A new hemoglobin gene from soybean: a role for hemoglobin in all plants.

We have isolated a new hemoglobin gene from soybean. It is expressed in cotyledons, stems of seedlings, roots, young leaves, and in some cells in the nodules that are associated with the nitrogen-fixing Bradyrhizobium symbiont. This contrasts with the expression of the leghemoglobins, which are active only in the infected cells of the nodules. The deduced protein sequence of the new gene shows only 58% similarity to one of the soybean leghemoglobins, but 85-87% similarity to hemoglobins from the nonlegumes Parasponia, Casuarina, and barley. The pattern of expression and the gene sequence indicate that this new gene is a nonsymbiotic legume hemoglobin. The finding of this gene in legumes and similar genes in other species strengthens our previous suggestion that genomes of all plants contain hemoglobin genes. The specialized leghemoglobin gene family may have arisen from a preexisting nonsymbiotic hemoglobin by gene duplication.

Caracterização fisiológica e do perfil de expressão gênica do transporte de nitrogênio em genótipos contrastantes para processo de fixação biológica de N2 de cana-de-açúcar (Saccharum spp.)

A cana-de-açúcar é uma cultura agrícola de grande importância econômica para o Brasil, e a expansão de seu cultivo para solos marginais requer uma maior utilização de fertilizantes à base de nitrogênio (N). Na maioria dos países produtores, a adubação nitrogenada se baseia em altas doses de aplicação, enquanto, no Brasil, o seu uso é relativamente baixo devido, em parte, ao processo de fixação biológica de nitrogênio (FBN) pela ação de bactérias diazotróficas. Além da FBN, as plantas adquirem fontes de N, como amônio e nitrato, por meio de transportadores de membranas localizados nas raízes. Há evidências que a associação com microrganismos pode favorecer as plantas por meio da regulação dos genes de transportadores de N. Desta forma, este trabalho teve como objetivo caracterizar o transporte de amônio e nitrato, avaliando a expressão gênica dos principais transportadores de N em cana-de-açúcar cultivada in vitro sob o efeito da associação com bactérias diazotróficas. Também foi descrita a comunidade bacteriana de plântulas in vitro, bem como o efeito da fertilização com N e da inoculação com bactérias diazotróficas em plantas maduras. Plântulas de \'SP70- 1143\' e \'Chunee\', que contrastam para FBN, foram empregadas em ensaios in vitro sob diversas concentrações e fontes de N em associação ou não com uma estirpe de Gluconacetobacter diazotrophicus ou um mistura de bactérias diazotróficas (G. diazotrophicus, Herbaspirillum seropedicae, H. rubrisubalbicans, Azospirillum amazonense e Burkholderia tropica). A caracterização do transporte de N por meio de ensaios de absorção de nitrato e amônio marcados (15N) revelou que a interação entre cana-de-açúcar x G. diazotrophicus induziu a expressão do gene do transportador de nitrato ScNRT2.1, o que levou a uma tendência no aumento no influxo de nitrato, assim como dos genes de transportadores de amônio ScAMT1.1 e ScAMT1.3, resultando em maiores influxos de amônio apenas para a cultivar \'SP70- 1143\'. Já a associação da cana-de-açúcar com a mistura de bactérias diazotróficas revelou que somente houve indução transcricional de ScAMT1.1, o que resultou na maior absorção de amônio em \'SP70-1143\'. Por sua vez, quando analisada a interação in vitro por 30 dias, a presença da bactéria, apesar de transiente, possivelmente favoreceu a expressão dos genes de transportadores de nitrato ScNRT1.1 e ScNRT2.1, e do transportador de amônio ScAMT1.1, resultando no maior acúmulo de 15N-nitrato de amônio nas plantas de \'SP70-1143\'. Foi detectada uma comunidade bacteriana associada a plântulas micropropagadas, a qual é distinta entre os genótipos \'SP70-1143\' e \'Chunee\' e se altera com a inoculação com G. diazotrophicus. Para as plantas cultivadas em campo, a comunidade bacteriana existente foi alterada pela fertilização de N, mas não pela inoculação com diazotróficas. Portanto, a inoculação com bactérias diazotróficas parece induzir a expressão dos principais genes transportadores de amônio e nitrato em plântulas do genótipo \'SP70-1143\' resultando na maior absorção de fontes inorgânicas de N.

Monitoramento da interação entre rizobactéria RZ2MS16 (Burkholderia ambifaria) promotora de crescimento e bioinoculantes comerciais aplicados nas culturas de soja e milho

As culturas da soja e milho são de grande importância econômica mundial e também para o Brasil, onde a área cultivada com essas duas culturas está estimada em 45.855.900 mil hectares, distribuídas em todos estados produtores conforme suas características. A estimativa da safra mundial de soja em 2015/16 apresentou uma redução na produção global da oleaginosa para 319,0 milhões de ton, volume 1,1 milhão de ton inferior ao levantamento de dezembro de 2015. Ainda assim, trata-se de um volume recorde. Para o milho, a produção global foi de 967,9 milhões de ton, com uma redução no volume de 5,9 milhões de ton em relação ao levantamento realizado em dezembro de 2015. Nessas duas culturas são comumente utilizadas bactérias fixadoras de nitrogênio (BFN), reduzindo ou até mesmo, eliminando a aplicação de adubos nitrogenados. Estudos apontam que a simbiose entre BFN e as culturas soja e milho pode ser otimizada mediante a coinoculação com rizobatérias promotoras de crescimento de plantas (RPCP). Apesar de promissora, o estudo da utilização de BFN em associação com RPCPs é incipiente no Brasil. Assim, o presente trabalho teve como objetivo monitorar, a partir da marcação bacteriana, a interação entre a linhagem de Burkholderia ambifaria (RZ2MS16), uma rizobactéria proveniente do guaranazeiro e previamente descrita como promotora de crescimento em soja e milho e linhagens das espécies Bradyrhizobium japonicum (SEMIA5079), Bradyrhizobium diazoefficiens (SEMIA5080) e Azospirillum brasilense (Ab-v5 e Ab-v6) que são comercialmente utilizadas como bioinoculantes nessas culturas respectivamente. Os efeitos sinergisticos da interação entre RZ2MS16 e bioinoculantes comercias foram avaliados em experimento de casa de vegetação. Também foi avaliado o efeito da coinoculação de bioinculantes com outra rizobactéria proveniente do guaranazeiro, Bacillus sp. (RZ2MS9). As linhagens foram inoculadas separadamente e coinoculadas, sendo melhores resultados observados com a coinoculação das linhagens. As linhagens marcadas com genes de fluorescência selecionadas para estudo de interação foram RZ2MS16, Ab-v5 e SEMIA5080, sendo essa interação observada por microscopia de fluorescência, com também pelo reisolamento das linhagens marcadas. As linhagens RZ2MS16:pNKGFP e Ab-v5: pWM1013 e SEMIA5080:pWM1013 colonizaram todos os nichos avaliados em milho e soja, respectivamente, sendo também caracterizadas como endofíticos. Assim se observa que estudos desta natureza são de grande importância para um melhor entendimento da interação entre bactéria planta e o efeito da coinoculação no melhor desenvolvimento de plantas comercialmente utilizadas.

Legume nodulation: successful symbiosis through short- and long-distance signalling

Nodulation in legumes provides a major conduit of available nitrogen into the biosphere. The development of nitrogen-fixing nodules results from a symbiotic interaction between soil bacteria, commonly called rhizobia, and legume plants. Molecular genetic analysis in both model and agriculturally important legume species has resulted in the identification of a variety of genes that are essential for the establishment, maintenance and regulation of this symbiosis. Autoregulation of nodulation (AON) is a major internal process by which nodule numbers are controlled through prior nodulation events. Characterisation of AON-deficient mutants has revealed a novel systemic signal transduction pathway controlled by a receptor-like kinase. This review reports our present level of understanding on the short- and long-distance signalling networks controlling early nodulation events and AON.

Statnote 32 : the partial correlation coefficient

In previous statnotes, the application of correlation and regression methods to the analysis of two variables (X,Y) was described. The most important statistic used to measure the degree of correlation between two variables is Pearson’s ‘product moment correlation coefficient’ (‘r’). The correlation between two variables may be due to their common relation to other variables. Hence, investigators using correlation studies need to be alert to the possibilities of spurious correlation and the methods of ‘partial correlation’ are one method of taking this into account. This statnote applies the methods of partial correlation to three scenarios. First, to a fairly obvious example of a spurious correlation resulting from the ‘size effect’ involving the relationship between the number of general practitioners (GP) and the number of deaths of patients in a town. Second, to the relationship between the abundance of the nitrogen-fixing bacterium Azotobacter in soil and three soil variables, and finally, to a more complex scenario, first introduced in Statnote 24involving the relationship between the growth of lichens in the field and climate.

Organic geochemistry of sediments from sapropel 94 of ODP Hole 161-974C

Analysis of the molecular composition of the organic matter (OM) from whole sediment samples can avoid analytical bias that might result from isolation of components from the sediment matrix, but has its own analytical challenges. We evaluated the use of GC * GC-ToFMS to analyze the pyrolysis products of six whole sediment samples obtained from above, within and below a 1 million year old OM-rich Mediterranean sapropel layer. We found differences in pyrolysis products nitrogen-fixing green sulfur bacteria contributed to the high productivity. Greater abundances of shorter chain aliphatic hydrocarbons, pyrroles, furans and alkyl aromatics in the pyrolysates of sapropel samples relative to the marls confirm better preservation of marine OM in the sapropels. In addition, the presence of greater amounts of thiophenes in the sapropels than in the marls is consistent with the existence of euxinic conditions during sapropel deposition. The combination of whole sediment pyrolysis and GC × GC-ToFMS is promising, but the procedure requires careful selection of its multiple analytical variables, particularly the pyrolysis temperature and the operational features of the GC columns.

Global distributions of diazotrophs abundance and biomass - Depth integrated values computed from a collection of source datasets - Contribution to the MAREDAT World Ocean Atlas of Plankton Functional Types

The MAREDAT atlas covers 11 types of plankton, ranging in size from bacteria to jellyfish. Together, these plankton groups determine the health and productivity of the global ocean and play a vital role in the global carbon cycle. Working within a uniform and consistent spatial and depth grid (map) of the global ocean, the researchers compiled thousands and tens of thousands of data points to identify regions of plankton abundance and scarcity as well as areas of data abundance and scarcity. At many of the grid points, the MAREDAT team accomplished the difficult conversion from abundance (numbers of organisms) to biomass (carbon mass of organisms). The MAREDAT atlas provides an unprecedented global data set for ecological and biochemical analysis and modeling as well as a clear mandate for compiling additional existing data and for focusing future data gathering efforts on key groups in key areas of the ocean. The present data set presents depth integrated values of diazotrophs abundance and biomass, computed from a collection of source data sets.

La face cachée de la dune : communautés fongiques du sol: dynamique, succession et interactions avec la végétation d’un écosystème dunaire côtier aux Îles de la Madeleine, Qc

Les écosystèmes dunaires remplissent plusieurs fonctions écologiques essentielles comme celle de protéger le littoral grâce à leur capacité d’amortissement face aux vents et vagues des tempêtes. Les dunes jouent aussi un rôle dans la filtration de l’eau, la recharge de la nappe phréatique, le maintien de la biodiversité, en plus de présenter un attrait culturel, récréatif et touristique. Les milieux dunaires sont très dynamiques et incluent plusieurs stades de succession végétale, passant de la plage de sable nu à la dune bordière stabilisée par l’ammophile à ligule courte, laquelle permet aussi l’établissement d’autres herbacées, d’arbustes et, éventuellement, d’arbres. Or, la survie de ces végétaux est intimement liée aux microorganismes du sol. Les champignons du sol interagissent intimement avec les racines des plantes, modifient la structure des sols, et contribuent à la décomposition de la matière organique et à la disponibilité des nutriments. Ils sont donc des acteurs clés de l’écologie des sols et contribuent à la stabilisation des dunes. Malgré cela, la diversité et la structure des communautés fongiques, ainsi que les mécanismes influençant leur dynamique écologique, demeurent relativement méconnus. Le travail présenté dans cette thèse explore la diversité des communautés fongiques à travers le gradient de succession et de conditions édaphiques d’un écosystème dunaire côtier afin d’améliorer la compréhension de la dynamique des sols en milieux dunaires. Une vaste collecte de données sur le terrain a été réalisée sur une plaine de dunes reliques se trouvant aux Îles de la Madeleine, Qc. J’ai échantillonné plus de 80 sites répartis sur l’ensemble de ce système dunaire et caractérisé les champignons du sol grâce au séquençage à haut débit. Dans un premier temps, j’ai dressé un portait d’ensemble des communautés fongiques du sol à travers les différentes zones des dunes. En plus d’une description taxonomique, les modes de vie fongiques ont été prédits afin de mieux comprendre comment les variations au niveau des communautés de champignons du sol peuvent se traduire en changements fonctionnels. J’ai observé un niveau de diversité fongique élevé (plus de 3400 unités taxonomiques opérationnelles au total) et des communautés taxonomiquement et fonctionnellement distinctes à travers un gradient de succession et de conditions édaphiques. Ces résultats ont aussi indiqué que toutes les zones des dunes, incluant la zone pionière, supportent des communautés fongiques diversifiées. Ensuite, le lien entre les communautés végétales et fongiques a été étudié à travers l’ensemble de la séquence dunaire. Ces résultats ont montré une augmentation claire de la richesse spécifique végétale, ainsi qu’une augmentation de la diversité des stratégies d’acquisition de nutriments (traits souterrains lié à la nutrition des plantes, soit mycorhizien à arbuscule, ectomycorhizien, mycorhizien éricoide, fixateur d’azote ou non spécialisé). J’ai aussi pu établir une forte corrélation entre les champignons du sol et la végétation, qui semblent tous deux réagir de façon similaire aux conditions physicochimiques du sol. Le pH du sol influençait fortement les communautés végétales et fongiques. Le lien observé entre les communautés végétales et fongiques met l’emphase sur l’importance des interactions biotiques positives au fil de la succession dans les environnements pauvres en nutriments. Finalement, j’ai comparé les communautés de champignons ectomycorhiziens associées aux principales espèces arborescentes dans les forêts dunaires. J’ai observé une richesse importante, avec un total de 200 unités taxonomiques opérationnelles ectomycorhiziennes, appartenant principalement aux Agaricomycètes. Une analyse de réseaux n’a pas permis de détecter de modules (c'est-à-dire des sous-groupes d’espèces en interaction), ce qui indique un faible niveau de spécificité des associations ectomycorhiziennes. De plus, je n’ai pas observé de différences en termes de richesse ou de structure des communautés entre les quatre espèces hôtes. En conclusion, j’ai pu observer à travers la succession dunaire des communautés diversifiées et des structures distinctes selon la zone de la dune, tant chez les champignons que chez les plantes. La succession semble toutefois moins marquée au niveau des communautés fongiques, par rapport aux patrons observés chez les plantes. Ces résultats ont alimenté une réflexion sur le potentiel et les perspectives, mais aussi sur les limitations des approches reposant sur le séquençage à haut-débit en écologie microbienne.

Cell- and Tissue-Specific Transcriptome Analyses of Medicago truncatula Root Nodules

Legumes have the unique ability to host nitrogen-fixing Rhizobium bacteria as symbiosomes inside root nodule cells. To get insight into this key process, which forms the heart of the endosymbiosis, we isolated specific cells/tissues at different stages of symbiosome formation from nodules of the model legume Medicago truncatula using laser-capture microdissection. Next, we determined their associated expression profiles using Affymetrix Medicago GeneChips. Cells were collected from the nodule infection zone divided into a distal (where symbiosome formation and division occur) and proximal region (where symbiosomes are mainly differentiating), as well as infected cells from the fixation zone containing mature nitrogen fixing symbiosomes. As non-infected cells/tissue we included nodule meristem cells and uninfected cells from the fixation zone. Here, we present a comprehensive gene expression map of an indeterminate Medicago nodule and selected genes that show specific enriched expression in the different cells or tissues. Validation of the obtained expression profiles, by comparison to published gene expression profiles and experimental verification, indicates that the data can be used as digital "in situ''. This digital "in situ'' offers a genome-wide insight into genes specifically associated with subsequent stages of symbiosome and nodule cell development, and can serve to guide future functional studies.

Inhibition of glutamine synthetase by phosphinothricin leads to transcriptome reprograming in root nodules of Medicago truncatula

Glutamine synthetase (GS) is a vital enzyme for the assimilation of ammonia into amino acids in higher plants. In legumes, GS plays a crucial role in the assimilation of the ammonium released by nitrogen-fixing bacteria in root nodules, constituting an important metabolic knob controlling the nitrogen (N) assimilatory pathways. To identify new regulators of nodule metabolism, we profiled the transcriptome of Medicago truncatula nodules impaired in N assimilation by specifically inhibiting GS activity using phosphinothricin (PPT). Global transcript expression of nodules collected before and after PPT addition (4, 8, and 24 h) was assessed using Affymetrix M. truncatula GeneChip arrays. Hundreds of genes were regulated at the three time points, illustrating the dramatic alterations in cell metabolism that are imposed on the nodules upon GS inhibition. The data indicate that GS inhibition triggers a fast plant defense response, induces premature nodule senescence, and promotes loss of root nodule identity. Consecutive metabolic changes were identified at the three time points analyzed. The results point to a fast repression of asparagine synthesis and of the glycolytic pathway and to the synthesis of glutamate via reactions alternative to the GS/GOGAT cycle. Several genes potentially involved in the molecular surveillance for internal organic N availability are identified and a number of transporters potentially important for nodule functioning are pinpointed. The data provided by this study contributes to the mapping of regulatory and metabolic networks involved in root nodule functioning and highlight candidate modulators for functional analysis.

Composts addition may improve biology in cotton soils

Composts can provide a source of organic carbon and nutrients for soil biota and increase soil fertility as well as provide other biological and structural benefits hence compost addition to cotton soils is seen as a way to improve cotton soil biological health and fertility. In a six month incubation experiment we analysed the changes in microbial populations and activities related to C and N cycling following the application of feedlot, poultry manure and gin trash compost materials. A significant variation in the chemical composition, e.g. major nutrients and trace elements, was found between the three compost products. The feedlot compost generally contained higher levels of dissolved organic carbon, total nitrogen and bicarbonate extractable phosphorus whereas the Gin trash compost had lower carbon and nutrient concentrations. The effect of compost addition @ 5 and 10t/ha generally increased microbial activity but the effect was only evident during the first two weeks of incubation. Composts effects on the abundance of total bacteria (16S), nitrifying (amoA), nitrogen fixing (nifH) and denitrifying bacteria (nosZ) and total fungi (ITS gene) varied between different composts. The addition of feedlot and poultry compost material significantly increased the levels of dissolved organic carbon (DOC) and nitrogen (DON) in soil compared to that in control soils while ‘Gin trash’ compost had no effect. These differences reflected in the microbial catabolic diversity changes in the compost amended soils. Therefore, chemical analysis of the compost material before application is recommended to more fully consider its’ potential benefits.

Pre-announcement of symbiotic guests: transcriptional reprogramming by mycorrhizal lipochitooligosaccharides shows a strict co-dependency on the GRAS transcription factors NSP1 and RAM1

BACKGROUND: More than 80 % of all terrestrial plant species establish an arbuscular mycorrhiza (AM) symbiosis with Glomeromycota fungi. This plant-microbe interaction primarily improves phosphate uptake, but also supports nitrogen, mineral, and water aquisition. During the pre-contact stage, the AM symbiosis is controled by an exchange of diffusible factors from either partner. Amongst others, fungal signals were identified as a mix of sulfated and non-sulfated lipochitooligosaccharides (LCOs), being structurally related to rhizobial nodulation (Nod)-factor LCOs that in legumes induce the formation of nitrogen-fixing root nodules. LCO signals are transduced via a common symbiotic signaling pathway (CSSP) that activates a group of GRAS transcription factors (TFs). Using complex gene expression fingerprints as molecular phenotypes, this study primarily intended to shed light on the importance of the GRAS TFs NSP1 and RAM1 for LCO-activated gene expression during pre-symbiotic signaling. RESULTS: We investigated the genome-wide transcriptional responses in 5 days old primary roots of the Medicago truncatula wild type and four symbiotic mutants to a 6 h challenge with LCO signals supplied at 10(-7/-8) M. We were able to show that during the pre-symbiotic stage, sulfated Myc-, non-sulfated Myc-, and Nod-LCO-activated gene expression almost exclusively depends on the LysM receptor kinase NFP and is largely controled by the CSSP, although responses independent of this pathway exist. Our results show that downstream of the CSSP, gene expression activation by Myc-LCOs supplied at 10(-7/-8) M strictly required both the GRAS transcription factors RAM1 and NSP1, whereas those genes either co- or specifically activated by Nod-LCOs displayed a preferential NSP1-dependency. RAM1, a central regulator of root colonization by AM fungi, controled genes activated by non-sulfated Myc-LCOs during the pre-symbiotic stage that are also up-regulated in areas with early physical contact, e.g. hyphopodia and infecting hyphae; linking responses to externally applied LCOs with early root colonization. CONCLUSIONS: Since both RAM1 and NSP1 were essential for the pre-symbiotic transcriptional reprogramming by Myc-LCOs, we propose that downstream of the CSSP, these GRAS transcription factors act synergistically in the transduction of those diffusible signals that pre-announce the presence of symbiotic fungi.