition of RSKVG 02 was found to be pH 7 at 30 °C utilizing 1% glucose and 0.05% ammonium sulfate as the sole carbon and nitrogen source. Plant growth-promoting traits such as IAA and ammonia were estimated to be 82.97 ± 0.01254a µg/ml and 80.49 ± 0.23699a mg/ml respectively. Additionally, their phosphate and potassium solubilization efficiency were evaluated to be 46.69 ± 0.00125 b mg/ml and 50.29 ± 0.000266 mg/ml. Morphological, and biochemical methods characterized the isolated bacterial culture, and molecularly identified by 16 S rRNA sequencing as Rhizobium mayense. The isolate was further tested for its effects on the growth of Finger millet (Eleusine coracana) and Green gram (Vigna radiata) under pot conditions. The pot study experiments indicated that the bacterial isolates used as bio inoculants increased the total plant growth compared to the control and their dry weight showed similar results. The chlorophyll content of Green gram and Finger millet was estimated to be 19.54 ± 0.2784a mg/L and 15.3 ± 0.0035 mg/L which suggested that Rhizobium sp. Possesses high nitrogenase activity. The enzyme activity proved to use this bacterium as a biofertilizer property to enhance soil fertility, efficient farming, and an alternative chemical fertilizer. Therefore, Rhizobium mayense can be potentially used as an efficient biofertilizer for crop production and increase yield and soil fertility.

Phenotypic, molecular, and symbiotic characterization of the rhizobial symbionts isolated from Acacia saligna grown in different regions in Morocco: a multivariate approach.

The introduced species Acacia saligna is a very promiscuous host as it can be efficiently nodulated with a wide range diversity of rhizobia taxa, including both fast and slow-growing strains. Fourteen nitrogen (N)-fixing bacteria were isolated from root nodules of wild Acacia saligna growing in distinct geographic locations in Morocco and were examined for their symbiotic efficiency and phenotypic properties. Multivariate tools, such as principal component analysis (PCA) and hierarchical clustering analysis (HCA), were used to study the correlation between phenotypic and symbiotic variables and discriminate and describe the similarities between different isolated bacteria with respect to all the phenotypic and symbiotic variables. Phenotypic characterization showed a variable response to extreme temperature, salinity and soil pH. At the plant level, the nodulation, nitrogen fixation, and the shoot and root dry weights were considered. The obtained results show that some of the tested isolates exhibit remarkable tolerances to the studied abiotic stresses while showing significant N2 fixation, indicating their usefulness as effective candidates for the inoculation of acacia trees. The PCA also allowed showing the isolates groups that present a similarity with evaluated phenotypic and symbiotic parameters. The genotypic identification of N2-fixing bacteria, carried out by the 16S rDNA approach, showed a variable genetic diversity among the 14 identified isolates, and their belonging to three different genera, namely Agrobacterium, Phyllobacterium and Rhizobium.

Relationship between nitrifying microorganisms and other microorganisms residing in the maize rhizosphere.

The microbial network of rhizosphere is unique as a result of root exudate. Insights into the relationship that exists with the energy metabolic functional groups will help in biofertilizer production. We hypothesize that there exists a relationship between nitrifying microorganisms and other energy metabolic functional microbial groups in the maize rhizosphere across different growth stages. Nucleospin soil DNA extraction kit was used to extract DNA from soil samples collected from maize rhizosphere. The 16S metagenomics sequencing was carried out on Illumina Miseq. The sequence obtained was analyzed on MG-RAST. Nitrospira genera were the most abundant in the nitrifying community. Nitrifying microorganisms were more than each of the studied functional groups except for nitrogen-fixing bacteria. Also, majority of the microorganisms were noticed at the fruiting stage and there was variation in the microbial structure across different growth stages. The result showed that there exists a substantial amount of both negative and positive correlation within the nitrifying microorganisms, and between them and other energy metabolic functional groups. The knowledge obtained from this study will help improve the growth and development of maize through modification of the rhizosphere microbial community structure.

Paenibacillus caui sp. nov., a nitrogen-fixing species isolated from the rhizosphere soil of a peach tree.

A nitrogen-fixing, endospore-forming, motile, rod-shaped, facultative aerobic bacterium, designated 81-11T, was isolated from rhizosphere soil of a peach tree collected from Handan, Hebei, PR China. From the comparison of 16S rRNA gene sequence, the strain is most closely related to Paenibacillus phoenicis DSM 27463T (96.9 %) and Paenibacillus faecis DSM 23593T (96.7 %). The genome size of strain 81-11T was 4.4 Mb, comprising 4879 predicted genes with a DNA G+C content of 50.0 mol%. The average nucleotide identity values of genome sequences between the novel isolate and the type strains of related species P. phoenicis DSM 27463T and P. faecis DSM 23593T were 71.8 and 72.1 %, respectively. The major cellular fatty acids were anteiso-C15 : 0(47.8 %), iso-C16 : 0 (15.5 %) and iso-C15 : 0 (13.0 %). Menaquinone-7 was the major respiratory quinone. The polar lipids contained phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, aminophospholipid, aminoglycopid, unknown polar lipids and unidentified aminophosphoglycolipid. Based on phylogenetic, genomic and phenotypic characteristics, strain 81-11T was classified as a novel species within the genus Paenibacillus, for which the name Paenibacillus caui sp. nov. is proposed. The type strain of Paenibacillus caui is 81-11T (=JCM 34618T=CGMCC 1.18907T).

Effect of Predation by Colpoda sp. in Nitrogen Fixation Rate of Two Free-Living Bacteria.

Biological nitrogen fixation is limited to several groups of prokaryotes, some of them reduce nitrogen as free-living nitrogen-fixing bacteria. Protozoa predation on these latter releases sequestered nitrogen that may enhance the formation of new bacterial biomass and possibly increase nitrogen fixation within soil microbial communities. We aim to evaluate the predation effect of Colpoda sp. on two nitrogen fixers: Azospirillum lipoferum and Stenotrophomonas sp. during their lag, early exponential, and exponential phases. The kinetics of bacterial population growth was determined in the predators' presence or absence and the effect of predation on the rate of N fixation was evaluated through the reduction of acetylene to ethylene technique. Colpoda sp. showed a non-significant difference in preferences between the two species offered as prey. Consequently, the abundance of A. lipoferum and Stenotrophomonas sp. decreased significantly due to predator's pressure and both species responded by increasing their specific growth rate. Likewise, predation promoted greater nitrogen fixation rate by CFU during the lag phase in A. lipoferum (0.20 nM/CFU with predation vs 0.09 nM/CFU without predation) and Stenotrophomonas sp. (0.22 nM/CFU vs 0.09 nM/CFU respectively). During early exponential phase (29 h), the rate diminished to 0.13 and 0.05 nM/CFU in A. lipoferum and to 0.09 nM/CFU and 0.05 nM/CFU in Stenotrophomonas sp. Finally, during the exponential phase (52 h), only A. lipoferum without predation produced 0.003 nM/CFU of ethylene. Thus, the nitrogenase activity was higher in the lag and the early exponential phases when predator activity was involved.

Vibrio salinus sp. nov., a marine nitrogen-fixing bacterium isolated from the lagoon sediment of an islet inside an atoll in the western Pacific Ocean.

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 C16:1 ω7c, 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.

Paenibacillus sinensis sp. nov., a nitrogen-fixing species isolated from plant rhizospheres.

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.

Medicago-Sinorhizobium-Ralstonia: A Model System to Investigate Pathogen-Triggered Inhibition of Nodulation.

How plants deal with beneficial and pathogenic microorganisms and how they can tolerate beneficial ones and face pathogens at the same time are questions that remain puzzling to plant biologists. Legume plants are good models to explore those issues, as their interactions with nitrogen-fixing bacteria called rhizobia results in a drastic and easy-to-follow phenotype of nodulation. Intriguingly, despite massive and chronic infection, legume defense reactions are essentially suppressed during the whole symbiotic process, raising a question about a potential negative effect of plant immune responses on the establishment of nodulation. In the present study, we used the model legume, Medicago truncatula, coinoculated with mutualistic and phytopathogenic bacteria, Sinorhizobium medicae and Ralstonia solanacearum, respectively. We show that the presence of R. solanacearum drastically inhibits the nodulation process. The type III secretion system of R. solanacearum, which is important for the inhibition of pathogen-associated molecular pattern-triggered immunity (PTI), strongly contributes to inhibit nodulation. Thus, our results question the negative effect of PTI on nodulation. By including a pathogenic bacterium in the interaction system, our study provides a new angle to address the influence of the biotic environment on the nodulation process.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Multiple Mutualism Effects generate synergistic selection and strengthen fitness alignment in the interaction between legumes, rhizobia and mycorrhizal fungi.

Nearly all organisms participate in multiple mutualisms, and complementarity within these complex interactions can result in synergistic fitness effects. However, it remains largely untested how multiple mutualisms impact eco-evolutionary dynamics in interacting species. We tested how multiple microbial mutualists-N-fixing bacteria and mycorrrhizal fungi-affected selection and heritability of traits in their shared host plant (Medicago truncatula), as well as fitness alignment between partners. Our results demonstrate for the first time that multiple mutualisms synergistically affect the selection and heritability of host traits and enhance fitness alignment between mutualists. Specifically, we found interaction with multiple microbial symbionts doubled the strength of natural selection on a plant architectural trait, resulted in 2- to 3-fold higher heritability of plant reproductive success, and more than doubled fitness alignment between N-fixing bacteria and plants. These findings show synergism generated by multiple mutualisms extends to key components of microevolutionary change, emphasising the importance of multiple mutualism effects on evolutionary trajectories.

Diversity of soil nitrogen-fixing bacteria in the rhizosphere and non-rhizophere soils of Ebinur Lake Wetland.

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.

Effect of PAHs on nitrogen-fixing and sulfate-reducing microbial communities in seagrass Enhalus acoroides sediment.

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.

Diversity and abundance of culturable nitrogen-fixing bacteria in the phyllosphere of maize.

AIMS: The present study aimed at gaining an insight into the abundance and genetic diversity of culturable N-fixing epiphyte bacteria on the phyllosphere of maize in arid and semi-arid regions of Iran. METHODS AND RESULTS: Leaf samples of the maize variety, 'single cross 704' (Zea mays L.) were collected from different locations in Iran. The community of culturable N-fixing epiphyte bacteria present was examined by 16S rRNA sequencing, BOXAIR-polymerase chain reaction (PCR) and restricted fragment length polymorphisms analysis of 16S rRNA gene (16S-RFLP). Approximately, 31·82% of the 242 isolates were identified as N-fixers by cultivation of bacteria in Rennie medium and detection of their nifH gene. The N-fixers were affiliated with four bacterial phyla: Firmicutes, Proteobacteria, Actinobacteria and Bacteroidetes. 16S rRNA sequencing detected 16 genera and 24 different species in the identified phyla. The most dominant genus was Bacillus and the species identified were B. pumilus, B. amyloliquefaciens, B. subtilis, B. paralicheniformis, B. licheniformis, B. niabensis and B. megaterium. In total, 22 RFLP groups were present among the isolates originally identified as N-fixing bacteria. BOXAIR-PCR showed that there was a low similarity level among the N-fixing bacteria isolates, and genetic differentiation of individual strains was relatively great. CONCLUSIONS: Our findings suggest that nitrogen-fixing epiphyte bacteria on the phyllosphere of maize may provide significant nitrogen input into arid and semi-arid ecosystem. SIGNIFICANCE AND IMPACT OF THE STUDY: This research implies that phyllosphere epiphyte diazotrophs have much to offer in sustainable agriculture and can be an alternative to chemical N-fertilizers for providing nitrogen to crops arid and semi-arid regions.

Vibrio nitrifigilis sp. nov., a marine nitrogen-fixing bacterium isolated from the lagoon sediment of an islet inside an atoll.

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 C16:1 ω7c, C16:0, and C18:1 ω7c. 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.

Integrated eco-strategies towards sustainable carbon and nitrogen cycling in agriculture.

To meet the ever-growing human demands for food, fuel, and fiber, agricultural activities have dramatically altered the global carbon (C) and nitrogen (N) cycles. These biogeochemical cycles along with water, phosphorus, and sulfur cycles are fundamental features of life on Earth. Human alteration of the global N cycle has had both positive and negative outcomes. To efficiently feed a growing population, crop-livestock production systems have been developed, however, these systems also contribute significantly to environmental pollution and global climate change. Management of agricultural waste (AW) and the application of N fertilizers are central to the issues of greenhouse gas (GHG) emissions and nutrient runoff that contributes to the eutrophication of water bodies. If managed properly, AW can provide nutrients for plants and contribute to the conservation of soil health. In order to achieve the long-term conservation of agricultural production systems, it is important to promote the proper recycling of AW in agroecosystems and to minimize the reliance on chemical N fertilizers. Composting is one of the sustainable and effective approaches for recycling AW in agriculture. However, the conventional composting process is dilatory and produces compost with low N content compared to chemical N fertilizers. For this reason, comprehensive research is required to improve the composting process and the N content of the soil organic amendments. This work aims to explore the beneficial effects of the integrated application of biochar and specific C and N cycling microorganisms to the composting process and the quality of the composted products. In pursuit of replacing chemical N fertilizers with bio/organic fertilizers, we further discussed the power of the combined application of compost, biochar, and N-fixing bacteria in agricultural production systems. The knowledge of smart integration of AW and microorganisms in agriculture could solve the main agricultural and environmental problems associated with human-induced flows of C and N. Building upon the knowledge disseminated in review to further extensive research will pave the way for better management of agricultural production systems and sustainable C and N cycling in agriculture.

Diversity of nitrogen-fixing rhizobacteria associated with sugarcane: a comprehensive study of plant-microbe interactions for growth enhancement in Saccharum spp.

BACKGROUND: Nitrogen is an essential element for sugarcane growth and development and is generally applied in the form of urea often much more than at recommended rates, causing serious soil degradation, particularly soil acidification, as well as groundwater and air pollution. In spite of the importance of nitrogen for plant growth, fewer reports are available to understand the application and biological role of N2 fixing bacteria to improve N2 nutrition in the sugarcane plant. RESULTS: In this study, a total of 350 different bacterial strains were isolated from rhizospheric soil samples of the sugarcane plants. Out of these, 22 isolates were selected based on plant growth promotion traits, biocontrol, and nitrogenase activity. The presence and activity of the nifH gene and the ability of nitrogen-fixation proved that all 22 selected strains have the ability to fix nitrogen. These strains were used to perform 16S rRNA and rpoB genes for their identification. The resulted amplicons were sequenced and phylogenetic analysis was constructed. Among the screened strains for nitrogen fixation, CY5 (Bacillus megaterium) and CA1 (Bacillus mycoides) were the most prominent. These two strains were examined for functional diversity using Biolog phenotyping, which confirmed the consumption of diverse carbon and nitrogen sources and tolerance to low pH and osmotic stress. The inoculated bacterial strains colonized the sugarcane rhizosphere successfully and were mostly located in root and leaf. The expression of the nifH gene in both sugarcane varieties (GT11 and GXB9) inoculated with CY5 and CA1 was confirmed. The gene expression studies showed enhanced expression of genes of various enzymes such as catalase, phenylalanine-ammonia-lyase, superoxide dismutase, chitinase and glucanase in bacterial-inoculated sugarcane plants. CONCLUSION: The results showed that a substantial number of Bacillus isolates have N-fixation and biocontrol property against two sugarcane pathogens Sporisorium scitamineum and Ceratocystis paradoxa. The increased activity of genes controlling free radical metabolism may at least in part accounts for the increased tolerance to pathogens. Nitrogen-fixation was confirmed in sugarcane inoculated with B. megaterium and B. mycoides strains using N-balance and 15N2 isotope dilution in different plant parts of sugarcane. This is the first report of Bacillus mycoides as a nitrogen-fixing rhizobacterium in sugarcane.