Showing papers on "Nitrogen fixation published in 2019"
TL;DR: It is suggested that biological carbon export in the ocean is higher than expected and that stabilizing nitrogen-cycle feedbacks are weaker than previously thought, and a role for top-down zooplankton grazing control is proposed in shaping the global patterns of nitrogen fixation.
Abstract: Uncertainty in the global patterns of marine nitrogen fixation limits our understanding of the response of the ocean’s nitrogen and carbon cycles to environmental change. The geographical distribution of and ecological controls on nitrogen fixation are difficult to constrain with limited in situ measurements. Here we present convergent estimates of nitrogen fixation from an inverse biogeochemical and a prognostic ocean model. Our results demonstrate strong spatial variability in the nitrogen-to-phosphorus ratio of exported organic matter that greatly increases the global nitrogen-fixation rate (because phytoplankton manage with less phosphorus when it is in short supply). We find that the input of newly fixed nitrogen from microbial fixation and external inputs (atmospheric deposition and river fluxes) accounts for up to 50 per cent of carbon export in subtropical gyres. We also find that nitrogen fixation and denitrification are spatially decoupled but that nevertheless nitrogen sources and sinks appear to be balanced over the past few decades. Moreover, we propose a role for top-down zooplankton grazing control in shaping the global patterns of nitrogen fixation. Our findings suggest that biological carbon export in the ocean is higher than expected and that stabilizing nitrogen-cycle feedbacks are weaker than previously thought. Convergent estimates of nitrogen fixation from an inverse biogeochemical and a prognostic ocean model show that biological carbon export in the ocean is higher than expected and that stabilizing nitrogen-cycle feedbacks are weaker than we thought.
183 citations
TL;DR: It is found that N fixation was drastically reduced after almost four decades of fertilization, and functionality losses were associated with reductions in the relative abundance of keystone and phylogenetically clustered N fixers such as Geobacter spp.
Abstract: N fixation is one of the most important microbially driven ecosystem processes on Earth, allowing N to enter the soil from the atmosphere, and regulating plant productivity. A question that remains to be answered is whether such a fundamental process would still be that important in an over-fertilized world, as the long-term effects of fertilization on N fixation and associated diazotrophic communities remain to be tested. Here, we used a 35-year fertilization experiment, and investigated the changes in N fixation rates and the diazotrophic community in response to long-term inorganic and organic fertilization. It was found that N fixation was drastically reduced (dropped by 50%) after almost four decades of fertilization. Our results further indicated that functionality losses were associated with reductions in the relative abundance of keystone and phylogenetically clustered N fixers such as Geobacter spp. Our work suggests that long-term fertilization might have selected against N fixation and specific groups of N fixers. Our study provides solid evidence that N fixation and certain groups of diazotrophic taxa will be largely suppressed in a more and more fertilized world, with implications for soil biodiversity and ecosystem functions.
182 citations
TL;DR: A generalized nitrogen budget for a C3 leaf cell is provided and the potential for improving photosynthesis from a nitrogen perspective is discussed.
Abstract: Global food security depends on three main cereal crops (wheat, rice and maize) achieving and maintaining high yields, as well as increasing their future yields. Fundamental to the production of this biomass is photosynthesis. The process of photosynthesis involves a large number of proteins that together account for the majority of the nitrogen in leaves. As large amounts of nitrogen are removed in the harvested grain, this needs to be replaced either from synthetic fertilizer or biological nitrogen fixation. Knowledge about photosynthetic properties of leaves in natural ecosystems is also important, particularly when we consider the potential impacts of climate change. While the relationship between nitrogen and photosynthetic capacity of a leaf differs between species, leaf nitrogen content provides a useful way to incorporate photosynthesis into models of ecosystems and the terrestrial biosphere. This review provides a generalized nitrogen budget for a C3 leaf cell and discusses the potential for improving photosynthesis from a nitrogen perspective.
182 citations
TL;DR: A mechanistic overview of FLNF is provided, including how various controls may influence FLNF in the rhizosphere in comparison with symbiotic N fixation occurring in plant nodules where environmental conditions are moderated by the plant.
Abstract: Free-living nitrogen fixation (FLNF) in the rhizosphere, or N fixation by heterotrophic bacteria living on/near root surfaces, is ubiquitous and a significant source of N in some terrestrial systems. FLNF is also of interest in crop production as an alternative to chemical fertilizer, potentially reducing production costs and ameliorating negative environmental impacts of fertilizer N additions. Despite this interest, a mechanistic understanding of controls (e.g., carbon, oxygen, nitrogen, and nutrient availability) on FLNF in the rhizosphere is lacking but necessary. FLNF is distinct from and occurs under more diverse and dynamic conditions than symbiotic N fixation; therefore, predicting FLNF rates and understanding controls on FLNF has proven difficult. This has led to large gaps in our understanding of FLNF, and studies aimed at identifying controls on FLNF are needed. Here, we provide a mechanistic overview of FLNF, including how various controls may influence FLNF in the rhizosphere in comparison with symbiotic N fixation occurring in plant nodules where environmental conditions are moderated by the plant. We apply this knowledge to a real-world example, the bioenergy crop switchgrass (Panicum virgatum), to provide context of how FLNF may function in a managed system. We also highlight future challenges to assessing FLNF and understanding how FLNF functions in the environment and significantly contributes to plant N availability and productivity.
107 citations
TL;DR: How genetic approaches in rhizobia and their legume hosts allowed tremendous progress in understanding the molecular mechanisms controlling root nodule symbioses is surveyed and how this knowledge paves the way for engineering such associations in non-legume crops.
Abstract: Nitrogen is an essential element of life, and nitrogen availability often limits crop yields. Since the Green Revolution, massive amounts of synthetic nitrogen fertilizers have been produced from atmospheric nitrogen and natural gas, threatening the sustainability of global food production and degrading the environment. There is a need for alternative means of bringing nitrogen to crops, and taking greater advantage of biological nitrogen fixation seems a logical option. Legumes are used in most cropping systems around the world because of the nitrogen-fixing symbiosis with rhizobia. However, the world's three major cereal crops—rice, wheat, and maize—do not associate with rhizobia. In this review, we will survey how genetic approaches in rhizobia and their legume hosts allowed tremendous progress in understanding the molecular mechanisms controlling root nodule symbioses, and how this knowledge paves the way for engineering such associations in non-legume crops. We will also discuss challenges in bringing these systems into the field and how they can be surmounted by interdisciplinary collaborations between synthetic biologists, microbiologists, plant biologists, breeders, agronomists, and policymakers.
101 citations
TL;DR: This review summarizes many of the research strategies that have been employed in the study of rhizobia and the unique knowledge gained from these diverse tools, with a focus on genome- and systems-level approaches.
Abstract: The rhizobium–legume symbiosis is a major source of fixed nitrogen (ammonia) in the biosphere. The potential for this process to increase agricultural yield while reducing the reliance on nitrogen-...
81 citations
TL;DR: The application of cyanobacteria in salt-affected soil remediation will reconstruct green agriculture and promote the sustainable development of human society.
77 citations
TL;DR: Bradyrhizobium japonicum SAY3-7 plus Bradyrh Izobium elkanii BLY3-8 and Streptomyces griseoflavus are effective bacteria that can be used together as biofertilizer for the production of economically important leguminous crops, especially soybean and mung bean.
Abstract: The use of biofertilizers is important for sustainable agriculture, and the use of nodule bacteria and endophytic actinomycetes is an attractive way to enhance plant growth and yield. This study tested the effects of a biofertilizer produced from Bradyrhizobium strains and Streptomyces griseoflavus on leguminous, cereal, and vegetable crops. Nitrogen fixation was measured using the acetylene reduction assay. Under N-limited or N-supplemented conditions, the biofertilizer significantly promoted the shoot and root growth of mung bean, cowpea, and soybean compared with the control. Therefore, the biofertilizer used in this study was effective in mung bean, cowpea, and soybean regardless of N application. In this study, significant increments in plant growth, nodulation, nitrogen fixation, nitrogen, phosphorus, and potassium (NPK) uptake, and seed yield were found in mung beans and soybeans. Therefore, Bradyrhizobium japonicum SAY3-7 plus Bradyrhizobium elkanii BLY3-8 and Streptomyces griseoflavus are effective bacteria that can be used together as biofertilizer for the production of economically important leguminous crops, especially soybean and mung bean. The biofertilizer produced from Bradyrhizobium and S. griseoflavus P4 will be useful for both soybean and mung bean production.
75 citations
TL;DR: Assessment of experiments that assessed how endophytic Pseudomonas stutzeri A1501 inoculated on maize improved plant growth and plant nitrogen content using a 15N dilution technique under two water regime conditions revealed that soil compartment and A 1501 inoculation treatments were the main factors affecting the distribution of the diazotrophic community.
73 citations
TL;DR: How the current knowledge of nitrogen metabolism and BNF regulation may allow strategies for genetic manipulation of diazotrophs for ammonia excretion and provide a contribution towards solving the nitrogen crisis is explored.
Abstract: Biological nitrogen fixation (BNF) is controlled by intricate regulatory mechanisms to ensure that fixed nitrogen is readily assimilated into biomass and not released to the environment. Understanding the complex regulatory circuits that couple nitrogen fixation to ammonium assimilation is a prerequisite for engineering diazotrophic strains that can potentially supply fixed nitrogen to non-legume crops. In this review, we explore how the current knowledge of nitrogen metabolism and BNF regulation may allow strategies for genetic manipulation of diazotrophs for ammonia excretion and provide a contribution towards solving the nitrogen crisis.
66 citations
TL;DR: The mechanisms of assimilation of ammonium, nitrate, urea and N2 , the latter involving heterocyst differentiation, are summarized and aspects of CO2 assimilation that involves a carbon concentration mechanism are described.
Abstract: Heterocyst-forming cyanobacteria are filamentous organisms that perform oxygenic photosynthesis and CO2 fixation in vegetative cells and nitrogen fixation in heterocysts, which are formed under deprivation of combined nitrogen. These organisms can acclimate to use different sources of nitrogen and respond to different levels of CO2 . Following work mainly done with the best studied heterocyst-forming cyanobacterium, Anabaena, here we summarize the mechanisms of assimilation of ammonium, nitrate, urea and N2 , the latter involving heterocyst differentiation, and describe aspects of CO2 assimilation that involves a carbon concentration mechanism. These processes are subjected to regulation establishing a hierarchy in the assimilation of nitrogen sources -with preference for the most reduced nitrogen forms- and a dependence on sufficient carbon. This regulation largely takes place at the level of gene expression and is exerted by a variety of transcription factors, including global and pathway-specific transcriptional regulators. NtcA is a CRP-family protein that adjusts global gene expression in response to the C-to-N balance in the cells, and PacR is a LysR-family transcriptional regulator (LTTR) that extensively acclimates the cells to oxygenic phototrophy. A cyanobacterial-specific transcription factor, HetR, is involved in heterocyst differentiation, and other LTTR factors are specifically involved in nitrate and CO2 assimilation.
TL;DR: In this article, the abundance, activity, and structure of symbiotic and asymbiotic diazotrophs under different nitrogen fertilizer applications in paddy soil were investigated.
Abstract: Biological nitrogen fixation (BNF) plays an important role in nitrogen cycling by transferring atmospheric dinitrogen to the soil. BNF is performed by symbiotic and asymbiotic nitrogen-fixing microorganisms. However, the abundance, activity, and community structure of diazotrophs under different nitrogen fertilizer application rates and how root exudates influence diazotrophs remain unclear. 15N-N2 and 13C-CO2 labeling, DNA-based stable isotope probing (SIP), and molecular biological techniques were used in this study. The abundance, activity, and structure of symbiotic and asymbiotic diazotrophs under different nitrogen fertilizer applications in paddy soil were investigated. We found that the nitrogen fixation capacity in milk vetch (Astragalus sinicus L.) and nifH gene abundance in the root nodules were significantly higher in the low-nitrogen treatment than in the control (zero) and high-nitrogen treatments. Nitrogen-fixing bacteria were abundant in the soils with a high biodiversity. Soil nifH gene sequences were dominated by α-, β-, and δ-proteobacteria, as well as by Cyanobacteria. The relative abundance of α-proteobacteria was lower, and the relative abundance of Cyanobacteria was higher under high nitrogen. Incubation of soil with 13CO2 and subsequent DNA-SIP analysis demonstrated that OTU65 from α-proteobacteria was relatively more abundant in heavy fractions of the 13C-labeled soils than that in the unlabeled soils, indicating that α-proteobacteria may prefer rhizodeposition carbon to other organic carbon. However, OTU24 and OTU73 from δ-proteobacteria had relatively high abundances in light fractions both in the 13C-labeled and unlabeled samples, indicating that δ-proteobacteria may prefer other soil organic carbon to rhizodeposition carbon. The results suggested that soil N availability and rhizodeposition strongly modified the microbial communities of nitrogen-fixing bacteria. Moderate nitrogen application increased the symbiotic biological N fixing activity in the Astragalus sinicus L. rhizosphere. The BNF activity in the legume-rhizobia system is regulated by the exchange of organic C and N nutrient between the host plant and N-fixing bacteria.
TL;DR: Fundamental advances in understanding of biological nitrogen fixation are reviewed in the context of the emergence, evolution, and taxonomic distribution of nitrogenase, with an emphasis placed on key events associated with its emergence and diversification from anoxic to oxic environments.
TL;DR: It is suggested that major functional N2-fixing bacteria in sorghum roots are unique bradyrhizobia that resemble photosynthetic B. oligotrophicum S58T and non-nodulating Bradyrhuzobium sp.
Abstract: Sorghum (Sorghum bicolor) is cultivated worldwide for food, bioethanol, and fodder production. Although nitrogen fixation in sorghum has been studied since the 1970s, N2-fixing bacteria have not been widely examined in field-grown sorghum plants because the identification of functional diazotrophs depends on the culture method used. The aim of this study was to identify functional N2-fixing bacteria associated with field-grown sorghum by using "omics" approaches. Four lines of sorghum (KM1, KM2, KM4, and KM5) were grown in a field in Fukushima, Japan. The nitrogen-fixing activities of the roots, leaves, and stems were evaluated by acetylene reduction and 15N2-feeding assays. The highest nitrogen-fixing activities were detected in the roots of lines KM1 and KM2 at the late growth stage. Bacterial cells extracted from KM1 and KM2 roots were analyzed by metagenome, proteome, and isolation approaches and their DNA was isolated and sequenced. Nitrogenase structural gene sequences in the metagenome sequences were retrieved using two nitrogenase databases. Most sequences were assigned to nifHDK of Bradyrhizobium species, including non-nodulating Bradyrhizobium sp. S23321 and photosynthetic B. oligotrophicum S58T. Amplicon sequence and metagenome analysis revealed a relatively higher abundance (2.9-3.6%) of Bradyrhizobium in the roots. Proteome analysis indicated that three NifHDK proteins of Bradyrhizobium species were consistently detected across sample replicates. By using oligotrophic media, we purified eight bradyrhizobial isolates. Among them, two bradyrhizobial isolates possessed 16S rRNA and nif genes similar to those in S23321 and S58T which were predicted as functional diazotrophs by omics approaches. Both free-living cells of the isolates expressed N2-fixing activity in a semi-solid medium according to an acetylene reduction assay. These results suggest that major functional N2-fixing bacteria in sorghum roots are unique bradyrhizobia that resemble photosynthetic B. oligotrophicum S58T and non-nodulating Bradyrhizobium sp. S23321. Based on our findings, we discuss the N2-fixing activity level of sorghum plants, phylogenetic and genomic comparison with diazotrophic bacteria in other crops, and Bradyrhizobium diversity in N2 fixation and nodulation.
TL;DR: Mo application in Mo-deficient paddy field could be a useful measure to increase soil N input under no N fertilization, and the relative abundances of the most abundant genera Leptolyngbya and Microcoleus were significantly increased by Mo application.
TL;DR: Isolated strains are promising PSRB that enhance plant growth and this research is a base for recommending the use of these bacterial strains for biofertilizer, as an alternative of chemical fertilizer, for Triticum aestivum L. production.
TL;DR: A diverse array of microbes inhabiting the rhizosphere, and possibly aboveground tissues, appear to be episodically contributing fixed N to switchgrass, suggesting that microbial communities were distinct among tissue types and influenced by N fertilizer application.
Abstract: Perennial grasses can assimilate nitrogen (N) fixed by non-nodulating bacteria living in the rhizosphere and the plant's own tissues, but many details of associative N fixation (ANF) remain unknown, including ANF's contribution to grass N nutrition, the exact location of fixation, and composition of the associated microbial community. We examined ANF in switchgrass (Panicum virgatum L.), a North American perennial grass, using 15N-enriched N2 isotopic tracer additions in a combination of in vitro, greenhouse, and field experiments to estimate how much N is assimilated, where fixation takes place, and the likely N-fixing taxa present. Using in vitro incubations, we documented fixation in root-free rhizosphere soil and on root surfaces, with average rates of 3.8 μg N g root−1 d−1 on roots and 0.81 μg N g soil−1 d−1 in soil. In greenhouse transplants, N fixation occurred only in the early growing season, but in the field, fixation was irregularly detectable throughout the 3-month growing season. Soil, leaves, stems, and roots all contained diazotrophs and incorporated fixed N2. Metagenomic analysis suggested that microbial communities were distinct among tissue types and influenced by N fertilizer application. A diverse array of microbes inhabiting the rhizosphere, and possibly aboveground tissues, appear to be episodically contributing fixed N to switchgrass.
TL;DR: The findings suggest that diazotrophs have various activity and distribution in the three soil types, which played different roles on nitrogen input in agricultural soil in China, being driven by multiple environmental factors.
TL;DR: The multispecies inoculum of PGPRs containing Rhizobium phaseoli, SinorhizOBium americanum and Azospirillum brasilense nitrogen-fixing strains and other plant-growth promoting bacteria exerted a beneficial effect on maize plants that was greater than that obtained with single-bacteria.
TL;DR: This study concluded that the intercropping system enriched the beneficial diazotrophs in the plant rhizosphere and endosphere and that these microbes could enhance plant growth and serve as effective bioinoculants to sustain sugarcane production.
Abstract: Sugarcane-legume intercrops have gained attention because of their ability to improve crop productivity in an ecofriendly manner. We investigated the roles of rhizospheric and endospheric diazotrophs in soil nutrient transformation. We conducted two field experiments with three treatments: sugarcane monoculture, sugarcane + peanut intercrop, and sugarcane + soybean intercrop. Soil and plant samples were collected and the nutrient content, enzymatic activity, and diazotroph population were assessed. The nitrogenase (nifH) gene and 16S rRNA gene were used for molecular characterization. Correlation analysis was performed to discover the relations among the soil variables, plant variables, and microbial communities. The multiple variance analysis results indicated that the intercropping systems had a significant (p < 0.05) effect on soil total P, available K, and soil enzyme dehydrogenase. Higher diazotrophic populations in the rhizosphere and plant endosphere were recovered by sugarcane intercropping. The soybean intercrop had the maximum unique operational taxonomic units (OTUs). A total of 64 nifH gene-positive bacteria were identified by 16S rRNA gene sequencing. The BLAST search results classified all diazotrophs into five taxonomic groups: γ-Proteobacteria (28%), Actinobacteria (28%), Firmicutes (25%), β-Proteobacteria (11%), and α-Proteobacteria (8%). All identified bacteria had multiple plant growth-promoting abilities, and only 58% of the bacteria utilized aminocyclopropane-1-carboxylic acid (ACC) as their sole carbon source. Furthermore, the higher yield and γ-Proteobacteria positively correlated with soil organic matter, and urease activity revealed that intercropping improved soil fertility. Our study concluded that the intercropping system enriched the beneficial diazotrophs in the plant rhizosphere and endosphere and that these microbes could enhance plant growth and serve as effective bioinoculants to sustain sugarcane production. Moreover, higher soil nutrients (NKP) and biological activity showed the significance of our intercropping practice of a short-duration leguminous crop and a long-duration grass crop, and this practice would be a good solution to reduce the overuse of chemical fertilizers.
TL;DR: This work shows that the choice of a bio-inoculum having the right composition is one of the key aspects to be considered for the inoculation of a specific host plant cultivar with microbial consortia.
Abstract: Several important bacterial characteristics, such as biological nitrogen fixation, phosphate solubilisation, 1-aminocyclopropane-1-carboxylate deaminase activity, and production of siderophores and phytohormones, can be assessed as plant growth promotion traits. Our aim was to evaluate the effects of nitrogen-fixing and indole-3-acetic acid (IAA) producing endophytes in two Oryza sativa cultivars (Baldo and Vialone Nano). Three bacteria, Herbaspirillum huttiense RCA24, Enterobacter asburiae RCA23 and Staphylococcus sp. 377, producing different IAA levels, were tested for their ability to enhance nifH gene expression and nitrogenase activity in Enterobacter cloacae RCA25. Results showed that H. huttiense RCA24 performed best. Improvement in nitrogen-fixation and changes in physiological parameters such as chlorophyll, nitrogen content and shoot dry weight were observed for plants co-inoculated with strains RCA25 and RCA24 in a 10:1 ratio. Based on confocal laser scanning microscopy analysis, strain RCA24 was the best colonizer of the root interior and the only IAA producer located in the same root niche occupied by RCA25 cells. This work shows that the choice of a bio-inoculum having the right composition is one of the key aspects to be considered for the inoculation of a specific host plant cultivar with microbial consortia. This article is protected by copyright. All rights reserved.
TL;DR: A cross-species comparison of rhizobia systems highlights differences in their roles and interconnections but reveals common regulatory patterns and themes.
Abstract: Rhizobia are α- and β-proteobacteria that form a symbiotic partnership with legumes, fixing atmospheric dinitrogen to ammonia and providing it to the plant. Oxygen regulation is key in this symbiosis. Fixation is performed by an oxygen-intolerant nitrogenase enzyme but requires respiration to meet its high energy demands. To satisfy these opposing constraints the symbiotic partners cooperate intimately, employing a variety of mechanisms to regulate and respond to oxygen concentration. During symbiosis rhizobia undergo significant changes in gene expression to differentiate into nitrogen-fixing bacteroids. Legumes host these bacteroids in specialized root organs called nodules. These generate a near-anoxic environment using an oxygen diffusion barrier, oxygen-binding leghemoglobin and control of mitochondria localization. Rhizobia sense oxygen using multiple interconnected systems which enable a finely-tuned response to the wide range of oxygen concentrations they experience when transitioning from soil to nodules. The oxygen-sensing FixL-FixJ and hybrid FixL-FxkR two-component systems activate at relatively high oxygen concentration and regulate fixK transcription. FixK activates the fixNOQP and fixGHIS operons producing a high-affinity terminal oxidase required for bacterial respiration in the microaerobic nodule. Additionally or alternatively, some rhizobia regulate expression of these operons by FnrN, an FNR-like oxygen-sensing protein. The final stage of symbiotic establishment is activated by the NifA protein, regulated by oxygen at both the transcriptional and protein level. A cross-species comparison of these systems highlights differences in their roles and interconnections but reveals common regulatory patterns and themes. Future work is needed to establish the complete regulon of these systems and identify other regulatory signals.
TL;DR: Use of these endophytic strains as a potential biofertilizer can help to reduce the dependence on chemical fertilizers while improving crop growth and soil health simultaneously.
Abstract: Chickpea is an important leguminous crop that improves soil fertility through atmospheric nitrogen fixation with the help of rhizobia present in nodules. Non-rhizobia endophytes are also capable of inducing nodulation and nitrogen fixation in leguminous crops. The aim of the current study was to isolate, characterize and identify the non-rhizobia endophytic bacterial strains from root nodules of chickpea. For this purpose, more than one hundred isolates were isolated from chickpea root nodules under aseptic conditions and were confirmed as endophytes through re-isolating them from root nodules of chickpea after their inoculation. Nineteen confirmed endophytic bacterial strains revealed significant production of indole acetic acid (IAA) both in presence and absence of L-tryptophan and showed their ability to grow under salt, pH and heavy metal stresses. These strains were evaluated for in vitro plant growth promoting (PGP) traits and results revealed that seven strains showed solubilization of P and colloidal chitin along with possessing catalase, oxidase, urease and chitinase activities. Seven P-solubilizing strains were further evaluated in a jar trial to explore their potential for promoting plant growth and induction of nodulation in chickpea roots. Two endophytic strains identified as Paenibacillus polymyxa ANM59 and Paenibacillus sp. ANM76 through partial sequencing of the 16S rRNA gene showed the maximum potential during in vitro PGP activities and improved plant growth and nodulation in chickpea under the jar trial. Use of these endophytic strains as a potential biofertilizer can help to reduce the dependence on chemical fertilizers while improving crop growth and soil health simultaneously.
TL;DR: The results show that host size or age within a single plant species can also structure diversity of at least one group of soil microbes, and suggests that hosts may modify the niche space of their surrounding soil enabling a higher richness of microbial taxa.
Abstract: A major goal in microbial ecology is to understand the factors that structure bacterial communities across space and time. For microbes that are plant symbionts, community assembly processes can lead to either a positive or negative relationship between plant size or age and soil microbe diversity. Here, we evaluated the extent to which such relationships exist within a single legume species (Acacia acuminata) and their naturally occurring symbiotic nitrogen‐fixing bacteria (rhizobia). We quantified the diversity of rhizobia that associate with A. acuminata trees of variable size spanning a large environmental gradient in southwest Australia (72 trees in 24 sites spread across ~300,000 km²), using metabarcoding. We modelled rhizobia diversity using 16S exact genetic variants, in a binomial multivariate statistical framework that controlled for climate and local soil characteristics. We identified two major phylogenetic clades of rhizobia that associate with A. acuminata. Soil sampled at the base of larger Acacia trees contained a higher richness of rhizobia genetic variants. Each major clade responds differently to environmental factors (climate and soil characteristics), but the positive association between tree size and rhizobia genetic diversity was mainly driven by responses from one of the two clades. Overall tree size explained more variation than any other factor, resulting in a ~3‐fold increase in total richness and clade diversity from the smallest to the largest trees. Synthesis. Previous studies have shown that plant host species is important in structuring microbial soil communities in the rhizosphere. Our results show that host size or age within a single plant species can also structure diversity of at least one group of soil microbes. A positive relationship between plant host size and rhizobia diversity suggests that hosts may modify the niche space of their surrounding soil (niche construction hypothesis) enabling a higher richness of microbial taxa. That different rhizobial groups responded differently to host size and other ecological factors suggests that rhizobia is not an ecologically uniform group, and that entirely neutral explanations for our results are unlikely. Host plants may be analogous to “islands,” where larger plant hosts may accumulate diversity over time, through migration opportunities.
TL;DR: This study showed that symbiosis between the N2-fixing cyanobacterium UCYN-A and its eukaryotic algal host has led to adaptation of its daily gene expression pattern in order to enable daytime aerobic N2 fixation, which is likely more energetically efficient than fixing N2 at night, as found in other unicellular marine cyanobacteria.
Abstract: Symbiosis between a marine alga and a N2-fixing cyanobacterium (Cyanobacterium UCYN-A) is geographically widespread in the oceans and is important in the marine N cycle. UCYN-A is uncultivated and is an unusual unicellular cyanobacterium because it lacks many metabolic functions, including oxygenic photosynthesis and carbon fixation, which are typical in cyanobacteria. It is now presumed to be an obligate symbiont of haptophytes closely related to Braarudosphaera bigelowii N2-fixing cyanobacteria use different strategies to avoid inhibition of N2 fixation by the oxygen evolved in photosynthesis. Most unicellular cyanobacteria temporally separate the two incompatible activities by fixing N2 only at night, but, surprisingly, UCYN-A appears to fix N2 during the day. The goal of this study was to determine how the unicellular UCYN-A strain coordinates N2 fixation and general metabolism compared to other marine cyanobacteria. We found that UCYN-A has distinct daily cycles of many genes despite the fact that it lacks two of the three circadian clock genes found in most cyanobacteria. We also found that the transcription patterns in UCYN-A are more similar to those in marine cyanobacteria that are capable of aerobic N2 fixation in the light, such as Trichodesmium and heterocyst-forming cyanobacteria, than to those in Crocosphaera or Cyanothece species, which are more closely related to unicellular marine cyanobacteria evolutionarily. Our findings suggest that the symbiotic interaction has resulted in a shift of transcriptional regulation to coordinate UCYN-A metabolism with that of the phototrophic eukaryotic host, thus allowing efficient coupling of N2 fixation (by the cyanobacterium) to the energy obtained from photosynthesis (by the eukaryotic unicellular alga) in the light.IMPORTANCE The symbiotic N2-fixing cyanobacterium UCYN-A, which is closely related to Braarudosphaera bigelowii, and its eukaryotic algal host have been shown to be globally distributed and important in open-ocean N2 fixation. These unique cyanobacteria have reduced metabolic capabilities, even lacking genes for oxygenic photosynthesis and carbon fixation. Cyanobacteria generally use energy from photosynthesis for nitrogen fixation but require mechanisms for avoiding inactivation of the oxygen-sensitive nitrogenase enzyme by ambient oxygen (O2) or the O2 evolved through photosynthesis. This study showed that symbiosis between the N2-fixing cyanobacterium UCYN-A and its eukaryotic algal host has led to adaptation of its daily gene expression pattern in order to enable daytime aerobic N2 fixation, which is likely more energetically efficient than fixing N2 at night, as found in other unicellular marine cyanobacteria.
TL;DR: It is demonstrated that the nitrogen cycle has largely recuperated by 19 yr following disturbance, allowing for rapid biomass regeneration at the site and provides important insight into the sources and dynamics of nitrogen that support growth and carbon capture in regenerating Neotropical forests.
Abstract: Regenerating tropical forests have an immense capacity to capture carbon and harbor biodiversity. The recuperation of the nitrogen cycle following disturbance can fuel biomass regeneration, but few studies have evaluated the successional dynamics of nitrogen and nitrogen inputs in tropical forests. We assessed symbiotic and asymbiotic nitrogen fixation, soil inorganic nitrogen concentrations, and tree growth in a well-studied series of five tropical forest plots ranging from 19 yr in age to old-growth forests. Wet-season soil inorganic nitrogen concentrations were high in all plots, peaking in the 29-yr-old plot. Inputs from symbiotic nitrogen fixation declined through succession, while asymbiotic nitrogen fixation peaked in the 37-yr-old plot. Consequently, the dominant nitrogen fixation input switched from symbiotic fixation in the younger plots to asymbiotic fixation in the older plots. Tree growth was highest in the youngest plots and declined through succession. Interestingly, symbiotic nitrogen fixation was negatively correlated with the basal area of nitrogen-fixing trees across our study plots, highlighting the danger in using nitrogen-fixing trees as a proxy for rates of symbiotic nitrogen fixation. Our results demonstrate that the nitrogen cycle has largely recuperated by 19 yr following disturbance, allowing for rapid biomass regeneration at our site. This work provides important insight into the sources and dynamics of nitrogen that support growth and carbon capture in regenerating Neotropical forests.
TL;DR: This study provides the first insight into the diversity and distribution of the diazotrophic communities in the Eastern Indian Ocean during the pre-southwest monsoon period and highlights distinct contributions of both non-cyanobacteria and cyanobacteria to N2 fixation.
Abstract: The diazotrophic communities play an important role in sustaining primary productivity through adding new nitrogen to oligotrophic marine ecosystems. Yet, their composition in the oligotrophic Indian Ocean is poorly understood. Here, we report the first observation of phylogenetic diversity and distribution of diazotrophs in the Eastern Indian Ocean (EIO) surface water (to 200 m) during the pre-southwest monsoon period. Through high throughput sequencing of nifH genes, we identified diverse groups of diazotrophs in the EIO including both non-cyanobacterial and cyanobacterial phylotypes. Proteobacteria (mainly Alpha-, Beta-, and Gamma-proteobacteria) were the most diverse and abundant groups within all the diazotrophs, which accounted for more than 86.9% of the total sequences. Cyanobacteria were also retrieved, and they were dominated by the filamentous non-heterocystous cyanobacteria Trichodesmium spp. Other cyanobacteria such as unicellular diazotrophic cyanobacteria were detected sporadically. Interestingly, our qPCR analysis demonstrated that the depth-integrated gene abundances of the diazotrophic communities exhibited spatial heterogeneity with Trichodesmium spp. appeared to be more abundant in the Bay of Bengal (p < 0.05), while Sagittula castanea (Alphaproteobacteria) was found to be more dominating in the equatorial region and offshores (p < 0.05). Non-metric multidimensional scaling analysis (NMDS) further confirmed distinct vertical and horizontal spatial variations in the EIO. Canonical correspondence analysis (CCA) indicated that temperature, salinity, and phosphate were the major environmental factors driving the distribution of the diazotroph communities. Overall, our study provides the first insight into the diversity and distribution of the diazotrophic communities in EIO. The findings from this study highlight distinct contributions of both non-cyanobacteria and cyanobacteria to N2 fixation. Moreover, our study reveals information that is critical for understanding spatial heterogeneity and distribution of diazotrophs, and their vital roles in nitrogen and carbon cycling.
TL;DR: In this article, the authors investigated the potential mechanism of the effect of biochar and irrigation on the soybean-Rhizobium symbiotic performance and soil biological activity in a field trial.
Abstract: Nitrogen (N) in soybean (Glycine max L.) plants derived from biological nitrogen fixation was shown to be a sustainable N resource to substitute for N fertilizer. However, the limited water supply in sandy soil is a critical factor for soybean nodulation and crop growth. This study investigated the potential mechanism of the effect of biochar and irrigation on the soybean-Rhizobium symbiotic performance and soil biological activity in a field trial. In the absence of N fertilizer, 10 t ha−1 of black cherry wood-derived biochar were applied under irrigated and rainfed conditions on an experimental, sandy field site. The plant biomass, plant nutrient concentrations, nodule number, nodule leghemoglobin content, soil enzyme activities, and soil-available nutrients were examined. Our results show that biochar application caused a significant increase in the nodule number by 35% in the irrigated condition. Shoot biomass and soil fluorescein diacetate hydrolytic activity were significantly increased by irrigation in comparison to the rainfed condition. The activity of soil protease reduced significantly, by 8%, with the biochar application in the irrigated condition. Further, a linear correlation analysis and redundancy analysis performed on the plant, nodule, and soil variables suggested that the biochar application may affect soybean N uptake in the sandy field. Nodulation was enhanced with biochar addition, however, the plant N concentration and nodule Lb content remained unaffected.
TL;DR: The results suggest that the addition of biochar or biochar compound fertilizer could increase the abundance and alter the community structure of diazotrophs, which may benefit N fixation in alkaline agricultural soil.
TL;DR: It is demonstrated that the quantified shifts in the soil microbial community and the observed increases in the expression of key functional genes involved in N-cycling were the result of reduced nitrogen application in this strip intercropping system.
Abstract: Soil microbes are essential links between above- and below-ground ecosystems and play an important role in regulating ecological functions in the soil. Dynamic interactions within the soil-microbial community in a cereal-legume intercropping ecosystem influence the composition and structure of N-cycling microbial groups (e.g. nitrogen-fixing bacteria). However, these effects have not been extensively studied in some intercropping patterns or in response to varying nitrogen fertilization levels. In the present study, we evaluated the effects of reduced and conventional nitrogen application in a sweet maize (Zea may L.)/soybean (Glycine max L.) strip intercropping system under three cropping patterns over a 3-year time period. High-throughput sequencing and quantitative PCR techniques were used to investigate changes to both the microbial community structure and the expression of key nitrogen-cycling genes in the rhizosphere. Our results indicate that reduced nitrogen application affected the microbial community structure in the rhizosphere, but microbial diversity in the sweet maize rhizosphere was relatively stable. Both the abundance and activity of functional marker genes for microbial nitrogen fixation (nifH), nitrification (amoA), denitrification (nirS, nirK, nosZ), and decomposition (chiA) increased significantly from 2013 to 2016. Taken together, these data demonstrate that the quantified shifts in the soil microbial community and the observed increases in the expression of key functional genes involved in N-cycling were the result of reduced nitrogen application in this strip intercropping system. This study, therefore, provides essential insight into the potential relationships between functional nitrogen-cycling genes and mitigation of nitrogen-loss and N2O emissions in a cereal-legume strip intercropping system.