Activity and Diversity of Microorganisms in Root Zone of Plant Species Spontaneously Inhabiting Smelter Waste Piles

Ecogenomic insights into the resilience of keystone Blastococcus Species in extreme environments: a comprehensive analysis

BACKGROUND

The stone-dwelling genus Blastococcus plays a key role in ecosystems facing extreme conditions such as drought, salinity, alkalinity, and heavy metal contamination. Despite its ecological significance, little is known about the genomic factors underpinning its adaptability and resilience in such harsh environments. This study investigates the genomic basis of Blastococcus's adaptability within its specific microniches, offering insights into its potential for biotechnological applications.

RESULTS

Comprehensive pangenome analysis revealed that Blastococcus possesses a highly dynamic genetic composition, characterized by a small core genome and a large accessory genome, indicating significant genomic plasticity. Ecogenomic assessments highlighted the genus's capabilities in substrate degradation, nutrient transport, and stress tolerance, particularly on stone surfaces and archaeological sites. The strains also exhibited plant growth-promoting traits, enhanced heavy metal resistance, and the ability to degrade environmental pollutants, positioning Blastococcus as a candidate for sustainable agriculture and bioremediation. Interestingly, no correlation was found between the ecological or plant growth-promoting traits (PGPR) of the strains and their isolation source, suggesting that these traits are not linked to their specific environments.

CONCLUSIONS

This research highlights the ecological and biotechnological potential of Blastococcus species in ecosystem health, soil fertility improvement, and stress mitigation strategies. It calls for further studies on the adaptation mechanisms of the genus, emphasizing the need to validate these findings through wet lab experiments. This study enhances our understanding of microbial ecology in extreme environments and supports the use of Blastococcus in environmental management, particularly in soil remediation and sustainable agricultural practices.

Blastococcus brunescens sp. nov., a member of the Geodermatophilaceae isolated from sandstone collected from the Sahara Desert in Tunisia

The taxonomic position of strain BMG 8361T, isolated from sandstone collected in the Sahara Desert of Southern Tunisia, was refined through a polyphasic taxonomic investigation. Colonies of BMG 8361T were pale-orange coloured, irregular with a dry surface and produced a diffusible pink or brown pigment depending on media. The Gram-positive cells were catalase-positive and oxidase-negative. The strain exhibited growth at 10-40 °C and pH values ranging from 5.5 to 9.0, with optima at 28-35 °C and pH 6.5-8.0. Additionally, BMG 8361T demonstrated the ability to grow in the presence of up to 1 % NaCl (w/v) concentration. The peptidoglycan of the cell wall contained meso-diaminopimelic acid, glucose, galactose, xylose, ribose, and rhamnose. The predominant menaquinones consisted of MK-9(H4) and MK-9. The main polar lipids were phosphatidylcholine, phosphatidylinositol, glycophosphatidylinositol, diphosphatidylglycerol, phosphatidylethanolamine, and two unidentified lipids. Major cellular fatty acids were iso-C16 : 0, iso-C16 : 1 h, and C17 : 1  ω8c. Phylogenetic analyses based on both the 16S rRNA gene and whole-genome sequences assigned strain BMG 8361T within the genus Blastococcus. The highest pairwise sequence similarity observed in the 16S rRNA gene was 99.5 % with Blastococcus haudaquaticus AT 7-14T. However, when considering digital DNA-DNA hybridization and average nucleotide identity, the highest values, 48.4 and 86.58 %, respectively, were obtained with Blastococcus colisei BMG 822T. These values significantly undershoot the recommended thresholds for establishing new species, corroborating the robust support for the distinctive taxonomic status of strain BMG 8361T within the genus Blastococcus. In conjunction with the phenotyping results, this compelling evidence leads to the proposal of a novel species we named Blastococcus brunescens sp. nov. with BMG 8361T (=DSM 46845T=CECT 8880T) as the type strain.

Technogenic soil salinisation, vegetation, and management shape microbial abundance, diversity, and activity

The importance of the microbiome in the functioning of degraded lands in industrialised zones is significant. However, little is known about how environmental parameters affect microbial abundance, structure, diversity, and especially specific guilds involved in the nitrogen cycle in saline soils influenced by the soda industry. To address this knowledge gap, our research focused on assessing the microbiota in relation to soil properties and plant species composition across two transects representing different types of land use: saline wasteland and arable fields. Our findings show that the microbial communities were the most affected not only by soil salinity but also by pH and the composition of plant species. Taxonomic variability was the most shaped by salinity together with management type and CaCO3 content. The impact of salinity on the soil microbiome was manifested in a reduced abundance of bacteria and fungi, a lower number of observed phylotypes, reduced modularity, and a lower abundance of the nitrifying guild. Denitrification and nitrogen fixation were less affected by salinity. The last process was correlated with calcium carbonate. CaCO3 was also associated with microbial taxonomic variability and the overall microbial activity caused by hydrolases, which could aid organic matter turnover in saline but carbonate-rich sites. Bacterial genera such as Bacillus, Peanibacillus, and Rhodomicrobium, in addition to fungal taxa such as Cadophora, Mortierella globalpina, Preussia flanaganii, and Chrysosporium pseudomerdarium, show potential as favourable candidates for possible bioremediation initiatives. These results can be applied to future land reclamation projects. FUNDING INFORMATION: This research received no specific grant from funding agencies in the public, commercial, or not-for-profit sectors.

Blastococcus carthaginiensis sp. nov., isolated from a monument sampled in Carthage, Tunisia

A comprehensive polyphasic investigation was conducted to elucidate the taxonomic position of an actinobacterium, designated BMG 814T, which was isolated from the historic ruins of Carthage city in Tunisia. It grew as pink-orange pigmented colonies and displayed versatile growth capabilities, thriving within a temperature range of 20-40 °C, across a pH spectrum ranging from pH 5.5 to 10 and in the presence of up to 4 % NaCl. Chemotaxonomic investigations unveiled specific cell components, including diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylinositol, glycophosphatidylinositol, an unidentified aminoglycophospholipid, six unidentified aminolipids, two unidentified phospholipids and one unidentified lipid in its polar lipid profile. Furthermore, galactose, glucose and ribose were identified as the primary cell-wall sugars. Major menaquinones identified were MK-9(H4), MK-9(H2) and MK-9, while major fatty acids comprised iso-C15 : 0, iso-C16 : 0, C17 : 1  ω8c and C18 : 1  ω9c. Through phylogenetic analysis based on the 16S rRNA gene sequence, the strain was positioned within the genus Blastococcus, with Blastococcus capsiensis BMG 804T showing the closest relationship (99.1 %). In light of this, draft genomes for both strains, BMG 814T and BMG 804T, were sequenced in this study, and comparative analysis revealed that strain BMG 814T exhibited digital DNA-DNA hybridization and average nucleotide identity values below the recommended thresholds for demarcating new species with all available genomes of type strains of validly names species. Based on the polyphasic taxonomy assessment, strain BMG 814T (=DSM 46848T=CECT 8878T) was proposed as the type strain of a novel species named Blastococcus carthaginiensis sp. nov.

Long-term improvement of sediment in situ restoration and REDOX characteristics by Vallisneria natans coupling with carbon fiber

China is conducting ecological restoration work in urban water bodies. Under anoxic and anaerobic conditions, pollutants transform and produce odorous and black substances, deteriorating the water quality, which is a significant problem in urban water bodies. Vallisneria natans has received widespread attention for its applications in water treatment and restoration. However, the efficiency by which V. natans reduces water pollution and allows sediment remediation requires further improvement. Therefore, in this study, we investigated the effect of V. natans coupled with carbon fiber on the restoration of water bodies and sediment compared with the control group that grew V. natans without carbon fiber. The oxidation-reduction potential (ORP) was selected as the main evaluation index for the water and sediment. Dissolved oxygen in the water and total organic carbon and total nitrogen (TN) in the sediment were also evaluated. V. natans coupled with carbon fiber significantly increased the ORP; that of surface sediment increased by 50 % and that of the water body increased by 60 % compared with the sediment without any bioremediation. Chemical oxygen demand, total phosphorous, and TN in water decreased by 61.2 %, 22.9 %, and 48.3 %, respectively. These results indicate that planting V. natans with carbon fiber can reduce pollutants in water (including humus) and sediments, effectively improving ORP in water and sediment.

Microbial Community Response to Various Types of Exogenous Organic Matter Applied to Soil

Recycling of solid biowaste and manure would reduce the dependence of agriculture on synthetic products. Most of the available studies on the effects of exogenous organic matter (EOM) application to soil were focused on nutrients and crop yield, with much less attention to microbiological processes in soil, especially using modern molecular methods. The aim of this study was to evaluate the effects of various types of manure, sewage sludge and bottom sediment on the biochemical activity and biodiversity of soil and plant yield in a pot experiment. The soil was treated with a range of EOM types: six types of manure (cattle, pig, goat, poultry, rabbit and horse manure; two bottom sediments (from urban and rural systems); and two types of municipal sewage sludge. All EOMs stimulated dehydrogenases activity at a rate of 20 t ha-1. Alkaline phosphatase was mostly stimulated by poultry manure and one of the sludges. In general, the two-fold greater rate of EOMs did not further accelerate the soil enzymes. The functional diversity of the soil microbiome was stimulated the most by cattle and goat manure. EOMs produce a shift in distribution of the most abundant bacterial phyla and additionally introduce exogenous bacterial genera to soil. Poultry and horse manure introduced the greatest number of new genera that were able to survive the strong competition in soil. EOMs differentiated plant growth in our study, which was correlated to the rate of nitrate release to soil. The detailed impacts of particular amendments were EOM-specific, but in general, no harm for microbial parameters was observed for manure and sludge application, regardless of their type. There was also no proof that the PAH and pesticide contents measured in manure or sludge had any effect on microbial activity and diversity.

Soil microbial community assembly model in response to heavy metal pollution

Heavy metal pollution affected the stability and function of soil ecosystem. The impact of heavy metals on soil microbial community and the interaction of microbial community has been widely studied, but little was known about the response of community assembly to the heavy metal pollution. In this study, we collected 30 soil samples from non (CON), moderately (CL) and severely (CH) contaminated fields. The prokaryotic community was studied using high-throughput Illumina sequencing of 16s rRNA gene amplicons, and community assembly were quantified using phylogenetic-bin-based null approach (iCAMP). Results showed that diversity and composition of both bacterial and archaeal community changed significantly in response to heavy metal pollution. The microbial community assembly tended to be more deterministic with the increase of heavy metal concentration. Among the assembly processes, the relative importance of homogeneous selection (deterministic process) increased significantly (increased by 16.2%), and the relative importance of drift and dispersal limitation (stochastic process) decreased significantly (decreased by 11.4% and 5.4%, respectively). The determinacy of bacterial and archaeal community assembly also increased with heavy metal stress, but the assembly models were different. The deterministic proportion of microorganisms tolerant to heavy metals, such as Thiobacillus, Euryarchaeota and Crenarchaeota (clustered in bin 32, bin59 and bin60, respectively) increased, while the stochastic proportion of microorganisms sensitive to heavy metals, such as Koribacteraceae (clustered in bin23) increased. Therefore, the heavy metal stress made the prokaryotic community be deterministic, however, the effects on the assembly process of different microbial groups differed obviously.

Coupling of desorption of phenanthrene from marine sediments and biodegradation of the sediment washing solution in a novel biochar immobilized-cell reactor

The recurrent dredging of marine sediments needs the use of ex-situ technologies such as sediment washing (SW) to effectively remove polycyclic aromatic hydrocarbons. Notwithstanding, the large volumes of generated spent SW effluents require adequate treatment by employing highly-efficient, inexpensive and environmentally-friendly solutions. This study proposes the phenanthrene (PHE) desorption from sediments using Tween® 80 (TW80) as extracting agent and the treatment of the resulting spent SW solution in a biochar (BC) immobilized-cell bioreactor. The SW process reached the highest PHE removal of about 91% using a surfactant solution containing 10,800 mg L^-1 of TW80. The generated amount of spent PHE-polluted SW solution can be controlled by keeping a solid to liquid ratio of 1:4. A PHE degradation of up to 96% was subsequently achieved after 43 days of continuous reactor operation, aerobically treating the TW80 solution in the BC immobilized-cell bioreactor with a hydraulic retention time of 3.5 days. Brevundimonas, Chryseobacterium, Dysgonomonas, Nubsella, and both uncultured Weeksellaceae and Xanthobacteraceae genera were mainly involved in PHE biodegradation. A rough economic study showed a total cost of 342.60 € ton^-1 of sediment, including the SW operations, TW80 and BC supply and the biological treatment of the SW solution.

Rhizosphere Microbial Communities and Geochemical Constraining Mechanism of Antimony Mine Waste-Adapted Plants in Southwestern China

Antimony (Sb) and arsenic (As) are two hazardous metalloid elements, and the biogeochemical cycle of Sb and As can be better understood by studying plant rhizosphere microorganisms associated with Sb mine waste. In the current study, samples of three types of mine waste—Sb mine tailing, waste rocks, and smelting slag—and associated rhizosphere microorganisms of adapted plants were collected from Qinglong Sb mine, southwest China. 16S rRNA was sequenced and used to study the composition of the mine waste microbial community. The most abundant phylum in all samples was Proteobacteria, followed by Bacteroidota, Acidobacteriota, and Actinobacteriota. The community composition varied among different mine waste types. Gammaproteobacteria was the most abundant microorganism in tailings, Actinobacteria was mainly distributed in waste rock, and Saccharimonadia, Acidobacteriae, and Ktedonobacteria were mainly present in slag. At the family level, the vast majority of Hydrogenophilaceae were found in tailings, Ktedonobacteraceae, Chthoniobacteraceae, and Acidobacteriaceae (Subgroup 1) were mostly found in slag, and Pseudomonadaceae and Micrococcaceae were mainly found in waste rock. Actinobacteriota and Arthrobacter are important taxa for reducing heavy metal(loid) mobility, vegetation restoration, and self-sustaining ecosystem construction on antimony mine waste. The high concentrations of Sb and As reduce microbial diversity.

The Effect of Sample Preparation and Measurement Techniques on Heavy Metals Concentrations in Soil: Case Study from Kraków, Poland, Europe

Accurate and reliable laboratory results are an extremely important and integral part of conducting scientific research. Many factors influence the results obtained, including the type of determination method, accuracy and precision of measurements, and laboratory equipment used for the tests. This paper presents the results of measurements of heavy metal concentration in soil using two methods for adding soil components into solution and different laboratory methods and types of measuring equipment. The first method used was hot digestion of soil samples with a mixture of concentrated HNO3 and HClO4, after prior ashing of organic matter (IUNG method). The second method was a two-stage decomposition, where soil samples were hot digested, initially with oxidizing acid (HNO3) and subsequently with non-oxidizing acid (HF) (two-stage decomposition). The concentrations of selected heavy metals (Cr, Cu, Fe, Mn, Ni, Pb and Zn) were determined in solutions obtained by both digestion methods. The solutions obtained from soil decomposition were determined twice using atomic absorption spectrometry (AAS) and inductively coupled plasma mass spectrometry (ICP MS) methods in different laboratories using different types of spectrometers. In most cases, the measured concentrations of heavy metals are the highest for the two-stage solution samples and the measurements of their concentrations carried out using ICP. The exceptions are the measurements of Cu and Ni concentrations. In the case of Cu, lack of significant differentiation in concentrations of this metal may result from different forms of occurrence of Cu in soil than in the case of other metals. For Ni, however, a reversal of the trends seen for the other metals is observed and the type of spectrometer used for measurements is important. There may be an interference of the spectrometric spectrum of Ni with the spectra of the other determined metals. However, this is not clear at the present stage of the study. In conclusion, the results of this study indicate that the choice of soil sample preparation and the type of spectrometer used for measurements can, in many cases, determine the value of laboratory results, even if it is in an expected range of standard material. Research of published papers proved that most of them show only results based on one selected course of methodology without comparison with others. The novelty of the paper is the comparison of the measurements of heavy metal concentration in soil using two methods for adding soil components into solution and different laboratory methods and types of measuring equipment. Additionally, the article includes a discussion of the importance of methodology. We believe that the conclusions may help to better understand how sample preparation and measurement methods applied may influence the results obtained.

Phylloplane Biodiversity and Activity in the City at Different Distances from the Traffic Pollution Source

The phylloplane is an integrated part of green infrastructure which interacts with plant health. Taxonomic characterization of the phylloplane with the aim to link it to ecosystem functioning under anthropogenic pressure is not sufficient because only active microorganisms drive biochemical processes. Activity of the phylloplane remains largely overlooked. We aimed to study the interactions among the biological characteristics of the phylloplane: taxonomic diversity, functional diversity and activity, and the pollution grade. Leaves of Betula pendula were sampled in Moscow at increasing distances from the road. For determination of phylloplane activity and functional diversity, a MicroResp tool was utilized. Taxonomic diversity of the phylloplane was assessed with a combination of microorganism cultivation and molecular techniques. Increase of anthropogenic load resulted in higher microbial respiration and lower DNA amount, which could be viewed as relative inefficiency of phylloplane functioning in comparison to less contaminated areas. Taxonomic diversity declined with road vicinity, similar to the functional diversity pattern. The content of Zn in leaf dust better explained the variation in phylloplane activity and the amount of DNA. Functional diversity was linked to variation in nutrient content. The fraction of pathogenic fungi of the phylloplane was not correlated with any of the studied elements, while it was significantly high at the roadsides. The bacterial classes Gammaproteobacteria and Cytophagia, as well as the Dothideomycetes class of fungi, are exposed to the maximal effect of distance from the highway. This study demonstrated the sensitivity of the phylloplane to road vicinity, which combines the effects of contaminants (mainly Zn according to this study) and potential stressful air microclimatic conditions (e.g., low relative air humidity, high temperature, and UV level). Microbial activity and taxonomic diversity of the phylloplane could be considered as an additional tool for bioindication.