Selenium hyperaccumulators harbor a diverse endophytic bacterial community characterized by high selenium resistance and plant growth promoting properties

Metabolism Interaction Between Bacillus cereus SESY and Brassica napus Contributes to Enhance Host Selenium Absorption and Accumulation

The use of beneficial bacteria to enhance selenium absorption in crops has been widely studied. However, it is unclear how the interaction between bacteria and plants affects selenium absorption in crops. Here, pot experiments and Murashige and Skoog medium (MS) experiments were performed. Transcriptomic analyses were used to reveal the interaction between Bacillus cereus SESY and Brassica napus. The results indicated that B. cereus SESY can significantly increase the biomass and selenium content of B. napus. The genes related to the colonization, IAA synthesis, and l-cysteine synthesis and metabolism of B. cereus SESY were significantly stimulated by B. napus through transcriptional regulation. Further verification results showed that l-cysteine increased selenium content in B. napus roots and shoots by 62.9% and 88.4%, respectively. B. cereus SESY and l-cysteine consistently regulated the relative expression level of genes involved in plant hormone, amino acid metabolism, selenium absorption, and Se enzymatic and nonenzymatic metabolic pathway of B. napus. These genes were significantly correlated with selenium content and biomass of B. napus (p < 0.05). Overall, IAA biosynthesis, and l-cysteine biosynthesis and metabolism in B. cereus SESY stimulated by interactions triggered molecular and metabolic responses of B. napus, underpinning host selenium absorption and accumulation.

Endophytic microbial communities and functional shifts in Hemarthria compressa grass in response to Silicon and Selenium amendment

BACKGROUND

Hemarthria compressa, a widely cultivated forage grass, is critical for supporting livestock production and maintaining the ecological balance in grassland ecosystems. Enhancing its stress resistance and productivity is crucial for sustainable grassland utilization and development. Silicon (Si) and Selenium (Se) are recognized as beneficial nutrients that promote plant growth and stress tolerance, and modulate of plant-microorganism interactions. However, the intricate linkages between the endophytes shifts and host grass growth induced by Si/Se amendments are poorly understood. In this study, a pot experiment was conducted to examine the effects of foliar-applied Si/Se on the growth and nutritional quality of H. compressa grass, as well as the composition, diversity and potential functions of endophytic bacteria in leaves.

RESULTS

Both Si and Se treatments significantly improved grass biomass by approximately 17%. Nutritional quality was also improved, with Si application increased plant Si and neutral detergent fiber contents by 25.6% and 5.8%, while Se significantly enhanced the grass Se content from 0.055 mg kg-1 to 0.636 mg kg-1. Furthermore, Si/Se amendments altered the structure of the leaf endophytic bacterial community, resulting in an increased alpha diversity and a more modularized co-occurrence network. Moreover, both Si and Se treatments enriched plant growth-promoting bacterial genera such as Brevundimonas and Truepera. Metabolic function analysis revealed that Si application promoted chlorophyllide biosynthesis by 152%, several carbon metabolism pathways by 35-152%, and redox-related pathways by 57-93%, while the starch biosynthesis pathway was downregulated by 79% of the endophytic bacterial community. In contrast, Se application mainly enhanced starch degradation, CMP-legionamine biosynthesis by 71% and TCA cycle-related pathways by 23-58%, while reducing L-threonine metabolism by 98%. These specific functional changes in the endophytic bacteria induced by Si/Se amendments were closely linked with the observed growth promotion and stress resistance of the host H. compressa grass.

CONCLUSIONS

Si and Se amendments not only enhanced the growth and nutritional quality of H. compressa grass, but also altered the community structure and functional traits of endophytic bacteria in grass. The enrichment of beneficial endophytes and the modification of community metabolic functions within the endophytic community may play important synergistic effects on improving grass growth.

Hyperaccumulation of nickel but not selenium drives floral microbiome differentiation: A study with six species of Brassicaceae

PREMISE

Intraspecific variation in flower microbiome composition can mediate pollination and reproduction, and so understanding the community assembly processes driving this variation is critical. Yet the relative importance of trait-based host filtering and dispersal in shaping among-species variation in floral microbiomes remains unknown.

METHODS

Within two clades of Brassicaceae, we compared diversity and composition of floral microbiomes in natural populations of focal nickel and selenium hyperaccumulator species and two of their non-accumulating relatives. We assessed the relative strengths of floral elemental composition, plant phylogenetic distance (host filtering), and geography (dispersal) in driving floral microbiome composition.

RESULTS

Species in the nickel hyperaccumulator clade had strongly divergent floral microbiomes, the most of that variation driven by floral elemental composition, followed by geographic distance between plant populations and, lastly, phylogenetic distance. Conversely, within the selenium hyperaccumulator clade, floral microbiome divergence was much lower among the species and elemental composition, geography, and plant phylogeny were far weaker determinants of microbiome variation.

CONCLUSIONS

Our results show that the strength of elemental hyperaccumulation's effect on floral microbiomes differs substantially among plant clades, possibly due to variation in elements as selective filters or in long-distance dispersal probability in different habitats.

Selenium spatial distribution and bioavailability of soil-plant systems in China: a comprehensive review

Selenium (Se) has a dual nature, with beneficial and harmful effects on plants, essential for both humans and animals, playing a crucial role in ecosystem regulation. Insufficient Se in specific terrestrial environments raises concerns due to its potential to cause diseases, while excess Se can lead to severe toxicity. Thus, maintaining an optimal Se level is essential for living organisms. This review focuses first on Se transformation, speciation, and geochemical properties in soil, and then provides a concise overview of Se distribution in Chinese soil and crops, with a focus on the relationship between soil Se levels and parent materials. Additionally, this paper explores Se bioavailability, considering parent materials and soil physicochemical properties, using partial least squares path modeling for analysis. This paper aimed to be a valuable resource for effectively managing Se-enriched soil resources, contributing to a better understanding of Se role in ecosystems.

Diversity and functional traits of seed endophytes of Dysphania ambrosioides from heavy metal contaminated and non-contaminated areas

Seed endophytes played a crucial role on host plants stress tolerance and heavy metal (HM) accumulation. Dysphania ambrosioides is a hyperaccumulator and showed strong tolerance and extraordinary accumulation capacities of multiple HMs. However, little is known about its seed endophytes response to field HM-contamination, and its role on host plants HM tolerance and accumulation. In this study, the seed endophytic community of D. ambrosioides from HM-contaminated area (H) and non-contaminated area (N) were investigated by both culture-dependent and independent methods. Moreover, Cd tolerance and the plant growth promoting (PGP) traits of dominant endophytes from site H and N were evaluated. The results showed that in both studies, HM-contamination reduced the diversity and richness of endophytic community and changed the most dominant endophyte, but increased resistant species abundance. By functional trait assessments, a great number of dominant endophytes displayed multiple PGP traits and Cd tolerance. Interestingly, soil HM-contamination significantly increased the percentage of Cd tolerance isolates of Agrobacterium and Epicoccum, but significantly decreased the ration of Agrobacterium with the siderophore production ability. However, the other PGP traits of isolates from site H and N showed no significant difference. Therefore, it was suggested that D. ambrosioides might improve its HM tolerance and accumulation through harboring more HM-resistant endophytes rather than PGP endophytes, but to prove this, more work need to be conducted in the future.

Cadmium levels and soil pH drive structure and function differentiation of endophytic bacterial communities in Sedum plumbizincicola: A field study

Sedum plumbizincicola is a promising hyperaccumulator for heavy metal phytoremediation. It grows in heavy metal polluted soil and stores specific endophyte resources with heavy metal tolerance or growth promotion characteristics. In this study, the endophyte communities of S. plumbizincicola, growing naturally in the field (two former mining locations and one natural location) were investigated, and their structure and function were comparatively studied. The bioaccumulation and translocation characteristics of cadmium (Cd) and selenium (Se) in S. plumbizincicola were also evaluated. The results showed that the heavy metal pollution reduced the richness and diversity of endophyte communities. Soil pH and Cd concentration could be the key factors affecting the composition of the endophyte community. Co-occurrence network analysis identified that 22 keystone taxa belonging to Actinobacteriota, Firmicutes, Myxococcota and Proteobacteria were positively correlated with Cd bioaccumulation and translocation. The predicted endophyte metabolic pathways were enriched in physiological metabolism, immune system, and genetic Information processing. These findings may help to understand how endophytes assist host plants to enhance their adaptability to harsh environments, and provide a basis for further exploration of plant-endophyte interactions and improvement in phytoremediation efficiency.

Comparative assessment of bacterial diversity and composition in arsenic hyperaccumulator, Pteris vittata L. and non-accumulator, Pteris ensiformis Burm

The use of arsenic (As) for various industrial and agricultural applications has led to worldwide environmental contamination. Phytoremediation using hyperaccumulators is a sustainable soil As mitigation strategy. Microbial processes play an important role in the tolerance and uptake of trace elements such as in plants. The rhizospheric and endophytic microbial communities are responsible for accelerating the mobility of trace elements around the roots and the production of plant growth-promoting compounds and enzymes. Several studies have reported that the As hyperaccumulator, Pteris vittata L. (PV) influences the microbial community in its rhizosphere and roots. Deciphering the differences in the microbiomes of hyperaccumulators and non-accumulators is crucial in understanding the mechanism of hyperaccumulation. We hypothesized that there are significant differences in the microbiome of roots, rhizospheric soil, and bulk soil between the hyperaccumulator PV and a non-accumulator of the same genus, Pteris ensiformis Burm. (PE), and that the differential recruitment of bacterial communities provides PV with an advantage in As contaminated soil. We compared root endophytic, rhizospheric, and bulk soil microbial communities between PV and PE species grown in As-contaminated soil in a greenhouse setting. There was a significant difference (p < 0.001) in the microbiome of the three compartments between the ferns. Differential abundance analysis showed 328 Amplicon Sequence Variants (ASVs) enriched in PV compared to 172 in PE. The bulk and rhizospheric soil of both ferns were abundant in As-resistant genera. However, As-tolerant root endophytic genera were present in PV but absent in PE. Our findings show that there is a difference between the bacterial composition of an As hyperaccumulator and a non-accumulator species grown in As-contaminated soil. These differences need to be further explored to develop strategies for improving the efficiency of metal uptake in plants growing in As polluted soil.

Differences and similarities in selenium biopathways in Astragalus, Neptunia (Fabaceae) and Stanleya (Brassicaceae) hyperaccumulators

BACKGROUND AND AIMS

Selenium hyperaccumulator species are of primary interest for studying the evolution of hyperaccumulation and for use in biofortification because selenium is an essential element in human nutrition. In this study, we aimed to determine whether the distributions of selenium in the three most studied hyperaccumulating taxa (Astragalus bisulcatus, Stanleya pinnata and Neptunia amplexicaulis) are similar or contrasting, in order to infer the underlying physiological mechanisms.

METHODS

This study used synchrotron-based micro-X-ray fluorescence (µXRF) techniques to visualize the distribution of selenium and other elements in fresh hydrated plant tissues of A. racemosus, S. pinnata and N. amplexicaulis.

KEY RESULTS

Selenium distribution differed widely in the three species: in the leaves of A. racemosus and N. amplexicaulis selenium was mainly concentrated in the pulvini, whereas in S. pinnata it was primarilylocalized in the leaf margins. In the roots and stems of all three species, selenium was absent in xylem cells, whereas it was particularly concentrated in the pith rays of S. pinnata and in the phloem cells of A. racemosus and N. amplexicaulis.

CONCLUSIONS

This study shows that Astragalus, Stanleya and Neptunia have different selenium-handling physiologies, with different mechanisms for translocation and storage of excess selenium. Important dissimilarities among the three analysed species suggest that selenium hyperaccumulation has probably evolved multiple times over under similar environmental pressures in the US and Australia.

Life-cycle selenium accumulation and its correlations with the rhizobacteria and endophytes in the hyperaccumulating plant Cardamine hupingshanensis

Cardamine hupingshanensis (C. hupingshanensis) is known for its ability to hyperaccumulate selenium (Se). However, the roles of the rhizobacteria or endophytes in Se hyperaccumulation have not been explored in C. hupingshanensis. Here, in-situ-like pot experiments were conducted to investigate the characteristics of Se accumulation throughout C. hupingshanensis growth stages and its correlations with rhizobacteria and endophytes under varying soil Se levels. Results showed that Se levels in roots, stems and leaves increased from the seedling to bolting stage, but remained relatively stable during the flowering and maturity. Leaves exhibited the highest Se levels (736.48 ± 6.51 mg/kg DW), followed by stems (575.39 ± 27.05 mg/kg DW), and lowest in roots (306.62 ± 65.45 mg/kg DW) under high-Se stress. The Se translocation factors from soils to C. hupingshanensis roots was significantly higher (p < 0.05) in low-Se soils compared to medium- and high-Se soils. Rhizobacterial diversity showed significant positive correlations (p < 0.05) with both total and bioavailable soil Se contents. The levels of soil Se and growth stages of C. hupingshanensis were found to have significant effects (p < 0.03) on the compositions of rhizosphere bacteria and C. hupingshanensis endophytes. Low-abundance bacteria (< 5%), including Gemmatimonadetes, Latescibacteria and Nitrospirae, were identified to potentially increase the bioavailable Se levels in the rhizosphere. The Se accumulation significantly decreased (p < 0.05) in C. hupingshanensis grown in sterilized low- (32.4%), medium- (17%) and high-Se (42%) soils. Endophytes in C. hupingshanensis, such as Firmicutes and Proteobacteria, were likely recruited from the rhizobacteria, as evidenced by the isolated bacterial strains, and played an important role in Se hyperaccumulation, particularly during the flowering stage. This study provides new insights into potential mechanism underlying Se hyperaccumulation in C. hupingshanensis.

Current Scenario and Future Prospects of Endophytic Microbes: Promising Candidates for Abiotic and Biotic Stress Management for Agricultural and Environmental Sustainability

Globally, substantial research into endophytic microbes is being conducted to increase agricultural and environmental sustainability. Endophytic microbes such as bacteria, actinomycetes, and fungi inhabit ubiquitously within the tissues of all plant species without causing any harm or disease. Endophytes form symbiotic relationships with diverse plant species and can regulate numerous host functions, including resistance to abiotic and biotic stresses, growth and development, and stimulating immune systems. Moreover, plant endophytes play a dominant role in nutrient cycling, biodegradation, and bioremediation, and are widely used in many industries. Endophytes have a stronger predisposition for enhancing mineral and metal solubility by cells through the secretion of organic acids with low molecular weight and metal-specific ligands (such as siderophores) that alter soil pH and boost binding activity. Finally, endophytes synthesize various bioactive compounds with high competence that are promising candidates for new drugs, antibiotics, and medicines. Bioprospecting of endophytic novel secondary metabolites has given momentum to sustainable agriculture for combating environmental stresses. Biotechnological interventions with the aid of endophytes played a pivotal role in crop improvement to mitigate biotic and abiotic stress conditions like drought, salinity, xenobiotic compounds, and heavy metals. Identification of putative genes from endophytes conferring resistance and tolerance to crop diseases, apart from those involved in the accumulation and degradation of contaminants, could open new avenues in agricultural research and development. Furthermore, a detailed molecular and biochemical understanding of endophyte entry and colonization strategy in the host would better help in manipulating crop productivity under changing climatic conditions. Therefore, the present review highlights current research trends based on the SCOPUS database, potential biotechnological interventions of endophytic microorganisms in combating environmental stresses influencing crop productivity, future opportunities of endophytes in improving plant stress tolerance, and their contribution to sustainable remediation of hazardous environmental contaminants.

Selenium in soil-plant system: Transport, detoxification and bioremediation

Selenium (Se) is an essential micronutrient for humans and a beneficial element for plants. However, high Se doses always exhibit hazardous effects. Recently, Se toxicity in plant-soil system has received increasing attention. This review will summarize (1) Se concentration in soils and its sources, (2) Se bioavailability in soils and influencing factors, (3) mechanisms on Se uptake and translocation in plants, (4) toxicity and detoxification of Se in plants and (5) strategies to remediate Se pollution. High Se concentration mainly results from wastewater discharge and industrial waste dumping. Selenate (Se [VI]) and selenite (Se [IV]) are the two primary forms absorbed by plants. Soil conditions such as pH, redox potential, organic matter and microorganisms will influence Se bioavailability. In plants, excessive Se will interfere with element uptake, depress photosynthetic pigment biosynthesis, generate oxidative damages and cause genotoxicity. Plants employ a series of strategies to detoxify Se, such as activating antioxidant defense systems and sequestrating excessive Se in the vacuole. In order to alleviate Se toxicity to plants, some strategies can be applied, including phytoremediation, OM remediation, microbial remediation, adsorption technique, chemical reduction technology and exogenous substances (such as Methyl jasmonate, Nitric oxide and Melatonin). This review is expected to expand the knowledge of Se toxicity/detoxicity in soil-plant system and offer valuable insights into soils Se pollution remediation strategies.

A systematic assessment of matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) application for rapid identification of pathogenic microbes that affect food crops: delivered and future deliverables

MALDI-TOF MS has decades of experience in the detection and identification of microbial pathogens. This has now become a valuable analytical tool when it comes to the identification and detection of clinical microbial pathogens. This review gives a brief synopsis of what has been achieved using MALDI-TOF MS in clinical microbiology. The major focus, however, is on summarizing and highlighting the effectiveness of MALDI-TOF MS as a novel tool for rapid identification of food crop microbial pathogens. The methods used and the sample preparation methodologies reported thus far have been highlighted and the challenges and gaps and recommendations for fine tuning the technique have been put forth. In an era where anything close to the health and welfare of humanity has been considered as the top priority, this review pitches on one such relevant research topics.

Selenium species transforming along soil-plant continuum and their beneficial roles for horticultural crops

Selenium (Se) acquirement from daily diet can help reduce the risk of many diseases. The edible parts of crop plants are the main source of dietary Se, while the Se content in crops is determined by Se bioavailability in soil. We summarize recent research on the biogeochemical cycle of Se driven by specific microorganisms and emphasize the oxidizing process in the Se cycle. Moreover, we discuss how plant root exudates and rhizosphere microorganisms affect soil Se availability. Finally, we cover beneficial microorganisms, including endophytes, that promote crop quality and improve crop tolerance to environmental stresses. Se availability to plants depends on the balance between adsorption and desorption, reduction, methylation and oxidation, which are determined by interactions among soil properties, microbial communities and plants. Reduction and methylation processes governed by bacteria or fungi lead to declined Se availability, while Se oxidation regulated by Se-oxidizing microorganisms increases Se availability to plants. Despite a much lower rate of Se oxidization compared to reduction and methylation, the potential roles of microbial communities in increasing Se bioavailability are probably largely underestimated. Enhancing Se oxidation and Se desorption are crucial for the promotion of Se bioavailability and uptake, particularly in Se-deficient soils. Beneficial roles of Se are reported in terms of improved crop growth and quality, and enhanced protection against fungal diseases and abiotic stress through improved photosynthetic traits, increased sugar and amino acid contents, and promoted defense systems. Understanding Se transformation along the plant-soil continuum is crucial for agricultural production and even for human health.

Micro-analytical and molecular approaches for understanding the distribution, biochemistry, and molecular biology of selenium in (hyperaccumulator) plants

Micro-analytical techniques to untangle Se distribution and chemical speciation in plants coupled with molecular biology analysis enable the deciphering of metabolic pathways responsible for Se tolerance and accumulation. Selenium (Se) is not essential for plants and is toxic at high concentrations. However, Se hyperaccumulator plants have evolved strategies to both tolerate and accumulate > 1000 µg Se g^-1 DW in their living above-ground tissues. Given the complexity of the biochemistry of Se, various approaches have been adopted to study Se metabolism in plants. These include X-ray-based techniques for assessing distribution and chemical speciation of Se, and molecular biology techniques to identify genes implicated in Se uptake, transport, and assimilation. This review presents these techniques, synthesises the current state of knowledge on Se metabolism in plants, and highlights future directions for research into Se (hyper)accumulation and tolerance. We conclude that powerful insights may be gained from coupling information on the distribution and chemical speciation of Se to genome-scale studies to identify gene functions and molecular mechanisms that underpin Se tolerance and accumulation in these ecologically and biotechnologically important plants species. The study of Se metabolism is challenging and is a useful testbed for developing novel analytical approaches that are potentially more widely applicable to the study of the regulation of a wide range of metal(loid)s in hyperaccumulator plants.

Selenium increases photosynthetic capacity, daidzein biosynthesis, nodulation and yield of peanuts plants (Arachis hypogaea L.)

This study aimed to investigate the roles of selenium (Se) application on the profile of photosynthetic pigments, oxidant metabolism, flavonoids biosynthesis, nodulation, and its relation to agronomic traits of peanut plants. Two independent experiments were carried out: one conducted in soil and the other in a nutrient solution. When the plants reached the V2 growth stage, five Se doses (0, 7.5, 15, 30, and 45 μg kg^-1) and four Se concentrations (0, 5, 10, and 15 μmol L^-1) were supplied as sodium selenate. The concentration of photosynthetic pigments, activity of antioxidant enzymes and the concentration of total sugars in peanut leaves increased in response to Se fertilization. In addition, Se improves nitrogen assimilation efficiency by increasing nitrate reductase activity which results in a higher concentration of ureides, amino acids and proteins. Se increases the synthesis of daidzein and genistein in the root, resulting in a greater number of nodules and concentration and transport of ureides to the leaves. Se-treated plants showed greater growth, biomass accumulation in shoots and roots, yield and Se concentration in leaves and grains. Our results contribute to food security and also to increase knowledge about the effects of Se on physiology, biochemistry and biological nitrogen fixation in legume plants.

Selenium: a potent regulator of ferroptosis and biomass production

Emerging evidence supports the notion that selenium (Se) plays a beneficial role in plant development for modern crop production and is considered an essential micronutrient and the predominant source of plants. However, the essential role of selenium in plant metabolism remains unclear. When used in moderate concentrations, selenium promotes plant physiological processes such as enhancing plant growth, increasing antioxidant capacity, reducing reactive oxygen species and lipid peroxidation and offering stress resistance by preventing ferroptosis cell death. Ferroptosis, a recently discovered mechanism of regulated cell death (RCD) with unique features such as iron-dependant accumulation of lipid peroxides, is distinctly different from other known forms of cell death. Glutathione peroxidase (GPX) activity plays a significant role in scavenging the toxic by-products of lipid peroxidation in plants. A low level of GPX activity in plants causes high oxidative stress, which leads to ferroptosis. An integrated view of ferroptosis and selenium in plants and the selenium-mediated nanofertilizers (SeNPs) have been discussed in more recent studies. For instance, selenium supplementation enhanced GPX4 expression and increased TFH cell (Follicular helper T) numbers and the gene transcriptional program, which prevent lipid peroxidase and protect cells from ferroptosis. However, though ferroptosis in plants is similar to that in animals, only few studies have focused on plant-specific ferroptosis; the research on ferroptosis in plants is still in its infancy. Understanding the implication of selenium with relevance to ferroptosis is indispensable for plant bioresource technology. In this review, we hypothesize that blocking ferroptosis cell death improves plant immunity and protects plants from abiotic and biotic stresses. We also examine how SeNPs can be the basis for emerging unconventional and advanced technologies for algae/bamboo biomass production. For instance, algae treated with SeNPs accumulate high lipid profile in algal cells that could thence be used for biodiesel production. We also suggest that further studies in the field of SeNPs are essential for the successful application of this technology for the large-scale production of plant biomass.

Advances in Research on the Involvement of Selenium in Regulating Plant Ecosystems

Selenium is an essential trace element which plays an important role in human immune regulation and disease prevention. Plants absorb inorganic selenium (selenite or selenate) from the soil and convert it into various organic selenides (such as seleno amino acids, selenoproteins, and volatile selenides) via the sulfur metabolic pathway. These organic selenides are important sources of dietary selenium supplementation for humans. Organoselenides can promote plant growth, improve nutritional quality, and play an important regulatory function in plant ecosystems. The release of selenium-containing compounds into the soil by Se hyperaccumulators can promote the growth of Se accumulators but inhibit the growth and distribution of non-Se accumulators. Volatile selenides with specific odors have a deterrent effect on herbivores, reducing their feeding on plants. Soil microorganisms can effectively promote the uptake and transformation of selenium in plants, and organic selenides in plants can improve the tolerance of plants to pathogenic bacteria. Although selenium is not an essential trace element for plants, the right amount of selenium has important physiological and ecological benefits for them. This review summarizes recent research related to the functions of selenium in plant ecosystems to provide a deeper understanding of the significance of this element in plant physiology and ecosystems and to serve as a theoretical basis and technical support for the full exploitation and rational application of the ecological functions of selenium-accumulating plants.

Application of MALDI-TOF MS for identification of environmental bacteria: A review

Bacteria play a variety of roles in the environment. They maintain the balance in the ecosystem and provide different ecosystem services such as in biogeochemical cycling of nutrients, biodegradation of toxic pollutants, and others. Therefore, isolation and identification of different environmental bacteria are important to most environmental research. Due to the high cost and time associated with the conventional molecular techniques, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has gained considerable attention for routine identification of bacteria. This review aims to provide an overview of the application of MALDI-TOF MS in various environmental studies through bibliometric analysis and literature review. The bibliometric analysis helped to understand the time-variable application of MALDI-TOF MS in various environmental studies. The categorical literature review covers various environmental studies comprising areas like ecology, food microbiology, environmental biotechnology, agriculture, and plant sciences, which show the application of the technique for identification and characterization of pollutant-degrading, plant-associated, disease-causing, soil-beneficial, and other environmental bacteria. Further research should focus on bridging the gap between the phylogenetic identity of bacteria and their specific environmental functions or metabolic traits that can help in rapid advancements in environmental research, thereby, improving time and cost savings.

Selenium in Soil-Plant-Microbe: A Review

Selenium (Se) plays an important role in geochemistry and is an essential trace element for humans and animals. This review summarizes the transformation and accumulation of Se in the plant-soil-microbe system. As one of the important reservoirs of Se, soil is an important material basis of its entry into the food chain through plants. Soil with an appropriate amount of Se is beneficial for plant growth and plays a valuable role in a stress-resistant environment. Among the many migration and transformation pathways, the transformation of Se by microorganisms is particularly important and is the main form of Se transformation in the soil environment. In this review, the role and form transformation of Se in plants, soil, and microorganisms; the role of Se in plants; the form, input, and output of Se in soil; the absorption and transformation of Se by plants; and the role of microorganisms in Se transformation are presented. In addition to describing the migration and transformation laws of Se in the environment, this review expounds on the main directions and trends of Se research in the agricultural field as well as current gaps and difficulties in Se-related research. Overall, this reviews aims to provide necessary information and theoretical references for the development of Se-rich agriculture.

The beneficial and hazardous effects of selenium on the health of the soil-plant-human system: An overview

Selenium (Se), which can be both hazardous and beneficial to plants, animals and humans, plays a pivotal role in regulating soil-plant-human ecosystem functions. The biogeochemical behavior of Se and its environmental impact on the soil-plant-human system has received broad attention in the last decades. This review provides a comprehensive understanding of Se biogeochemistry in the soil-plant-human system. The speciation, transformation, bioavailability as well as the beneficial and hazardous effects of Se in the soil-plant-human system are summarized. Several important aspects in Se in the soil-plant-human system are detailed mentioned, including (1) strategies for biofortification in Se-deficient areas and phytoremediation of soil Se in seleniferous areas; (2) factors affecting Se uptake and transport by plants; (3) metabolic pathways of Se in the human body; (4) the interactions between Se and other trace elements in plant and animals, in particular, the detoxification of heavy metals by Se. Important research hotspots of Se biogeochemistry are outlined, including (1) the coupling of soil microbial activity and the Se biogeochemical cycle; (2) the molecular mechanism of Se metabolic in plants and animals; and (3) the application of Se isotopes as a biogeochemical tracer in research. This review provides up-to-date knowledge and guidelines on Se biogeochemistry research.

Assessment of the Ecotoxicity of Pollution by Potentially Toxic Elements by Biological Indicators of Haplic Chernozem of Southern Russia (Rostov region)

The content of various chemical elements such as metals, metalloids, and nonmetals in the environment is associated with natural and anthropogenic sources. It is necessary to normalize the content of metals, metalloids, and nonmetals as potentially toxic elements (PTE) in the Haplic Chernozem. The soils of the Southern Russia are of high quality and fertility. However, this type of soil, like Haplic Chernozem, is subject to contamination with a wide range of PTE. The aim of the work was to rank metals, metalloids, and nonmetals by ecotoxicity in Haplic Chernozem. To assess the ecotoxicity of chernozem, data for 15 years (2005-2020) were used. Biological indicators used to assess the ecotoxicity of Haplic Chernozem: catalase activity, cellulolytic activity, number of bacteria, Azotobacter spp. abundance, to change of length of radish's roots. Based on these biological indicators, an integral indicator of the state of Haplic Chernozem was calculated. The ecotoxicity of 23 metals (Cd, Hg, Pb, Cr, Cu, Zn, Ni, Co, Mo, Mn, Ba, Sr, Sn, V, W, Ag, Bi, Ga, Nb, Sc, Tl, Y, Yb), 5 metalloids (B, As, Ge, Sb, Te) and 2 nonmetals (F, Se) as priority pollutants. It is proposed to distinguish three hazard classes of metals, metalloids, and nonmetals to Haplic Chernozem: I class - Te, Ag, Se, Cr, Bi, Ge, Sn, Tl, Hg, Yb, W, Cd; II class - As, Co, Sc, Sb, Cu, Ni, B, Nb, Pb, Ga; III class - Sr, Y, Mo, Zn, V, Ba, Mn, F. It is advisable to use the results of the study for predictive assessment of the impact of metals, metalloids, and nonmetals on the ecological state of the soil during pollution.

Microbial reduction and resistance to selenium: Mechanisms, applications and prospects

Selenium is an essential trace element for humans, animals and microorganisms. Microbial transformations, in particular, selenium dissimilatory reduction and bioremediation applications have received increasing attention in recent years. This review focuses on multiple Se-reducing pathways under anaerobic and aerobic conditions, and the phylogenetic clustering of selenium reducing enzymes that are involved in these processes. It is emphasized that a selenium reductase may have more than one metabolic function, meanwhile, there are several Se(VI) and/or Se(IV) reduction pathways in a bacterial strain. It is noted that Se(IV)-reducing efficiency is inconsistent with Se(IV) resistance in bacteria. Moreover, we discussed the links of selenium transformations to biogeochemical cycling of other elements, roles of Se-reducing bacteria in soil, plant and digestion system, and the possibility of using functional genes involved in Se transformation as biomarker in different environments. In addition, we point out the gaps and perspectives both on Se transformation mechanisms and applications in terms of bioremediation, Se fortification or dietary supplementation.

Microbes: a potential tool for selenium biofortification

Selenium (Se) is a component of many enzymes and indispensable for human health due to its characteristics of reducing oxidative stress and enhancing immunity. Human beings take Se mainly from Se-containing crops. Taking measures to biofortify crops with Se may lead to improved public health. Se accumulation in plants mainly depends on the content and bioavailability of Se in soil. Beneficial microbes may change the chemical form and bioavailability of Se. This review highlights the potential role of microbes in promoting Se uptake and accumulation in crops and the related mechanisms. The potential approaches of microbial enhancement of Se biofortification can be summarized in the following four aspects: (1) microbes alter soil properties and impact the redox chemistry of Se to improve the bioavailability of Se in soil; (2) beneficial microbes regulate root morphology and stimulate the development of plants through the release of certain secretions, facilitating Se uptake in plants; (3) microbes upregulate the expression of certain genes and proteins that are related to Se metabolism in plants; and (4) the inoculation of microbes give rise to the generation of certain metabolites in plants contributing to Se absorption. Considering the ecological safety and economic feasibility, microbial enhancement is a potential tool for Se biofortification. For further study, the recombination and establishment of synthesis microbes is of potential benefit in Se-enrichment agriculture.

Roles of Oxygen in Methane-dependent Selenate Reduction in a Membrane Biofilm Reactor: Stimulation or Suppression

Although methane (CH₄) has been proven to be able to serve as an electron donor for bio-reducing various oxidized contaminants (e.g., selenate (SeO₄^2-)), little is known regarding the roles of oxygen in methane-based reduction processes. Here, a methane-based membrane biofilm reactor (MBfR) was established for evaluating the effects of oxygen supply rates on selenate reduction performance and microbial communities. The oxygen supply rate played a dual role (stimulatory or suppressive effect) in selenate reduction rates, depending on the presence or absence of dissolved oxygen (DO). Specifically, selenate reduction rate was substantially enhanced when an appropriate oxygen rate (e.g., 12 to 184 mg/L^.d in this study) was supplied but with negligible DO. The highest selenate reduction rate (up to 34 mg-Se/L^.d) was obtained under an oxygen supply rate of 184 mg/L^.d. In contrast, excessive oxygen supply rate (626 mg/L^.d) would significantly suppress selenate reduction rate under DO level of 3 mg/L. Accordingly, though the high oxygen supply rate (626 mg/L^.d) would promote the expression of pmoA (5.9 × 10⁹ copies g^-1), the expression level of narG (a recognized gene to mediate selenate reduction) would be significantly downregulated (6.1 × 10⁹ copies g^-1), thus suppressing selenate reduction. In contrast, the expression of narG gene significantly increased to 2.8 × 10¹⁰ copies g^-1, and the expression of pmoA gene could still maintain at 1.1 × 10⁹ copies g^-1 under an oxygen supply rate of 184 mg/L^.d. High-throughput sequencing targeting 16S rRNA gene, pmoA, and narG collectively suggested Methylocystis acts as the major aerobic methanotroph, in synergy with Arthrobacter and Variovorax which likely jointly reduce selenate to selenite (SeO₃^2-), and further to elemental selenium (Se⁰). Methylocystis was predominant in the biofilm regardless of variations of oxygen supply rates, while Arthrobacter and Variovorax were sensitive to oxygen fluctuation. These findings provide insights into the effects of oxygen on methane-dependent selenate reduction and suggest that it is feasible to achieve a higher selenate removal by regulating oxygen supply rates.

Selenium respiration in anaerobic bacteria: Does energy generation pay off?

Selenium (Se) respiration in bacteria was revealed for the first time at the end of 1980s. Although thermodynamically-favorable, energy-dense and documented in phylogenetically-diverse bacteria, this metabolic process appears to be accompanied by a number of challenges and numerous unanswered questions. Selenium oxyanions, SeO₄^2- and SeO₃^2-, are reduced to elemental Se (Se⁰) through anaerobic respiration, the end product being solid and displaying a considerable size (up to 500 nm) at the bacterial scale. Compared to other electron acceptors used in anaerobic respiration (e.g. N, S, Fe, Mn, and As), Se is one of the few elements whose end product is solid. Furthermore, unlike other known bacterial intracellular accumulations such as volutin (inorganic polyphosphate), S⁰, glycogen or magnetite, Se⁰ has not been shown to play a nutritional or ecological role for its host. In the context of anaerobic respiration of Se oxyanions, biogenic Se⁰ appears to be a by-product, a waste that needs proper handling, and this raises the question of the evolutionary implications of this process. Why would bacteria use a respiratory substrate that is useful, in the first place, and then highly detrimental? Interestingly, in certain artificial ecosystems (e.g. upflow bioreactors) Se⁰ might help bacterial cells to increase their density and buoyancy and thus avoid biomass wash-out, ensuring survival. This review article provides an in-depth analysis of selenium respiration (model selenium respiring bacteria, thermodynamics, respiratory enzymes, and genetic determinants), complemented by an extensive discussion about the evolutionary implications and the properties of biogenic Se⁰ using published and original/unpublished results.

Diversity of Endophytic Bacteria in Cardamine hupingshanensis and Potential of Culturable Selenium-Resistant Endophytes to Enhance Seed Germination Under Selenate Stress

The endophytic bacterial communities of Se hyperaccumulator Cardamine hupingshanensis collected from greenhouse and selenium mining area in Enshi City were investigated by Illumina sequencing technology. In addition, 14 culturable endophytic selenium-resistant strains were isolated and their selenium tolerance and plant growth promotion abilities were studied. The results showed that phylum Proteobacteria predominated in all the plants (> 70%) regardless of their habitats, with most of the OTUs related to Betaproteobacteria, Alphaproteobacteria, and Gammaproteobacteria. Roots harbored many more OTUs and showed higher alpha diversities than the leaves. Both growing environment and specific microflora selection of plants were found to have noticeable effects on endophytic bacterial community structure. The 14 culturable endophytes belonging to 11 bacterial genera were able to resist different levels of selenite and selenate, with their MIC ranges of 10-120 mM and 100-600 mM. Among them, Oceanobacillus and Terribacillus genera were firstly reported for the selenium-tolerant properties of their members. Inoculation experiment revealed that three endophytic strains (CHP07, CHP08, and CHP14) with excellent plant growth-promoting traits were beneficial for growth of Brassica chinensis seeds at germination stage under 0.19 mM selenate stress.

Complete genome sequence of plant growth-promoting and heavy metal-tolerant Enterobacter tabaci 4M9 (CCB-MBL 5004)

Enterobacter tabaci 4M9 (CCB-MBL 5004) was reported to have plant growth-promoting and heavy metal tolerance traits. It was able to tolerate more than 300 mg/L Cd, 600 mg/L As, and 500 mg/L Pb and still maintained the ability to produce plant growth-promoting substances under metal stress conditions. To explore the genetic basis of these beneficial traits, the complete genome sequencing of 4M9 was carried out using Pacific Bioscience (PacBio) sequencing technology. The complete genome consisted of one chromosome of 4,654,430 bp with a GC content of 54.6% and one plasmid of 51,135 bp with a GC content of 49.4%. Genome annotation revealed several genes involved in plant growth-promoting traits, including the production of siderophore, indole acetic acid, and 1-aminocyclopropane-1-carboxylate deaminase; solubilization of phosphate and potassium; and nitrogen metabolism. Similarly, genes involved in heavy metals (As, Co, Zn, Cu, Mn, Se, Cd, and Fe) tolerance were detected. These support its potential as a heavy metal-tolerant plant growth-promoting bacterium and a good genetic resource that can be employed to improve phytoremediation efficiency of heavy metal-contaminated soil via biotechnological techniques. This, to the best of our knowledge, is the first report on the complete genome sequence of heavy metal-tolerant plant growth-promoting E. tabaci.

Cadmium level and soil type played a selective role in the endophytic bacterial community of hyperaccumulator Sedum alfredii Hance

Phytoremediation technology has been applied for heavy metal elimination for many years, however little research about the difference of remediation efficiency of hyperaccumulator in different soils was reported. Here, a pot experiment was conducted with a cadmium (Cd)/zinc hyperaccumulator Sedum alfredii Hance grown on different types of soils and the differences of its endophytic bacterial community were elucidated. The results showed that the biomass of S. alfredii grown on black soil under both low and high Cd treatment was much heavier than that grown on other soils, and Cd uptake and Cd accumulation of S. alfredii in paddy soil was the highest, suggesting that black soil was more suitable for S. alfredii growth while paddy soil was more efficient for Cd phytoextraction. Moreover, Cd treated level and soil type both affected the structure of plant endophytic bacterial community. The two shared genera in the four representative soils were Caulobacter and Acinetobacter under low Cd level, and Caulobacter and Lactobacillus under high Cd level. Cd treatment shifted the structure and abundance of plant endophytes in different types of soils, while black soil and paddy soil were more similar in the distribution and abundance of S. alfredii endophytic community. This study highlighted the understanding of response to Cd within S. alfredii endophytic community in different types of soils, which could be beneficial for enhanced phytoremediation efficiency and better S. alfredii cultivation.

Keep and promote biodiversity at polluted sites under phytomanagement

The phytomanagement concept combines a sustainable reduction of pollutant linkages at risk-assessed contaminated sites with the generation of both valuable biomass for the (bio)economy and ecosystem services. One of the potential benefits of phytomanagement is the possibility to increase biodiversity in polluted sites. However, the unique biodiversity present in some polluted sites can be severely impacted by the implementation of phytomanagement practices, even resulting in the local extinction of endemic ecotypes or species of great conservation value. Here, we highlight the importance of promoting measures to minimise the potential adverse impact of phytomanagement on biodiversity at polluted sites, as well as recommend practices to increase biodiversity at phytomanaged sites without compromising its effectiveness in terms of reduction of pollutant linkages and the generation of valuable biomass and ecosystem services.

The invisible life inside plants: Deciphering the riddles of endophytic bacterial diversity

Endophytic bacteria often promote plant growth and protect their host plant against pathogens, herbivores, and abiotic stresses including drought, increased salinity or pollution. Current agricultural practices are being challenged in terms of climate change and the ever-increasing demand for food. Therefore, the rational exploitation of bacterial endophytes to increase the productivity and resistance of crops appears to be very promising. However, the efficient and larger-scale use of bacterial endophytes for more effective and sustainable agriculture is hindered by very little knowledge on molecular aspects of plant-endophyte interactions and mechanisms driving bacterial communities in planta. In addition, since most of the information on bacterial endophytes has been obtained through culture-dependent techniques, endophytic bacterial diversity and its full biotechnological potential still remain highly unexplored. In this study, we discuss the diversity and role of endophytic populations as well as complex interactions that the endophytes have with the plant and vice versa, including the interactions leading to plant colonization. A description of biotic and abiotic factors influencing endophytic bacterial communities is provided, along with a summary of different methodologies suitable for determining the diversity of bacterial endophytes, mechanisms governing the assembly and structure of bacterial communities in the endosphere, and potential biotechnological applications of endophytes in the future.

The diversity and distribution of endophytes across biomes, plant phylogeny and host tissues: how far have we come and where do we go from here?

The interiors of plants are colonized by diverse microorganisms that are referred to as endophytes. Endophytes have received much attention over the past few decades, yet many questions remain unanswered regarding patterns in their biodiversity at local to global scales. To characterize research effort to date, we synthesized results from ~600 published studies. Our survey revealed a global research interest and highlighted several gaps in knowledge. For instance, of the 17 biomes encompassed by our survey, 7 were understudied and together composed only 7% of the studies that we considered. We found that fungal endophyte diversity has been characterized in at least one host from 30% of embryophyte families, while bacterial endophytes have been surveyed in hosts from only 10.5% of families. We complimented our survey with a vote counting procedure to determine endophyte richness patterns among plant tissue types. We found that variation in endophyte assemblages in above-ground tissues varied with host growth habit. Stems were the richest tissue in woody plants, whereas roots were the richest tissue in graminoids. For forbs, we found no consistent differences in relative tissue richness among studies. We propose future directions to fill the gaps in knowledge we uncovered and inspire further research.

Accumulation of Cu, Cd, Pb, Zn and total P from synthetic stormwater in 30 bioretention plants

The uptake and distribution of four heavy metals, including copper (Cu), cadmium (Cd), lead (Pb) and zinc (Zn), and those of total phosphorus (TP) in 30 plants in North China were investigated through pot trial experiments. Accumulation and distribution of heavy metals or TP were associated with plant species, tissues, metal elements and pollutant loading. The highest amount of heavy metal and TP accumulation was found in the whole plants of Hylotelephium erythrostictum (Miq.) H. Ohba (C1) and Chlorophytum laxum R. Br. (L4), respectively. Considering the biological concentration factor, translocation factor, retention factor and biomass indices, C1 is the suitable plant for Cd and Cu uptake, whereas Hosta plantaginea (Lam.) Aschers (L3) and Viola verecunda A. Gray (V1) are the suitable plants for Pb removal. Rehmannia glutinosa (Gaetn.) Libosch. ex Fisch. (S1) and L4 can be chosen for Zn and TP removal, respectively. Cluster analysis was applied to select suitable plants for heavy metal and TP removal. Results showed that C1, L4 and Pennisetum alopecuroides (L.) Spreng (G1) have a good capability of accumulating heavy metals and TP. Results demonstrated that the plant species rather than the families considerably influenced the accumulation of pollutants.

Selenium Biofortification of Crop Food by Beneficial Microorganisms

Selenium (Se) is essential for human health, however, Se is deficient in soil in many places all around the world, resulting in human diseases, such as notorious Keshan disease and Keshin–Beck disease. Therefore, Se biofortification is a popular approach to improve Se uptake and maintain human health. Beneficial microorganisms, including mycorrhizal and root endophytic fungi, dark septate fungi, and plant growth-promoting rhizobacteria (PGPRs), show multiple functions, especially increased plant nutrition uptake, growth and yield, and resistance to abiotic stresses. Such functions can be used for Se biofortification and increased growth and yield under drought and salt stress. The present review summarizes the use of mycorrhizal fungi and PGPRs in Se biofortification, aiming to improving their practical use.

The diversity and distribution of endophytes across biomes, plant phylogeny and host tissues: how far have we come and where do we go from here?

The interiors of plants are colonized by diverse microorganisms that are referred to as endophytes. Endophytes have received much attention over the past few decades, yet many questions remain unanswered regarding patterns in their biodiversity at local to global scales. To characterize research effort to date, we synthesized results from ~600 published studies. Our survey revealed a global research interest and highlighted several gaps in knowledge. For instance, of the 17 biomes encompassed by our survey, 7 were understudied and together composed only 7% of the studies that we considered. We found that fungal endophyte diversity has been characterized in at least one host from 30% of embryophyte families, while bacterial endophytes have been surveyed in hosts from only 10.5% of families. We complimented our survey with a vote counting procedure to determine endophyte richness patterns among plant tissue types. We found that variation in endophyte assemblages in above-ground tissues varied with host growth habit. Stems were the richest tissue in woody plants, whereas roots were the richest tissue in graminoids. For forbs, we found no consistent differences in relative tissue richness among studies. We propose future directions to fill the gaps in knowledge we uncovered and inspire further research.

The reduction of selenium(IV) by boreal Pseudomonas sp. strain T5-6-I - Effects on selenium(IV) uptake in Brassica oleracea

Selenium (Se) is an essential micronutrient but toxic when taken in excessive amounts. Therefore, understanding the metabolic processes related to selenium uptake and bacteria-plant interactions coupled with selenium metabolism are of high importance. We cultivated Brassica oleracea with the previously isolated heterotrophic aerobic Se(IV)-reducing Pseudomonas sp. T5-6-I strain to better understand the phenomena of bacteria-mediated Se(IV) reduction on selenium availability to the plants. B. oleracea grown on Murashige and Skoog medium (MS-salt agar) with and without of Pseudomonas sp. were amended with Se(IV)/⁷⁵Se(IV), and selenium transfer into plants was studied using autoradiography and gamma spectroscopy. XANES was in addition used to study the speciation of selenium in the B. oleracea plants. In addition, the effects of Se(IV) on the protein expression in B. oleracea was studied using HPLC-SEC. TEM and confocal microscopy were used to follow the bacterial/Se-aggregate accumulation in plants and the effects of bacterial inoculation on root-hair growth. In the tests using ⁷⁵Se(IV) on average 130% more selenium was translocated to the B. oleracea plants grown with Pseudomonas sp. compared to the plants grown with selenium, but without Pseudomonas sp.. In addition, these bacteria notably increased root hair density. Changes in the protein expression of B. oleracea were observed on the ∼30-58 kDa regions in the Se(IV) treated samples, probably connected e.g. to the oxidative stress induced by Se(IV) or expression of proteins connected to the Se(IV) metabolism. Based on the XANES measurements, selenium appears to accumulate in B. oleracea mainly in organic C-Se-H and C-Se-C bonds with and without bacteria inoculation. We conclude that the Pseudomonas sp. T5-6-I strain seems to contribute positively to the selenium accumulation in plants, establishing the high potential of Se⁰-producing bacteria in the use of phytoremediation and biofortification of selenium.

The applicability of gene sequencing and MALDI-TOF to identify less common gram-negative rods (Advenella, Castellaniella, Kaistia, Pusillimonas and Sphingobacterium) from environmental isolates

Our aim was to identify less common non-fermenting gram-negative rods during the bioremediation process. Five genera were found: Advenella, Castellaniella, Kaistia, Pusillimonas and Sphingobacterium, for a total of 15 isolates. Therefore, we evaluated the applicability of four methods currently available for bacteria identification: (1) conventional biochemical methods, (2) the VITEK^®-2 system, (3) MALDI-TOF mass spectrometry and (4) 16S rRNA gene sequencing. The biochemical methods and the VITEK^®-2 system were reliable only for the Sphingobacterium isolate and solely at the genus level. Both MALDI-TOF mass spectrometry platforms (Bruker and VITEK^® MS) did not achieve reliable identification results for any of these genera. 16S rRNA gene sequencing identified eight isolates to the species level but not to the subspecies level, when applicable. The remaining seven isolates were reliably identified through 16S rRNA gene sequencing to the genus level only. Our findings suggest that the detection and identification of less common genera (and species) that appeared at certain moments during the bioremediation process can be a challenge to microbiologists considering the most used techniques. In addition, more studies are required to confirm our results.

The bumble bee microbiome increases survival of bees exposed to selenate toxicity

Bumble bees are important and widespread insect pollinators who face many environmental challenges. For example, bees are exposed to the metalloid selenate when foraging on pollen and nectar from plants growing in contaminated soils. As it has been shown that the microbiome of animals reduces metalloid toxicity, we assayed the ability of the bee microbiome to increase survivorship against selenate challenge. We exposed uninoculated or microbiota-inoculated Bombus impatiens workers to a field-realistic dose of 0.75 mg l^-1 selenate and found that microbiota-inoculated bees survive slightly but significantly longer than uninoculated bees. Using 16S rRNA gene sequencing, we found that selenate exposure altered gut microbial community composition and relative abundance of specific core bacteria. We also grew two core bumble bee microbes - Snodgrassella alvi and Lactobacillus bombicola - in selenate-spiked media and found that these bacteria grew in the tested concentrations of 0.001-10 mg l^-1 selenate. Furthermore, the genomes of these microbes harbour genes involved in selenate detoxification. The bumble bee microbiome slightly increases survivorship when the host is exposed to selenate, but the specific mechanisms and colony-level benefits under natural settings require further study.

Getting to the Root of Selenium Hyperaccumulation—Localization and Speciation of Root Selenium and Its Effects on Nematodes

Elemental hyperaccumulation protects plants from many aboveground herbivores. Little is known about effects of hyperaccumulation on belowground herbivores or their ecological interactions. To examine effects of plant selenium (Se) hyperaccumulation on nematode root herbivory, we investigated spatial distribution and speciation of Se in hyperaccumulator roots using X-ray microprobe analysis, and effects of root Se concentration on root-associated nematode communities. Perennial hyperaccumulators Stanleya pinnata and Astragalus bisulcatus, collected from a natural seleniferous grassland contained 100–1500 mg Se kg−1 root dry weight (DW). Selenium was concentrated in the cortex and epidermis of hyperaccumulator roots, with lower levels in the stele. The accumulated Se consisted of organic (C-Se-C) compounds, indistinguishable from methyl-selenocysteine. The field-collected roots yielded 5–400 nematodes g−1 DW in Baermann funnel extraction, with no correlation between root Se concentration and nematode densities. Even roots containing > 1000 mg Se kg−1 DW yielded herbivorous nematodes. However, greenhouse-grown S. pinnata plants treated with Se had fewer total nematodes than those without Se. Thus, while root Se hyperaccumulation may protect plants from non-specialist herbivorous nematodes, Se-resistant nematode taxa appear to associate with hyperaccumulators in seleniferous habitats, and may utilize high-Se hyperaccumulator roots as food source. These findings give new insight into the ecological implications of plant Se (hyper)accumulation.

On the Ecology of Selenium Accumulation in Plants

Plants accumulate and tolerate Se to varying degrees, up to 15,000 mg Se/kg dry weight for Se hyperaccumulators. Plant Se accumulation may exert positive or negative effects on other species in the community. The movement of plant Se into ecological partners may benefit them at low concentrations, but cause toxicity at high concentrations. Thus, Se accumulation can protect plants against Se-sensitive herbivores and pathogens (elemental defense) and reduce surrounding vegetation cover via high-Se litter deposition (elemental allelopathy). While hyperaccumulators negatively impact Se-sensitive ecological partners, they offer a niche for Se-tolerant partners, including beneficial microbial and pollinator symbionts as well as detrimental herbivores, pathogens, and competing plant species. These ecological effects of plant Se accumulation may facilitate the evolution of Se resistance in symbionts. Conversely, Se hyperaccumulation may evolve driven by increasing Se resistance in herbivores, pathogens, or plant neighbors; Se resistance also evolves in mutualist symbionts, minimizing the plant's ecological cost. Interesting topics to address in future research are whether the ecological impacts of plant Se accumulation may affect species composition across trophic levels (favoring Se resistant taxa), and to what extent Se hyperaccumulators form a portal for Se into the local food chain and are important for Se cycling in the local ecosystem.

Culturomics of the plant prokaryotic microbiome and the dawn of plant-based culture media - A review

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The plant microbiome culturomics is substantially lagging behind the human microbiome.

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Conventional chemically-synthetic culture media recover < 10% of plant-associated microbiota.

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Plant-based culture media (PCM) are introduced as a novel tool for plant microbiome culturomics.

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PCM extended the microbiota culturability to recover unculturable bacterial taxa.

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Streamlined- and large-genomes conspicuously contribute to the dilemma of unculturability.

Improving cultivability of a wider range of bacterial and archaeal community members, living natively in natural environments and within plants, is a prerequisite to better understanding plant-microbiota interactions and their functions in such very complex systems. Sequencing, assembling, and annotation of pure microbial strain genomes provide higher quality data compared to environmental metagenome analyses, and can substantially improve gene and protein database information. Despite the comprehensive knowledge which already was gained using metagenomic and metatranscriptomic methods, there still exists a big gap in understanding in vivo microbial gene functioning in planta, since many differentially expressed genes or gene families are not yet annotated. Here, the progress in culturing procedures for plant microbiota depending on plant-based culture media, and their proficiency in obtaining single prokaryotic isolates of novel and rapidly increasing candidate phyla are reviewed. As well, the great success of culturomics of the human microbiota is considered with the main objective of encouraging microbiologists to continue minimizing the gap between the microbial richness in nature and the number of species in culture, for the benefit of both basic and applied microbiology. The clear message to fellow plant microbiologists is to apply plant-tailored culturomic techniques that might open up novel procedures to obtain not-yet-cultured organisms and extend the known plant microbiota repertoire to unprecedented levels.

Rapid dereplication of microbial isolates using matrix-assisted laser desorption ionization time-of-flight mass spectrometry: A mini-review

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MALDI-TOF MS is applicable as high-resolution and high-throughput tool.

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The classification and characterization of cultivable microorganisms is targeted.

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Advantageous are its simple sample preparation and short measurement time.

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It accelerates the dereplication of isolates from large-scale screening campaigns.

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Applications for studying microbial diversity and future trends are discussed.

Matrix-Assisted Laser Desorption Ionization Time-Of-Flight Mass Spectrometry (MALDI-TOF MS) has become one of the most popular methods for the rapid, cost-effective and accurate classification and characterization of cultivable microorganisms. Due to its simple sample preparation and short measurement time, MALDI-TOF MS is an excellent choice for the high-throughput study of microbial isolates from rhizospheres or plants grown under diverse environmental conditions. While clinical isolates have a higher identification rate than environmental isolates due to the focus of commercial mass spectral libraries on the former, no identification is necessary in the dereplication step of large environmental studies. The grouping of large sets of isolates according to their intact protein profiles can be performed without knowledge of their taxonomy. Thus, this method is easily applicable to environmental samples containing microorganisms from yet undescribed phylogenetic origins. The main strategies applied to achieve effective dereplication are, first, expanding existing mass spectral libraries and, second, using an additional statistical analysis step to group measured mass spectra and identify unique isolates. In this review, these aspects are addressed. It closes with a prospective view on how MALDI-TOF MS-based microbial characterisation can accelerate the exploitation of plant-associated microbiota.

Fungal Endophyte Alternaria tenuissima Can Affect Growth and Selenium Accumulation in Its Hyperaccumulator Host Astragalus bisulcatus

Endophytes can enhance plant stress tolerance by promoting growth and affecting elemental accumulation, which may be useful in phytoremediation. In earlier studies, up to 35% elemental selenium (Se0) was found in Se hyperaccumulator Astragalus bisulcatus. Since Se0 can be produced by microbes, the plant Se0 was hypothesized to be microbe-derived. Here we characterize a fungal endophyte of A. bisulcatus named A2. It is common in seeds from natural seleniferous habitat containing 1,000-10,000 mg kg-1 Se. We identified A2 as Alternaria tenuissima via 18S rRNA sequence analysis and morphological characterization. X-ray microprobe analysis of A. bisulcatus seeds that did or did not harbor Alternaria, showed that both contained >90% organic seleno-compounds with C-Se-C configuration, likely methylselenocysteine and glutamyl-methylselenocysteine. The seed Se was concentrated in the embryo, not the seed coat. X-ray microprobe analysis of A2 in pure culture showed the fungus produced Se0 when supplied with selenite, but accumulated mainly organic C-Se-C compounds when supplied with selenate. A2 was completely resistant to selenate up to 300 mg L-1, moderately resistant to selenite (50% inhibition at ∼50 mg Se L-1), but relatively sensitive to methylselenocysteine and to Se extracted from A. bisulcatus (50% inhibition at 25 mg Se L-1). Four-week old A. bisulcatus seedlings derived from surface-sterilized seeds containing endophytic Alternaria were up to threefold larger than seeds obtained from seeds not showing evidence of fungal colonization. When supplied with Se, the Alternaria-colonized seedlings had lower shoot Se and sulfur levels than seedlings from uncolonized seeds. In conclusion, A. tenuissima may contribute to the Se0 observed earlier in A. bisulcatus, and affect host growth and Se accumulation. A2 is sensitive to the Se levels found in its host's tissues, but may avoid Se toxicity by occupying low-Se areas (seed coat, apoplast) and converting plant Se to non-toxic Se0. These findings illustrate the potential for hyperaccumulator endophytes to affect plant properties relevant for phytoremediation. Facultative endophytes may also be applicable in bioremediation and biofortification, owing to their capacity to turn toxic inorganic forms of Se into non-toxic or even beneficial, organic forms with anticarcinogenic properties.

Mechanisms of selenium hyperaccumulation in plants: A survey of molecular, biochemical and ecological cues

BACKGROUND

Selenium (Se) is a micronutrient required for many life forms, but toxic at higher concentration. Plants do not have a Se requirement, but can benefit from Se via enhanced antioxidant activity. Some plant species can accumulate Se to concentrations above 0.1% of dry weight and seem to possess mechanisms that distinguish Se from its analog sulfur (S). Research on these so-called Se hyperaccumulators aims to identify key genes for this remarkable trait and to understand ecological implications.

SCOPE OF REVIEW

This review gives a broad overview of the current knowledge about Se uptake and metabolism in plants, with a special emphasis on hypothesized mechanisms of Se hyperaccumulation. The role of Se in plant defense responses and the associated ecological implications are discussed.

MAJOR CONCLUSIONS

Hyperaccumulators have enhanced expression of S transport and assimilation genes, and may possess transporters with higher specificity for selenate over sulfate. Genes involved in antioxidant reactions and biotic stress resistance are also upregulated. Key regulators in these processes appear to be the growth regulators jasmonic acid, salicylic acid and ethylene. Hyperaccumulation may have evolved owing to associated ecological benefits, particularly protection against pathogens and herbivores, and as a form of elemental allelopathy.

GENERAL SIGNIFICANCE

Understanding plant Se uptake and metabolism in hyperaccumulators has broad relevance for the environment, agriculture and human and animal nutrition and may help generate crops with selenate-specific uptake and high capacity to convert selenate to less toxic, anticarcinogenic, organic Se compounds.

Plant Materials are Sustainable Substrates Supporting New Technologies of Plant-Only-Based Culture Media for in vitro Culturing of the Plant Microbiota

In order to improve the culturability and biomass production of rhizobacteria, we previously introduced plant-only-based culture media. We herein attempted to widen the scope of plant materials suitable for the preparation of plant-only-based culture media. We chemically analyzed the refuse of turfgrass, cactus, and clover. They were sufficiently rich to support good in vitro growth by rhizobacteria isolates representing Proteobacteria and Firmicutes. They were also adequate and efficient to produce a cell biomass in liquid batch cultures. These culture media were as sufficient as artificial culture media for the cultivation and recovery of the in situ rhizobacteria of barley (Hordeum murinum L.). Based on culture-dependent (CFU plate counting) and culture-independent analyses (qPCR), mowed turfgrass, in particular, supported the highest culturable population of barley endophytes, representing >16% of the total bacterial number quantified with qPCR. This accurately reflected the endophytic community composition, in terms of diversity indices (S', H', and D') based on PCR-DGGE, and clustered the plant culture media together with the qPCR root populations away from the artificial culture media. Despite the promiscuous nature of the plant materials tested to culture the plant microbiome, our results indicated that plant materials of a homologous nature to the tested host plant, at least at the family level, and/or of the same environment were more likely to be selected. Plant-only-based culture media require further refinements in order to provide selectivity for the in vitro growth of members of the plant microbiome, particularly difficult-to-culture bacteria. This will provide insights into their hidden roles in the environment and support future culturomic studies.

Endophytic Paecilomyces formosus LHL10 Augments Glycine max L. Adaptation to Ni-Contamination through Affecting Endogenous Phytohormones and Oxidative Stress

This study investigated the Ni-removal efficiency of phytohormone-producing endophytic fungi Penicillium janthinellum, Paecilomyces formosus, Exophiala sp., and Preussia sp. Among four different endophytes, P. formosus LHL10 was able to tolerate up to 1 mM Ni in contaminated media as compared to copper and cadmium. P. formosus LHL10 was further assessed for its potential to enhance the phytoremediation of Glycine max (soybean) in response to dose-dependent increases in soil Ni (0.5, 1.0, and 5.0 mM). Inoculation with P. formosus LHL10 significantly increased plant biomass and growth attributes as compared to non-inoculated control plants with or without Ni contamination. LHL10 enhanced the translocation of Ni from the root to the shoot as compared to the control. In addition, P. formosus LHL10 modulated the physio-chemical apparatus of soybean plants during Ni-contamination by reducing lipid peroxidation and the accumulation of linolenic acid, glutathione, peroxidase, polyphenol oxidase, catalase, and superoxide dismutase. Stress-responsive phytohormones such as abscisic acid and jasmonic acid were significantly down-regulated in fungal-inoculated soybean plants under Ni stress. LHL10 Ni-remediation potential can be attributed to its phytohormonal synthesis related genetic makeup. RT-PCR analysis showed the expression of indole-3-acetamide hydrolase, aldehyde dehydrogenase for indole-acetic acid and geranylgeranyl-diphosphate synthase, ent-kaurene oxidase (P450-4), C13-oxidase (P450-3) for gibberellins synthesis. In conclusion, the inoculation of P. formosus can significantly improve plant growth in Ni-polluted soils, and assist in improving the phytoremediation abilities of economically important crops.