Soil Microbiota Research Articles

Microbial metabolic activity in Amazon floodplain forest and agricultural soils.

Microorganisms play an essential role in ecosystem functions. An increasingly used method for conducting functional analyses of a soil microbial community is based on the physiological profile at the community level. This method allows the metabolic capacity of microorganisms to be assessed based on patterns of carbon consumption and derived indices. In the present study, the functional diversity of microbial communities was assessed in soils from seasonally flooded-forest (FOR) and -traditional farming systems (TFS) in Amazonian floodplains flooded with black, clear, and white water. The soils of the Amazon floodplains showed differences in the metabolic activity of their microbial communities, with a general trend in activity level of clear water floodplain > black water floodplain > white water floodplain. The redundancy analysis (RDA) indicated that soil moisture (flood pulse) was the most important environmental parameter in determining the metabolic activity of the soil microbial communities in the black, clear, and white floodplains. In addition, the variance partitioning analysis (VPA) indicated that the microbial metabolic activity of the soil was more influenced by water type (41.72%) than by seasonality (19.55%) and land use type (15.28%). The soil microbiota of the white water floodplain was different from that of the clear water and black water floodplains in terms of metabolic richness, as the white water floodplain was mainly influenced by the low substrate use during the non-flooded period. Taken together, the results show the importance of considering soils under the influence of flood pulses, water types, and land use as environmental factors when recognizing functional diversity and ecosystem functioning in Amazonian floodplains.

Recent Advances in Bio-management of Plant Diseases

Constantly increasing global human populations has put agricultural sector under astounding pressure to fulfil food demands growing worldwide. In order to optimize crop production, usage of agrochemicals in intensive agronomic practices have increased alarmingly. The negative impact of excessive application of agrichemicals on food production, human health and environment raises concerns about its long-term field application. Exploration of alternative means of crop protection and optimization, therefore, warrants inexpensive and environmentally friendly strategy. Use of microbes or microbes-based products among many options is one such important strategy that provides solution to the problems. In this regard, many biocontrol measures have been practiced over time, and some of them have shown exceptional potential and success. Realizing the importance of soil microbiota in crop optimization while reducing the chemical inputs, significance of plant beneficial bacteria in the amelioration of biotic stresses especially the phytopathogens employing microbiome management, microbial volatilomes, and nano-bioformulations is discussed. The relationship between the agriculturally useful soil microbiomes and food crops enables the development of microbes-based antagonist strategies for low-cost production of food crops in worrying open field environment.

Combined Application of Organic and Inorganic Nitrogen and Seed Inoculation with Rhizobacteria (Stenotrophomonas maltophilia FA-9) Improved Productivity, Nitrogen Use Efficiency, and Economic Returns of Pearl Millet

Nitrogen (N) availability and soil microbiota exert significant impacts on plant metabolic systems and yield. Different studies have indicated that yield and nitrogen use efficiency (NUE) of pearl millet (Pennisetum glaucum L.R.Br.) can be improved by the inoculation of N-fixing bacteria. However, the interactive effects of different N sources and bacteria inoculation on growth, productivity, and NUE of pearl millet have been less explored. Therefore, individual and interactive effects of different N sources (organic and inorganic) and bacteria inoculation on growth, productivity, and NUE of pearl millet were investigated in this study. Two different N sources, i.e., organic (farmyard manure) and inorganic (urea) alone or in 50% + 50% combinations (urea + FYM), were used to supply the recommended amount of N. Similarly, seeds were inoculated with two different N-fixing bacteria, i.e., endobacteria (Enterobacter sp. MN17) and rhizobacteria (Stenotrophomonas maltophilia FA-9). Urea + farmyard manure (FYM) and seed inoculation rhizobacteria improved soil attributes, yield-related traits, grain quality, NUE, and net economic returns. Soil porosity was significantly improved by seed inoculation with both bacteria and FYM application. Similarly, seed inoculation with rhizobacteria increased soil organic carbon by 45.45% and 34.88% during the 1st and 2nd year of the study, respectively. Urea + FYM application combined with rhizobacteria seed inoculation improved the number of grains per ear (23.49 and 23.63%), 1000-grain weight (5.76% and 7.85%), grain yield (23.19% and 25.0%), and NUE (33.83 and 48.15%). Similarly, grain quality was significantly improved by seed inoculation with both bacteria. Likewise, urea + FYM combined with rhizobacteria improved nitrogen use efficiency (NUE) by 33.83% and 48.15% in 2020 and 2021, respectively, compared to no N application and no seed inoculation. The highest economic returns (1506.4 and 1506.9 USD) were noted for urea + FYM application combined with rhizobacteria seed inoculation. Therefore, urea + FYM application combined with rhizobacteria (S. maltophilia FA-9) seed inoculation seemed a viable approach to improve grain yield, grain quality, NUE, and net economic returns of pearl millet.

Combined effects of dry-wet irrigation, redox changes and microbial diversity on soil nutrient bioavailability in the rice field

Sustainable development goals (SDGs) by United Nations are some of the high-priority areas of research and this article established the sustainable agronomic practices converging soil chemistry, crop productivity and soil microbial involvement in nutrient modulation. Alternate wetting-drying (AWD) cultivation with implications on soil microbiome, nutritional dynamics and rice yield during pre-monsoon (boro) and monsoon (aman) season are not well studied. In the present 4-year field study, the impact of AWD irrigation in pre-monsoon and flooded irrigation in monsoon on soil microbiota and the nutrient pool has been studied. Nutrient-less pond water has been used to avoid any external nutrient input from irrigation water to ensure the sole elemental flux within the soil itself. The release of soil nutrients into the soil-aqueous system, influencing microbial populations and modulating the redox status was explored. Results indicated an increase in total concentration as well as bioavailability of selected nutritional elements (N, P, K, Fe, Ca, Mg, Cu and Zn) by 16–54% in the pre-monsoon cultivation relative to monsoon cultivation. Three plant growth phases (developing, milking and harvest) were considered to check the nutrient modulations in soil and plant tissues along with the plant growth and elemental uptake continuum. Crop plant measurements were improved and grain yields were found to be 5.2–6.46% increased under AWD and microbial activity. Krona charts, relative abundance, rarefaction curve and multivariate analysis of metagenomics data showed that the pre-monsoon soil was more enriched and maintained a balance between soil pH and microbial biomass than the monsoon soil. Microbial community diversity associated with plant growth phases was also found to be different depending on the seasonal alterations. Bacillus sp., Acidothiobacillus sp., Pseudomonas sp., Rhizobium sp., Burkholderia sp. were predominant in pre-monsoon soil releasing pulses of N, P, K, Ca and Mg whereas Verrucomicrobia was found to be dominant in monsoon soil where Fe was released. This study is a first of its kind that showed the combined effect of season and some specific groups of soil microbes on macro-micro nutritional availability in soil and enhanced plant quality.

Cyanobacteria as a potential bioasset for restoring degraded land

AbstractDegradation and pollution of land resources is a severe issue worldwide. Rapid urbanization and increased food demand have necessitated the restoration of degraded and highly contaminated land resources in a sustainable manner. The role of soil microorganism in maintaining nutrient balance, texture, fertility, and soil health is widely acknowledged. Cyanobacteria, one of the major components of soil microbiota, have been explored for their role as biofertilizers in improving plant growth and increasing soil fertility; however, less attention has been paid to their potential in restoring degraded lands. Cyanobacteria aids in nutrient cycling, production of plant growth‐promoting substances, desalination, and degradation of diverse organic as well as inorganic contaminants. They use diverse mechanisms for bioremediation (such as biosorption, bioaccumulation, and biotransformation) of contaminants in addition to the specific mechanism employed. They occur in symbiotic relationships with various hosts in natural as well as anthropogenically disturbed environments. Therefore, their use in restoration of highly degraded lands is justified and needs to be recognized worldwide. Identifying and exploring cyanobacterial species thriving in stress conditions and multiomics approaches would help in reconnoitering the complex plant–soil‐cyanobacteria interactions and enable scientists to design robust and well‐integrated biotechnological tools for soil remediation. Nevertheless, several technical challenges need to be addressed for rendering cyanobacteria as a realistic and viable bioasset. In this article, we summarize the role of cyanobacteria in addressing the reclamation of various types of degraded and polluted soils. And, it also examines the remaining knowledge gaps that limit its applicability in diverse environmental settings in a sustainable manner.

Lysogenic bacteriophages encoding arsenic resistance determinants promote bacterial community adaptation to arsenic toxicity

Emerging evidence from genomics gives us a glimpse into the potential contribution of lysogenic bacteriophages (phages) to the environmental adaptability of their hosts. However, it is challenging to quantify this kind of contribution due to the lack of appropriate genetic markers and the associated controllable environmental factors. Here, based on the unique transformable nature of arsenic (the controllable environmental factor), a series of flooding microcosms was established to investigate the contribution of arsM-bearing lysogenic phages to their hosts’ adaptation to trivalent arsenic [As(III)] toxicity, where arsM is the marker gene associated with microbial As(III) detoxification. In the 15-day flooding period, the concentration of As(III) was significantly increased, and this elevated As(III) toxicity visibly inhibited the bacterial population, but the latter quickly adapted to As(III) toxicity. During the flooding period, some lysogenic phages re-infected new hosts after an early burst, while others persistently followed the productive cycle (i.e., lytic cycle). The unique phage-host interplay contributed to the rapid spread of arsM among soil microbiota, enabling the quick recovery of the bacterial community. Moreover, the higher abundance of arsM imparted a greater arsenic methylation capability to soil microbiota. Collectively, this study provides experimental evidence for lysogenic phages assisting their hosts in adapting to an extreme environment, which highlights the ecological perspectives on lysogenic phage-host mutualism.

Crop rotation significantly influences the composition of soil, rhizosphere, and root microbiota in canola (Brassica napus L.)

BackgroundCrop rotation is an agronomic practice that is known to enhance productivity and yield, and decrease pest and disease pressure. Economic and other factors have increased the frequency of certain crops, including canola, with unknown effects on the below ground microbial communities that impact plant health and performance. This study investigated the effect of 12 years of crop rotation including canola-wheat; canola-pea-barley; and unrotated canola across three geographic sites in Western Canada with diverse soil types and environmental conditions. To provide data on mature, established crop rotation strategies, root exudate profiles, soil nutrient fluxes, and bacterial and fungal microbial community profiles were determined at the flowering stage in the final two (canola) years of the 12-year rotations.ResultsAfter 12 years of rotation, nutrient fluxes were affected in the soil in an inconsistent manner, with K, NO3, Mg, Ca, P, and Fe fluxes variably impacted by rotation depending on the year and site of sampling. As expected, rotation positively influenced yield and oil content, and decreased disease pressure from Leptosphaeria and Alternaria. In two of the three sites, root exudate profiles were significantly influenced by crop rotation. Bacterial soil, root, and rhizosphere communities were less impacted by crop rotation than the fungal communities. Fungal sequences that were associated with specific rotation strategies were identified in the bulk soil, and included known fungal pathogens in the canola-only strategy. Two closely related fungal sequences identified as Olpidium brassicae were extremely abundant at all sites in both years. One of these sequences was observed uniquely at a single site and was significantly associated with monocropped canola; moreover, its abundance correlated negatively with yield in both years.ConclusionsLong-term canola monoculture affected root exudate profiles and soil nutrient fluxes differently in the three geographic locations. Bacterial communities were less impacted by rotation compared to the fungal communities, which consistently exhibited changes in composition in all ecological niches at all sites, in both years. Fungal sequences identified as O. brassicae were highly abundant at all sites, one of which was strongly associated with canola monoculture. Soil management decisions should include consideration of the effects on the microbial ecosystems associated with the plants in order to inform best management practices.

Veterinary drug albendazole inhibits root colonization and symbiotic function of the arbuscular mycorrhizal fungus Rhizophagus irregularis.

Arbuscular mycorrhizal fungi (AMF) are plant symbionts that have a pivotal role in maintaining soil fertility and nutrient cycling. However, these microsymbionts may be exposed to organic pollutants like pesticides or veterinary drugs known to occur in agricultural soils. Anthelminthics are veterinary drugs that reach soils through the application of contaminated manures in agricultural settings. Their presence might threaten the function of AMF, considered as sensitive indicators of the toxicity of agrochemicals to the soil microbiota. We determined the impact of the anthelminthic compounds albendazole and ivermectin on the establishment and functionality of the symbiosis between the model-legume Lotus japonicus and the AMF Rhizophagus irregularis. Our analyses revealed negative effects of albendazole on the development and functionality of arbuscules, the symbiotic organelle of AMF, at a concentration of 0.75μg g-1. The impairment of the symbiotic function was verified by the reduced expression of genes SbtM1, PT4 and AMT2;2 involved in arbuscules formation, P and N uptake, and the lower phosphorus shoot content detected in the albendazole-treated plants. Our results provide first evidence for the toxicity of albendazole on the colonization capacity and function of R. irregularis at concentrations that may occur in agricultural soils systematically amended with drug-containing manures.

Pseudomonas sivasensis 2RO45 inoculation alters the taxonomic structure and functioning of the canola rhizosphere microbial community.

Inoculation with plant growth-promoting rhizobacteria (PGPR) is an eco-friendly sustainable strategy for improving crop productivity in diverse environments under different conditions. Our earlier study demonstrated that Pseudomonas sivasensis 2RO45 significantly stimulated canola (Brassica napus L. var. napus) growth. The aim of the present study was to investigate the structural and functional dynamics in the canola rhizosphere microbiome after inoculation with PGPR P. sivasensis 2RO45. The results based on alpha diversity metrics showed that P. sivasensis 2RO45 did not significantly alter the diversity of the native soil microbiota. However, the introduced strain modified the taxonomic structure of microbial communities, increasing the abundance of plant beneficial microorganisms, e.g., bacteria affiliated with families Comamonadaceae, Vicinamibacteraceae, genus Streptomyces, and fungi assigned to Nectriaceae, Didymellaceae, Exophiala, Cyphellophora vermispora, and Mortierella minutissima. The analysis of community level physiological profiling (CLPP) revealed that microbial communities in the P. sivasensis 2RO45 treated canola rhizospheres were more metabolically active than those in the non-treated canola rhizosphere. Four carbon sources (phenols, polymers, carboxylic acids, and amino acids) were better metabolized by the microbial communities from the rhizosphere of plants inoculated with the P. sivasensis 2RO45 than non-inoculated canola rhizospheres. Based on the community-level physiological profiles, the functional diversity of the rhizosphere microbiome was altered by the P. sivasensis 2RO45 inoculation. Substrate utilization Shannon diversity (H) index and evenness (E) index were significantly increased in the treated canola plants. The study provides new insight into PGPR-canola interactions for sustainable agriculture development.

Windstorm disturbance sets off plant species invasion, microbiota shift, and soilborne pathogens spread in an urban Mediterranean forest

We investigated the effects of a severe windstorm on vegetation, soil chemistry, understory microclimate, and soil microbiota in a Mediterranean holm oak forest. Plant species composition remained almost unchanged in the undisturbed area, whereas highly diverse plant communities were found in the disturbed area (e.g. gap area). Specifically, 11 invasive plant species were detected in 2015, but four years after, five disappeared and another five decreased, with only Ailanthus altissima increasing. Soil in disturbed areas has higher pH, Na, P, K, Ca, Cu, and Mn, but lower total limestone, organic carbon, total nitrogen, Mg, Fe, and standing litter compared to undisturbed areas. Disturbed areas had higher light availability at the ground and large variations in soil and air temperature and air relative humidity compared to undisturbed areas. The storm disturbance increased soil bacterial and fungal species richness and diversity. Moreover, the microbial co-occurrence network in the undisturbed area was more heterogeneous and complex, while modularity and number of positive correlations were higher in the disturbed area, which suggests that the structural composition of microbial communities and their co-occurrence patterns have been altered by windstorm disturbance. In the gaps, soil microbial community composition indicated a shift toward an opportunistic microbiota dominated by fast-growing but less competitive species. In addition, we found a large increase in putative plant pathogens but a decrease in simbiotrophic and ectomycorrhizal fungi in the gaps. The present work demonstrate the multiple effects of storm damage on the above- and belowground structure and diversity of forest ecosystems.

Repeated applications of fipronil, propyzamide and flutriafol affect soil microbial functions and community composition: A laboratory-to-field assessment

Pesticides play an important role in conventional agriculture by controlling pests, weeds, and plant diseases. However, repeated applications of pesticides may have long lasting effects on non-target microorganisms. Most studies have investigated the short-term effects of pesticides on soil microbial communities at the laboratory scale. Here, we assessed the ecotoxicological impact of fipronil (insecticide), propyzamide (herbicide) and flutriafol (fungicide) on (i) soil microbial enzymatic activities, (ii) potential nitrification, (iii) abundance of the fungal and bacterial community and key functional genes (nifH, amoA, chiA, cbhl and phosphatase) and (iii) diversity of bacteria, fungi, ammonia oxidizing bacteria (AOB) and archaea (AOA) after repeated pesticide applications in laboratory and field experiments. Our results showed that repeated applications of propyzamide and flutriafol affected the soil microbial community structure in the field and had significant inhibitory effects on enzymatic activities. The abundances of soil microbiota affected by pesticides recovered to levels similar to the control following a second application, suggesting that they might be able to recover from the pesticide effects. However, the persistent pesticide inhibitory effects on soil enzymatic activities suggests that the ability of the microbial community to cope with the repeated application was not accompanied by functional recovery. Overall, our results suggest that repeated pesticide applications may influence soil health and microbial functionalities and that more information should be collected to inform risk-based policy development.

Evaluation of Phytotoxicity of Common Chernozem in the Application of <i>Bacillus</i> sp. and Biochar for Stimulation of Decomposition of Winter Wheat Harvest Residues (<i>Triticum aestivum</i> L.)

Stable functioning of agricultural lands is impossible without maintaining soil fertility. However, there are often a lot of crop residues in the fields, which decompose for a long time and turn into available organic matter. To increase the rate of decomposition of crop residues of grain crops (wheat, barley and others), it is necessary to introduce biostimulants. Biostimulants are a variety of substances that stimulate the decomposition of organic substances and have a beneficial effect on the soil microbiota. The article examines the influence of Bacillus sp. on the processes of decomposition of crop residues of wheat both independently and together with biochar. The aim of the study was to evaluate the phytotoxicity of ordinary chernozem during the decomposition of crop residues of winter wheat under the influence of Bacillus sp. and biochar. To assess the ecological state of the soil, the following research methods were used: assessment of the rate of decomposition of cellulose (determination of cellulolytic activity), assessment of the ecological state of the soil (intensity of CO2 emissions, changes in the intensity of initial growth and development of winter barley (Hordeum vulgare L.)). Introduction of Bacillus sp. × 100 and the joint use of biochar and Bacillus sp. it stimulated the decomposition of cellulose up to 14–15% of the background content. Inoculation of Bacillus sp. on the biochar, it was effective already at the recommended dose both for the decomposition of the cellulose web and for restoring the ecological state of the soil, demonstrating a synergistic effect. The results obtained should be used in carrying out measures to increase soil fertility of agricultural lands and environmental monitoring of soil conditions.

Nitrogen‐fixing cushion Astragalus siculus modulates soil fertility, microclimate, plant facilitation, bacterial and fungal microbiota along an elevation gradient

AbstractQuestionCushion‐forming vascular plants are adapted to alpine environments and act as ecosystem engineers by moderating microclimate and creating a fertility island under their canopy. Most of the available studies on cushion ecology have been devoted to plant facilitation, but none used a holistic approach that considers the response of co‐existing plant species with other key ecosystem players. Here, we quantified the biogenic effect and facilitation capacity of Astragalus siculus, a spiny nitrogen‐fixing cushion plant, and test the hypothesis that the facilitation effect would increase with elevation as stress gradient.LocationMount Etna, the highest active volcano in the Mediterranean Basin.MethodsWe combined chemical characterization of the soil with a description of the soil microbiota by high‐throughput sequencing of bacterial and eukaryotic rRNA gene markers carried out at three elevations, that is 1650, 1900 and 2210 m a.s.l. In addition, we analysed the microclimate outside and inside the Astragalus canopy to assess the linkages between above‐ and below‐ground ecosystem compartments and quantified the occurrence of co‐existing vascular plants.ResultsAstragalus cushions have strong biogenic effects on above‐ and below‐ground conditions by dramatically increasing soil organic carbon and total nitrogen stocks at 1900 and 2210 m elevation. Moreover, a buffering of soil temperature and moisture regimes was recorded, with lower temperatures in summer but higher in winter inside the cushions. Cushions harbour a specific bacterial and fungal microbiota compared to external bare soil. Stem density and cushion height increase significantly with altitude, as does the nurse effect of the cushion on the growth and survival of co‐existing vascular plants.ConclusionsAs a result of cushion biogenic environmental changes, the effect of Astragalus on some of the co‐existing species shifted from negative or null at 1650 m to facilitative along the elevation gradient. Furthermore, our data show a relationship between Astragalus morphological traits and soil biogenic changes related to soil chemistry and microbiota that affect plant interaction and coexistence.

Effect of Fresh Organic Matter of Straw on Microbiological Parameters of Sod-Podzolic Soil

The loss of soil organic matter (SOM) due to agricultural land use has a negative impact on soil properties and is one of the major contributors to the increase in atmospheric CO2 concentrations. An appropriate way for simultaneous restoration of POM stocks and deposition of sequestered carbon is the straw application to the soil. The aim of the study was to evaluate the effect of straw on the quantitative indicators of different groups of microorganisms in sod-podzolic soil (Umbric Retisol) in a long-term field experiment. Introduction of straw increased microbial biomass carbon (Cmic) by 1.25–2 times, with the greatest increase in microbial biomass observed in the variants without fertilizer. Basal respiration and respiration coefficient (qCO2) increased in the row: control NPK NPK + straw straw. Application of straw increased the gene copy number of fungi and bacteria up to 2 times and archaea up to 1.5 times. Mineral fertilizer application without straw reduced qCO2, fungi biomass and archaeal gene copy number by 1.5–3.0 times. The fungi/bacteria ratio varied from 4 to 15 determined by fluorescent microscopy and from 0.17 to 0.33 by quantitative PCR. The lowest values of fungi/bacteria ratios were found in soils with the application of mineral fertilizers, and the highest – with the incorporation of straw. Thus, the regular introduction of fresh organic matter of straw is an important technological procedure to increase the microbiological activity of soil and leveling the negative impact of mineral fertilizers on soil microbiota.

Analysis of the microbiological composition of the domestic winery in Rzeszów

Abstract Aim of this study is to analyse the microbiological composition of grapes and soil from a home vineyard located in Rzeszów. During the research, the following tasks were undertaken: determination of the total number of microorganisms, isolation of the microbial cultures from grapes and soil, and identification of the bacterial strains and yeast using the MALDI-TOF MS Biotyper mass spectrometry. Natural microbiota of grapes and soil are very diverse. Microbiological analysis showed that the total number of microorganisms is higher in the soil, compared to grapes. As the result of the analysis of the microbiota of the home vineyard using the MALDI-TOF MS Biotyper mass spectrometry, five species of yeasts and eight species of bacteria were identified. Microbiological evaluation of the tested vineyard showed the presence of the yeast strains as Saccharomyces spp., Dekkera anomala, and Candida spp., and the strains of bacteria as Lactobacillus spp., Pantoea agglomerans, Lactococcus spp., Staphylococcus warneri, and Acetobacter spp.

The impact of antibiotic residues on resistance patterns in leek at harvest

When crops are cultivated on fields fertilized with animal manure, the risk exists that plants may take up antibiotic residues and may be exposed to antibiotic resistance genes and antibiotic resistant bacteria. During cultivation in a greenhouse pot experiment, leek (Allium porrum) was fertilized with either pig slurry or mineral fertilizer and exposed to either no antibiotics, doxycycline (10,000 μg/kg manure), sulfadiazine (1000 μg/kg manure), or lincomycin (1000 μg/kg manure). At harvest, 4.5 months later, lincomycin, sulfadiazine or doxycycline were not detected in any of the leek samples nor in their corresponding soil samples. Further, antimicrobial susceptibility testing was performed on 181 Bacillus cereus group isolates and 52 Pseudomonas aeruginosa isolates from the grown leek. For the B. cereus group isolates, only a small shift in MIC50 for lincomycin was observed among isolates from the lincomycin and control treatment. For P. aeruginosa, only in the setup with doxycycline treatment a higher MIC50 for doxycycline was observed compared to the control, specifically the isolates selected from growth media supplemented with 8 mg/L doxycycline. Nine antibiotic resistance genes (tet(B), tet(L), tet(M), tet(O), tet(Q), tet(W), erm(B), erm(F) and sul2) were investigated at harvest in the leek and soil samples. In the leek samples, none of the antibiotic resistance genes were detected. In the soil samples fertilized with pig slurry, the genes erm(B), erm(F), tet(M), sul2, tet(W) and tet(O) were detected in significantly higher copy numbers in the lincomycin treatment as compared to the other antibiotic treatments. This could be due to a shift in soil microbiota induced by the addition of lincomycin. The results of this study indicate that consumption of leek carries a low risk of exposure to antibiotic residues or antibiotic resistance to doxycycline, sulfadiazine or lincomycin.

Long-term warming-induced trophic downgrading in the soil microbial food web

Climatic warming has been hypothesized to accelerate organic matter decomposition by soil microorganisms and thereby enhance carbon (C) release to the atmosphere. However, the long-term consequences of soil warming on belowground biota interactions are poorly understood. Here we investigate how geothermal warming by 6 °C for more than 50 years affects soil microbiota. Using metatranscriptomics we obtained comprehensive profiles of the prokaryotic, eukaryotic and viral players of the soil microbial food web. When compared to ambient soil temperature conditions, we found pronounced differences in taxa abundances within and between trophic modules of the soil food web. Specifically, we observed a ‘trophic downgrading’ at elevated temperature, with soil fauna decreasing in abundance, while predatory bacteria and viruses became relatively more abundant. We propose that the drivers for this shift are previously observed decreases in microbial biomass and soil organic carbon, and the increase in soil bulk density (decrease in soil porosity) at elevated temperature. We conclude that a trophic downgrading may have important implications for soil carbon sequestration and nutrient dynamics in a warming world.

Impact of sterilization and chemical fertilizer on the microbiota of oil palm seedlings.

Soil nutrients and microbiota are known as essential components for healthy plant growth and crop productivity. However, limited studies have been conducted on the importance of soil microbiota in the early growth of oil palm seedlings (Elaeis guineensis Jacq.) under the influence of nitrogen, phosphorus and potassium (NPK) compound fertilizer (nitrogen, phosphorus, and potassium). In this study, we analyzed the root microbial community associated with seedlings grown under normal and sterilized soil conditions to ascertain the microbial strains potentially associated with soil, plant health and chemical fertilizer efficiency. Oil palm seedlings were grown under four treatments: (i) fertilized normal soil (+FN), (ii) unfertilized normal soil (-FN), (iii) fertilized sterilized soil (+FS) and (iv) unfertilized sterilized soil (-FS). Our findings revealed that chemical fertilizer promoted the growth of the copiotrophs Pseudomonadota and Bacteroidota in the control +FN, which are known to degrade complex polysaccharides. After autoclaving, the soil macronutrient content did not change, but soil sterilization reduced microbial diversity in the +FS and -FS treatments and altered the soil microbiota composition. Sterilized soil with a depleted microbial population adversely affected crop growth, which was exacerbated by fertilizer use. In the rhizosphere and rhizoplane compartments, a total of 412 and 868 amplicon sequence variances (ASVs) were found depleted in the +FS and -FS treatments, respectively. Several genera were identified in the ASVs with diminished abundance, including Humibacter, Microbacterium, Mycobacterium, 1921-2, HSB OF53-F07, Mucilaginibacter, Bacillus, Paenibacillus, and several unclassified genera, suggesting their possible roles in promoting the plant growth of oil palm seedlings. Soil sterilization might remove these beneficial microbes from the bulk soil pool, affecting the colonization ability in the rhizocompartments as well as their role in nutrient transformation. Therefore, this study provides useful insights concerning the benefits of a soil microbiome survey before making fertilizer recommendations.

Intensive management facilitates bacterial invasion on soil microbial community

Intensive management has greatly altered natural forests, especially forests around the world are increasingly being converted into economic plantations. Soil microbiota are critical for community functions in all ecosystems, but the effects of microbial disturbance during economic plantation remain unclear. Here, we used Escherichia coli O157:H7, a model pathogenic species for bacterial invasion, to assess the invasion impacts on the soil microbial community under intensive management. The E. coli invasion was tracked for 135 days to explore the instant and legacy impacts on the resident community. Our results showed that bamboo economic plantations altered soil abiotic and biotic properties, especially increasing pH and community diversity. Higher pH in bamboo soils resulted in longer pathogen survivals than in natural hardwood soils, indicating that pathogen suppression during intensive management should arouse our attention. A longer invasion legacy effect on the resident community (P < 0.05) were found in bamboo soils underlines the need to quantify the soil resilience even when the invasion was unsuccessful. Deterministic processes drove community assembly in bamboo plantations, and this selection acted more strongly during by E. coli invasion than in hardwood soils. We also showed more associated co-occurrence patterns in bamboo plantations, suggesting more complex potential interactions within the microbial community. Apart from community structure, community functions are also strongly related to the resident species associated with invaders. These findings provide new perspectives to understand intensive management facilitates the bacterial invasion, and the impacts would leave potential risks on environmental and human health.

Dynamics of microbial community composition during degradation of silks in burial environment

The silk residues in the soil formed the unique niche, termed “silksphere.” Here, we proposed a hypothesis that silksphere microbiota have great potential as a biomarker for unraveling the degradation of the ancient silk textiles with great archaeological and conservation values. To test our hypothesis, in this study, we monitored the dynamics of microbial community composition during silk degradation via both indoor soil microcosmos model and outdoor environment with amplicon sequencing against 16S and ITS gene. Microbial community divergence was evaluated with Welch two sample t-test, PCoA, negative binomial generalized log-linear model and clustering, etc. Community assembly mechanisms differences between silksphere and bulk soil microbiota were compared with dissimilarity-overlap curve (DOC) model, Neutral model and Null model. A well-established machine learning algorithm, random forest, was also applied to the screening of potential biomarkers of silk degradation. The results illustrated the ecological and microbial variability during the microbial degradation of silk. Vast majority of microbes populating the silksphere microbiota strongly diverged from those in bulk soil. Certain microbial flora can serve as an indicator of silk degradation, which would lead to a novel perspective to perform identification of archaeological silk residues in the field. To sum up, this study provides a new perspective to perform the identification of archaeological silk residue through the dynamics of microbial communities.