Symbiotic ectomycorrhizal tree roots represent an important niche for interaction with bacteria since the fungi colonizing them have a large surface area and receive a direct supply of photosynthetically derived carbon. We examined individual root tips of Pinus sylvestris at defined time points between 5 days and 24 weeks, identified the dominant fungi colonizing each root tip using Sanger sequencing and the bacterial communities colonizing individual root tips by 454 pyrosequencing. Bacterial colonization was extremely dynamic with statistically significant variation in time and increasing species richness until week 16 (3477 operational taxonomic units). Bacterial community structure of roots colonized by Russula sp. 6 GJ-2013b, Piloderma spp., Meliniomyces variabilis and Paxillus involutus differed significantly at weeks 8 and 16 but diversity declined and significant differences were no longer apparent at week 24. The most common genera were Burkholderia, Sphingopyxsis, Dyella, Pseudomonas, Acinetobacter, Actinospica, Aquaspirillum, Acidobacter Gp1, Sphingomonas, Terriglobus, Enhydrobacter, Herbaspirillum and Bradyrhizobium. Many genera had high initial abundance at week 8, declining with time but Dyella and Terriglobus increased in abundance at later time points. In roots colonized by Piloderma spp. several other bacterial genera, such as Actinospica, Bradyrhizobium, Acidobacter Gp1 and Rhizomicrobium appeared to increase in abundance at later sampling points.
Scientists in Brazil and the UK are joining forces to help solve urgent food and energy security issues in South America's most populous country, by establishing a virtual centre that will investigate how to reduce the use of fertilisers and engineer nitrogen fixation - a biological process essential for all forms of life on the planet – in food and energy crops.
The project, led in the UK by the John Innes Centre and including researchers based at the James Hutton Institute in Dundee, will carry out world-class research on biological nitrogen fixation to increase scientific knowledge, with the aim of introducing changes in agricultural practices in Brazil.
Professor Euan James, from the James Hutton Institute’s Ecological Sciences group, said: “Nitrogen is one of the essential building blocks of life as we know it. It amounts to about 79% of the air we breathe, but the vast majority of living organisms cannot access nitrogen directly, so it has to be made available to them, or ‘fixed’, by micro-organisms.
This manual brings together state-of-the-art methods for the study of root-nodule bacteria, both in the free-living state and in symbiosis with legumes.
In each chapter, the manual introduces a topic and provides guidance on how study of the symbiosis might best be tackled.
Detailed descriptions of the protocols that need to be followed, potential problems and pitfalls are provided. Topics covered include acquiring, recognising, growing and storing rhizobia, experimenting with strains in the laboratory, glasshouse and field, and applying contemporary molecular and genetic methodologies to assist in the study of rhizobia.
Serratia species-affiliated DNA sequences have recently been discovered in the root nodules of two chickpea cultivars; however, little is known about their potential influence on chickpea plant growth. All Serratia-affiliated sequences (1136) could be grouped into two clusters at 98 % DNA similarity. The major cluster, represented by 96 % of sequences, was closely associated with Serratia marcescens sequences from GenBank. In the current study, we isolated two Serratia strains, 5D and RTL100, from root nodules of a field-grown Desi cultivar from Faisalabad and Thal areas, respectively. In vitro, strain 5D showed significantly higher phosphate (P) solubilization and lactic acid production than RTL100, whereas a comparable concentration of phytohormone was produced by both isolates. The application of Serratia strain 5D as an inoculum resulted in 25.55 % and 30.85 % increases in the grain yield of crops grown on fertile soil in irrigated areas and nutrient-deficient soil in rainfed areas, respectively, compared to the non-inoculated control. Results of plant inoculations indicated that Serratia sp. 5D and RTL100 can serve as effective microbial inoculants, particularly in nutrient-deficient soils in rainfed areas, where chickpea is the only major crop grown during the entire year.
It is important to study the response of plant pathogens to the antibiosis traits of biocontrol microbes to design the efficient biocontrol strategies. In this study, we evaluated the role of volatile organic compounds (VOCs) produced by a biocontrol strain Bacillus amyloliquefaciens SQR-9 on the growth and virulence traits of tomato wilt pathogen Ralstonia solanacearum (RS). The VOCs of SQR-9 significantly inhibited the growth of RS on agar medium and in soil. In addition, the VOCs significantly inhibited the motility traits, production of antioxidant enzymes and exopolysaccharides, biofilm formation and tomato root colonization by RS. The strain SQR-9 produced 22 VOCs, but only nine VOCs showed 1–11% antibacterial activity against RS in their corresponding amounts; however, the consortium of all VOCs showed 70% growth inhibition of RS. The proteomics analysis showed that the VOCs of SQR-9 downregulated RS proteins related to the antioxidant activity, virulence, carbohydrate and amino acid metabolism, protein folding and translation, while the proteins involved in the ABC transporter system, amino acid synthesis, detoxification of aldehydes and ketones, methylation, protein translation and folding, and energy transfer were upregulated. This study describes the significance and effectiveness of VOCs produced by a biocontrol strain against tomato wilt pathogen.
Nitrogen is one of the most paradoxical elements in the periodic table. Flames are extinguished and animals die in an atmosphere of pure nitrogen - so it was once known as "azote", Greek for "lifeless". And yet this colourless, odourless gas, making up 78% of the atmosphere, has a highly explosive nature.
Scientists at the University of California, Riverside have discovered that a strain of beneficial nitrogen-fixing bacteria has spread across California, demonstrating that beneficial bacteria can share some of the same features that are characteristic of pathogens.
The bacteria, called Bradyrhizobium, form tumor-like nodules on the roots of plants and are able to 'fix' nitrogen by breaking it down and rendering it into forms that plants can easily metabolize. "Bacterial epidemics are commonplace, but except for notable pathogens we rarely understand what drives bacteria to spread among populations," said Joel Sachs, an associate professor of biology, who led the research effort. "Why some strains spread epidemically while others do not is not well understood." Sachs and his team gathered genetic data from more than 350 bacterial nodules that were cultured from host plants across California. The host plant the researchers focused on was Acmispon strigosus, a common herb native to the southwestern United States that exhibits a near continuous range across California.
Previously, 159 bacterial strains were isolated from the root nodules of wild perennial Glycyrrhiza legume species grown on 40 sites in central and north-western China, in which 57 strains were classified as “true symbionts” belonging to the genus Mesorhizobium based on amplified fragment length polymorphism (AFLP) genomic fingerprinting and partial sequences of the 16S rRNA gene . In the present work, the phylogeny of Glycyrrhiza nodulating mesorhizobia was further examined by multilocus sequence analysis (MLSA). The concatenated gene tree of three housekeeping genes (16S rRNA, recA, and rpoB) of 59 strains including the 29 mesorhizobial test strains and 30 type mesorhizobial species, was constructed applying the maximum likelihood method and Bayesian inference. In the concatenated gene tree, the 29 test strains were distributed in seven separate clades. Seventeen test strains clustered with Mesorhizobium tianshanense, Mesorhizobium temperatum, Mesorhizobium muleiense, and Mesorhizobium alhagi with high bootstrap support (BS > 85%). Eight test strains did not cluster with any of the described Mesorhizobium species. Based on the results, we proposed these eight test strains might belong to a putative new species of the genus Mesorhizobium. The sequences of three accessory genes (nodA, nodC, and nifH) of the test strains were also analyzed and were compared with those of representatives of the 30 described mesorhizobial species. The results showed that mesorhizobia involved in symbiosis with Glycyrrhiza plants probably have acquired some genetic material from other rhizobia in co-evolution with Glycyrrhiza and other legume species.
We have a number of collaborations we’ve done in the biologicals space such as with Marrone Biosciences. In 2011, Syngenta agreed to exclusively distribute biofungicide, Regalia, which has had an impact in the European market. Clariva Complete Beans seed treatment has had an impact for soybeans in the US and was a result of our acquisition of Pasteuria Bioscience. We have other examples in the biological space but I think that it’s an area where, at least for the US farmer, they’re looking for efficacy and performance, and they may not be thinking about it in terms of using a biological. US farmers are looking for performance and control, and it’s an added benefit when a biological can actually provide that level of performance and control and with low impact on the environment.
As you start to get into specialty crops like fruit and vegetables, that mindset begins to shift because managing chemical residues is extremely important. But farmers are still going to measure biologicals on their performance and ROI, from what I see in the US market.
Currently, most biologicals are being used in integrated pest management programs in rotation with synthetic chemical products or combination. The good news is that there is a focus in the industry to continue to advance the performance of bio-compounds and realization that investment in improving performance will be a big benefit to the grower in the end.
Conservation agriculture is a sustainable alternative to conventional agriculture. However, little is known about their effect on the environment and on the soil microbial community. It was established as a hypothesis that the bacterial community structure would be defined by the different agronomic practices. The objective of this study was, therefore, to investigate how crop residue management, tillage and fertilizer application affected the bacterial community and those groups involved in the degradation of applied plant residues, and increase the knowledge to predict the sustainability of a soil under a specific agronomic practice. Samples from an arable soil from the state of Sonora (México), i.e. Hyposodic Vertisol (Calcaric, Chromic) (IUSS Working Group, 2007), cultivated with wheat (Triticum spp.) and maize (Zea mays L.) in succession on conventionally tilled beds (CTB) with crop residue incorporated, permanent beds (PB) with residue burned or retained, left unfertilized or fertilized (300 kg N ha−1 for wheat and 103 kg N ha−1 for maize) was improved with dried young wheat plants to stimulate microbial growth, while the bacterial community structure and C and N mineralization were monitored in an aerobic incubation of 56 days. The soil organic C was significantly higher in the PB-residue retained treatments (average 13.1 g kg−1 dry soil) compared with PB-residue burned (average 9.9 g kg−1 dry soil) or CTB-residue incorporated (average 10.5 g kg−1 dry soil), while pH and EC were significantly higher in the PB-residue burned (averages 8.85 and 1.06 dS m−1) compared with the fertilized or unfertilized soil in PB-residue retained (averages 8.65 and 0.78 dS m−1) or CTB-residue incorporated (averages 8.75 and 0.95 dS m−1). In the unimproved soil, we found a significant effect of soil organic C, application of N fertilizer (highly significant on Nitrosovibrio) and tillage-residue management (principally in fertilized soil) on the bacterial community structure, but not in the improved soil. Treatment had no significant effect on the decomposition of the applied organic material, and on average 48% and 9.4% of the applied C and N, respectively, were mineralized in 56 days. Improvement of soil with wheat plant material increased mainly the relative abundance of Actinobacteria and Firmicutes and decreased a wide range of bacterial groups. On the bacterial level of genus, tillage-residue management was the most important defining factor of the bacterial community inducing differences in the genera involved in the degradation of applied plant material, i.e. Promicromonospora, Bacillus, Agromyces, Streptomyces, Sinorhizobium and Lysobacter, in different treatments. It was found that nitrogen fertilization and tillage-crop residue management defined the soil bacterial community structure in the unimproved soil, but were less determinant in improved soil, and these results supported the hypothesis tested. It was concluded that all the factors tested, i.e. tillage, crop-residue management and fertilizer application, affect the soil bacterial community structure, while the mineralization potential of the soil was preserved. This study contributes to our understanding of how soil use and management practices define the soil bacterial community structure.
Ornamental plants play an important role in human society since flowers are considered a vital component due to their beauty, texture, color, shape and fragrance. To produce high quality ornamentals, growers in general have intensified the use of agrochemicals without considering their deleterious impact on floral attributes. Also, the agrochemicals (including fertilizers and pesticides) used in floriculture are expensive and their excessive application results in emergence of pathogens resistant to such chemicals. It has, therefore, become imperative to develop renewable, inexpensive and eco-friendly fertilizers without producing any disturbing impact on quality of ornamentals. In this regard, phosphate solubilizing microorganisms (PSM) among plant growth promoting rhizobacteria have been identified as an efficient alternative to agrochemicals in floriculture. Even though, there are adequate reports on the effect of PSM on growth and development of numerous plants, information on the impact of PSM on production and quality of ornamental plants is, however, critically scarce. Considering these gaps and success of PSM application in floriculture achieved so far, efforts have been directed to highlight the impact of PSM on the production of ornamentals grown distinctively in different production systems. Also, the role of PSM in the management of ornamental diseases is discussed and considered. The review will conclude by identifying several PSM for future researches aiming to improve the health and quality of ornamentals grown in different production systems. Use of PSM is also likely to reduce the use of chemicals in floriculture.
The 78th volume of this series features in-depth and up-to-date reviews by recognized experts on a range of topics related to the genomes and evolution of charophytes, bryophytes, lycophytes, and ferns, discussing how the sequencing of genomes of various species in both the animal and plant kingdoms has greatly informed our understanding of evolution.
Soil harbors several beneficial microorganisms and some of them colonize in the rhizospheric zone and enhance plant growth. Such bacteria are generally designated as PGPR (Plant Growth-Promoting Rhizobacteria). Plant growth-promoting rhizobacteria (PGPR) was first defined by Kloepper and Schrot to describe soil bacteria that colonize the roots of plants following inoculation onto seed and that enhance plant growth.
Marama bean (Tylosema esculentum) is an indigenous non-nodulating legume to the arid agro-ecological parts of Southern Africa. It is a staple food for the Khoisan and Bantu people from these areas. It is intriguing how it is able to synthesize the high protein content in the seeds since its natural habitat is nitrogen-deficient. The aim of the study was to determine the presence of seed-transmittable bacterial endophytes that may have growth promoting effects, which may be particularly important for the harsh conditions. Marama bean seeds were surface sterilized and gnotobiotically grown to 2 weeks old seedlings. From surface-sterilized shoots and roots, 123 distinct bacterial isolates were cultured using three media, and identified by BOX-PCR fingerprinting and sequence analyses of the 16S rRNA and nifH genes. Phylogenetic analyses of 73 putative endophytes assigned them to bacterial species from 14 genera including Proteobacteria (Rhizobium, Massilia, Kosakonia, Pseudorhodoferax, Caulobacter, Pantoea, Sphingomonas, Burkholderia, Methylobacterium), Firmicutes (Bacillus), Actinobacteria (Curtobacterium, Microbacterium) and Bacteroidetes (Mucilaginibacter, Chitinophaga). Screening for plant growth-promoting activities revealed that the isolates showed production of IAA, ACC deaminase, siderophores, endoglucanase, protease, AHLs, and capacities to solubilize phosphate and fix nitrogen. This is the first report that marama bean seeds may harbor endophytes that can be cultivated from seedlings; in this community of bacteria, physiological characteristics that are potentially plant growth promoting are widespread.
One group of bacteria, rhizobia, are soil-dwelling and underappreciated powerhouses of agricultural productivity. These bacteria form a specialized relationship with leguminous plants (soybean, bean, lentils, peanuts, etc.) in which they supply nitrogen, a globally limiting resource, in exchange for carbon. When undisturbed, this interaction naturally increases soil nitrogen content. Agricultural soils are frequently nitrogen limited which causes farmers to deposit approximately 80 million tons of nitrogen fertilizers on agricultural fields each year! This practice has resulted in increased crop yields at the expense of the environment. Toxic algal blooms pollute water sources, microbial communities have been destroyed, fossil fuels are burned to produce the fertilizers, and gaseous nitrogen compounds are released into the atmosphere as consequences of modern fertilizer production and use. Fortunately, the relationship between legumes and rhizobia offers an opportunity to offset the excessive use of fertilizers and begin shifting away from these environmentally detrimental practices.
Rhizobium leguminosarum bv trifolii is the effective nitrogen fixing microsymbiont of a diverse range of annual and perennial Trifolium (clover) species. Strain WSM2304 is an aerobic, motile, non-spore forming, Gram-negative rod, isolated from Trifolium polymorphum in Uruguay in 1998. This microsymbiont predominated in the perennial grasslands of Glencoe Research Station, in Uruguay, to competitively nodulate its host, and fix atmospheric nitrogen. Here we describe the basic features of WSM2304, together with the complete genome sequence, and annotation. This is the first completed genome sequence for a nitrogen fixing microsymbiont of a clover species from the American center of origin. We reveal that its genome size is 6,872,702 bp encoding 6,643 protein-coding genes and 62 RNA only encoding genes. This multipartite genome was found to contain 5 distinct replicons; a chromosome of size 4,537,948 bp and four circular plasmids of size 1,266,105 bp, 501,946 bp, 308,747 bp and 257,956 bp.
In Sinorhizobium meliloti, the nodG gene is located in the nodFEG operon of the symbiotic plasmid. Although strong sequence similarity (53% amino acid identities) between S. meliloti NodG and Escherichia coli FabG was reported in 1992, it has not been determined whether S. meliloti NodG plays a role in fatty acid synthesis. We report that expression of S. meliloti NodG restores the growth of the E. coli fabG temperature-sensitive mutant CL104 under nonpermissive conditions. Using in vitro assays, we demonstrated that NodG is able to catalyze the reduction of the 3-oxoacyl-ACP intermediates in E. coli fatty acid synthetic reaction. Moreover, although deletion of the S. meliloti nodG gene does not cause any growth defects, upon overexpression of nodG from a plasmid, the S. meliloti fabG gene encoding the canonical 3-oxoacyl-ACP reductase (OAR) can be disrupted without any effects on growth or fatty acid composition. This indicates that S. meliloti nodG encodes an OAR and can play a role in fatty acid synthesis when expressed at sufficiently high levels. Thus, a bacterium can simultaneously possess two or more OARs that can play a role in fatty acid synthesis. Our data also showed that, although SmnodG increases alfalfa nodulation efficiency, it is not essential for alfalfa nodulation.
Root nodule-forming rhizobia exhibit a bipartite lifestyle, replicating in soil and also within plant cells where they fix nitrogen for legume hosts. Host control models posit that legume hosts act as a predominant selective force on rhizobia, but few studies have examined rhizobial fitness in natural populations. Here, we genotyped and phenotyped Bradyrhizobium isolates across more than 800 km of the native Acmispon strigosus host range. We sequenced chromosomal genes expressed under free-living conditions and accessory symbiosis loci expressed in planta and encoded on an integrated ‘symbiosis island’ (SI). We uncovered a massive clonal expansion restricted to the Bradyrhizobium chromosome, with a single chromosomal haplotype dominating populations, ranging more than 700 km, and acquiring 42 divergent SI haplotypes, none of which were spatially widespread. For focal genotypes, we quantified utilization of 190 sole-carbon sources relevant to soil fitness. Chromosomal haplotypes that were both widespread and dominant exhibited superior growth on diverse carbon sources, whereas these patterns were not mirrored among SI haplotypes. Abundance, spatial range and catabolic superiority of chromosomal, but not symbiosis genotypes suggests that fitness in the soil environment, rather than symbiosis with hosts, might be the key driver of Bradyrhizobium dominance.
This work expects to supplement information on soil biological processes, particularly for fruit production systems in a semiarid region, by comparing soil microbial diversity and density, and nutrient concentration in soil as well as plant tissues in organic and conventional production systems for different varieties of apple and peach. Organic and conventional practices were compared by taking soil samples and analyzing soil microbial populations and plant and soil nutrients using several laboratory procedures. Significantly higher active and total fungal biomass, flagellate, and Actinobacteria populations and plant nutrients, P and Cu in plant tissues and OM, P, and S in soils were observed in organic compared to the conventional practices, irrespective of crops and varieties. In peach, protozoa and nematode populations were significantly higher in organic than in conventional soils, but not in apple. Organic fruit production practices harbored both greater microbial activity and higher concentrations of some plant and soil nutrients and are anticipated to promote better soil health and productivity than conventional practices. However, introduction and/or enhancement of certain microbes, especially mycorrhizae in both production systems, expected to increase soil health and productivity, are suggested. Use of ranges of microbial population to estimate soil health and management strategy is proposed.
Soybean cyst nematode Heterodera glycines is one of the most serious soil-borne pathogens in soybean production. However, the researches were limited in China due to lack of an effective pathosystem. In this study, we screened 21 legume Medicago plants in both Medicago truncatula and Medicago sativa to obtain candidate model plants for establishing a new pathosystem for legume-H. glycines interactions. The nematode infection of tested plants was assayed with Race 3 and 4 respectively, which were two dominant H. glycines inbred races in China soybean producing areas. The results showed that the model legume plant M. truncatula A17 failed to allow Race 3 of H. glycines to complete its life cycle, in contrast, it provided the Race 4 population to form several cyst nematodes, however, the female index (FI) value was approximately 1.6. Three M. sativa cultivars, including Xunlu, Aergangjin and Junren, provided either Race 3 or 4 of H. glycines to develop into mature cysts with their FI value below 5 as well. Our results demonstrated that legume plants in both M. truncatula and M. sativa were not likely to be a model plant for H. glycines because of an extreme high resistance.
Soybean has the unique ability to form a symbiotic relationship with a soil bacterium, Bradyrhizobium japonicum. This relationship results in biological nitrogen fixation, a process in which atmospheric nitrogen (N) is converted to plant-available N in exchange for photosynthetically derived carbon. Because of this symbiotic relationship, soybean growers typically do not apply N fertil- izer, but will apply inoculants containing B. japonicum on or near the seed to ensure that adequate bacterial infection and subsequent biological nitrogen fixation can occur (Schulz and Thelen, 2008). Current university recommenda- tions suggest using inoculants when planting in fields with no previous history of soybean, where soybean has not been planted in the last 3 to 5 years, for soils with pH <6.0, and for sandy texture soils (i.e., low organic matter soils) (Pedersen, 2004; Abendroth et al., 2006). Although much work has examined soybean yield response to inoculant use in fields with or without a previous history of soybean, there is a general lack of information examining inoculant use under different crop rotations and tillage systems. Our objective was to measure soybean yield response to seed-applied inoculants as influenced by crop rotation and tillage system.
Field trials were conducted from 2009 through 2011 within a long-term corn- soybean rotation study established in 1983 near Arlington, WI. This study contains two tillage systems: conventional and no-till. Conventional tillage was accomplished with one pass of a chisel plow in the fall and two passes with a field cultivator in the spring before planting. Within each tillage system, there are seven crop rotations containing soybean: continuous soybean (SS); soybean rotated annually with corn (SC); first-year soybean after 5 consecutive years of corn (1S); and two (2S), three (3S), four (4S), and 5 years (5S) of con- tinuous soybean after 5 years of corn. Finally, within each crop rotation, there were three seed-applied rhizobia inoculant treatments: a non-treated control; Optimize Soybean (contains B. japonicum); and Excalibre (contains B. japoni- cum and B. elkanii). To view the results of the study and read the full article, please follow the link below:
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