Microbiological characterization of a semi-arid meadow soil seeded with different proportions of orchard grass and alfalfa

1 póster donde se muestran los resultados de su investigación.-- Póster presentado al XV Congress of the Spanish Society of Nitrogen Fixation, and the IV Portuguese-Spanish Congress on Nitrogen Fixation. En León (España). 16, 17 y 18 de junio de 2015Soil is a pivotal component of the environment and the maintenance of soil quality is critical for ensuring the sustainability of the biosphere. The use of fertilizers has increased at a faster rate than global food production. Modern agriculture is dependent on phosphorus derived from phosphate rock, which is a non‐renewable resource. It is needed to improve P acquisition efficiency for both low input and intensive agroecosystems. However, few studies have focused on cereal‐legume interactions with regard to soil P. The objective of this work was to study the effects of grass‐legume mixtures and phosphorus fertilization on soil microbial community structure and biomass [determined by fatty acid methyl ester (FAME) profiling] as well as on the soil nitrogen (N) mineralisation rate.Peer reviewe

Culturable bacterial diversity from the chestnut (Castanea sativa Mill.) phyllosphere and antagonism against the fungi causing the chestnut blight and ink diseases

22 páginas, 3 tablas, 5 figurasThe phyllosphere supports a large and complex bacterial community that varies both across plant species and geographical locations. Phyllosphere bacteria can have important effects on plant health. The sweet chestnut (Castanea sativa Mill.) is an economically important tree species affected worldwide by the fungal pathogens Cryphonectria parasitica and Phytophthora cinnamomi. We examined the culturable phyllosphere bacterial community of the sweet chestnut at two nearby locations in Central Spain in order to know its geographical variability and to explore its potential as source of biological control agents against these two pathogenic fungi. The bacterial diversity at strain level was high but it varied significantly between locations; however, phylotype richness and diversity were more comparable. The isolates were affiliated with the phyla Actinobacteria, Firmicutes and Proteobacteria. Most of them were members of recognized bacterial species, with a notable proportion of representative of the genera Dietzia and Lonsdalea, but a small fraction of the strains revealed the existence of several potential novel species or even genera. Antagonism tests showed the occurrence in the chestnut phyllosphere of bacterial strains potentially useful as biological control agents against the two pathogenic fungi, some of which belong to species never before described as fungal antagonists. Chestnut phyllosphere, therefore, contains a great diversity of culturable bacteria and may represent an untapped source of potential biocontrol agents against the fungi causing blight and ink diseases of this tree species.This work was supported by grant no. QLK5-CT-2001-00029 (MANCHEST project) from the European Union.Peer reviewe

Novel lichen-dominated hypolithic communities in the Namib Desert

The ventral surfaces of translucent rocks from hot desert pavements often harbor hypolithic microbial communities, which are mostly dominated by cyanobacteria. The Namib Desert fog belt supports extensive hypolithic colonization of quartz rocks, which are also colonized by lichens on their dorsal surfaces. Here, we aim to evaluate whether lichens colonize the ventral surface of the rocks (i.e., show hypolithic lifestyle) and compare the bacterial composition of these coastal hypolithic communities with those found inland. Fungal DNA barcoding and fungal and bacterial Illumina metabarcoding were combined with electron microscopy to characterize the composition and spatial structure of hypolithic communities from two (coastal and inland) areas in the Namib Desert. We report, for the first time, the structure and composition of lichen-dominated hypolithic communities found in the coastal zone of the Namib Desert with extensive epilithic lichen cover. Lichen modified areoles with inverted morphology of the genus Stellarangia (three lineages) and Buellia (two lineages) were the main components of these hypolithic communities. Some of these lineages were also found in epilithic habitats. These lichen-dominated hypolithic communities differed in structural organization and bacterial community composition from those found in inland areas. The hypolithic lichen colonization characterized here seems not to be an extension of epilithic or biological soil crust lichen growths but the result of specific sublithic microenvironmental conditions. Moisture derived from fog and dew could be the main driver of this unique colonization.Open Access funding provided thanks to the CRUE-CSIC agreement with Springer Nature. DC acknowledges the financial support of the University of Pretoria and the National Research Foundation of South Africa. AV was supported by the project “CLU-2019–05 – IRNASA/CSIC Unit of Excellence,” funded by the Junta de Castilla y León and co-financed by the European Union (ERDF “Europe drives our growth”). This work was supported by grants CTM2015-64728-C2- 2-R (MINECO/FEDER, EU) and PID2019-105469RB-C22 (MICINN).http://link.springer.com/journal/248am2022BiochemistryGeneticsMicrobiology and Plant Patholog

Taxonomía polifásica de poblaciones de microorganismos que establecen simbiosis con Phaseolus vulgaris

La alubia, Phaseolus vulgaris, es un cultivo de gran importancia en la Península Ibérica, lo que la convierte en un modelo muy adecuado para el estudio de poblaciones endófitas en distintos suelos. En este estudio se han elegido una serie de suelos en el Noroeste de Portugal, que presentan la particularidad de ser suelos de montaña que han sido sometidos a técnicas de cultivo tradicional, sin abonos químicos, durante muchísimos años, y sobre los que se ha cultivado alubias de una variedad local de generación en generación. Se han aislado microorganismos endosimbiontes a partir de nódulos de plantas de Phaseolus vulgaris, y se ha realizado la caracterización polifásica de las cepas aisladas mediante la utilización de métodos fenotípicos y moleculares. Los resultados más sobresaliente fueron: Se aislaron 186 cepas de microorganismos endófitos de Phaseolus vulgaris, de las cuales 180 fueron capaces de producir nódulos efectivos y el resto fueron capaces de penetrar en sus raíces sin originar estructuras diferenciadas. La caracterización genotípica y fenotípica permitió la identificación de todas las cepas aisladas a nivel de especie y/o subespecie. De acuerdo con los resultados obtenidos, el 82% de las cepas fueron identificadas como Rhizobium rhizogenes, el 15% como Rhizobium tropici tipo A y el 3% como cepas del género Herbaspirillum. Por primera vez se aislaron cepas de R. rhizogenes (Agrobacterium rhizogenes) capaces de formar nódulos en plantas de Phaseolus vulgaris. De acuerdo con los resultados de los perfiles de TP-RAPD dentro de la especie Rhizobium rhizogenes puede haber más de una subespecie, hecho que será necesario comprobar en posteriores estudios. Se ha demostrado que existen cepas de Rhizobium tropici tipo A en la Península Ibérica y que, además, estas cepas portan en el gen 16S el mismo “inserto” que las cepas americanas. Se ha caracterizado e identificado una nueva especie del género Herbaspirillum que se ha denominado Herbaspirillum lusitanum. La especie Herbaspirillum lusitanum es la primera que se describe como endófito de leguminosas.The common bean, Phaseolus vulgaris, is a staple grain-legume in the Iberian Peninsula and, therefore, a very appropriate model for studying the soil bacterial endophytic populations. In this study, different mountain soils from the north-west of Portugal were chosen because they have been cultivated following traditional agronomical practices from the antiquity, avoiding the use of chemical fertilizers, and where a local genotype of of Phaseolus has been recurrently planted. Endosymbiont microorganisms were isolated from nodules of Phaseolus vulgaris plants, and their polyphasic characterization performed by using phenotypic and genotypic methods. The main results were: From a total of 186 isolates, 180 formed effective root nodules in Phaseolus vulgaris plants. The remainder six strains were able to infect Phaseolus vulgaris roots but they did not form any differentiated structure. Their genotypic and phenotypic characterization allowed to identify all these isolates at a taxonomic level of species and/or subspecies. From the 186 isolates, the 82% was identified as Rhizobium rhizogenes, 15 % as Rhizobium tropici type A, and the remaining 3 % as members of the genus Herbaspirillum. To the best of our knowledge, strains of R. rhizogenes (Agrobacterium rhizogenes) able to nodulate Phaseolus vulgaris plants were isolated by the first time. The TP-RAPD profiles indicated that there could be more than one subespecies of Rhizobium rhizogenes, although more detailled studies should be done to verify that result. It has been demonstrated that Rhizobium tropici type A strains can be found in soils from the Iberian Peninsula. These strains showed a “insert” in its 16S rRNA gen that is identical to that found in strains from American origen. It has been characterized and identified a new species of the genus Herbaspirillum designated as Herbaspirillum lusitanum. To our knowledge, this is the first report on the undoubted association of a bacterium of the genus Herbaspirillum with a leguminous plant.Peer reviewe

Arable agriculture changes soil microbial communities in the South African Grassland Biome

7 páginas, 3 figuras, 1 tabla. -- This article is available at http://www.sajs.co.zaMany studies, mostly in temperate regions of the northern hemisphere, have demonstrated that agricultural practices affect the composition and diversity of soil microbial communities. However, very little is known about the impact of agriculture on the microbial communities in other regions of the world, most particularly on the African continent. In this study, we used MiSeq amplicon sequencing of bacterial 16S rRNA genes and fungal ITS regions to characterise microbial communities in agricultural and natural grassland soils located in the Mpumalanga Province of South Africa. Nine soil chemical parameters were also measured to evaluate the effects of edaphic factors on microbial community diversity. Bacterial and fungal communities were significantly richer and more diverse in natural grassland than in agricultural soils. Microbial taxonomic composition was also significantly different between the two habitat types. The phylum Acidobacteria was significantly more abundant in natural grassland than in agricultural soils, while Actinobacteria and the family Nectriaceae showed the opposite pattern. Soil pH and phosphorus significantly influenced bacterial communities, whereas phosphorus and calcium influenced fungal communities. These findings may be interpreted as a negative impact of land-use change on soil microbial diversity and composition.National Research Foundation (South Africa); University of PretoriaPeer reviewe

Polyphasic characterization of phosphate-solubilizing bacteria isolated from rhizospheric soil of the north-eastern region of Portugal.

First International Meeting on Microbial Phosphate Solubilization. Salamanca, Spain, 16-19 july 2002. 4 p.Phosphate-solubilizing microorganisms are often used as plant growth promoters. In the frame of a project focused on the isolation of endosymbionts and ectorhizospheric bacteria associated with Phaseolus vulgaris plants growing in a mountain soil at the north-east of Portugal, we obtained six bacterial strains with high phosphate-solubilizing capability, as demonstrated by the formation of ‘halos’ when plated in YED medium supplemented with tricalcium-phosphate. These bacterial strains were characterized by a polyphasic approach using both phenotypic (API 20 NE) and molecular assays (RAPD, with M13 primer, TP-RAPD, and 16S rDNA sequencing). TP-RAPD yielded an identical band patterns in the six strains indicating that they belong to the same bacterial species. The 16S rRNA sequence analysis of a group-representative strain (P4-22) revealed a sequence similarity value of 99.27% with Pseudomonas jessenii. Moreover, the RAPD fingerprints of these six strains did not show differences, indicating that they form a highly homogenous group. This high homogeneity could be a consequence of the recurring agronomical practices used in this region from the antiquity that include organic fertilization and monoculture of Phaseolus vulgaris.Peer reviewe

Endophytic seed mycobiome of six sorghum (Sorghum bicolor) cultivars from commercial seedlots using an Illumina sequencing approach

18 páginas, 6 figuras, 2 tablasPathogen-free seeds are important for the establishment of young seedlings, prevention of health problems upon consumption by animals and livestock, and inadvertent movement of pathogens into and out of countries. However, testing for the presence of fungi, including pathogens from seeds is a time consuming and difficult process. In this study, we characterized the seed fungal microbiome (mycobiome) of six commercial sorghum cultivars from South Africa using a deep amplicon next generation sequencing approach based on the Internal Transcribed Spacer (ITS) region of the ribosomal operon. Sorghum is the fifth most important crop in the world, and widely used by African farmers. We found that the fungi present in each of the seedlots were similar to those reported by cultural studies. By comparing phylotypes of certain key families and genera to phylotypes used in established phylogenies and reputed sequences from public databases, the diagnostic value of the NGS method was also investigated. We showed that a number of molecular operational taxonomic units (MOTUs) could be identified at the species level and established that certain known pathogens are not present in the tested seeds, for instance in the Aspergillus group. Other groups could not be identified, not even to genus level. While acknowledging the shortcomings of using partial ITS data, we demonstrated that deep amplicon sequencing is a valuable diagnostic tool for seed disease control and prevention in some cases.Research funding was provided by the Agricultural Research Council Collaborative Consortium to Broaden the Food Base.Peer reviewe

Cyanobacteria and Alphaproteobacteria may facilitate cooperative interactions in niche communities

11 páginas, 5 figuras, 2 tablas. -- The first publication by Frontiers Media is avalilable at https://www.frontiersin.org/articles/10.3389/fmicb.2017.02099/fullHypoliths, microbial assemblages found below translucent rocks, provide important ecosystem services in deserts. While several studies have assessed microbial diversity of hot desert hypoliths and whether these communities are metabolically active, the interactions among taxa remain unclear. Here, we assessed the structure, diversity, and co-occurrence patterns of hypolithic communities from the hyperarid Namib Desert by comparing total (DNA) and potentially active (RNA) communities. The potentially active and total hypolithic communities differed in their composition and diversity, with significantly higher levels of Cyanobacteria and Alphaproteobacteria in potentially active hypoliths. Several phyla known to be abundant in total hypolithic communities were metabolically inactive, indicating that some hypolithic taxa may be dormant or dead. The potentially active hypolith network was highly modular in structure with almost exclusively positive co-occurrences (>95% of the total) between taxa. Members of the Cyanobacteria and Alphaproteobacteria were identified as potential keystone taxa, and exhibited numerous positive co-occurrences with other microbes, suggesting that these groups might have important roles in maintaining network topological structure despite their low abundance.The authors gratefully acknowledge the financial support provided by the National Research Foundation of South Africa (Grant no. 97891 to MWVG and TTK13061018773 to AV) and the University of Pretoria (MWVG, AV, TPM, and DAC).Peer reviewe

Natural diversity of nodular microsymbionts of Alnus glutinosa in the Tormes River basin.

The genetic diversity of Frankia strains nodulating Alnus glutinosa along the basin of the Tormes River was studied on DNA extracted directly from nodules. Frankia strains inhabiting root nodules at 12 different locations, ranging in altitude from 409 to 1181 m, were characterized. For that, we amplified the whole IGS region between 16S–23S rDNA and performed a restriction fragment length polymorphism (RFLP) analysis with four restriction enzymes. Two different RFLP patterns (termed A and B) were obtained with HaeIII, indicating the existence of two different groups of Frankia strains. Three different nodule extracts from each of the two RFLP groups were selected for further analyses. Sequencing of the 16S–23S rDNA IGS showed a 100% of intragroup homology and also confirmed the difference (98.4% level of similarity) between the Frankia strains in the two nodule extract groups. The phylogenetic analyses based on the two 16S–23S rDNA IGS sequences obtained in this study and other previously published sequences indicated that Frankia strains TFAg5 and TFAg23 (chosen as representative of HaeIII–RFLP group A and B, respectively) are quite similar to other strains nodulating plants of A. rhombifolia and A. viridis in California (pairwise levels of similarity including gaps ranged from 97.8% to 98.6%), together with which they form a single group. To put the Frankia strains representative of each HaeIII–RFLP group in the context of overall Frankia diversity we amplified and sequenced the 16S rDNA and glnII gene from nodular DNA. An also remarkable fact found in this study was that Frankia strains belonging to the HaeIII–RFLP group A were distributed all along the river course, from the lowest site sampled to the highest, while Frankia strains placed into RFLP group B were restricted to the upper Tormes River, being exclusively found at altitudes of 946 m or higher.Peer reviewe

Relationship between plant species diversity and plant biomass of orchard grass and lucerne sown in different ratios in the province of Salamanca, Spain

16 páginas, 3 tablas y 5 figurasA field experiment was carried out at the CSIC Muñovela farm belonging to the Spanish National Research Council (CSIC) in order to evaluate the effect of sowing orchard grass (Dactylis glomerata var. Trerano) and lucerne (Medicago sativa var. Aragon) in monoculture and in combination. The experiment was based on a randomized block designed with a factorial arrangement (5 × 2). Experimental units were 40 plots distributed in four blocks. The phosphorus fertilization (P) factor included two types of conditions: basal fertilization without phosphorus (-P) and basal fertilization with phosphorus (+P), and the vegetation cover factor (T) included five conditions depending on the grass (G) and the legume (L). Above-ground biomass showed statistically significant differences among seasons and years (P < 0.05). However, no statistically significant differences treatments were found among various treatments. The presence of the grass species Lolium perenne L. and Poa pratensis L. throughout the three years indicated that both species significantly increased their presence over time regardless of the treatments applied. The analysis performed for the other plant species (those other than grasses and legumes) allowed us to determine that the T1 and T5 treatments, which correspond to single species not treated with the application of phosphorus, influenced the presence of 70% of other species planted. Our specific aim was to explore how changing plant biotic diversity affects productivity under a given set of conditions. We manipulated plant species richness as an experimental factor to determine if productivity would be affected by changes in the ratios of plants sown.GRICA Sustainability Project 2016-2017Peer reviewe