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The accumulation of metals in natural environments is a growing concern of modern societies since they constitute persistent, non-degradable contaminants. Microorganisms are involved in redox processes and participate to the biogeochemical cycling of metals. Some endospore-forming Firmicutes (EFF) are known to oxidize and reduce specific metals and have been isolated from metal-contaminated sites. However, whether EFF isolated from uncontaminated sites have the same capabilities has not been thoroughly studied. In this study, we measured manganese oxidation and copper resistance of aerobic EFF from uncontaminated sites. For the purposes of this study we have sampled 22 natural habitats and isolated 109 EFF strains. Manganese oxidation and copper resistance were evaluated by growth tests as well as by molecular biology. Overall, manganese oxidation and tolerance to over 2 mM copper was widespread among the isolates (more than 44% of the isolates exhibited Mn (II)-oxidizing activity through visible Birnessite formation and 9.1% tolerate over 2 mM copper). The co-occurrence of these properties in the isolates was also studied. Manganese oxidation and tolerance to copper were not consistently found among phylogenetically related isolates. Additional analysis correlating the physicochemical parameters measured on the sampling sites and the metabolic capabilities of the isolates showed a positive correlation between in situ alkaline conditions and the ability of the strains to perform manganese oxidation. Likewise, a negative correlation between temperature in the habitat and copper tolerance of the strains was observed. Our results lead to the conclusion that metal tolerance is a wide spread phenomenon in unrelated aerobic EFF from natural uncontaminated environments. [ABSTRACT FROM AUTHOR]

Oxalate is present in environments as diverse as soils or gastrointestinal tracts. This organic acid can be found as free acid or forming metal salts (e.g. calcium, magnesium). Oxalotrophy, the ability to use oxalate as carbon and energy sources, is mainly the result of bacterial catabolism, which can be either aerobic or anaerobic. Although some oxalotrophic bacterial strains are commonly used as probiotics, little is known about the diversity and ecology of this functional group. This review aims at exploring the taxonomic distribution and the phylogenetic diversity of oxalotrophic bacteria across biomes. In silico analyses were conducted using the two key enzymes involved in oxalotrophy: formyl-coenzyme A (CoA) transferase (EC 2.8.3.16) and oxalyl-CoA decarboxylase (EC 4.1.1.8), encoded by the frc and oxc genes, respectively. Our analyses revealed that oxalate-degrading bacteria are restricted to three phyla, namely Actinobacteria, Firmicutes and Proteobacteria and originated from terrestrial, aquatic and clinical environments. Diversity analyses at the protein level suggest that total Oxc diversity is more constrained than Frc diversity and that bacterial oxalotrophic diversity is not yet fully described. Finally, the contribution of oxalotrophic bacteria to ecosystem functioning as well as to the carbon cycle is discussed. [ABSTRACT FROM AUTHOR]

Fungi and bacteria form various associations that are central to numerous environmental processes. In the so-called fungal highway, bacteria disperse along fungal mycelium. We developed a novel tool for the in situ isolation of bacteria moving along fungal hyphae as well as for the recovery of fungi potentially involved in dispersal, both of which are attracted towards a target culture medium. We present the validation and the results of the first in situ test. Couples of fungi and bacteria were isolated from soil. Amongst the enriched organisms, we identified several species of fast-growing fungi (Fusarium sp. and Chaetomium sp.), as well as various potentially associated bacterial groups, including Variovorax soli, Olivibacter soli, Acinetobacter calcoaceticus, and several species of the genera Stenotrophomonas, Achromobacter and Ochrobactrum. Migration of bacteria along fungal hyphae across a discontinuous medium was confirmed in most of the cases. Although the majority of the bacteria for which migration was confirmed were also positive for flagellar motility, not all motile bacteria dispersed using their potential fungal partner. In addition, the importance of hydrophobicity of the fungal mycelial surface was confirmed. Future applications of the columns include targeting different types of microorganisms and their interactions, either by enrichment or by state of the art molecular biological methods. [ABSTRACT FROM AUTHOR]

In this study, the role of native plant growth-promoting rhizobacteria (PGPR) as bio-inoculants was assessed as an alternative to ameliorate Ilex paraguariensis St. Hill. growth in nursery comparing poorer (soil) versus richer (compost) substrates. Twelve rhizospheric strains isolated from yerba mate plantations were evaluated in vitro for their potential as PGPRs. Three isolates, identified as Kosakonia radicincitans YD4, Rhizobium pusense YP3, and Pseudomonas putida YP2, were selected on the basis of their N fixation activity, IAA-like compound and siderophore production, and phosphate solubilization. A highly significant positive effect of bio-inoculation with the native isolates was observed in 5-month-old seedlings cultivated in soil. The highest increase was observed in seedlings inoculated with K. radicincitans YD4 with an increase of 183 % in the dry shoot weight and a 30 % increase in shoot N content. In contrast, in compost, no increment in the dry weight was observed; however, an increase in content in some macronutrients in shoots was observed. Remarkably, when plant biomass was compared between soil and compost, seedlings inoculated with K. radicincitans YD4 in soil produced the highest yields, even though higher yields could be expected in compost due to the richness of this substrate. In conclusion, bio-inoculation of yerba mate seedlings with native PGPR increases the yield of this crop in nursery and could represent a promising sustainable strategy to improve yerba mate growth in low-fertility soils. [ABSTRACT FROM AUTHOR]

The oxalate-carbonate pathway (OCP) is a biogeochemical set of reactions that involves the conversion of atmospheric CO fixed by plants into biomass and, after the biological recycling of calcium oxalate by fungi and bacteria, into calcium carbonate in terrestrial environments. Oxalotrophic bacteria are a key element of this process because of their ability to oxidize calcium oxalate. However, the diversity and alternative carbon sources of oxalotrophs participating to this pathway are unknown. Therefore, the aim of this study was to characterize oxalotrophic bacteria in tropical OCP systems from Bolivia, India, and Cameroon. Ninety-five oxalotrophic strains were isolated and identified by sequencing of the 16S rRNA gene. Four genera corresponded to newly reported oxalotrophs ( Afipia, Polaromonas, Humihabitans, and Psychrobacillus). Ten strains were selected to perform a more detailed characterization. Kinetic curves and microcalorimetry analyses showed that Variovorax soli C18 has the highest oxalate consumption rate with 0.240 µM h. Moreover, Streptomyces achromogenes A9 displays the highest metabolic plasticity. This study highlights the phylogenetic and physiological diversity of oxalotrophic bacteria in tropical soils under the influence of the oxalate-carbonate pathway. [ABSTRACT FROM AUTHOR]

We present a method for the physical isolation of endospores from environmental samples allowing the specific targeting of endospore-forming bacteria for sequencing (endospore-enriched community). The efficiency of the method was tested on lake sediment samples. After 16 S rRNA gene amplicon sequencing, the composition in the endospore-enriched community was compared with the community from untreated control samples (whole community). In the whole community, Firmicutes had a relative abundance of 8% and 19% in the two different lake sediments. In contrast, in the endospore-enriched community, Firmicutes abundance increased to 90.6% and 83.9%, respectively, confirming the efficiency of the endospore enrichment. The relative abundance of other microbial groups that form spore-like resisting states (i.e. actinobacteria, cyanobacteria and myxococcales) was below 2% in the endospore-enriched community, indicating that the method is adapted to true endospores. Representatives from two out of the three known classes of Firmicutes ( Bacilli and Clostridia) were detected and supposedly asporogenic groups (e.g. E thanoligenes and T richococcus) could be detected. The method presented here is a leap forward for ecological studies of endospore-forming Firmicutes. It can be applied to other types of samples in order to reveal the diversity and metabolic potential of this bacterial group in the environment. [ABSTRACT FROM AUTHOR]

Highlights: [•] Genetic diversity of rhizobia present in nodules of beans in two Chilean soils is very low. [•] The genetic diversity was independent of soil origin and previous use. [•] Indigenous rhizobial populations play a minor role symbiotic partner selection. [Copyright &y& Elsevier]

Measurements of chemical composition and biological parameters of sediment cores are used as proxies for changes in past environmental conditions and more recently the human impact on ecosystem health. In this study, endospore-forming bacteria are proposed as a new biological proxy for such paleoecological reconstructions. A sediment core providing a record for the past 90 years (Cs and magnetic susceptibility dating) was retrieved from the Rhone Delta of Lake Geneva. X-ray fluorescence was analyzed at a 0.2-cm resolution, while DNA extracts, elemental geochemistry and grain size were obtained at 4-cm intervals. The total number of bacteria and endospore-forming bacteria were quantified by qPCR using the 16S rRNA gene and the endosporulation-specific spo0A gene. Furthermore, a spo0A fragment was subjected to amplicon sequencing to define OTUs (operational taxonomic units) and the phylogenetic affiliation of the endospore formers. The results showed that despite the fact that the quantity of extracted DNA decreased with the age of the sediment, the abundance of endospore-forming bacteria remained constant. However, the diversity of this group of bacteria changed significantly, reflecting the eutrophication of the lake from 1960 to 1990. The shift in community composition was linked to the dominance of anaerobic clostridia-like endospore formers. This trend has reversed in the last 10 years of the record, suggesting a recovery after perturbation. This study shows that the abundance and diversity of endospore-forming bacteria can be used as proxies to reconstruct lake history. We hereby successfully introduce a new strategy for paleoecology that could also be applied to ocean sediments and long sediment cores. [ABSTRACT FROM AUTHOR]

The interactions between bacteria and fungi, the main actors of the soil microbiome, remain poorly studied. Here, we show that the saprotrophic and ectomycorrhizal soil fungus Morchella crassipes acts as a bacterial farmer of Pseudomonas putida, which serves as a model soil bacterium. Farming by M. crassipes consists of bacterial dispersal, bacterial rearing with fungal exudates, as well as harvesting and translocation of bacterial carbon. The different phases were confirmed experimentally using cell counting and 13C probing. Common criteria met by other non-human farming systems are also valid for M. crassipes farming, including habitual planting, cultivation and harvesting. Specific traits include delocalization of food production and consumption and separation of roles in the colony (source versus sink areas), which are also found in human agriculture. Our study evidences a hitherto unknown mutualistic association in which bacteria gain through dispersal and rearing, while the fungus gains through the harvesting of an additional carbon source and increased stress resistance of the mycelium. This type of interaction between fungi and bacteria may play a key role in soils. [ABSTRACT FROM AUTHOR]

In this study, we developed and validated a culture-independent method for diversity surveys to specifically detect endospore-forming Firmicutes. The global transcription regulator of sporulation ( spo0A) was identified as a gene marker for endospore-forming Firmicutes. To enable phylogenetic classification, we designed a set of primers amplifying a 602 bp fragment of spo0A that we evaluated in pure cultures and environmental samples. The amplification was positive for 35 strains from 11 genera, yet negative for strains from Alicyclobacillus and Sulfobacillus. We also evaluated various DNA extraction methods because endospores often result in reduced yields. Our results demonstrate that procedures utilizing increased physical force improve DNA extraction. An optimized DNA extraction method on biomass pre-extracted from the environmental sample source (indirect DNA extraction) followed by amplification with the aforementioned primers for spo0A was then tested in sediments from two different sources. Specifically, we validated our culture-independent diversity survey methodology on a set of 8338 environmental spo0A sequences obtained from the sediments of Lakes Geneva ( Switzerland) and Baikal ( Russia). The phylogenetic affiliation of the environmental sequences revealed a substantial number of new clades within endospore-formers. This novel culture-independent approach provides a significant experimental improvement that enables exploration of the diversity of endospore-forming Firmicutes. [ABSTRACT FROM AUTHOR]

The oxalate-carbonate pathway involves the oxidation of calcium oxalate to low-magnesium calcite and represents a potential long-term terrestrial sink for atmospheric CO2. In this pathway, bacterial oxalate degradation is associated with a strong local alkalinization and subsequent carbonate precipitation. In order to test whether this process occurs in soil, the role of bacteria, fungi and calcium oxalate amendments was studied using microcosms. In a model system with sterile soil amended with laboratory cultures of oxalotrophic bacteria and fungi, the addition of calcium oxalate induced a distinct pH shift and led to the final precipitation of calcite. However, the simultaneous presence of bacteria and fungi was essential to drive this pH shift. Growth of both oxalotrophic bacteria and fungi was confirmed by qPCR on the frc (oxalotrophic bacteria) and 16 S rRNA genes, and the quantification of ergosterol (active fungal biomass) respectively. The experiment was replicated in microcosms with non-sterilized soil. In this case, the bacterial and fungal contribution to oxalate degradation was evaluated by treatments with specific biocides (cycloheximide and bronopol). Results showed that the autochthonous microflora oxidized calcium oxalate and induced a significant soil alkalinization. Moreover, data confirmed the results from the model soil showing that bacteria are essentially responsible for the pH shift, but require the presence of fungi for their oxalotrophic activity. The combined results highlight that the interaction between bacteria and fungi is essential to drive metabolic processes in complex environments such as soil. [ABSTRACT FROM AUTHOR]

Desulfotomaculum reducens is the first Gram-positive sulfate- and metal- reducing bacterium for which the transcriptomic response to uranium exposure has been evaluated. The genes upregulated during fermentative growth in the presence of U(VI) as compared to its absence included those encoding for proteins involved in respiration such as NADH quinone oxidoreductase and heterodisulfide reductase. This finding suggested that electrons were shuttled to the electron transport chain during fermentation and points to the reduction of U(VI) as a metabolic process. Although U(IV) is typically insoluble and readily removable by filtration, U(IV) produced during active growth was not retained by a 0.2 μm pore size filter and filtration was not sufficient to differentiate between U(VI) and U(IV). In addition, genes involved in iron homeostasis were upregulated in the presence of uranium, which was consistent with the upregulation of genes involved in c-type cytochrome biogenesis. Despite the upregulation of cytochrome biosynthesis genes, the sole c-type cytochrome encoded in the genome was not differentially expressed. Finally, genes encoding metal efflux pumps were also upregulated indicating the toxic nature of uranium. Analysis of the time-dependent gene expression showed that sporulation was the dominant process at the early stationary phase and that the presence of U at that stage did not impact expression. [ABSTRACT FROM AUTHOR]

We have studied the distribution and community composition of denitrifying bacteria in the stratified water column and at the sediment-water interface in lakes Plußsee and Schöhsee, and a near-shore site in the Baltic Sea in Germany. Although environmental changes induced by the stratification of the water column in marine environments are known to affect specific populations of denitrifying bacteria, little information is available for stratified freshwater lakes and brackish water. The aim of the present study was to fill this gap and to demonstrate specific distribution patterns of denitrifying bacteria in specific aquatic habitats using two functional markers for the nitrite reductase ( nirK and nirS genes) as a proxy for the communities. The leading question to be answered was whether communities containing the genes nirK and nirS have similar, identical, or different distribution patterns, and occupy the same or different ecological niches. The genes nirK and nirS were analyzed by PCR amplification with specific primers followed by terminal restriction fragment length polymorphism (T-RFLP) and by cloning and sequence analysis. Overall, nirS-denitrifiers were more diverse than nirK-denitrifiers. Denitrifying communities in sediments were clearly different from those in the water column in all aquatic systems, regardless of the gene analyzed. A differential distribution of denitrifying assemblages was observed for each particular site. In the Baltic Sea and Lake Plußsee, nirK-denitrifiers were more diverse throughout the water column, while nirS-denitrifiers were more diverse in the sediment. In Lake Schöhsee, nirS-denitrifiers showed high diversity across the whole water body. Habitat-specific clusters of nirS sequences were observed for the freshwater lakes, while nirK sequences from both freshwater lakes and the Baltic Sea were found in common phylogenetic clusters. These results demonstrated differences in the distribution of bacteria containing nirS and those containing nirK indicating that both types of denitrifiers apparently occupy different ecological niches. [ABSTRACT FROM AUTHOR]

Summary Spore-forming, Gram-positive sulfate-reducing bacteria (SRB) represent a group of SRB that dominates the deep subsurface as well as niches in which resistance to oxygen and dessication is an advantage. Desulfotomaculum reducens strain MI-1 is one of the few cultured representatives of that group with a complete genome sequence available. The metabolic versatility of this organism is reflected in the presence of genes encoding for the oxidation of various electron donors, including three- and four-carbon fatty acids and alcohols. Synteny in genes involved in sulfate reduction across all four sequenced Gram-positive SRB suggests a distinct sulfate-reduction mechanism for this group of bacteria. Based on the genomic information obtained for sulfate reduction in D. reducens, the transfer of electrons to the sulfite and APS reductases is proposed to take place via the quinone pool and heterodisulfide reductases respectively. In addition, both H2-evolving and H2-consuming cytoplasmic hydrogenases were identified in the genome, pointing to potential cytoplasmic H2 cycling in the bacterium. The mechanism of metal reduction remains unknown. [ABSTRACT FROM AUTHOR]

The biological reduction of soluble U(VI) to the less soluble U(IV) has been proposed as a strategy to remediate uranium-contaminated sites. However, the majority of the contaminated sites contain, in addition to U(VI), competing electron acceptors (CEAs) that can either enhance or inhibit U(VI) reduction. Desulfotomaculum reducens MI-1 is a sulfate-reducing bacterium able to reduce a variety of electron acceptors including U(VI). We characterized U(VI) reduction by D. reducens in the presence of pyruvate and three CEAs: sulfate, nitrate or soluble ferric iron. In the presence of sulfate or ferric iron and U(VI), cell growth was driven by respiration of the CEA. Nitrate was not used as an electron acceptor for growth and vegetative cells grew instead by fermenting pyruvate. Sulfate remaining after sulfate reduction has ceased or the presence of nitrate did not affect U(VI) reduction. However, in the case of sulfate, the addition of H2 after the depletion of pyruvate greatly enhanced U(VI) reduction. Contrary to sulfate and nitrate, the presence of Fe(II), the product of Fe(III) reduction, abolished U(VI) reduction. The results from this investigation suggest that this microorganism and others with similar characteristics may play a role in U(VI) bioremediation efforts but only after the soluble Fe(II) produced by Fe(III) reduction has been advected away. [ABSTRACT FROM AUTHOR]

The oxidation of ammonia plays a significant role in the transformation of fixed nitrogen in the global nitrogen cycle. Autotrophic ammonia oxidation is known in three groups of microorganisms. Aerobic ammonia-oxidizing bacteria and archaea convert ammonia into nitrite during nitrification. Anaerobic ammonia-oxidizing bacteria (anammox) oxidize ammonia using nitrite as electron acceptor and producing atmospheric dinitrogen. The isolation and cultivation of all three groups in the laboratory are quite problematic due to their slow growth rates, poor growth yields, unpredictable lag phases, and sensitivity to certain organic compounds. Culture-independent approaches have contributed importantly to our understanding of the diversity and distribution of these microorganisms in the environment. In this review, we present an overview of approaches that have been used for the molecular study of ammonia oxidizers and discuss their application in different environments. [ABSTRACT FROM AUTHOR]

The bioremediation of uranium-contaminated sites is designed to stimulate the activity of microorganisms able to catalyze the reduction of soluble U(VI) to the less soluble mineral UO2. U(VI) reduction does not necessarily support growth in previously studied bacteria, but it typically involves viable vegetative cells and the presence of an appropriate electron donor. We characterized U(VI) reduction by the sulfate-reducing bacterium Desulfotomaculum reducens strain MI-1 grown fermentatively on pyruvate and observed that spores were capable of U(VI) reduction. Hydrogen gas – a product of pyruvate fermentation – rather than pyruvate, served as the electron donor. The presence of spent growth medium was required for the process, suggesting that an unknown factor produced by the cells was necessary for reduction. Ultrafiltration of the spent medium followed by U(VI) reduction assays revealed that the factor's molecular size was below 3 kDa. Pre-reduced spent medium displayed short-term U(VI) reduction activity, suggesting that the missing factor may be an electron shuttle, but neither anthraquinone-2,6-disulfonic acid nor riboflavin rescued spore activity in fresh medium. Spores of D. reducens also reduced Fe(III)-citrate under experimental conditions similar to those for U(VI) reduction. This is the first report of a bacterium able to reduce metals while in a sporulated state and underscores the novel nature of the mechanism of metal reduction by strain MI-1. [ABSTRACT FROM AUTHOR]

The genes and intergenic regions of the amoCAB operon were analyzed to establish their potential as molecular markers for analyzing ammonia-oxidizing betaproteobacterial (beta-AOB) communities. Initially, sequence similarity for related taxa, evolutionary rates from linear regressions, and the presence of conserved and variable regions were analyzed for all available sequences of the complete amoCAB operon. The gene amoB showed the highest sequence variability of the three amo genes, suggesting that it might be a better molecular marker than the most frequently used amoA to resolve closely related AOB species. To test the suitability of using the amoCAB genes for community studies, a strategy involving nested PCR was employed. Primers to amplify the whole amoCAB operon and each individual gene were tested. The specificity of the products generated was analyzed by denaturing gradient gel electrophoresis, cloning, and sequencing. The fragments obtained showed different grades of sequence identity to amoCAB sequences in the GenBank database. The nested PCR approach provides a possibility to increase the sensitivity of detection of amo genes in samples with low abundance of AOB. It also allows the amplification of the almost complete amoA gene, with about 300 bp more sequence information than the previous approaches. The coupled study of all three amo genes and the intergenic spacer regions that are under different selection pressure might allow a more detailed analysis of the evolutionary processes, which are responsible for the differentiation of AOB communities in different habitats. [ABSTRACT FROM AUTHOR]

ABSTRACT: The community composition of ammonia-oxidizing bacteria (AOB) was studied during four stages of plant development in soil cultivated with Phaseolus vulgaris in comparison to unplanted soil, using an alfisol previously harboring the legume Medicago sativa. Denaturing gradient gel electrophoresis (DGGE) patterns of 16S rRNA gene and clone libraries of the same gene suggested that bacteria related to Nitrosospira cluster 3 were dominant in both planted and unplanted soil. Bacteria related to Nitrosomonas cluster 8 (Nitrosomonas communis cluster) were found at all times in planted soil, but appeared only randomly in unplanted soil. Analysis of PCR products of the gene encoding the alpha-subunit of ammonia monooxygenase (amoA) by DGGE and clone libraries only detected Nitrosospira cluster 3-like organisms, but failed to detect sequences related to Nitrosomonas. The results suggest that P. vulgaris does not affect the dominant members of AOB communities (Nitrosospira cluster 3), but could have an effect on the prevalence of Nitrosomonas cluster 8 in this type of legume-planted alfisol. [Copyright &y& Elsevier]

Abstract: The effect of common bean (Phaseolus vulgaris L.) on the composition of nitrogen fixing bacterial assemblages in soil was studied by comparing planted and unplanted soil. The community composition was studied by terminal restriction fragment length polymorphism (T-RFLP) of the nitrogenase reductase gene (nifH). Principal component analysis (PCA) of T-RFLP profiles showed the separation of profiles from planted and unplanted soil. Terminal restriction fragments (T-RFs) corresponding to rhizobial bacteria were identified preferentially in planted soil; however most nifH T-RFs in soil could not be assigned to T-RFs simulated from a database of known diazotrophs. To specifically study rhizobial bacteria in the soil and nodules, PCR products from the alpha subunit of the nitrogenase enzyme (nifD) were analyzed by denaturing gradient gel electrophoresis (DGGE). DGGE results showed the specific stimulation of the rhizobial microsymbionts in planted soil. [Copyright &y& Elsevier]

The functional gene amoA was used to compare the diversity of ammonia-oxidizing bacteria (AOB) in the water column and sediment–water interface of the two freshwater lakes Plußsee and Schöhsee and the Baltic Sea. Nested amplifications were used to increase the sensitivity of amoA detection, and to amplify a 789-bp fragment from which clone libraries were prepared. The larger part of the sequences was only distantly related to any of the cultured AOB and is considered to represent new clusters of AOB within the Nitrosomonas/ Nitrosospira group. Almost all sequences from the water column of the Baltic Sea and from 1-m depth of Schöhsee were related to different Nitrosospira clusters 0 and 2, respectively. The majority of sequences from Plußsee and Schöhsee were associated with sequences from Chesapeake Bay, from a previous study of Plußsee and from rice roots in Nitrosospira-like cluster A, which lacks sequences from Baltic Sea. Two groups of sequences from Baltic Sea sediment were related to clonal sequences from other brackish/marine habitats in the purely environmental Nitrosospira-like cluster B and the Nitrosomonas-like cluster. This confirms previous results from 16S rRNA gene libraries that indicated the existence of hitherto uncultivated AOB in lake and Baltic Sea samples, and showed a differential distribution of AOB along the water column and sediment of these environments. [ABSTRACT FROM AUTHOR]

The oxalate-carbonate pathway (OCP) is a biogeochemical process linking oxalate oxidation and carbonate precipitation. Currently, this pathway is described as a tripartite association involving oxalogenic plants, oxalogenic fungi, and oxalotrophic bacteria. While the OCP has recently received increasing interest given its potential for capturing carbon in soils, there are still many unknowns, especially regarding the taxonomic and functional diversity of the fungi involved in this pathway. To fill this gap, we described an active OCP site in Madagascar, under the influence of the oxalogenic tree Tamarindus indica, and isolated, identified, and characterized 50 fungal strains from the leaf litter. The fungal diversity encompassed three phyla, namely Mucoromycota, Ascomycota, and Basidiomycota, and 23 genera. Using various media, we further investigated their functional potential. Most of the fungal strains produced siderophores and presented proteolytic activities. The majority were also able to decompose cellulose and xylan, but only a few were able to solubilize inorganic phosphate. Regarding oxalate metabolism, several strains were able to produce calcium oxalate crystals while others decomposed calcium oxalate. These results challenge the current view of the OCP by indicating that fungi are both oxalate producers and degraders. Moreover, they strengthen the importance of the role of fungi in C, N, Ca, and Fe cycles. [ABSTRACT FROM AUTHOR]

This study evaluates mechanisms of biogenic mineral formation induced by bacterial iron reduction for the stabilization of corroded iron. As an example, the Desulfitobacterium hafniense strain TCE1 was employed to treat corroded coupons presenting urban natural atmospheric corrosion, and spectroscopic investigations were performed on the samples' cross-sections to evaluate the corrosion stratigraphy. The treated samples presented a protective continuous layer of iron phosphates (vivianite Fe2+3(PO4)2·8H2O and barbosalite Fe2+Fe3+2(PO4)2(OH)2), which covered 92% of the surface and was associated with a decrease in the thickness of the original corrosion layer. The results allow us to better understand the conversion of reactive corrosion products into stable biogenic minerals, as well as to identify important criteria for the design of a green alternative treatment for the stabilization of corroded iron. [ABSTRACT FROM AUTHOR]

Morchella helvetica, sp. nov. (Morchella sect. Distantes) is a new species of true morels discovered in Switzerland. It is formally described in the present study using an integrative approach based on micro- and macromorphological characteristics, multilocus phylogenetics, and a brief description of its habitat. Molecular analyses clearly indicated that Morchella helvetica is a sister species to M. eximioides, M. angusticeps, and M. confusa. It can be distinguished by the two phylogenetic markers RNA polymerase II subunit 2 (RPB2) and translation elongation factor-1 alpha (TEF1-α). In addition, M. helvetica exhibits particular morphological features, notably the presence of pale hairs on the pileus, a mealy stipe, and darkening ridges when aging. [ABSTRACT FROM AUTHOR]

Background: Spores are highly resistant dormant cells, adapted for survival and dispersal, that can withstand unfavourable environmental conditions for extended periods of time and later reactivate. Understanding the germination process of microbial spores is important in numerous areas including agriculture, food safety and health, and other sectors of biotechnology. Microfluidics combined with high-resolution microscopy allows to study spore germination at the single-cell level, revealing behaviours that would be hidden in standard population-level studies. Methods: Here, we present a microfluidic platform – the so-called four-conditions microfluidic chemostat (4CMC) – for germination studies where spores are confined to monolayers inside microchambers, allowing the testing of four growth conditions in parallel. This platform can be used with multiple species, including non-model organisms, and is compatible with existing image analysis software. Results: In this study, we focused on three soil dwellers, two bacteria and one fungus, and revealed new insights into their germination. We studied endospores of the model bacterium Bacillus subtilis and demonstrated a correlation between spore density and germination in rich media. We then investigated the germination of the obligate-oxalotrophic environmental bacterium Ammoniphilus oxalaticus in a concentration gradient of potassium oxalate, showing that lower concentrations result in more spores germinating compared to higher concentrations. We also used this microfluidic platform to study the soil beneficial filamentous fungus Trichoderma rossicum, showing for the first time that the size of the spores and hyphae increase in response to increased nutrient availability, while germination times remain the same. Discussion: Our platform allows to better understand microbial behaviour at the single-cell level, under a variety of controlled conditions. While we used it to decipher the responsiveness of soil dwellers' spores, it would also be suitable for other spores from bacteria or filamentous fungi, but also vegetative cells and yeast, and even microbial communities. [ABSTRACT FROM AUTHOR]

Filamentous fungi and fungal-like organisms contribute to a wide range of important ecosystem functions. Evidence has shown the movement of liquid across mycelial networks in unsaturated environments, such as soil. However, tools to investigate liquid movement along hyphae at the level of the single cell are still lacking. Microfluidic devices permit the study of fungal and fungal-like organisms with cellular resolution as they can confine hyphae to a single optical plane, which is compatible with microscopy imaging over longer timescales and allows for precise control of the microchannel environment. The aim of this study was to develop a method that enables the visualization and quantification of liquid movement on hyphae of fungal and fungal-like microorganisms. For this, the fungal–fungal interaction microfluidic device was modified to allow for the maintenance of unsaturated microchannel conditions. Fluorescein-containing growth medium solidified with agar was used to track liquid transported by hyphae via fluorescence microscopy. Our key findings highlight the suitability of this novel methodology for the visualization of liquid movement by hyphae over varying time scales and the ability to quantify the movement of liquid along hyphae. Furthermore, we showed that at the cellular level, extracellular movement of liquid along hyphae can be bidirectional and highly dynamic, uncovering a possible link between liquid movement and hyphal growth characteristics. We envisage that this method can be applied to facilitate future research probing the parameters contributing to hyphal liquid movement and is an essential step for studying the phenomenon of fungal highways. [ABSTRACT FROM AUTHOR]

One of the most challenging types of artifact occurring within museum collections is unstable chloride-contaminated archaeological iron. A high chloride concentration causes cracking, flaking and leads to full mineralization, in effect making objects fragile. Consequently, removal of chloride ions plays a key role in stabilization treatment, while preserving the integrity of the corroded iron object. Despite the variety of stabilization methods, all have significant disadvantages, including a lack of sustainability. Within the framework of the Horizon Europe project GoGreen the potential of microbial biosorption to stabilize archaeological iron artefacts is being investigated. Dry biomass of the fungi Meyerozyma sp. and Saccharomyces cerevisiae was studied to remove chloride ions. Preliminary tests were carried out on artificially-aged steel samples. To assess the activities of the microorganisms' functional groups and biosorption capabilities as a potential green stabilization treatment, analytical techniques including FTIR, Raman spectroscopy, and SEM-EDX were used. The results demonstrate two promising paths for the development of green stabilization treatments based on fungal biomass: passive adsorption into the cell wall and conversion of reactive corrosion products into more stable compounds. The use of microbial biomass opens up promising perspectives for the development of more sustainable solutions in archaeological iron stabilization, while avoiding the generation of toxic waste in our environment. [ABSTRACT FROM AUTHOR]

The effect of three plant growth-promoting Bacillus strains inoculated either alone or as a consortium was tested on oat (Avena sativa) growth. The bioinoculants were applied as vegetative cells or endospores at low cell densities on the seeds and their effect was tested in sterile in vitro conditions, pot experiments, and a field trial. The in vitro seed germination assay showed that both individual bacterial inocula and bacterial consortia had positive effects on seed germination. Greenhouse pot experiments with sterile and non-sterile soil showed that consortia increased the total dry biomass of oat plants as compared to single strain inoculation and uninoculated controls. However, the positive impact on plant growth was less prominent when the bioinoculated strains had to compete with native soil microbes. Finally, the field experiment demonstrated that the consortium of vegetative cells was more efficient in promoting oat growth than the endospore consortium and the uninoculated control. Moreover, both consortia successfully colonized the roots and the rhizosphere of oat plants, without modifying the overall structure of the autochthonous soil microbial communities. [ABSTRACT FROM AUTHOR]

Bacteria swim and swarm by rotating the micrometers long, helical filaments of their flagella. They change direction by reversing their flagellar rotation, which switches the handedness of the filament's supercoil. So far, all studied functional filaments are composed of a mixture of L- and R-state flagellin monomers. Here we show in a study of the wild type Firmicute Kurthia sp., that curved, functional filaments can adopt a conformation in vivo that is closely related to a uniform, all-L-state. This sheds additional light on transitions of the flagellar supercoil and uniquely reveals the atomic structure of a wild-type flagellar filament in vivo, including six residues showing clearly densities of O-linked glycosylation. [ABSTRACT FROM AUTHOR]