Cloning method for taxonomic interpretation of T-RFLP patterns.

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Trade, diplomacy, and warfare: The Quest for elite rhizobia inoculant strains

Rhizobia form symbiotic nitrogen-fixing nodules on leguminous plants, which provides an important source of fixed nitrogen input into the soil ecosystem. The improvement of symbiotic nitrogen fixation is one of the main challenges facing agriculture research. Doing so will reduce the usage of chemical nitrogen fertilizer, contributing to the development of sustainable agriculture practices to deal with the increasing global human population. Sociomicrobiological studies of rhizobia have become a model for the study of the evolution of mutualistic interactions. The exploitation of the wide range of social interactions rhizobia establish among themselves, with the soil and root microbiota, and with the host plant, could constitute a great advantage in the development of a new generation of highly effective rhizobia inoculants. Here, we provide a brief overview of the current knowledge on three main aspects of rhizobia interaction: trade of fixed nitrogen with the plant; diplomacy in terms of communication and possible synergistic effects; and warfare, as antagonism and plant control over symbiosis. Then, we propose new areas of investigation and the selection of strains based on the combination of the genetic determinants for the relevant rhizobia symbiotic behavioral phenotypes

Genetic diversity and salt tolerance of bacterial communities from two Tunisian soils

Microbial ecology studies on arid soils are particularly important for the analysis of biological functions during desertification. Although much is known about the arid saline flora, few researches have directly compared the bacterial communities of saline arid soils with cultivated soils in Northern Africa. Bacterial communities present in two soils from Soliman (north of Tunisia), one salty and neglected, and the other cultivated, were investigated by using both cultivation dependent and independent approaches. The first approach was used to assess the presence of salt tolerant bacteria and the relationships among salt (NaCl) resistance phenotype, soil characteristics and phylogenetic assignment of strains. Total community analysis, performed by T-RFLP on total DNA, was carried out to investigate the relationships between total community fingerprinting with cultivated isolates diversity. The cultivated isolates from salty soil were more genetically diverse, harbouring strains that can grow at high salt concentration. Moreover, the salt resistance of isolates was found not to be related to any particular phylogenetic group, being widespread among isolates belonging to different bacterial subdivisions. Ribotype richness, evaluated as number of different T-RFLP bands (TRFs), was shown to be higher in the agricultural soil than in the salty soil and several agricultural soil-specific TRFs were detected

Polyphenol characterization and skin-preserving properties of hydroalcoholic flower extract from Himantoglossum robertianum (Orchidaceae)

Himantoglossum robertianum (Loisel.) P. Delforge is a Mediterranean orchid whose propagation in vitro has been achieved, making it eligible as a source of bioactive substances. Flowers were analyzed by light and SEM microscopy and used to obtain a polyphenol-rich, hydroalcoholic flower extract (HFE). HFE was characterized for total phenols, flavonoids and proanthocyanidins, and for polyphenol profile by RP-LC-DAD. Antioxidant assays, in vitro collagenase and elastase inhibition, and MTT and cell motility assays on HaCaT keratinocytes were done. Microscopy showed epidermal cells containing anthocyanins in the flower labellum. Flavonoids (flavones and flavan-3-ols) represented the most abundant compounds (42.91%), followed by scopoletin (33.79%), and phenolic acids (23.3%). Antioxidant assays showed strong activities, rating ORAC > FRAP > TEAC > \u3b2-carotene bleaching > DPPH > iron-chelation. Biological assays showed elastase and collagenase inhibition (up to 42% and 78%, respectively), improvement of HaCaT cell viability after treatment with 500 \u3bcM H2O2 (from 30% to 84% of control), and stimulation of cell migration rate up to 210% of control. In summary, HFE counteracted different free radicals, while protective properties were shown by cell-free and cell-based bioassays, suggesting the possible use of H. robertianum flowers for skin-preserving, repair, and anti-aging applications

Metabolic modelling reveals the specialization of secondary replicons for niche adaptation in Sinorhizobium meliloti

The genome of about 10% of bacterial species is divided among two or more large chromosome-sized replicons. The contribution of each replicon to the microbial life cycle (for example, environmental adaptations and/or niche switching) remains unclear. Here we report a genome-scale metabolic model of the legume symbiont Sinorhizobium meliloti that is integrated with carbon utilization data for 1,500 genes with 192 carbon substrates. Growth of S. meliloti is modelled in three ecological niches (bulk soil, rhizosphere and nodule) with a focus on the role of each of its three replicons. We observe clear metabolic differences during growth in the tested ecological niches and an overall reprogramming following niche switching. In silico examination of the inferred fitness of gene deletion mutants suggests that secondary replicons evolved to fulfil a specialized function, particularly host-associated niche adaptation. Thus, genes on secondary replicons might potentially be manipulated to promote or suppress host interactions for biotechnological purposes

Mixed nodule infection in Sinorhizobium meliloti-medicago sativa symbiosis suggest the presence of cheating behavior

In the symbiosis between rhizobia and legumes, host plants can forms ymbiotic root nodules with multiple rhizobial strains, potentially showing different symbiotic performances in nitrogen fixation. Here, we investigated the presence of mixed nodules, containing rhizobia with different degrees of mutualisms, and evaluate their relative fitness in the Sinorhizobium meliloti-Medicago sativa model symbiosis. We used three S. meliloti strains, the mutualist strains Rm1021 and BL225C and the non-mutualist AK83. We performed competition experiments involving both in vitro and in vivo symbiotic assays with M. sativa host plants. We show the occurrence of a high number (from 27 to 100%) of mixed nodules with no negative effect on both nitrogen fixation and plant growth. The estimation of the relative fitness as non-mutualist/mutualist ratios in single nodules shows that in some nodules the non-mutualist strain efficiently colonized root nodules along with the mutualist ones. In conclusion, we can support the hypothesis that in S. meliloti-M. sativa symbiosis mixed nodules are formed and allow non-mutualist or less-mutualist bacterial partners to be less or not sanctioned by the host plant, hence allowing a potential form of cheating behavior to be present in the nitrogen fixing symbiosis

Role and regulation of ACC deaminase gene in Sinorhizobium meliloti: Is it a symbiotic, rhizospheric or endophytic gene?

Plant-associated bacteria exhibit a number of different strategies and specific genes allow bacteria to communicate and metabolically interact with plant tissues. Among the genes found in the genomes of plant-associated bacteria, the gene encoding the enzyme 1-aminocyclopropane-1-carboxylate (ACC) deaminase (acdS) is one of the most diffused. This gene is supposed to be involved in the cleaving of plant-produced ACC, the precursor of the plant stress-hormone ethylene toning down the plant response to infection. However, few reports are present on the actual role in rhizobia, one of the most investigated groups of plant-associated bacteria. In particular, still unclear is the origin and the role of acdS in symbiotic competitiveness and on the selective benefit it may confer to plant symbiotic rhizobia. Here we present a phylogenetic and functional analysis of acdS orthologs in the rhizobium model-species Sinorhizobium meliloti. Results showed that acdS orthologs present in S. meliloti pangenome have polyphyletic origin and likely spread through horizontal gene transfer, mediated by mobile genetic elements. When acdS ortholog from AK83 strain was cloned and assayed in S. meliloti 1021 (lacking acdS), no modulation of plant ethylene levels was detected, as well as no increase in fitness for nodule occupancy was found in the acdS-derivative strain compared to the parental one. Surprisingly, AcdS was shown to confer the ability to utilize formamide and some dipeptides as sole nitrogen source. Finally, acdS was shown to be negatively regulated by a putative leucine-responsive regulator (LrpL) located upstream to acdS sequence (acdR). acdS expression was induced by root exudates of both legumes and non-leguminous plants. We conclude that acdS in S. meliloti is not directly related to symbiotic interaction, but it could likely be involved in the rhizospheric colonization or in the endophytic behavior

Metabolic modelling reveals the specialization of secondary replicons for niche adaptation in Sinorhizobium meliloti

The genome of about 10% of bacterial species is divided among two or more large chromosome-sized replicons. The contribution of each replicon to the microbial life cycle (for example, environmental adaptations and/or niche switching) remains unclear. Here we report a genome-scale metabolic model of the legume symbiont Sinorhizobium meliloti that is integrated with carbon utilization data for 1,500 genes with 192 carbon substrates. Growth of S. meliloti is modelled in three ecological niches (bulk soil, rhizosphere and nodule) with a focus on the role of each of its three replicons. We observe clear metabolic differences during growth in the tested ecological niches and an overall reprogramming following niche switching. In silico examination of the inferred fitness of gene deletion mutants suggests that secondary replicons evolved to fulfil a specialized function, particularly host-associated niche adaptation. Thus, genes on secondary replicons might potentially be manipulated to promote or suppress host interactions for biotechnological purposes

Genetic diversity of dinitrogen-fixing bacterial communities in soil amended with olive husks

The industrial production of olive oil is accompanied by the accumulation of large quantities of by-products from the olive milling industry that are commonly dispersed as fertilisers, which are nowadays suspected to have potential toxic effects on is omicroflora. The aim of this work has been the investigation of the genetic diversity of bacterial communities present in soil treated with olive husks focusing on the dinitrogen-fixing bacteria.nifH genes were amplified from total soil DNA using universal primers, cloned and typed by restriction analysis and sequencing of representative haplotypes. On the same samples, DGGE analysis on amplified 16S rDNA was performed aiming at monitoring modifications in the total community pattern. Results showed a high genetic diversity ofnifH genes within the community, which was well in agreement with the total community profiles obtained by DGGE on 16SrDNA. Most of thenifH gene fragments (19 out of 32) were found to be similar to sequences related with clostridia

Climate variability during MIS 20–18 as recorded by alkenone-SST and calcareous plankton in the Ionian Basin (central Mediterranean)

This study shows the first Mediterranean high-resolution record of alkenone-derived sea surface temperature (SST) in the marine sediments outcropping at the Ideale section (IS) (southern Italy, central Mediterranean) from late marine isotope stage (MIS) 20 - through early MIS 18. The SST pattern evidences glacial-interglacial up to submillennial-scale temperature variation, with lower values (~13 °C) in late MIS 20 and substage 19b, and higher values (up to 21 °C) in MIS 19c and in the interstadials of MIS 19a. The SST data are combined with the new calcareous plankton analysis and the available, chronologically well-constrained carbon and oxygen isotope records in the IS. The multi-proxy approach, together with the location of the IS near the Italian coasts, the lower circalittoral-upper bathyal depositional setting, and high sedimentation rate allow to document long-and short-term paleoenvironmental modifications (sea level, rainfall, inorganic/organic/fresh water input to the basin), as a response to regional and global climate changes. The combined proxies reveal the occurrence of a terminal stadial event in late MIS 20 (here Med-HTIX), and warm-cold episodes (here Med-BATIX and Med-YDTIX) during Termination IX (TIX), which recall those that occurred through the last termination (TI). During these periods and the following ghost sapropel layer (insolation cycle 74, 784 ka) in the early MIS 19, high frequency internal changes are synchronously recorded by all proxies. The substage MIS 19c is warm but quite unstable, with several episodes of paleoenvironmental changes, associated with fluctuating tropical-subtropical water inflow through the Gibraltar Strait, variations of the cyclonic regime in the Ionian basin, and the southward shift of westerly winds and winter precipitation over southern Europe and Mediterranean basin. Three high-amplitude millennial-scale oscillations in the patterns of SST and calcareous plankton key taxa during MIS 19a are interpreted as linked to changes in temperature as well as in salinity due to periodical water column stratification and mixing. The main processes involved in the climate variability include changes in oceanographic exchanges through the Gibraltar Strait during modulations of Atlantic meridional overturning circulation and/or variations in atmospheric dynamics related to the influence of westerly and polar winds acting in the paleo-Ionian basin. A strong climate teleconnection between the North Atlantic and Mediterranean is discussed, and a prominent role of atmospheric processes in the central Mediterranean is evidenced by comparing data sets at the IS with Italian and extra-Mediterranean marine and terrestrial records