Population genomics resolves cryptic species of the ecologically flexible genus Laspinema (cyanobacteria).

Cyanobacterial taxonomy is entering the genomic era, but only a few taxonomic studies have employed population genomics, which provides a framework and a multitude of tools to understand species boundaries. Phylogenomic and population genomic analyses previously suggested that several cryptic lineages emerged within the genus Laspinema. Here, we apply population genomics to define boundaries between these lineages and propose two new cryptic species, Laspinema olomoucense and L. palackyanum. Moreover, we sampled soil and puddles across Central Europe and sequenced the 16S rRNA gene and 16S-23S ITS region of the isolated Laspinema strains. Together with database mining of 16S rRNA gene sequences, we determined that the genus Laspinema has a cosmopolitan distribution and inhabits a wide variety of habitats, including freshwater, saline water, mangroves, soil crusts, soils, puddles, and the human body.

The global speciation continuum of the cyanobacterium Microcoleus.

Speciation is a continuous process driven by genetic, geographic, and ecological barriers to gene flow. It is widely investigated in multicellular eukaryotes, yet we are only beginning to comprehend the relative importance of mechanisms driving the emergence of barriers to gene flow in microbial populations. Here, we explored the diversification of the nearly ubiquitous soil cyanobacterium Microcoleus. Our dataset consisted of 291 genomes, of which 202 strains and eight herbarium specimens were sequenced for this study. We found that Microcoleus represents a global speciation continuum of at least 12 lineages, which radiated during Eocene/Oligocene aridification and exhibit varying degrees of divergence and gene flow. The lineage divergence has been driven by selection, geographical distance, and the environment. Evidence of genetic divergence and selection was widespread across the genome, but we identified regions of exceptional differentiation containing candidate genes associated with stress response and biosynthesis of secondary metabolites.

Population genomics and morphological data bridge the centuries of cyanobacterial taxonomy along the continuum of Microcoleus species.

The filamentous cyanobacterium Microcoleus is among the most important global primary producers, especially in hot and cold desert ecosystems. This taxon represents a continuum consisting of a minimum of 12 distinct species with varying levels of gene flow and divergence. The notion of a species continuum is poorly understood in most lineages but is especially challenging in cyanobacteria. Here we show that genomic diversification of the Microcoleus continuum is reflected by morphological adaptation. We compiled a dataset of morphological data from 180 cultured strains and 300 whole genome sequences, including eight herbarium specimens and the type specimen of Microcoleus. We employed a combination of phylogenomic, population genomic, and population-level morphological data analyses to delimit species boundaries. Finally, we suggest that the shape of the filament apices may have an adaptive function to environmental conditions in the soil.

High genomic differentiation and limited gene flow indicate recent cryptic speciation within the genus Laspinema (cyanobacteria).

The sympatric occurrence of closely related lineages displaying conserved morphological and ecological traits is often characteristic of free-living microbes. Gene flow, recombination, selection, and mutations govern the genetic variability between these cryptic lineages and drive their differentiation. However, sequencing conservative molecular markers (e.g., 16S rRNA) coupled with insufficient population-level sampling hindered the study of intra-species genetic diversity and speciation in cyanobacteria. We used phylogenomics and a population genomic approach to investigate the extent of local genomic diversity and the mechanisms underlying sympatric speciation of Laspinema thermale. We found two cryptic lineages of Laspinema. The lineages were highly genetically diverse, with recombination occurring more frequently within than between them. That suggests the existence of a barrier to gene flow, which further maintains divergence. Genomic regions of high population differentiation harbored genes associated with possible adaptations to high/low light conditions and stress stimuli, although with a weak diversifying selection. Overall, the diversification of Laspinema species might have been affected by both genomic and ecological processes.

New cyanobacterial genus Argonema is hidding in soil crusts around the world.

Cyanobacteria are crucial primary producers in soil and soil crusts. However, their biodiversity in these habitats remains poorly understood, especially in the tropical and polar regions. We employed whole genome sequencing, morphology, and ecology to describe a novel cyanobacterial genus Argonema isolated from Antarctica. Extreme environments are renowned for their relatively high number of endemic species, but whether cyanobacteria are endemic or not is open to much current debate. To determine if a cyanobacterial lineage is endemic is a time consuming, elaborate, and expensive global sampling effort. Thus, we propose an approach that will help to overcome the limits of the sampling effort and better understand the global distribution of cyanobacterial clades. We employed a Sequencing Read Archive, which provides a rich source of data from thousands of environmental samples. We developed a framework for a characterization of the global distribution of any microbial species using Sequencing Read Archive. Using this approach, we found that Argonema is actually cosmopolitan in arid regions. It provides further evidence that endemic microbial taxa are likely to be much rarer than expected.

Case Study upon Foliar Application of Biofertilizers Affecting Microbial Biomass and Enzyme Activity in Soil and Yield Related Properties of Maize and Wheat Grains.

This study evaluated the effects of the application of microbial inoculants (N-fixing Klebsiella planticola and Enterobacter spp.), two rates of composite mineral fertilizers, and their combination on microbial biomass carbon (MBC), dehydrogenase (DHA), and proteinase activity (PTA) in Lessivated Cambisol and yield-related properties of maize and wheat grains in a two-year trial. Unfertilized soil was used as a control variant. MBC was measured using the chloroform fumigation-extraction method, DHA was determined spectrophotometrically by measuring the intensity of the formed red-colored triphenyl formazan, while PTA was determined using a titration method by measuring the degree of gelatine decomposition. In grain samples, P was determined spectrophotometrically, K-by flame emission photometry, N-on an elemental carbon/nitrogen/sulfur (CNS) analyzer, and crude proteins-by calculation of N content. Measuring both crops' yield was carried out at the end of the vegetation. The results indicated that mineral fertilizers are not, in general, negative for soil microbiota when used in the context of sustainable agriculture without monoculture. There is a significant increase in the values of soil MBC, DHA, and PTA in the variants with combined application of bacterial inoculants and lower rates of mineral fertilizers. The highest values of these parameters were determined in the period with a better distribution of precipitation during the vegetation period of the year. The mentioned combination also resulted in a higher grain yield of maize and wheat comparing to the application of lower rates of the NPK nutrients solely. The combined application of high rates of mineral fertilizers and bacterial inoculants resulted in significantly increased N, P, K, and protein content in the grains of crops, and the same applied to yield. Concluding, studied bacterial inoculants can be used to specify the replacement of nitrogen fertilizers, stimulating the microbial biomass and enzyme activity in the soil, helping to ensure that the supply of nutrients contributing to an optimized yield of crops is maintained.

Oxidative Stress, Endoparasite Prevalence and Social Immunity in Bee Colonies Kept Traditionally vs. Those Kept for Commercial Purposes.

Commercially and traditionally managed bees were compared for oxidative stress (superoxide dismutase (SOD), catalase (CAT), glutathione S-transferase (GST) and malondialdehyde (MDA)), the prevalence of parasites (Lotmaria passim, Crithidia mellificae and Nosema ceranae/apis) and social immunity (glucose oxidase gene expression). The research was conducted on Pester plateau (Serbia-the Balkan Peninsula), on seemingly healthy colonies. Significant differences in CAT, GST and SOD activities (p < 0.01), and MDA concentrations (p < 0.002) were detected between commercial and traditional colonies. In the former, the prevalence of both L. passim and N. ceranae was significantly (p < 0.05 and p < 0.01, respectively) higher. For the first time, L. passim was detected in honey bee brood. In commercial colonies, the prevalence of L. passim was significantly (p < 0.01) lower in brood than in adult bees, whilst in traditionally kept colonies the prevalence in adult bees and brood did not differ significantly. In commercially kept colonies, the GOX gene expression level was significantly (p < 0.01) higher, which probably results from their increased need to strengthen their social immunity. Commercially kept colonies were under higher oxidative stress, had higher parasite burdens and higher GOX gene transcript levels. It may be assumed that anthropogenic influence contributed to these differences, but further investigations are necessary to confirm that.

Microelements and Heavy Metals Content in Frequently Utilized Medicinal Plants Collected from the Power Plant Area.

The effectiveness of medicinal plants is mainly associated with their active constituents, but one of the major quality problems frequently encountered is their high trace metals content that can be associated to extensive pollution of the environment where medicinal plants grow. Therefore the aim of this research was to evaluate the content of Cd, Co, Cr, Cu, Fe, Mn, Ni, Pb, Zn and As in selected and frequently used medicinal plants, including chicory, broadleaf, common comfrey and dandelion. The plant material was collected from their wild habitats in the area of highly developed power plant activity during the summer of 2015. Plant analyses were done according to ICP methodology, using ICAP 6300 ICP optical emission spectrometer. The obtained results showed that the content of As, Cd, Co, Mn, Ni and Zn in the investigated medicinal plant species was below the maximum permissible concentration, while in all parts of all studied plants the concentration of Cr was toxic. The toxic concentrations of Cu were determined in root and aerial parts of chicory and common comfrey, and the toxic concentrations of Fe in root and aerial parts of dandelion and broadleaf plantain, and in aerial parts of common comfrey. However, high but not toxic content of Pb was found in aerial parts of chicory. It can be concluded that medicinal plants from the studied growing site are not appropriate for use in alternative medicine and that a determination of trace metals content in these plants must become a standard criterion for evaluation of their quality.