Aspects of nitrogen-fixing Actinobacteria, in particular free-living and symbiotic Frankia

Harnessing the power of microbes: Enhancing soybean growth in an acidic soil through AMF inoculation rather than P-fertilization

The low phosphorus (P) availability of acidic soils severely limits leguminous plant growth and productivity. Improving the soil P nutritional status can be achieved by increasing the P-content through P-fertilization or stimulating the mineralization of organic P via arbuscular mycorrhizal fungi (AMF) application; however, their corresponding impacts on plant and soil microbiome still remain to be explored. Here, we examined the effects of AMF-inoculation and P-fertilization on the growth of soybean with different P-efficiencies, as well as the composition of rhizo-microbiome in an acidic soil. The growth of recipient soybean NY-1001, which has a lower P-efficiency, was not significantly enhanced by AMF-inoculation or P-fertilization. However, the plant biomass of higher P-efficiency transgenic soybean PT6 was significantly increased by 46.74%-65.22% through AMF-inoculation. Although there was no discernible difference in plant biomass between PT6 and NY-1001 in the absence of AMF-inoculation and P-fertilization, PT6 had approximately 1.9-2.5 times the plant biomass of NY-1001 after AMF-inoculation. Therefore, the growth advantage of higher P-efficiency soybean was achieved through the assistance of AMF rather than P-fertilization in available P-deficient acidic soil. Most nitrogen (N)-fixing bacteria and some functional genes related to N-fixation were abundant in endospheric layer, as were the P-solubilizing Pseudomonas plecoglossicida, and annotated P-metabolism genes. These N-fixing and P-solubilizing bacteria were positive correlated with each other. Lastly, the two most abundant phytopathogenic fungi species accumulated in endospheric layer, they exhibited positive correlations with N-fixing bacteria, but displayed negative interactions with the majority of the other dominant non-pathogenic genera with potential antagonistic activity.

Sub-micron microplastics affect nitrogen cycling by altering microbial abundance and activities in a soil-legume system

Recently, the environmental and agricultural impact of plastic waste has attracted considerable attention. Here, we investigated the impact of sub-micron polyethylene (PE) and polypropylene (PP) microplastics (MPs) on nitrogen cycling, with emphasis on bacterial abundance and diversity in a soil-soybean (Glycine max) system. Exposure to soil containing MPs (50 and 500 mg kg-1) did not affect soybean growth, but significantly increased plant nitrogen uptake, which was confirmed by increased activities of nitrogenase in the soil and glutamine synthetase in soybean root. Additionally, there was an increase in 16S gene copy number and carbon and nitrogen substrate utilization, indicating increased abundance and activity of rhizosphere microbial communities. Moreover, MP contamination affected the taxonomic profile of rhizosphere bacteria, especially the abundance of symbiotic and free-living bacteria involved in nitrogen cycling. Furthermore, qPCR analysis of nitrogen-related genes and Kyoto Encyclopedia of Genes and Genomes analysis of 16S rRNA gene sequencing data revealed an increased abundance of functional genes associated with nitrogen fixation and nitrification. However, the concentration and polymer type of MPs did not have a significant impact in our system. Overall, these results provide insights into the interactions between MPs and rhizosphere bacterial communities in the soil-legume system.

Compost, plants and endophytes versus metal contamination: choice of a restoration strategy steers the microbiome in polymetallic mine waste

Finding solutions for the remediation and restoration of abandoned mining areas is of great environmental importance as they pose a risk to ecosystem health. In this study, our aim was to determine how remediation strategies with (i) compost amendment, (ii) planting a metal-tolerant grass Bouteloua curtipendula, and (iii) its inoculation with beneficial endophytes influenced the microbiome of metal-contaminated tailings originating from the abandoned Blue Nose Mine, SE Arizona, near Patagonia (USA). We conducted an indoor microcosm experiment followed by a metataxonomic analysis of the mine tailings, compost, and root samples. Our results showed that each remediation strategy promoted a distinct pattern of microbial community structure in the mine tailings, which correlated with changes in their chemical properties. The combination of compost amendment and endophyte inoculation led to the highest prokaryotic diversity and total nitrogen and organic carbon, but also induced shifts in microbial community structure that significantly correlated with an enhanced potential for mobilization of Cu and Sb. Our findings show that soil health metrics (total nitrogen, organic carbon and pH) improved, and microbial community changed, due to organic matter input and endophyte inoculation, which enhanced metal leaching from the mine waste and potentially increased environmental risks posed by Cu and Sb. We further emphasize that because the initial choice of remediation strategy can significantly impact trace element mobility via modulation of both soil chemistry and microbial communities, site specific, bench-scale preliminary tests, as reported here, can help determine the potential risk of a chosen strategy.

Hyperarid soil microbial community response to simulated rainfall

The exceptionally long and protracted aridity in the Atacama Desert (AD), Chile, provides an extreme, terrestrial ecosystem that is ideal for studying microbial community dynamics under hyperarid conditions. Our aim was to characterize the temporal response of hyperarid soil AD microbial communities to ex situ simulated rainfall (5% g water/g dry soil for 4 weeks) without nutrient amendment. We conducted replicated microcosm experiments with surface soils from two previously well-characterized AD hyperarid locations near Yungay at 1242 and 1609 masl (YUN1242 and YUN1609) with distinct microbial community compositions and average soil relative humidity levels of 21 and 17%, respectively. The bacterial and archaeal response to soil wetting was evaluated by 16S rRNA gene qPCR, and amplicon sequencing. Initial YUN1242 bacterial and archaeal 16S rRNA gene copy numbers were significantly higher than for YUN1609. Over the next 4 weeks, qPCR results showed significant increases in viable bacterial abundance, whereas archaeal abundance decreased. Both communities were dominated by 10 prokaryotic phyla (Actinobacteriota, Proteobacteria, Chloroflexota, Gemmatimonadota, Firmicutes, Bacteroidota, Planctomycetota, Nitrospirota, Cyanobacteriota, and Crenarchaeota) but there were significant site differences in the relative abundances of Gemmatimonadota and Chloroflexota, and specific actinobacterial orders. The response to simulated rainfall was distinct for the two communities. The actinobacterial taxa in the YUN1242 community showed rapid changes while the same taxa in the YUN1609 community remained relatively stable until day 30. Analysis of inferred function of the YUN1242 microbiome response implied an increase in the relative abundance of known spore-forming taxa with the capacity for mixotrophy at the expense of more oligotrophic taxa, whereas the YUN1609 community retained a stable profile of oligotrophic, facultative chemolithoautotrophic and mixotrophic taxa. These results indicate that bacterial communities in extreme hyperarid soils have the capacity for growth in response to simulated rainfall; however, historic variations in long-term hyperaridity exposure produce communities with distinct putative metabolic capacities.

Trichoderma harzianum inoculation promotes sweet sorghum growth in the saline soil by modulating rhizosphere available nutrients and bacterial community

As one of the major abiotic stresses, salinity can affect crop growth and plant productivity worldwide. The inoculation of rhizosphere or endophytic microorganisms can enhance plant tolerance to salt stresses, but the potential mechanism is not clear. In this study, Trichoderma harzianum ST02 was applied on sweet sorghum [Sorghum bicolor (L.) Moench] in a field trial to investigate the effects on microbiome community and physiochemical properties in the rhizosphere soil. Compared with the non-inoculated control, Trichoderma inoculation significantly increased the stem yield, plant height, stem diameter, and total sugar content in stem by 35.52%, 32.68%, 32.09%, and 36.82%, respectively. In addition, Trichoderma inoculation improved the nutrient availability (e.g., N, P, and K) and organic matter in the rhizosphere soil and changed the bacterial community structure and function in both bulk and rhizosphere soil by particularly increasing the relative abundance of Actinobacter and N-cycling genes (nifH, archaeal and bacterial amoA). We proposed that T. harzianum ST02 could promote sweet sorghum growth under saline conditions by regulating available nutrients and the bacterial community in the rhizosphere soil.

Effect of organic amendments obtained from different pretreatment technologies on soil microbial community

The application of organic amendments (OAs) obtained from biological treatment technologies is a common agricultural practice to increase soil functionality and fertility. OAs and their respective pretreatment processes have been extensively studied. However, comparing the properties of OAs obtained from different pretreatment processes remains challenging. In most cases, the organic residues used to produce OAs exhibit intrinsic variability and differ in origin and composition. In addition, few studies have focused on comparing OAs from different pretreatment processes in the soil microbiome, and the extent to which OAs affect the soil microbial community remains unclear. This limits the design and implementation of effective pretreatments aimed at reusing organic residues and facilitating sustainable agricultural practices. In this study, we used the same model residues to produce OAs to enable meaningful comparisons among compost, digestate, and ferment. These three OAs contained different microbial communities. Compost had higher bacterial but lower fungal alpha diversity than ferment and digestate. Compost-associated microbes were more prevalent in the soil than ferment- and digestate-associated microbes. More than 80% of the bacterial ASVs and fungal OTUs from the compost were detected 3 months after incorporation into the soil. However, the addition of compost had less influence on the resulting soil microbial biomass and community composition than the addition of ferment or digestate. Specific native soil microbes, members from Chloroflexi, Acidobacteria, and Mortierellomycota, were absent after ferment and digestate application. The addition of OAs increased the soil pH, particularly in the compost-amended soil, whereas the addition of digestate enhanced the concentrations of dissolved organic carbon (DOC) and available nutrients (such as ammonium and potassium). These physicochemical variables were key factors that influenced soil microbial communities. This study furthers our understanding of the effective recycling of organic resources for the development of sustainable soils.

Diversity and regulation of symbiotic nitrogen fixation in plants

Plants associate with nitrogen-fixing bacteria to secure nitrogen, which is generally the most limiting nutrient for plant growth. Endosymbiotic nitrogen-fixing associations are widespread among diverse plant lineages, ranging from microalgae to angiosperms, and are primarily one of three types: cyanobacterial, actinorhizal or rhizobial. The large overlap in the signaling pathways and infection components of arbuscular mycorrhizal, actinorhizal and rhizobial symbioses reflects their evolutionary relatedness. These beneficial associations are influenced by environmental factors and other microorganisms in the rhizosphere. In this review, we summarize the diversity of nitrogen-fixing symbioses, key signal transduction pathways and colonization mechanisms relevant to such interactions, and compare and contrast these interactions with arbuscular mycorrhizal associations from an evolutionary standpoint. Additionally, we highlight recent studies on environmental factors regulating nitrogen-fixing symbioses to provide insights into the adaptation of symbiotic plants to complex environments.

The microbiome of buried soils demonstrates significant shifts in taxonomic structure and a general trend towards mineral horizons

Burial mounds represent a challenge for microbiologists. Could ancient buried soils preserve microbiomes as they do archaeological artifacts? To investigate this question, we studied the soil microbiome under a burial mound dating from 2500 years ago in Western Kazakhstan. Two soil profile cuts were established: one under the burial mound and another adjacent to the mound surface steppe soil. Both soils represented the same dark chestnut soil type and had the same horizontal stratification (A, B, C horizons) with slight alterations. DNA samples isolated from all horizons were studied with molecular techniques including qPCR and high throughput sequencing of amplicon libraries of the 16S rRNA gene fragment. The taxonomic structure of the microbiome of the buried horizons demonstrated a deep divergence from ones of the surface, comparable to the variation between different soil types (representatives of the soil types were included in the survey). The cause of this divergence could be attributed to diagenetic processes characterized by the reduction of organic matter content and changes in its structure. Corresponding trends in the microbiome structure are obvious from the beta-diversity pattern: the A and B horizons of the buried soils form one cluster with the C horizons of both buried and surface soil. This trend could generally be designated as 'mineralization'. Statistically significant changes between the buried and surface soils microbiomes were detected in the number of phylogenetic clusters, the biology of which is in the line of diagenesis. The trend of 'mineralization' was also supported by PICRUSt2 functional prediction, demonstrating a higher occurrence of the processes of degradation in the buried microbiome. Our results show a profound shift in the buried microbiome relatively the "surface" microbiome, indicating the deep difference between the original and buried microbiomes.

Bacterial community succession in aerobic-anaerobic-coupled and aerobic composting with mown hay affected C and N losses

The primary objective of this work was to investigate how the dominant microbial species change and affect C and N losses under aerobic and aerobic-anaerobic-coupled composting of mown hay (MH, ryegrass) and corn stover (CS) mix. Results showed that C and N losses in aerobic compost of MH-CS were significantly decreased by 19.57-31.47% and 29.04-41.18%, respectively. 16S rRNA gene sequencing indicated that the bacterial microbiota showed significant differences in aerobic and aerobic-anaerobic-coupled composting. LEfSe analyses showed that aerobic composting promoted the growth of bacteria related to lignocellulosic degradation and nitrogen fixation, while aerobic-anaerobic-coupled composting promoted the growth of bacteria related to denitrification. Correlation analysis between bacterial community and environmental factors indicated that moisture content (MC) was the most important environmental factor influencing the differentiation of bacterial growth. KEGG analysis showed that aerobic composting enhanced the amino acid, carbohydrate, and other advantageous metabolic functions compared to that of aerobic-anaerobic-coupled composting. As a conclusion, the addition of 10-20% corn stover (w/w) to new-mown hay (ryegrass) appeared to inhibit anaerobic composting and prompt aerobic composting in MH-CS mix, which led to the effective utilization of mown hay as a resource for composting.

Inoculation with Actinobacteria spp. Isolated from a Hyper-Arid Environment Enhances Tolerance to Salinity in Lettuce Plants (Lactuca sativa L.)

Irrigated agriculture is responsible for a third of global agricultural production, but the overuse of water resources and intensification of farming practices threaten its sustainability. The use of saline water in irrigation has become an alternative in areas subjected to frequent drought, but this practice affects plant growth due to osmotic impact and excess of ions. Plant-growth-promoting rhizobacteria (PGPR) can mitigate the negative impacts of salinity and other abiotic factors on crop yields. Actinobacteria from the hyper-arid Atacama Desert could increase the plant tolerance to salinity, allowing their use as biofertilizers for lettuce crops using waters with high salt contents. In this work, rhizosphere samples of halophytic Metharme lanata were obtained from Atacama Desert, and actinobacteria were isolated and identified by 16S gene sequencing. The PGPR activities of phosphate solubilization, nitrogen fixation, and the production of siderophore and auxin were assessed at increasing concentrations of NaCl, as well as the enhancement of salt tolerance in lettuce plants irrigated with 100 mM of NaCl. Photosynthesis activity and chlorophyll content, proline content, lipid peroxidation, cation and P concentration, and the identification and quantification of phenolic compounds were assessed. The strains S. niveoruber ATMLC132021 and S. lienomycini ATMLC122021 were positive for nitrogen fixation and P solubilization activities and produced auxin up to 200 mM NaCl. In lettuce plants, both strains were able to improve salt stress tolerance by increasing proline contents, carotenoids, chlorophyll, water use efficiency (WUE), stomatal conductance (gs), and net photosynthesis (A), concomitantly with the overproduction of the phenolic compound dicaffeoylquinic acid. All these traits were positively correlated with the biomass production under saltwater irrigation, suggesting its possible use as bioinoculants for the agriculture in areas where the water resources are scarce and usually with high salt concentrations.

Changes of bacterial community structure,monosaccharide composition and CO2 exchange along the successional stages of biological soil crusts

Biological soil crusts (BSCs) are a dominant ecological landscape of drylands, which have a significant impact on global biogeochemical flux. However, it is unclear how bacterial community and physiological characteristics vary along the BSCs successional stages. In this study, bacterial community composition, physiological characteristics, and monosaccharide composition of extracellular polysaccharides (EPSs) were compared among different successional stages. Our findings demonstrated that besides the dominant bacterial species, the bacterial communities also showed considerable differences between these two stages. Cyanobacteria were keystone taxa in the early stage, while heterotrophic bacteria (Proteobacteria, Actinobacteria and Acidobacteria) were keystone taxa in the later stages. According to the results of CO₂ exchange, cyanobacterial crusts accumulated net carbon faster than moss crusts, while moss crusts had a significantly higher respiration rate. The monosaccharide analysis indicated that the EPSs components also varied depending on BSCs' successional stages. Specifically, the contents of rhamnose and arabinose were higher in the cyanobacterial crusts than other types of crusts, while the contents of fucose, xylose, mannose and glucose were the highest in cyanobacterial-lichen crusts, and galactose content was highest in the moss crusts. Altogether, our results stress the heterogeneous variation of BSCs along with succession, and this work offered a fresh viewpoint for a deeper comprehension of the interactions between the monosaccharide components of EPS and the networks of bacterial communities in BSCs.

Development of a Multicomponent Microbiological Soil Inoculant and Its Performance in Sweet Potato Cultivation

The cultivation and consumption of sweet potato (Ipomoea batatas) are increasing globally. As the usage of chemical fertilizers and pest control agents during its cultivation may lead to soil, water and air pollution, there is an emerging need for environment-friendly, biological solutions enabling increased amounts of healthy crop and efficient disease management. Microbiological agents for agricultural purposes gained increasing importance in the past few decades. Our goal was to develop an agricultural soil inoculant from multiple microorganisms and test its application potential in sweet potato cultivation. Two Trichoderma strains were selected: Trichoderma ghanense strain SZMC 25217 based on its extracellular enzyme activities for the biodegradation of plant residues, and Trichoderma afroharzianum strain SZMC 25231 for biocontrol purposes against fungal plant pathogens. The Bacillus velezensis strain SZMC 24986 proved to be the best growth inhibitor of most of the nine tested strains of fungal species known as plant pathogens, therefore it was also selected for biocontrol purposes against fungal plant pathogens. Arthrobacter globiformis strain SZMC 25081, showing the fastest growth on nitrogen-free medium, was selected as a component with possible nitrogen-fixing potential. A Pseudomonas resinovorans strain, SZMC 25872, was selected for its ability to produce indole-3-acetic acid, which is among the important traits of potential plant growth-promoting rhizobacteria (PGPR). A series of experiments were performed to test the selected strains for their tolerance to abiotic stress factors such as pH, temperature, water activity and fungicides, influencing the survivability in agricultural environments. The selected strains were used to treat sweet potato in two separate field experiments. Yield increase was observed for the plants treated with the selected microbial consortium (synthetic community) in comparison with the control group in both cases. Our results suggest that the developed microbial inoculant has the potential to be used in sweet potato plantations. To the best of our knowledge, this is the first report about the successful application of a fungal-bacterial consortium in sweet potato cultivation.

Bioactive Metabolite Survey of Actinobacteria Showing Plant Growth Promoting Traits to Develop Novel Biofertilizers

The use of chemical fertilizers and pesticides has caused harmful impacts on the environment with the increase in economic burden. Biofertilizers are biological products containing living microorganisms capable of improving plant growth through eco-friendly mechanisms. In this work, three actinobacterial strains Streptomyces violaceoruber, Streptomyces coelicolor, and Kocuria rhizophila were characterized for multiple plant growth promoting (PGP) traits such as indole acetic acid production, phosphate solubilization, N2-fixation, and drought and salt tolerance. Then, these strains were investigated for their secreted and cellular metabolome, revealing a rich arsenal of bioactive molecules, including antibiotics and siderophores, with S. violaceoruber being the most prolific strain. Furthermore, the in vivo assays, performed on tomato (Solanum lycopersicum L.), resulted in an improved germination index and the growth of seedlings from seeds treated with PGP actinobacteria, with a particular focus on S. violaceoruber cultures. In particular, this last strain, producing volatile organic compounds having antimicrobial activity, was able to modulate volatilome and exert control on the global DNA methylation of tomato seedlings. Thus, these results, confirming the efficacy of the selected actinobacteria strains in promoting plant growth and development by producing volatile and non-volatile bioactive molecules, can promote eco-friendly alternatives in sustainable agriculture.

Replacement of water yam (Dioscorea alata L.) indigenous root endophytes and rhizosphere bacterial communities via inoculation with a synthetic bacterial community of dominant nitrogen-fixing bacteria

Biofertilizers containing high-density plant growth-promoting bacteria are gaining interest as a sustainable solution to environmental problems caused by eutrophication. However, owing to the limitations of current investigative techniques, the selected microorganisms are not always preferred by the host plant, preventing recruitment into the native microbiota or failing to induce plant growth-promoting effects. To address this, five nitrogen-fixing bacteria previously isolated from water yam (Dioscorea alata L.) plants and showing dominant abundance of 1% or more in the water yam microbiota were selected for analysis of their plant growth-promoting activities when used as a synthetic bacterial inoculant. Water yam cv. A-19 plants were inoculated twice at 10 and 12 weeks after planting under greenhouse conditions. Bacterial communities in root, rhizosphere, and bulk soil samples were characterized using high-throughput 16S rRNA amplicon sequencing. Compared with non-inoculated plants, all bacterial communities were significantly altered by inoculation, mainly at the genus level. The inoculation effects were apparently found in the root communities at 16 weeks after planting, with all inoculated genera showing dominance (in the top 35 genera) compared with the control samples. However, no significant differences in any of the growth parameters or nitrogen contents were observed between treatments. At 20 weeks after planting, the dominance of Stenotrophomonas in the inoculated roots decreased, indicating a decline in the inoculation effects. Interestingly, only the Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium clade was dominant (>1% relative abundance) across all samples, suggesting that bacteria related to this clade are essential core bacteria for water yam growth. This is the first report on addition of a synthetic nitrogen-fixing bacterial community in water yam plants showing that native bacterial communities can be replaced by a synthetic bacterial community, with declining in the effects of Stenotrophomonas on the modified communities several weeks after inoculation.

Heavy metal contamination affects the core microbiome and assembly processes in metal mine soils across Eastern China

Mining activities in metal mine areas cause serious environmental pollution, thereby imposing stresses to soil ecosystems. Investigating the ecological pattern underlying contaminated soil microbial diversity is essential to understand ecosystem responses to environment changes. Here we collected 624 soil samples from 49 representative metal mines across eastern China and analyzed their soil microbial diversity and biogeographic patterns by using 16 S rRNA gene amplicons. The results showed that deterministic factors dominated in regulating the microbial community in non-contaminated and contaminated soils. Soil pH played a key role in climatic influences on the heavy metal-contaminated soil microbial community. A core microbiome consisting of 25 taxa, which could be employed for the restoration of contaminated soils, was identified. Unlike the non-contaminated soil, stochastic processes were important in shaping the heavy metal-contaminated soil microbial community. The largest source of variations in the soil microbial community was land use type. This result suggests that varied specific ecological remediation strategy ought to be developed for differed land use types. These findings will enhance our understanding of the microbial responses to anthropogenically induced environmental changes and will further help to improve the practices of soil heavy metal contamination remediation.

Reviewing and renewing the use of beneficial root and soil bacteria for plant growth and sustainability in nutrient-poor, arid soils

A rapidly increasing human population coupled with climate change and several decades of over-reliance on synthetic fertilizers has led to two pressing global challenges: food insecurity and land degradation. Therefore, it is crucial that practices enabling both soil and plant health as well as sustainability be even more actively pursued. Sustainability and soil fertility encompass practices such as improving plant productivity in poor and arid soils, maintaining soil health, and minimizing harmful impacts on ecosystems brought about by poor soil management, including run-off of agricultural chemicals and other contaminants into waterways. Plant growth promoting bacteria (PGPB) can improve food production in numerous ways: by facilitating resource acquisition of macro- and micronutrients (especially N and P), modulating phytohormone levels, antagonizing pathogenic agents and maintaining soil fertility. The PGPB comprise different functional and taxonomic groups of bacteria belonging to multiple phyla, including Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria, among others. This review summarizes many of the mechanisms and methods these beneficial soil bacteria use to promote plant health and asks whether they can be further developed into effective, potentially commercially available plant stimulants that substantially reduce or replace various harmful practices involved in food production and ecosystem stability. Our goal is to describe the various mechanisms involved in beneficial plant-microbe interactions and how they can help us attain sustainability.

Tracking the nitrogen cycle in a vulnerable alluvial system using a multi proxy approach: Case study Varaždin alluvial aquifer, Croatia

At high concentrations nitrate is considered a serious environmental pollutant which degrades the quality of ground and surface waters. Such high nitrate concentrations (>50 mg NO₃/L) have been observed for decades in the alluvial aquifer in the Varaždin region of Croatia. Here we employ a novel cross disciplinary approach (dual isotopes, chemical, bacteria diversity and mixing modelling) to determine sources of nitrate and processes that can influence nitrate concentration within this vulnerable alluvial aquifer. Ten groundwater wells were sampled across the region and in different hydrological conditions for basic chemical, stable isotopes (δ¹⁸O-H₂O, δ²H-H₂O, δ¹⁵N-NO₃ and δ¹⁸O-NO₃), and bacterial diversity analyses. In addition, solid samples, i.e. soil samples and fertilizers were collected and analysed for bulk δ¹⁵N. The primary nitrate sources were manure, sewage, soil organic N, and ammonia fertilizers, however we observe no clear evidence to indicate that synthetic fertilizers are a major contributor to groundwater nitrate concentrations. Whilst denitrification was observed in the parts of the study area with dissolved oxygen (DO) deficiency, i.e. anoxic conditions, nitrification has been identified as the major process responsible for nitrate behaviour within the aquifer system. Our results will facilitate the creation of a conceptual model of nitrate behaviour in the study area and from this, a numerical groundwater nitrate transport model. These data, understanding of nitrate dynamics and subsequent models will be critical for future sustainable water and agricultural management of the study area.

Biocrusts from Iceland and Svalbard: Does microbial community composition differ substantially?

A wide range of microorganisms inhabit biocrusts of arctic and sub-arctic regions. These taxa live and thrive under extreme conditions and, moreover, play important roles in biogeochemical cycling. Nevertheless, their diversity and abundance remain ambiguous. Here, we studied microbial community composition in biocrusts from Svalbard and Iceland using amplicon sequencing and epifluorescence microscopy. Sequencing of 16S rRNA gene revealed the dominance of Chloroflexi in the biocrusts from Iceland and Longyearbyen, and Acidobacteria in the biocrusts from Ny-Ålesund and South Svalbard. Within the 18S rRNA gene sequencing dataset, Chloroplastida prevailed in all the samples with dominance of Trebouxiophyceae in the biocrusts from Ny-Ålesund and Embryophyta in the biocrusts from the other localities. Furthermore, cyanobacterial number of cells and biovolume exceeded the microalgal in the biocrusts. Community compositions in the studied sites were correlated to the measured chemical parameters such as conductivity, pH, soil organic matter and mineral nitrogen contents. In addition, co-occurrence analysis showed the dominance of positive potential interactions and, bacterial and eukaryotic taxa co-occurred more frequently together.

Diversity, mechanisms and beneficial features of phosphate-solubilizing Streptomyces in sustainable agriculture: A review

Currently, the use of phosphate (P) biofertilizers among many bioformulations has attracted a large amount of interest for sustainable agriculture. By acting as growth promoters, members of the Streptomyces genus can positively interact with plants. Several studies have shown the great potential of this bacterial group in supplementing P in a soluble, plant-available form by several mechanisms. Furthermore, some P-solubilizing Streptomyces (PSS) species are known as plant growth-promoting rhizobacteria that are able to promote plant growth through other means, such as increasing the availability of soil nutrients and producing a wide range of antibiotics, phytohormones, bioactive compounds, and secondary metabolites other than antimicrobial compounds. Therefore, the use of PSS with multiple plant growth-promoting activities as an alternative strategy appears to limit the negative impacts of chemical fertilizers in agricultural practices on environmental and human health, and the potential effects of these PSS on enhancing plant fitness and crop yields have been explored. However, compared with studies on the use of other gram-positive bacteria, studies on the use of Streptomyces as P solubilizers are still lacking, and their results are unclear. Although PSS have been reported as potential bioinoculants in both greenhouse and field experiments, no PSS-based biofertilizers have been commercialized to date. In this regard, this review provides an overview mainly of the P solubilization activity of Streptomyces species, including their use as P biofertilizers in competitive agronomic practices and the mechanisms through which they release P by solubilization/mineralization, for both increasing P use efficiency in the soil and plant growth. This review further highlights and discusses the beneficial association of PSS with plants in detail with the latest developments and research to expand the knowledge concerning the use of PSS as P biofertilizers for field applications by exploiting their numerous advantages in improving crop production to meet global food demands.

Non-rhizobia are the alternative sustainable solution for growth and development of the nonlegume plants

The major research focus for biological nitrogen fixation (BNF) has mostly been on typical rhizobia with legumes. But the newly identified non-rhizobial bacteria, both individually or in combination could also be an alternative for nitrogen supplementation in both legumes and nonlegume plants. Although about 90% of BNF is derived from a legume - rhizobia symbiosis, the non-legumes specially the cereals lack canonical nitrogen fixation system through root-nodule organogenesis. The non-rhizobia may colonize in the rhizosphere or present in endophytic/associative nature. The non-rhizobia are well known for facilitating plant growth through their potential to alleviate various stresses (salt, drought, and pathogens), acquisition of minerals (P, K, etc.), or by producing phytohormones. Bacterial symbiosis in non-legumes represents by the Gram-positive Frankia having a major contribution in overall fortification of usable nitrogenous material in soil where they are associated with their hosts. This review discusses the recent updates on the diversity and association of the non-rhizobial species and their impact on the growth and productivity of their host plants with particular emphasis on major economically important cereal plants. The future application possibilities of non-rhizobia for soil fertility and plant growth enhancement for sustainable agriculture have been discussed.

Rootstock Priming with Shikimic Acid and Streptomyces griseus for Growth, Productivity, Physio-Biochemical, and Anatomical Characterisation of Tomato Grown under Cold Stress

With this research, we aimed to determine the impact of grafting and rootstock seed treated with Streptomyces griseus (MT210913) (S. griseus) or shikimic acid (SA) at a 60 ppm concentration on tomato (Solanum lycopersicum L.) production grown under low-temperature conditions. Two open-field trials were performed during both winter seasons of 2020 and 2021 at the Experimental Farm, Faculty of Agriculture, Cairo University, Giza, Egypt. A tomato cultivar (Peto 86) was used as a scion and two tomato phenotypes were employed as rootstocks (Solanum cheesmaniae L. (line LA 524) and GS hybrid), as well as self-grafted as a control. Effects of sub-optimal temperature on vegetative growth, yield, and fruit quality were tested. The results indicate that, under cold stress, rootstock seed priming, especially with S. griseus, enhanced plant growth, total yield, and fruit quality properties. GS hybrid rootstock was more effective than that of S. cheesmaniae rootstock in terms of mitigating the negative effect of cold stress. GS hybrid, inoculated with S. griseus, increased the total yield per plant by 10.5% and 5.7% in the first and second seasons, respectively. Higher levels of GA3 and mineral content were noticed in leaves that were grafted and treated with S. griseus compared to the control treatment. Additionally, the great enhancing effects of all anatomical features of tomato plants were recorded with GS hybrid rootstock, inoculated by S. griseus. These results prove that grafting on GS hybrid rootstock treated with S. griseus is a potential choice to alleviate the cold stress of commercial tomato varieties.

Potential of lignocellulose degrading microorganisms for agricultural residue decomposition in soil: A review

Lignocellulosic crop residues (LCCRs) hold a significant share of the terrestrial biomass, estimated at 5 billion Mg per annum globally. A massive amount of these LCCRs are burnt in many countries resulting in immense environmental pollution; hence, its proper disposal in a cost-effective and eco-friendly manner is a significant challenge. Among the different options for management of LCCRs, the use of lignocellulose degrading microorganisms (LCDMOs), like fungi and bacteria, has emerged as an eco-friendly and effective way for its on-site disposal. LCDMOs achieve degradation through various mechanisms, including multiple supportive enzymes, causing oxidative attacks by which recalcitrance of lignocellulose material is reduced, paving the way to further activity by depolymerizing enzymes. This improves the physical properties of soil, recycles plant nutrients, promotes plant growth and thus helps improve productivity. Rapid and proper microbial degradation may be achieved through the correct combination of the LCDMOs, supplementing nutrients and controlling different factors affecting microbial activity in the field. The review is a critical discussion of previous studies revealing the potential of individuals or a set of LCDMOs, factors controlling the rate of degradation and the key researchable areas for better understanding of the role of these decomposers for future use.

Nostoc Talks Back: Temporal Patterns of Differential Gene Expression During Establishment of Anthoceros-Nostoc Symbiosis

Endosymbiotic associations between hornworts and nitrogen-fixing cyanobacteria form when the plant is limited for combined nitrogen (N). We generated RNA-seq data to examine temporal gene expression patterns during the culturing of N-starved Anthoceros punctatus in the absence and the presence of symbiotic cyanobacterium Nostoc punctiforme. In symbiont-free A. punctatus gametophytes, N starvation caused downregulation of chlorophyll content and chlorophyll fluorescence characteristics as well as transcription of photosynthesis-related genes. This downregulation was reversed in A. punctatus cocultured with N. punctiforme, corresponding to the provision by the symbiont of N₂-derived NH₄⁺, which commenced within 5 days of coculture and reached a maximum by 14 days. We also observed transient increases in transcription of ammonium and nitrate transporters in a N. punctiforme-dependent manner as well as that of a SWEET transporter that was initially independent of N₂-derived NH₄⁺. The temporal patterns of differential gene expression indicated that N. punctiforme transmits signals that impact gene expression to A. punctatus both prior to and after its provision of fixed N. This study is the first illustrating the temporal patterns of gene expression during establishment of an endosymbiotic nitrogen-fixing association in this monophyletic evolutionary lineage of land plants. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Paradigms of actinorhizal symbiosis under the regime of global climatic changes: New insights and perspectives

Nitrogen occurs as inert and inaccessible dinitrogen gaseous form (N₂ ) in the atmosphere. Biological nitrogen fixation is a chief process that makes this dinitrogen (N₂ ) accessible and bioavailable in the form of ammonium (NH₄ ⁺ ) ions. The key organisms to fix nitrogen are certain prokaryotes, called diazotrophs either in the free-living form or establishing significant mutual relationships with a variety of plants. On such examples is ~95-100 MY old incomparable symbiosis between dicotyledonous trees and a unique actinobacterial diazotroph in diverse ecosystems. In this association, the root of the certain dicotyledonous tree (~25 genera and 225 species) belonging to three different taxonomic orders, Fagales, Cucurbitales, and Rosales (FaCuRo) known as actinorhizal trees can host a diazotroph, Frankia of order Frankiales. Frankia is gram-positive, branched, filamentous, sporulating, and free-living soil actinobacterium. It resides in the specialized, multilobed, and coralloid organs (lateral roots but without caps), the root nodules of actinorhizal tress. This review aims to provide systematic information on the distribution and the phylogenetic diversity of hosts from FaCuRo and their micro-endosymbionts (Frankia spp.), colonization mechanisms, and signaling pathways. We also aim to provide details on developmental and physiological imperatives for gene regulation and functional genomics of symbiosis, phenomenal restoration ecology, influences of contemporary global climatic changes, and anthropogenic impacts on plant-Frankia interactions for the functioning of ecosystems and the biosphere.

Inter-cluster competition and resource partitioning may govern the ecology of Frankia

Microbes live in a complex communal ecosystem. The structural complexity of microbial community reflects diversity, functionality, as well as habitat type. Delineation of ecologically important microbial populations along with exploration of their roles in environmental adaptation or host-microbe interaction has a crucial role in modern microbiology. In this scenario, reverse ecology (the use of genomics to study ecology) plays a pivotal role. Since the co-existence of two different genera in one small niche should maintain a strict direct interaction, it will be interesting to utilize the concept of reverse ecology in this scenario. Here, we exploited an 'R' package, the RevEcoR, to resolve the issue of co-existing microbes which are proven to be a crucial tool for identifying the nature of their relationship (competition or complementation) persisting among them. Our target organism here is Frankia, a nitrogen-fixing actinobacterium popular for its genetic and host-specific nature. According to their plant host, Frankia has already been sub-divided into four clusters C-I, C-II, C-III, and C-IV. Our results revealed a strong competing nature of CI Frankia. Among the clusters of Frankia studied, the competition index between C-I and C-III was the largest. The other interesting result was the co-occurrence of C-II and C-IV groups. It was revealed that these two groups follow the theory of resource partitioning in their lifestyle. Metabolic analysis along with their differential transporter machinery validated our hypothesis of resource partitioning among C-II and C-IV groups.

Nutrients, temperature, and oxygen mediate microbial antibiotic resistance in sea bass (Lateolabrax maculatus) ponds

Antibiotic resistance genes (ARGs) have drawn increasing attention as novel environmental pollutants because of the threat they impose on human and animal health. The sea bass (Lateolabrax maculatus) is the third most cultured marine fish in China. Therefore, a study of ARG pollution in the sea bass culture environment is of great significance for the healthy and sustainable development of the sea bass industry. Here, we systematic investigated the contents of 23 antibiotic resistance-related genes (ARRGs), including 19 ARGs and four mobile genetic elements, and analyzed bacterial community composition and environmental parameters in sea bass ponds. The relative abundance (ARRG copies/16S ribosomal RNA gene copies) of ARRGs was up to 3.83 × 10^-2. Sul1 was the most abundant ARRG, followed by ereA, intI-1, sul2, dfrA1, and aadA. Both the ARRG changes and aquatic microbiota succession were mainly driven by water temperature (WT), dissolved oxygen (DO), and NO₃^-. WT is positively correlated with the most ARGs and some of the top 38 Operational Taxonomic Units (OTUs) belonging to the orders of Frankiales, Micrococcales, Chitinophagales, and Sphingomonadales. Furthermore, WT is negatively related with some other OTUs of the orders Frankiales, Xanthomonadales, Micrococcales, and Rhizobiales. However, DO and NO₃^- have the opposite function with WT on specific taxa and ARGs. These results indicate that sea bass ponds are reservoirs of ARGs, and are driven mainly by the nutrient, temperature, and oxygen with inducing specific microbial taxa. The regulation of environmental factors (increasing DO and NO₃^-) can be conducted to reduce drug resistance risk in aquaculture ponds. Therefore, environmental factors and specific taxa could be the indicators of ARG contamination and can be used to establish an antibiotic elimination system and consequently realize a sustainable aquaculture industry.

Bacterial community succession and influencing factors for Imperata cylindrica litter decomposition in a copper tailings area of China

Litter decomposition is a critical component of the ecological nutritional transformation process. In a copper mining area, the litter from Imperata cylindrica is the major indicator for restoring heavy metal-polluted copper mining lands. Large amounts of litter are generated at the end of the plant growing season during the process of vegetation restoration in copper mining areas, and the microbial dynamics play an important role in soil nutrient turnover during the decomposition of litter. Investigating the characteristics and interactions of bacterial communities during litter decomposition will clarify the driving mechanisms of organic matter and nutrient cycling in copper mining areas that harbor contaminated soils. Here, we report the results of an in situ decomposition experiment that lasted for a total of 460 days from three of the 16 copper mining subdams with heavy metal pollution and different phytoremediation histories (e.g., 50, 22 and 5 years) to explore the bacterial communities as the driving factors of litter decomposition. The total carbon contents of the litter decreased by 62.6% and 71.5% in the decomposition process at those sites with phytoremediation histories of 50 and 22 years (S516 and S536), respectively, but decreased by only 25.8% at the site with a phytoremediation history of 5 years (S560). The optimal C/N ratios in the three different restoration stages varied and were 65.5, 86.7 and 39.3 in S516, S536, S560, respectively. Litter decomposition enriched the heavy metal contents such as cadmium, copper (Cu), lead and zinc (P < 0.05) in litter. Proteobacteria and Actinobacteriota were the dominant bacterial phyla during the different litter decomposition stages, which accounted for 91.66% of the relative abundances in the bacterial communities. Moreover, the role of Friedmanniella, which had the highest betweenness centrality (BC) value, was critical in sustaining both the structure and function of the bacterial communities during the early decomposition stage. However, Quadrisphaera, with the maximum BC value (1074.8), became the dominant genus as litter decomposition progressed. The most crucial factors that affected the litter bacterial communities were the litter pH and copper contents. The obtained results will be helpful to provide a further understanding of litter decomposition mechanisms and will provide a scientific basis for improving the effectiveness of material circulation and nutrient transformation in degraded copper mining ecosystems.

Genetically related genotypes of cowpea present similar bacterial community in the rhizosphere

Plant breeding reduces the genetic diversity of plants and could influence the composition, structure, and diversity of the rhizosphere microbiome, selecting more homogeneous and specialized microbes. In this study, we used 16S rRNA sequencing to assess the bacterial community in the rhizosphere of different lines and modern cowpea cultivars, to investigate the effect of cowpea breeding on bacterial community assembly. Thus, two African lines (IT85F-2687 and IT82D-60) and two Brazilian cultivars (BRS-Guariba and BRS-Tumucumaque) of cowpea were assessed to verify if the generation advance and genetic breeding influence the bacterial community in the rhizosphere. No significant differences were found in the structure, richness, and diversity of bacterial community structure between the rhizosphere of the different cowpea genotypes, and only slight differences were found at the OTU level. The complexity of the co-occurrence network decreased from African lines to Brazilian cultivars. Regarding functional prediction, the core functions were significantly altered according to the genotypes. In general, African lines presented a more abundance of groups related to chemoheterotrophy, while the rhizosphere of the modern cultivars decreased functions related to cellulolysis. This study showed that the genetic breeding process affects the dynamics of the rhizosphere community, decreasing the complexity of interaction in one cultivar. As these cowpea genotypes are genetically related, it could suggest a new hypothesis of how genetic breeding of similar genotypes could influence the rhizosphere microbiome.

Inoculation with Native Actinobacteria May Improve Desert Plant Growth and Survival with Potential Use for Restoration Practices

Soil microorganisms, together with water, play a key role in arid ecosystems, being responsible for the nutrient cycle, facilitating nutrient incorporation into plants, influencing plant drought tolerance, and enhancing their establishment. Therefore, their use for restoration practices is promising. We tested the potential of native strains of Actinobacteria from Monte Desert as growth promoters of native vegetation, isolating them from two substrates from their habitat (bare soil and leaf-cutting ant refuse dumps). Strains were inoculated into the soil where seedlings of three native plant species (Atriplex lampa, Grindelia chiloensis, Gutierrezia solbrigii) were growing. Seedlings were grown following a full factorial design experiment under greenhouse and field conditions comparing native Actinobacteria effects with a known growth-promoting strain, Streptomyces sp. (BCRU-MM40 GenBank accession number: FJ771041), and control treatments. Seedlings survived greenhouse condition but species survival and growth were different among treatments at field conditions, varying over time. The highest survival was observed in a native soil strain (S20) while the lowest in MM40. The low survival in MM40 and in the other treatments may be explained by the higher herbivory observed in those seedlings compared to control ones, suggesting a higher nutritional status in inoculated plants. Strains from refuse dumps were the best at enhancing seedling growth, while strains from soil were the best at maintaining their survival. Native Actinobacteria studied may increase plant species survival and growth by improving their nutritional status, suggesting their potential to facilitate vegetation establishment and, therefore, being good candidates for restoration practices. Furthermore, plant species respond differently to different strains, highlighting the importance of microorganism diversity for ecosystem functioning.

Phylosymbiosis in the Rhizosphere Microbiome Extends to Nitrogen Cycle Functional Potential

Most plants rely on specialized root-associated microbes to obtain essential nitrogen (N), yet not much is known about the evolutionary history of the rhizosphere–plant interaction. We conducted a common garden experiment to investigate the plant root–rhizosphere microbiome association using chloridoid grasses sampled from around the world and grown from seed in a greenhouse. We sought to test whether plants that are more closely related phylogenetically have more similar root bacterial microbiomes than plants that are more distantly related. Using metagenome sequencing, we found that there is a conserved core and a variable rhizosphere bacterial microbiome across the chloridoid grasses. Additionally, phylogenetic distance among the host plant species was correlated with bacterial community composition, suggesting the plant hosts prefer specific bacterial lineages. The functional potential for N utilization across microbiomes fluctuated extensively and mirrored variation in the microbial community composition across host plants. Variation in the bacterial potential for N fixation was strongly affected by the host plants’ phylogeny, whereas variation in N recycling, nitrification, and denitrification was unaffected. This study highlights the evolutionary linkage between the N fixation traits of the microbial community and the plant host and suggests that not all functional traits are equally important for plant–microbe associations.

Evolutionary genomics and biosynthetic potential of novel environmental Actinobacteria

Actinobacteria embroil Gram-positive microbes with high guanine and cytosine contents in their DNA. They are the source of most antimicrobials of bacterial origin utilized in medicine today. Their genomes are among the richest in novel secondary metabolites with high biotechnological potential. Actinobacteria reveal complex patterns of evolution, responses, and adaptations to their environment, which are not yet well understood. We analyzed three novel plant isolates and explored their habitat adaptation, evolutionary patterns, and potential secondary metabolite production. The phylogenomically characterized isolates belonged to Actinoplanes sp. TFC3, Streptomyces sp. L06, and Embleya sp. NF3. Positively selected genes, relevant in strain evolution, encoded enzymes for stress resistance in all strains, including porphyrin, chlorophyll, and ubiquinone biosynthesis in Embleya sp. NF3. Streptomyces sp. L06 encoded for pantothenate and proteins for CoA biosynthesis with evidence of positive selection; furthermore, Actinoplanes sp. TFC3 encoded for a c-di-GMP synthetase, with adaptive mutations. Notably, the genomes harbored many genes involved in the biosynthesis of at least ten novel secondary metabolites, with many avenues for future new bioactive compound characterization-specifically, Streptomyces sp. L06 could make new ribosomally synthesized and post-translationally modified peptides, while Embleya sp. NF3 could produce new non-ribosomal peptide synthetases and ribosomally synthesized and post-translationally modified peptides. At the same time, TFC3 has particularly enriched in terpene and polyketide synthases. All the strains harbored conserved genes in response to diverse environmental stresses, plant growth promotion factors, and degradation of various carbohydrates, which supported their endophytic lifestyle and showed their capacity to colonize other niches. This study aims to provide a comprehensive estimation of the genomic features of novel Actinobacteria. It sets the groundwork for future research into experimental tests with new bioactive metabolites with potential application in medicine, biofertilizers, and plant biomass residue utilization, with potential application in medicine, as biofertilizers and in plant biomass residues utilization. KEY POINTS: • Potential of novel environmental bacteria for secondary metabolites production • Exploring the genomes of three novel endophytes isolated from a medicinal tree • Pan-genome analysis of Actinobacteria genera.

Mycolicibacterium sp. strain PAM1, an alfalfa rhizosphere dweller, catabolizes PAHs and promotes partner-plant growth

This research was focused on the isolation and characterization of a PAH-catabolizing mycobacterial strain from the petroleum hydrocarbon-contaminated rhizosphere of alfalfa, as well as on revealing some points of interaction between the microorganism and the plant. Mycolicibacterium sp. PAM1, a pyrene degrader isolated from the niche of interest to us, can catabolize fluoranthene, anthracene, fluorene, and phenanthrene. On the basis of curves of PAM1 growth with different PAHs as the sole carbon sources and on the basis of PAH-degradation rates, we found that pollutant availability to the strain decreased in the sequence phenanthrene > fluorene > fluoranthene ∼ pyrene > anthracene. For each PAH, the catabolic products were identified. PAM1 was found to have the functional genes nidA and nidB. New data modeling the 2D and 3D structures, intrinsic structural disorder, and molecular dynamics of the nidA and nidB gene products were obtained. The identified genes and intermediates of pyrene degradation indicate that PAM1 has a PAH catabolic pathway that is peculiar to known mycobacterial pyrene degraders. PAM1 utilized some components of alfalfa root exudates as nutrients and promoted plant growth. The use of mycobacterial partners of alfalfa is attractive for enhancing the phytoremediation of PAH-contaminated soils.

Plant-Microbe Interaction: Aboveground to Belowground, from the Good to the Bad

Soil health and fertility issues are constantly addressed in the agricultural industry. Through the continuous and prolonged use of chemical heavy agricultural systems, most agricultural lands have been impacted, resulting in plateaued or reduced productivity. As such, to invigorate the agricultural industry, we would have to resort to alternative practices that will restore soil health and fertility. Therefore, in recent decades, studies have been directed towards taking a Magellan voyage of the soil rhizosphere region, to identify the diversity, density, and microbial population structure of the soil, and predict possible ways to restore soil health. Microbes that inhabit this region possess niche functions, such as the stimulation or promotion of plant growth, disease suppression, management of toxicity, and the cycling and utilization of nutrients. Therefore, studies should be conducted to identify microbes or groups of organisms that have assigned niche functions. Based on the above, this article reviews the aboveground and below-ground microbiomes, their roles in plant immunity, physiological functions, and challenges and tools available in studying these organisms. The information collected over the years may contribute toward future applications, and in designing sustainable agriculture.

A Taxon-Wise Insight Into Rock Weathering and Nitrogen Fixation Functional Profiles of Proglacial Systems

The Arctic environment is particularly affected by global warming, and a clear trend of the ice retreat is observed worldwide. In proglacial systems, the newly exposed terrain represents different environmental and nutrient conditions compared to later soil stages. Therefore, proglacial systems show several environmental gradients along the soil succession where microorganisms are active protagonists of the soil and carbon pool formation through nitrogen fixation and rock weathering. We studied the microbial succession of three Arctic proglacial systems located in Svalbard (Midtre Lovénbreen), Sweden (Storglaciären), and Greenland (foreland close to Kangerlussuaq). We analyzed 65 whole shotgun metagenomic soil samples for a total of more than 400 Gb of sequencing data. Microbial succession showed common trends typical of proglacial systems with increasing diversity observed along the forefield chronosequence. Microbial trends were explained by the distance from the ice edge in the Midtre Lovénbreen and Storglaciären forefields and by total nitrogen (TN) and total organic carbon (TOC) in the Greenland proglacial system. Furthermore, we focused specifically on genes associated with nitrogen fixation and biotic rock weathering processes, such as nitrogenase genes, obcA genes, and genes involved in cyanide and siderophore synthesis and transport. Whereas we confirmed the presence of these genes in known nitrogen-fixing and/or rock weathering organisms (e.g., Nostoc, Burkholderia), in this study, we also detected organisms that, even if often found in soil and proglacial systems, have never been related to nitrogen-fixing or rock weathering processes before (e.g., Fimbriiglobus, Streptomyces). The different genera showed different gene trends within and among the studied systems, indicating a community constituted by a plurality of organisms involved in nitrogen fixation and biotic rock weathering, and where the latter were driven by different organisms at different soil succession stages.

Diversity and function of culturable actinobacteria in the root-associated of Salvia miltiorrhiza Bunge

The root-associated actinobacteria play important roles in plant growth, nutrient use, and disease resistance due to their functional diversity. Salvia miltiorrhiza is a critical medicinal plant in China. The root actinobacterial community structure has been studied; however, the functions of root-associated actinobacteria of S. miltiorrhiza have not been elucidated. This study aimed to decipher the diversity and function of the culturable root-associated actinobacteria in plant growth using culture-dependent technology and culturable microbe metagenomes. We isolated 369 strains from the root-associated actinobacteria, belonging to four genera, among which Streptomyces was dominant. Besides, the functional prediction revealed some pathways related to plant growth, nitrogen and phosphorus metabolism, and antagonistic pathogens. We systematically described the diversity and functions of the culturable root-associated actinobacteria community. Our results demonstrated that the culturable root-associated actinobacteria of S. miltiorrhiza have rich functionalities, explaining the possible contribution of culturable root-associated actinobacteria to S. miltiorrhiza's growth and development. This study provides new insights into understanding the function of the culturable root-associated actinobacteria and can be used as a knowledge base for plant growth promoters and biological control agent development in agriculture.

Cometabolic degradation of 1,4-dioxane by a tetrahydrofuran-growing Arthrobacter sp. WN18

1,4-Dioxane (dioxane), an emerging groundwater contaminant, is frequently detected in landfill leachates with its structural analog, tetrahydrofuran (THF). Along with undesirable leakage of landfill leachates, dioxane and THF inevitably percolate into groundwater leading to a broader region of contamination. Cometabolic bioremediation is an effective approach to manage commingled THF and dioxane pollution. In this study, a newly isolated bacterium Arthrobacter sp. WN18 is able to co-oxidize dioxane with THF as the primary substrate. Meanwhile, the THF-induced thmADBC gene cluster was responsible for the dioxane degradation rate indicating THF monooxygenase is the essential enzyme that initializing α-hydroxylation of THF and dioxane. Further, γ-butyrolactone and HEAA were characterized as the key metabolites of THF and dioxane, respectively. In addition, WN18 can tolerate the inhibition of trichloroethylene (5.0 mg/L) as a representative of co-existing leachate constituent, and sustain its activity at various pH (5-11), temperatures (15-42 °C), and salinities (up to 4%, as NaCl wt). Like other Arthrobacter species, WN18 also exhibited the capability of fixing nitrogen. All this evidence indicates the feasibility and advantage of WN18 as a thmADBC-catalyzed inoculator to bioremediate co-contamination of THF and dioxane.

Impact of Olive Saplings and Organic Amendments on Soil Microbial Communities and Effects of Mineral Fertilization

Plant communities and fertilization may have an impact on soil microbiome. Most commercial olive trees are minerally fertilized, while this practice is being replaced by the use of organic amendments. Organic amendments can both fertilize and promote plant growth-promoting organisms. Our aims were (i) to describe the changes in soil bacterial and fungal communities induced by the presence of young olive trees and their interaction with organic amendments and (ii) to compare the effects of mineral and organic fertilization. We set up two parallel experiments in pots using a previously homogenized soil collected from a commercial olive orchard: in the first one, we grew olive saplings in unamended and organically amended soils with two distinct composts and compared these two soils incubated without a plant, while in the second experiment, we comparatively tested the effects of organic and mineral fertilization. OTUs and the relative abundances of bacterial and fungal genera and phyla were analyzed by 16S rRNA and ITS1 gene amplicon using high-throughput sequencing. Basal respiration and substrate-induced respiration were measured by MicroResp^TM. The effects of the different treatments were analyzed in all phyla and in the 100 most abundant genera. The presence of olive saplings increased substrate-induced respiration and bacterial and fungal richness and diversity. Organic amendments greatly affected both bacterial and fungal phyla and increased bacterial richness while not affecting fungal richness. Mineral fertilization increased the relative abundance of the less metabolically active bacterial phyla (Actinobacteria and Firmicutes), while it reduced the most metabolically active phylum, Bacteroidetes. Mineral fertilization increased the relative abundance of three N₂-fixing Actinobacteria genera, while organic fertilization only increased one genus of Proteobacteria. In organically and minerally fertilized soils, high basal respiration rates were associated with low fungal diversity. Basidiomycota and Chytridiomycota relative abundances positively correlated with basal respiration and substrate-induced respiration, while Ascomycota correlated negatively. Indeed, the Ascomycota phyla comprised most of the fungal genera decreased by organic amendments. The symbiotrophic phylum Glomeromycota did not correlate with any of the C sources. The relative abundance of this phylum was promoted by the presence of plants but decreased when amending soils with composts.

Diversity of nitrogen cycling genes at a Midwest long-term ecological research site with different management practices

Nitrogen fertilizer results in the release of nitrous oxide (N₂O), a concern because N₂O is an ozone-depleting substance and a greenhouse gas. Although the reduction of N₂O to nitrogen gas can control emissions, the factors impacting the enzymes involved have not been fully explored. The current study investigated the abundance and diversity of genes involved in nitrogen cycling (primarily denitrification) under four agricultural management practices (no tillage [NT], conventional tillage [CT], reduced input, biologically-based). The work involved examining soil shotgun sequencing data for nine genes (napA, narG, nirK, nirS, norB, nosZ, nirA, nirB, nifH). For each gene, relative abundance values, diversity and richness indices, and taxonomic classification were determined. Additionally, the genes associated with nitrogen metabolism (defined by the KEGG hierarchy) were examined. The data generated were statistically compared between the four management practices. The relative abundance of four genes (nifH, nirK, nirS, and norB) were significantly lower in the NT treatment compared to one or more of the other soils. The abundance values of napA, narG, nifH, nirA, and nirB were not significantly different between NT and CT. The relative abundance of nirS was significantly higher in the CT treatment compared to the others. Diversity and richness values were higher for four of the nine genes (napA, narG, nirA, nirB). Based on nirS/nirK ratios, CT represents the highest N₂O consumption potential in four soils. In conclusion, the microbial communities involved in nitrogen metabolism were sensitive to different agricultural practices, which in turn, likely has implications for N₂O emissions. KEY POINTS: • Four genes were less abundant in NT compared to one or more of the others soils (nifH, nirK, nirS, norB). • The most abundant sequences for many of the genes classified within the Proteobacteria. • Higher diversity and richness indices were observed for four genes (napA, narG, nirA, nirB). • Based on nirS/nirK ratios, CT represents the highest N₂O consumption potential.

Improvement of Medicago sativa Crops Productivity by the Co-inoculation of Sinorhizobium meliloti-Actinobacteria Under Salt Stress

Biotic and abiotic stresses are severely limiting plant production and productivity. Of notable importance is salt stress that not only limits plant growth and survival, but affects the soil fertility and threatens agricultural ecosystems sustainability. The problem is exacerbated in fragile arid and semi-arid areas where high evaporation, low precipitation and the use of salty water for irrigation is accelerating soil salinization. Legumes, considered very nutritious foods for people and providing essential nutrients for ecosystems are a fundamental element of sustainable agriculture. They can restore soil health by their ability to fix nitrogen in a symbiotic interaction with the rhizobia of the soil. However, salt stress is severely limiting productivity and nitrogen fixation ability in legumes. Plant growth-promoting rhizobacteria (PGPR) and mainly actinobacteria promote plant growth by producing phytohormones, siderophores, antibiotics and antifungal compounds, solubilizing phosphate and providing antagonism to phytopathogenic microorganisms. In addition, actinobacteria have beneficial effects on nodulation and growth of legumes. In this study, actinobacteria isolated from different niches and having PGP activities were used in co-inoculation experiments with rhizobia in Medicago sativa plants rhizosphere submitted to salt stress. The results indicate that drought- and salinity-tolerant Actinobacteria with multiple PGP traits can potentially increase alfalfa growth under saline conditions, in the presence or absence of symbiotic rhizobial bacteria. Actinobacteria discovered in this study can, therefore, be suitable biofertilizers in the formulation of agricultural products improving plant development, health and productivity in saline soils, a necessary alternative for modern agriculture and sustainable development.

Nutrient availability is a dominant predictor of soil bacterial and fungal community composition after nitrogen addition in subtropical acidic forests

Nutrient addition to forest ecosystems significantly influences belowground microbial diversity, community structure, and ecosystem functioning. Nitrogen (N) addition in forests is common in China, especially in the southeast region. However, the influence of N addition on belowground soil microbial community diversity in subtropical forests remains unclear. In May 2018, we randomly selected 12 experimental plots in a Pinus taiwanensis forest within the Daiyun Mountain Nature Reserve, Fujian Province, China, and subjected them to N addition treatments for one year. We investigated the responses of the soil microbial communities and identified the major elements that influenced microbial community composition in the experimental plots. The present study included three N treatments, i.e., the control (CT), low N addition (LN, 40 kg N ha^-1 yr^-1), and high N addition (HN, 80 kg N ha^-1 yr^-1), and two depths, 0−10 cm (topsoil) and 10−20 cm (subsoil), which were all sampled in the growing season (May) of 2019. Soil microbial diversity and community composition in the topsoil and subsoil were investigated using high-throughput sequencing of bacterial 16S rDNA genes and fungal internal transcribed spacer sequences. According to our results, 1) soil dissolved organic carbon (DOC) significantly decreased after HN addition, and available nitrogen (AN) significantly declined after LN addition, 2) bacterial α-diversity in the subsoil significantly decreased with HN addition, which was affected significantly by the interaction between N addition and soil layer, and 3) soil DOC, rather than pH, was the dominant environmental factor influencing soil bacterial community composition, while AN and MBN were the best predictors of soil fungal community structure dynamics. Moreover, N addition influence both diversity and community composition of soil bacteria more than those of fungi in the subtropical forests. The results of the present study provide further evidence to support shifts in soil microbial community structure in acidic subtropical forests in response to increasing N deposition.

Transition from unclassified Ktedonobacterales to Actinobacteria during amorphous silica precipitation in a quartzite cave environment

The orthoquartzite Imawarì Yeuta cave hosts exceptional silica speleothems and represents a unique model system to study the geomicrobiology associated to silica amorphization processes under aphotic and stable physical-chemical conditions. In this study, three consecutive evolution steps in the formation of a peculiar blackish coralloid silica speleothem were studied using a combination of morphological, mineralogical/elemental and microbiological analyses. Microbial communities were characterized using Illumina sequencing of 16S rRNA gene and clone library analysis of carbon monoxide dehydrogenase (coxL) and hydrogenase (hypD) genes involved in atmospheric trace gases utilization. The first stage of the silica amorphization process was dominated by members of a still undescribed microbial lineage belonging to the Ktedonobacterales order, probably involved in the pioneering colonization of quartzitic environments. Actinobacteria of the Pseudonocardiaceae and Acidothermaceae families dominated the intermediate amorphous silica speleothem and the final coralloid silica speleothem, respectively. The atmospheric trace gases oxidizers mostly corresponded to the main bacterial taxa present in each speleothem stage. These results provide novel understanding of the microbial community structure accompanying amorphization processes and of coxL and hypD gene expression possibly driving atmospheric trace gases metabolism in dark oligotrophic caves.

Unraveling Mechanisms and Impact of Microbial Recruitment on Oilseed Rape (Brassica napus L.) and the Rhizosphere Mediated by Plant Growth-Promoting Rhizobacteria

Plant growth-promoting rhizobacteria (PGPR) are noticeably applied to enhance plant nutrient acquisition and improve plant growth and health. However, limited information is available on the compositional dynamics of rhizobacteria communities with PGPR inoculation. In this study, we investigated the effects of three PGPR strains, Stenotrophomonas rhizophila, Rhodobacter sphaeroides, and Bacillus amyloliquefaciens on the ecophysiological properties of Oilseed rape (Brassica napus L.), rhizosphere, and bulk soil; moreover, we assessed rhizobacterial community composition using high-throughput Illumina sequencing of 16S rRNA genes. Inoculation with S. rhizophila, R. sphaeroides, and B. amyloliquefaciens, significantly increased the plant total N (TN) (p < 0.01) content. R. sphaeroides and B. amyloliquefaciens selectively enhanced the growth of Pseudomonadacea and Flavobacteriaceae, whereas S. rhizophila could recruit diazotrophic rhizobacteria, members of Cyanobacteria and Actinobacteria, whose abundance was positively correlated with inoculation, and improved the transformation of organic nitrogen into inorganic nitrogen through the promotion of ammonification. Initial colonization by PGPR in the rhizosphere affected the rhizobacterial community composition throughout the plant life cycle. Network analysis indicated that PGPR had species-dependent effects on niche competition in the rhizosphere. These results provide a better understanding of PGPR-plant-rhizobacteria interactions, which is necessary to develop the application of PGPR.

Distribution of Mixotrophy and Desiccation Survival Mechanisms across Microbial Genomes in an Arid Biological Soil Crust Community

Desert surface soils devoid of plant cover are populated by a variety of microorganisms, many with yet unresolved physiologies and lifestyles. Nevertheless, a common feature vital for these microorganisms inhabiting arid soils is their ability to survive long drought periods and reactivate rapidly in rare incidents of rain. Chemolithotrophic processes such as oxidation of atmospheric hydrogen and carbon monoxide are suggested to be a widespread energy source to support dormancy and resuscitation in desert soil microorganisms. Here, we assessed the distribution of chemolithotrophic, phototrophic, and desiccation-related metabolic potential among microbial populations in arid biological soil crusts (BSCs) from the Negev Desert, Israel, via population-resolved metagenomic analysis. While the potential to utilize light and atmospheric hydrogen as additional energy sources was widespread, carbon monoxide oxidation was less common than expected. The ability to utilize continuously available energy sources might decrease the dependency of mixotrophic populations on organic storage compounds and carbon provided by the BSC-founding cyanobacteria. Several populations from five different phyla besides the cyanobacteria encoded CO2 fixation potential, indicating further potential independence from photoautotrophs. However, we also found population genomes with a strictly heterotrophic genetic repertoire. The highly abundant Rubrobacteraceae (Actinobacteriota) genomes showed particular specialization for this extreme habitat, different from their closest cultured relatives. Besides the ability to use light and hydrogen as energy sources, they encoded extensive O2 stress protection and unique DNA repair potential. The uncovered differences in metabolic potential between individual, co-occurring microbial populations enable predictions of their ecological niches and generation of hypotheses on the dynamics and interactions among them.IMPORTANCE This study represents a comprehensive community-wide genome-centered metagenome analysis of biological soil crust (BSC) communities in arid environments, providing insights into the distribution of genes encoding different energy generation mechanisms, as well as survival strategies, among populations in an arid soil ecosystem. It reveals the metabolic potential of several uncultured and previously unsequenced microbial genera, families, and orders, as well as differences in the metabolic potential between the most abundant BSC populations and their cultured relatives, highlighting once more the danger of inferring function on the basis of taxonomy. Assigning functional potential to individual populations allows for the generation of hypotheses on trophic interactions and activity patterns in arid soil microbial communities and represents the basis for future resuscitation and activity studies of the system, e.g., involving metatranscriptomics.

High nitrogen concentration alter microbial community in Allium fistulosum rhizosphere

Welsh onion (Allium fistulosum L.) constitutes an important plant species cultivated in China due the benefits and applications in different areas. Moreover, nitrogen is an essential nutrient during the growth and development of plant. Here, we present the effects of nitrogen on soil microbiome in welsh onion plants. We used High-throughput sequencing analysis to determine the diversity and abundances of microbes associated to soil rhizosphere in welsh onion under the influence of nitrogen application. Nitrogen application significantly influenced in the diversity of fungal community. The relative abundance of Orbiliomycetes increased with the nitrogen concentration. Nitrogen application did not affect the diversity of bacterial community, whereas the relative abundance of Acidobacteria_Gp2, Verrucomicrobiae and Sphingobacteriia decreased with the nitrogen condition. In this work, we introduced evidences of the effect of nitrogen fertilization on microbial community in welsh onion rhizosphere, and the change of microbial community may interfere the growth and development of welsh onion.

An Update on Molecular Tools for Genetic Engineering of Actinomycetes-The Source of Important Antibiotics and Other Valuable Compounds

The first antibiotic-producing actinomycete (Streptomyces antibioticus) was described by Waksman and Woodruff in 1940. This discovery initiated the "actinomycetes era", in which several species were identified and demonstrated to be a great source of bioactive compounds. However, the remarkable group of microorganisms and their potential for the production of bioactive agents were only partially exploited. This is caused by the fact that the growth of many actinomycetes cannot be reproduced on artificial media at laboratory conditions. In addition, sequencing, genome mining and bioactivity screening disclosed that numerous biosynthetic gene clusters (BGCs), encoded in actinomycetes genomes are not expressed and thus, the respective potential products remain uncharacterized. Therefore, a lot of effort was put into the development of technologies that facilitate the access to actinomycetes genomes and activation of their biosynthetic pathways. In this review, we mainly focus on molecular tools and methods for genetic engineering of actinomycetes that have emerged in the field in the past five years (2015-2020). In addition, we highlight examples of successful application of the recently developed technologies in genetic engineering of actinomycetes for activation and/or improvement of the biosynthesis of secondary metabolites.

P-Solubilizing Streptomyces roseocinereus MS1B15 With Multiple Plant Growth-Promoting Traits Enhance Barley Development and Regulate Rhizosphere Microbial Population

Phosphate-solubilizing bacteria (PSB) have been reported to increase phosphate (P) content and plant growth. Their application in agricultural systems is an eco-friendly alternative strategy for limiting negative environmental impact of chemical fertilizers and increasing costs. Therefore, the aim of this study was to isolate and characterize new putative PSB to use as inoculum to enhance plant growth and increase P bioavailability in soil. Sixteen bacteria were isolated from Moroccan oat rhizosphere and were screened for their putative P-solubilization by semi-quantitative agar spot method. The two strains MS1B15 and MS1B13, identified as Streptomyces roseocinereus and Streptomyces natalensis, respectively, showed the maximum phosphate solubilization index (PSI = 1.75 and PSI = 1.63). After quantitative assay to determine phosphate solubilization activity, S. roseocinereus MS1B15 was selected for evaluating its putative plant growth promotion activities including production of siderophores, indole-3-acetic acid (IAA) and amino-cyclopropane-1-carboxylate (ACC) deaminase, nitrogen fixation and antimicrobial activity against soil-borne plant pathogens. Under greenhouse condition, barley plants inoculated with S. roseocinereus MS1B15 significantly increased shoot and ear length as well as available phosphorus in ears and leaves and P and N contents in the soil. Overall results showed that the selected strain S. roseocinereus MS1B15 could represent a potential candidate as biofertilizer to increase plant growth as well as P uptake.