Search

Summary: Microbial communities can rapidly respond to stress, meaning plants may encounter altered soil microbial communities in stressful environments. These altered microbial communities may then affect natural selection on plants. Because stress can cause lasting changes to microbial communities, microbes may also cause legacy effects on plant selection that persist even after the stress ceases.To explore how microbial responses to stress and persistent microbial legacy effects of stress affect natural selection, we grew Chamaecrista fasciculata plants in stressful (salt, herbicide, or herbivory) or nonstressful conditions with microbes that had experienced each of these environments in the previous generation.Microbial community responses to stress generally counteracted the effects of stress itself on plant selection, thereby weakening the strength of stress as a selective agent. Microbial legacy effects of stress altered plant selection in nonstressful environments, suggesting that stress‐induced changes to microbes may continue to affect selection after stress is lifted.These results suggest that soil microbes may play a cryptic role in plant adaptation to stress, potentially reducing the strength of stress as a selective agent and altering the evolutionary trajectory of plant populations. [ABSTRACT FROM AUTHOR]

An efficient conversion of ortho, meta and para fluoro- and trifluoromethyl-substituted benzoic acids to the corresponding benzamides in fermentations of the soil bacterium Streptomyces sp. JCM9888 is described. We also report the efficient reduction of the same class of substrates to the corresponding benzyl alcohols with the fungi Cunninghamella elegans. These biotransformations were surprisingly efficient and may have value as disruptive technologies in process chemistry. [ABSTRACT FROM AUTHOR]

Summary: Nonmycorrhizal cluster root‐forming species enhance the phosphorus (P) acquisition of mycorrhizal neighbours in P‐impoverished megadiverse systems. However, whether mycorrhizal plants facilitate the defence of nonmycorrhizal plants against soil‐borne pathogens, in return and via their symbiosis, remains unknown.We characterised growth and defence‐related compounds in Banksia menziesii (nonmycorrhizal) and Eucalyptus todtiana (ectomycorrhizal, ECM) seedlings grown either in monoculture or mixture in a multifactorial glasshouse experiment involving ECM fungi and native oomycete pathogens.Roots of B. menziesii had higher levels of phytohormones (salicylic and jasmonic acids, jasmonoyl‐isoleucine and 12‐oxo‐phytodienoic acid) than E. todtiana which further activated a salicylic acid‐mediated defence response in roots of B. menziesii, but only in the presence of ECM fungi. We also found that B. menziesii induced a shift in the defence strategy of E. todtiana, from defence‐related secondary metabolites (phenolic and flavonoid) towards induced phytohormone response pathways.We conclude that ECM fungi play a vital role in the interactions between mycorrhizal and nonmycorrhizal plants in a severely P‐impoverished environment, by introducing a competitive component within the facilitation interaction between the two plant species with contrasting nutrient‐acquisition strategies. This study sheds light on the interplay between beneficial and detrimental soil microbes that shape plant–plant interaction in severely nutrient‐impoverished ecosystems. [ABSTRACT FROM AUTHOR]

Summary: Optimizing agroecosystems and crops for micronutrient uptake while reducing issues with inorganic contaminants (metal(loid)s) is a challenging task. One promising approach is to use arbuscular mycorrhizal fungi (AMF) and investigate the physiological, molecular and epigenetic changes that occur in their presence and that lead to changes in plant metal(loid) concentration (biofortification of micronutrients or mitigation of contaminants). Moreover, it is important to understand these mechanisms in the context of the soil microbiome, particularly those interactions of AMF with other soil microbes that can further shape crop nutrition. To address these challenges, a two‐pronged approach is recommended: exploring molecular mechanisms and investigating microbiome management and engineering. Combining both approaches can lead to benefits in human health by balancing nutrition and contamination caused by metal(loid)s in the agro‐ecosystem. [ABSTRACT FROM AUTHOR]

The capacity for bacterial extracellular electron transfer via secreted metabolites is widespread in natural, clinical, and industrial environments. Recently, we discovered biological oxidation of phenazine-1-carboxylic acid (PCA), the first example of biological regeneration of a naturally produced extracellular electron shuttle. However, it remained unclear how PCA oxidation was catalyzed. Here, we report the mechanism, which we uncovered by genetically perturbing the branched electron transport chain (ETC) of the soil isolate Citrobacter portucalensis MBL. Biological PCA oxidation is coupled to anaerobic respiration with nitrate, fumarate, dimethyl sulfoxide, or trimethylamine-N-oxide as terminal electron acceptors. Genetically inactivating the catalytic subunits for all redundant complexes for a given terminal electron acceptor abolishes PCA oxidation. In the absence of quinones, PCA can still donate electrons to certain terminal reductases, albeit much less efficiently. In C. portucalensis MBL, PCA oxidation is largely driven by flux through the ETC, which suggests a generalizable mechanism that may be employed by any anaerobically respiring bacterium with an accessible cytoplasmic membrane. This model is supported by analogous genetic experiments during nitrate respiration by Pseudomonas aeruginosa. Author summary: Many bacteria have extremely flexible metabolisms, and we are only beginning to understand how they manifest in the environment. Our study focuses on the role of phenazine-1-carboxylic acid (PCA), a molecule that some bacteria synthesize and secrete into their surroundings. PCA is an "extracellular electron shuttle," a molecule that readily transfers electrons between cells and oxidizing/reducing compounds or other cells. Until our investigation, the role of PCA electron-shuttling had only been studied in one direction: how it takes electrons away from cells, and the effect this has on their viability. Here we present a detailed account of the opposite process and its mechanism: what happens when PCA delivers electrons to cells? Our findings indicate that this previously underappreciated process is generalizable to any anaerobically respiring bacterium. Consequently, we expect that electron donation by PCA is widespread in environments where PCA is plentiful and oxygen is sparse, such as in some agricultural soils. The universality of the extracellular electron shuttle oxidation mechanism we describe for PCA suggests that it should also occur with similar small molecules, of which there are thousands, deepening the implication that this is a significant process in the environment and motivating further research into its consequences. [ABSTRACT FROM AUTHOR]

Simple Summary: This study shows the common occurrence of entomopathogenic fungi (EF) in the habitats of Ixodes ricinus, which indicates the necessity to consider EF as a potential factor influencing the tick population. However, the obtained results highlight the need for further research to fully understand the interaction between soil microorganisms and tick occurrence. (1) Background: In addition to the microclimate, host availability, and tick microbiota, soil environmental microorganisms can affect tick populations. This study aimed to (1) determine the presence and diversity of entomopathogenic fungi (EF) in forests, where ticks are abundant, and (2) estimate the effectiveness of the isolated EF strains against Ixodes ricinus. (2) Methods: EF were isolated using the trap insect method from soil collected from tick sites. A bioassay was used to estimate the effectiveness of EF against ticks. (3) Results: The presence of EF was found in all tested forest habitat types. A total of 53 strains belonging to the genera Metarhizium, Beauveria, and Isaria were isolated. All the six strains subjected to the bioassay showed potential efficacy against both adult and nymphal stages of I. ricinus; however, the strains differed in their effectiveness. The most effective isolate against I. ricinus was the soil environmental strain of Metarhizium anisopliae. (4) Conclusion: The study indicates that tick habitats can be the source of entomopathogenic fungi, which have a lethal effect on ticks, as demonstrated in preliminary laboratory tests with I. ricinus. However, for practical use, extensive field tests and further research on application methods and long-term effects are necessary to develop effective and sustainable tick management strategies. [ABSTRACT FROM AUTHOR]

Microbial inoculants derived from plant growth-promoting rhizobacteria (PGPR) offer eco-friendly alternatives to traditional chemical fertilizers, maintaining microbiota balance in agricultural systems. However, limited research has explored the combined effects of microbial inoculants and chemical fertilizers on crop growth and soil properties. In this study, we investigated seven fertilizer combinations, ranging from no fertilizer to various proportions of chemical fertilizers with microbial inoculants, on timothy (Phleum pratense L.) growth, chlorophyll content, soil properties, enzyme activities, and soil microbial communities. A randomized block design was employed to analyze these effects. The results indicate that the combination of 85% chemical fertilizer with microbial inoculants significantly increased timothy yield and chlorophyll content. In addition, a reduction to 55% chemical fertilizer in conjunction with microbial inoculants resulted in comparable yield to that of 100% fertilizer with no inoculants. The microbial inoculants treatments notably elevated soil catalase, urease, acid phosphatase, and invertase activities, along with soil fast-acting nutrient content. The sequencing results show that the abundance of beneficial bacteria increased, while that of fungi decreased in the soil rhizosphere after the application of microbial inoculants. This study underscored the potential of microbial inoculants combined with reductions in chemical fertilizers to enhance soil microbiology, nutrient content, and beneficial microbial abundance while suppressing pathogenic fungi, thereby promoting timothy growth and yield. These findings provide a theoretical basis for the use of microbial inoculants in sustainable agricultural practices, providing valuable insights for optimizing microbial inoculants and chemical fertilizer formulations to mitigate the sustainability challenges posed by conventional fertilizers. [ABSTRACT FROM AUTHOR]

The biological interactions between plants and their root microbiomes are essential for plant growth, and even though plant genotype (G), soil microbiome (M), and growth conditions (environment; E) are the core factors shaping root microbiome, their relationships remain unclear. In this study, we investigated the effects of G, M, and E and their interactions on the Lotus root microbiome and plant growth using an in vitro cross-inoculation approach, which reconstructed the interactions between nine Lotus accessions and four soil microbiomes under two different environmental conditions. Results suggested that a large proportion of the root microbiome composition is determined by M and E, while G-related (G, G × M, and G × E) effects were significant but small. In contrast, the interaction between G and M had a more pronounced effect on plant shoot growth than M alone. Our findings also indicated that most microbiome variations controlled by M have little effect on plant phenotypes, whereas G × M interactions have more significant effects. Plant genotype-dependent interactions with soil microbes warrant more attention to optimize crop yield and resilience. [ABSTRACT FROM AUTHOR]

[Display omitted] • Recent advances in microbial diversity and key taxa in saline soils are summarized. • The threshold effect of salinity on soil C and N turnover exists in salinized soils. • Soil microorganisms have higher resistance to salt stress in already salinized soils. • Salt-tolerant microorganisms promote plant growth in a variety of ways. • Microbial resources developed by multi-omics are beneficial to saline ecosystems. Soil salinization threatens food security and ecosystem health, and is one of the important drivers to the degradation of many ecosystems around the world. Soil microorganisms have extremely high diversity and participate in a variety of key ecological processes. They are important guarantees for soil health and sustainable ecosystem development. However, our understanding of the diversity and function of soil microorganisms under the change of increased soil salinization is fragmented. Here, we summarize the changes in soil microbial diversity and function under the influence of soil salinization in diverse natural ecosystems. We particularly focus on the diversity of soil bacteria and fungi under salt stress and the changes in their emerging functions (such as their mediated biogeochemical processes). This study also discusses how to use the soil microbiome in saline soils to deal with soil salinization for supporting sustainable ecosystems, and puts forward the knowledge gaps and the research directions that need to be strengthened in the future. Due to the rapid development of molecular-based biotechnology (especially high-throughput sequencing technology), the diversity and community composition and functional genes of soil microorganisms have been extensively characterized in different habitats. Clarifying the responding pattern of microbial-mediated nutrient cycling under salt stress and developing and utilizing microorganisms to weaken the adverse effects of salt stress on plants and soil, which are of guiding significance for agricultural production and ecosystem management in saline lands. [ABSTRACT FROM AUTHOR]

Crop-specific cultivation practices including crop rotation, cover cropping, and fertilisation are key measures for sustainable farming, for which soil microorganisms are important components. This study aims at identifying links between agronomic practices, potato yield and quality as well as soil microorganisms. We analysed the roles of cover crops and of the soil prokaryotic, fungal, and protistan communities in a long-term trial, differing in crop rotation, i.e. winter wheat or silage maize as pre-crop, presence and positioning of oil radish within the rotation, and fertilisation, i.e. mineral fertiliser, straw, manure, or slurry. Up to 16% higher yields were observed when oil radish grew directly before potatoes. Losses of potato quality due to infection with Rhizoctonia solani-induced diseases and common scab was 43–63% lower when wheat + oil radish was pre-crop under manure or straw + slurry fertilisation than for maize as pre-crop. This contrast was also reflected by 42% higher fungal abundance and differences in β-diversity of prokaryotes, fungi, and protists. Those amplicon sequence variants, which were found in the treatments with highest potato qualities and differed in their abundances from other treatments, belonged to Firmicutes (2.4% of the sequences) and Mortierellaceae (28%), which both comprise potential antagonists of phytopathogens. Among protists, Lobosa, especially Copromyxa, was 62% more abundant in the high potato quality plots compared to all others, suggesting that specific higher trophic organisms can improve crop performance. Our findings suggest that successful potato cultivation is related (1) to planting of oil radish before potatoes for increasing yield and (2) to fertilisation with manure or straw + slurry for enriching the microbiome with crop-beneficial taxa. [ABSTRACT FROM AUTHOR]

d‐amino acids are the d stereoisomers of the common l‐amino acids found in proteins. Over the past two decades, the occurrence of d‐amino acids in plants has been reported and circumstantial evidence for a role in various processes, including interaction with soil microorganisms or interference with cellular signalling, has been provided. However, examples are not numerous and d‐amino acids can also be detrimental, some of them inhibiting growth and development. Thus, the persistence of d‐amino acid metabolism in plants is rather surprising, and the evolutionary origins of d‐amino acid metabolism are currently unclear. Systemic analysis of sequences associated with d‐amino acid metabolism enzymes shows that they are not simply inherited from cyanobacterial metabolism. In fact, the history of plant d‐amino acid metabolism enzymes likely involves multiple steps, cellular compartments, gene transfers and losses. Regardless of evolutionary steps, enzymes of d‐amino acid metabolism, such as d‐amino acid transferases or racemases, have been retained by higher plants and have not simply been eliminated, so it is likely that they fulfil important metabolic roles such as serine, folate or plastid peptidoglycan metabolism. We suggest that d‐amino acid metabolism may have been critical to support metabolic functions required during the evolution of land plants. Summary statement: d‐amino acids are d enantiomers of natural, l‐amino acids. Their metabolism is still incompletely known and here, we review how it is linked to the origin of higher plants. [ABSTRACT FROM AUTHOR]

The adverse impact of total petroleum hydrocarbons (TPH) can be mitigated through bioremediation. However, the efficiency of bioremediation is often compromised due to its slow speed. Therefore, this study aimed to evaluate the promoting effect of organic and inorganic biostimulants on the bioremediation rate of autochthonous microorganisms. The study examined the impact of rapeseed meal (biostimulation-BS1), soybean meal (BS2), and NPK fertilizer (BS3), as biostimulants on pH, bacterial and fungal count, enzymatic activities, and also TPH values of diesel-contaminated soil. The results revealed that amending the soil with rapeseed meal, soybean meal, and NPK fertilizer resulted in a significant increase in dehydrogenase and catalase activities, with 9.96, 7.7, and 6.75-fold and 2.52, 2.4, and 2.52-fold enhancement, respectively, compared to natural attenuation (NA-as control) which contains diesel-contaminated soil without any organic or inorganic amendments. Moreover, the pH value of the BS1 (6.4) and BS2 (6.77) groups was almost neutral. The growth of heterotrophic and hydrocarbon-utilizing bacteria and fungi was significantly improved with organic matter amendment (P <.05). The TPH removal efficiencies in natural attenuation, BS1, BS2, BS3, and rapeseed meal+ soybean meal+ NPK fertilizer (BS4) groups were 49.22%, 71.65%, 90.55%, 65.77%, and 55.25%, respectively. Molecular identification revealed that three hydrocarbon-utilizing bacteria belonged to various genera, including Nocardiopsis, Streptomyces, and Mammaliicoccus. Overall, this study suggests that amending organic compounds to contaminated soil is an effective, cost-effective, and eco-friendly strategy to improve the bioremediation rate of autochthonous microorganisms. [ABSTRACT FROM AUTHOR]

Streptomyces are well-known for producing bioactive secondary metabolites, with numerous antimicrobials essential to fight against infectious diseases. Globally, multidrug-resistant (MDR) microorganisms significantly challenge human and veterinary diseases. To tackle this issue, there is an urgent need for alternative antimicrobials. In the search for potent agents, we have isolated four Streptomyces species PC1, BT1, BT2, and BT3 from soils collected from various geographical regions of the Himalayan country Nepal, which were then identified based on morphology and 16S rRNA gene sequencing. The relationship of soil microbes with different Streptomyces species has been shown in phylogenetic trees. Antimicrobial potency of isolates was carried out against Staphylococcus aureus American Type Culture Collection (ATCC) 43300, Shigella sonnei ATCC 25931, Salmonella typhi ATCC 14028, Klebsiella pneumoniae ATCC 700603, and Escherichia coli ATCC 25922. Among them, Streptomyces species PC1 showed the highest zone of inhibition against tested pathogens. Furthermore, ethyl acetate extracts of shake flask fermentation of these Streptomyces strains were subjected to liquid chromatography-tandem mass spectrometric (LC-MS/MS) analysis for their metabolic comparison and Global Natural Products Social Molecular Networking (GNPS) web-based molecular networking. We found very similar metabolite composition in four strains, despite their geographical variation. In addition, we have identified thirty-seven metabolites using LC-MS/MS analysis, with the majority belonging to the diketopiperazine class. Among these, to the best of our knowledge, four metabolites, namely cyclo-(Ile-Ser), 2-n-hexyl-5-n-propylresorcinol, 3-[(6-methylpyrazin-2-yl) methyl]-1H-indole, and cyclo-(d-Leu-l-Trp), were detected for the first time in Streptomyces species. Besides these, other 23 metabolites including surfactin B, surfactin C, surfactin D, and valinomycin were identified with the help of GNPS-based molecular networking. [ABSTRACT FROM AUTHOR]

Simple Summary: Coffee pulp is a byproduct of the coffee industry and represents an environmental problem; therefore, alternatives are being sought regarding its use in other industries, such as for animal feed. The study evaluated the feasibility of replacing part of the wheat bran provided in broiler chickens' diets during the finishing stage with extruded coffee pulp meal. The results indicated that coffee pulp can replace up to 25% of wheat bran in chicken feed in that phase of production, which could offer a viable alternative, in addition to contributing to a more sustainable and environmentally friendly production process. Coffee pulp is a by-product of the coffee industry. Due to conventional management techniques, it represents a severe environmental problem due to its negative impact on the soil (anaerobic fermentation and pH changes), water sources (the infiltration of pollutants into streams, acidification of water sources, and modification of microorganisms), and biodiversity (soil microbiology, fish, crustaceans, and other vertebrates). Therefore, it is essential to develop protocols for the treatment of this waste so that it can be used again in other productive activities under the circular economy approach. This means that all the waste from a production process can be reused, can generate value for the benefit of the producer, and, in turn, mitigate the environmental impact. The objective of this study was to evaluate the replacement of 5 levels of wheat bran (WB) with extruded coffee pulp flour (ECPF) as an alternative to a conventional fiber source in broiler finisher diets. A total of 300 Cobb 500 chickens in the finishing phase were assessed in the study, grouped in 5 treatments: T1, a conventional diet or control treatment (100% WB and 0% ECPF), T2 (75% WB and 25% ECPF), T3 (50% WB and 50% ECPF), T4 (25% WB and 75% ECPF), and T5 (0% WB and 100% ECPF). Feed intake, weight gain, feed conversion ratio (FCR), and intestinal morphometry (villus length: VL, villus width: VW, crypt depth: CD, villus height/crypt depth ratio: V/C, and villus surface area: VSA) were evaluated at the level of the duodenum, jejunum, and ileum. Feed intake decreased correspondingly as the ECPF in the diet was increased, with statistical differences (p < 0.01) between their averages; the most significant weight gain (834.61 g) was evidenced with the T2 treatment, this being statistically different (p < 0.01) from T4 and T5; similarly, the best FCR (1.58) was evidenced with the T2 treatment, followed by the control treatment T1 (with 1.64); however, they were not statistically different (p > 0.05). All treatment results were similar to the VL control samples in the three intestinal portions, except for the T5 in the jejunum, which showed statistical differences from the control. In VW, the treatment results were similar to the control samples of the jejunum and ileum; however, in the duodenum, the T5 results showed the highest value (172.18 μm), being statistically different (p < 0.05) from the other treatments being evaluated. For CD, it was only in the duodenum that the T2 and T3 treatments were similar to the control. Likewise, for V/C in the duodenum, only the T2 results were similar to the control. There was no significant difference in the VSA among the different treatment groups. T2 showed better production parameters without altering the intestinal villi. In conclusion, ECPF is a potential input for use to replace up to 25% of WB in the feed of broilers in the finishing phase. [ABSTRACT FROM AUTHOR]

Background: Rhizosphere microorganisms are vital in plants' growth and development and these beneficial microbes are recruited to the root-zone soil when experiencing various environmental stresses. However, the effect of white grub (Maladera verticalis) larvae feeding on the structure and function of rhizosphere microbial communities of aerobic rice (Oryza sativa L.) is unclear. Results: In this study, we compared physicochemical properties, enzyme activities, and microbial communities using 18 samples under healthy and M. verticalis larvae-feeding aerobic rice rhizosphere soils at the Yunnan of China. 16 S rRNA and ITS amplicons were sequenced using Illumina high throughput sequencing. M. verticalis larvae feeding on aerobic rice can influence rhizosphere soil physicochemical properties and enzyme activities, which also change rhizosphere microbial communities. The healthy and M. verticalis larvae-feeding aerobic rice rhizosphere soil microorganisms had distinct genus signatures, such as possible_genus_04 and Knoellia genera in healthy aerobic rice rhizosphere soils and norank_f__SC − I−84 and norank_f__Roseiflexaceae genera in M. verticalis larvae-feeding aerobic rice rhizosphere soils. The pathway of the metabolism of terpenoids and polyketides and carbohydrate metabolism in rhizosphere bacteria were significantly decreased after M. verticalis larvae feeding. Fungal parasite–wood saprotroph and fungal parasites were significantly decreased after M. verticalis larvae feeding, and plant pathogen–wood saprotroph and animal pathogen–undefined saprotroph were increased after larvae feeding. Additionally, the relative abundance of Bradyrhizobium and Talaromyces genera gradually increased with the elevation of the larvae density. Bacterial and fungal communities significantly correlated with soil physicochemical properties and enzyme activities, respectively. Conclusions: Based on the results we provide new insight for understanding the adaptation of aerobic rice to M. verticalis larvae feeding via regulating the rhizosphere environment, which would allow us to facilitate translation to more effective measures. [ABSTRACT FROM AUTHOR]

Environmental parameters vary in time, and variability is inherent in soils, where microbial activity follows precipitation pulses. The expanded pulse-reserve paradigm (EPRP) contends that arid soil microorganisms have adaptively diversified in response to pulse regimes differing in frequency and duration. To test this, we incubate Chihuahuan Desert soil microbiomes under separate treatments in which 60 h of hydration was reached with pulses of different pulse duration (PD), punctuated by intervening periods of desiccation. Using 16S rRNA gene amplicon data, we measure treatment effects on microbiome net growth, growth efficiency, diversity, and species composition, tracking the fate of 370 phylotypes (23% of those detected). Consistent with predictions, microbial diversity is a direct, saturating function of PD. Increasingly larger shifts in community composition are detected with decreasing PD, as specialist phylotypes become more prominent. One in five phylotypes whose fate was tracked responds consistently to PD, some preferring short pulses (nimble responders; NIRs) and some longer pulses (torpid responders; TORs). For pulses shorter than a day, microbiome growth efficiency is an inverse function of PD, as predicted. We conclude that PD in pulsed soil environments constitutes a major driver of microbial community assembly and function, largely consistent with the EPRP predictions. Theory predicts that bacteria living under pulsed growth regimes adapt to pulse duration by adopting different strategies ranging from nimble to torpid responders. Physiological responses to pulse duration of soil bacteria fit the predictions. [ABSTRACT FROM AUTHOR]

Reductions in sequencing costs have enabled widespread use of shotgun metagenomics and amplicon sequencing, which have drastically improved our understanding of the microbial world. However, large sequencing projects are now hampered by the cost of library preparation and low sample throughput, comparatively to the actual sequencing costs. Here, we benchmarked three high-throughput DNA extraction methods: ZymoBIOMICS™ 96 MagBead DNA Kit, MP BiomedicalsTM FastDNATM-96 Soil Microbe DNA Kit, and DNeasy® 96 PowerSoil® Pro QIAcube® HT Kit. The DNA extractions were evaluated based on length, quality, quantity, and the observed microbial community across five diverse soil types. DNA extraction of all soil types was successful for all kits, however DNeasy® 96 PowerSoil® Pro QIAcube® HT Kit excelled across all performance parameters. We further used the nanoliter dispensing system I.DOT One to miniaturize Illumina amplicon and metagenomic library preparation volumes by a factor of 5 and 10, respectively, with no significant impact on the observed microbial communities. With these protocols, DNA extraction, metagenomic, or amplicon library preparation for one 96-well plate are approx. 3, 5, and 6 hours, respectively. Furthermore, the miniaturization of amplicon and metagenome library preparation reduces the chemical and plastic costs from 5.0 to 3.6 and 59 to 7.3 USD pr. sample. This enhanced efficiency and cost-effectiveness will enable researchers to undertake studies with greater sample sizes and diversity, thereby providing a richer, more detailed view of microbial communities and their dynamics. [ABSTRACT FROM AUTHOR]

This article presents research findings on 3H in abiotic environmental compartments, specifically, the 'water-soil-air' system. All of the research areas are located within the Semipalatinsk Test Site (STS): the perimeter of the 'Degelen' site, the riverside zone of the Shagan river and the 'background' area–the southeastern part of the STS (SEP). As research progressed, numerical values of 3H and its species were revealed in various environmental compartments. The presence of 3H was registered not only in underground nuclear test locations but also in the 'background' area–SEP. Maximum 3H tritium concentrations in the water were detected at the 'Degelen' site (up to 57000±5000 Bq/kg) and the Shagan riv (up to 61500±6000 Bq/kg), in the air of the 'Degelen' site (up to 56±11 Bq/m3), in the soil of the 'Degelen' site (up to 5170±500 Bq/kg) and the Shagan riv (4100±400 Bq/kg) in the free water, at SEP (up to 1710±170 Bq/kg) in the organic constituent. Based upon all of the findings, 3H was found to be readily distributed in abiotic environmental compartments depending on certain conditions. Research suggests that water plays a key role in 3H migration processes in the natural system of interest. The second most but equally important constituent is soil and microorganisms of plant and animal origin living there. These assumptions are indirectly proven by research findings that show the HTO and HT air concentration dynamics depending on the sampling location. [ABSTRACT FROM AUTHOR]

What is the effect of phyllosphere microorganisms on litter decomposition in the absence of colonization by soil microorganisms? Here, we simulated the litter standing decomposition stage in the field to study the differences in the composition and structure of the phyllosphere microbial community after the mixed decomposition of Populus × canadensis and Pinus sylvestris var. mongolica litter. After 15 months of mixed decomposition, we discovered that litters that were not in contact with soil had an antagonistic effect (the actual decomposition rate was 18.18%, which is lower than the expected decomposition rate) and the difference between the litters themselves resulted in a negative response to litter decomposition. In addition, there was no significant difference in bacterial and fungal community diversity after litter decomposition. The litter bacterial community was negatively responsive to litter properties and positively responsive to the fungal community. Importantly, we found that bacterial communities had a greater impact on litter decomposition than fungi. This study has enriched our understanding of the decomposition of litter itself and provided a theoretical basis for further exploring the "additive and non-additive effects" of litter decomposition and the mechanism of microbial drive. IMPORTANCE The study of litter decomposition mechanism plays an important role in the material circulation of the global ecosystem. However, previous studies have often looked at contact with soil as the starting point for decomposition. But actually, standing litter is very common in forest ecosystems. Therefore, we used field simulation experiments to simulate the decomposition of litters without contact with soil for 15 months, to explore the combined and non-added benefits of the decomposition of mixed litters, and to study the influence of microbial community composition on the decomposition rate while comparing the differences of microbial communities. [ABSTRACT FROM AUTHOR]

Sulfate-reducing prokaryotes (SRPs) are essential microorganisms that play crucial roles in various ecological processes. Even though SRPs have been studied for over a century, there are still gaps in our understanding of their biology. In the past two decades, a significant amount of data on SRP ecology has been accumulated. This review aims to consolidate that information, focusing on SRPs in soils, their relation to the rare biosphere, uncultured sulfate reducers, and their interactions with other organisms in terrestrial ecosystems. SRPs in soils form part of the rare biosphere and contribute to various processes as a low-density population. The data reveal a diverse range of sulfate-reducing taxa intricately involved in terrestrial carbon and sulfur cycles. While some taxa like Desulfitobacterium and Desulfosporosinus are well studied, others are more enigmatic. For example, members of the Acidobacteriota phylum appear to hold significant importance for the terrestrial sulfur cycle. Many aspects of SRP ecology remain mysterious, including sulfate reduction in different bacterial phyla, interactions with bacteria and fungi in soils, and the existence of soil sulfate-reducing archaea. Utilizing metagenomic, metatranscriptomic, and culture-dependent approaches will help uncover the diversity, functional potential, and adaptations of SRPs in the global environment. [ABSTRACT FROM AUTHOR]

Tricholoma matsutake is a kind of ectomycorrhizal fungus. In addition to its vital influence on symbiotic plants, the impact of the soil microbial community on the growth and development of T. matsutake has been garnering attention. To clarify the differences in soil microflora between "T. matsutake Shangri-la" and "T. matsutake Nanhua", and the effects of soil bacteria and fungi on the growth and development of T. matsutake, this study took the soil of "T. matsutake Shangri-la" and "T. matsutake Nanhua" at different developmental stages. A total of 7694 bacterial OTUs and 2170 fungal OTUs were obtained through microbial omics based on amplicon sequencing. The results indicate that the α diversity and composition of the soil microorganisms in the T. matsutake Shangri-la shiro were higher than those of the T. matsutake Nanhua. It is affected by species, geographical locations, and the growth period of matsutake. Matsutake mycelia also recruit certain types of bacteria and fungi in the stage of fruiting body development. Both bacteria and fungi positively and negatively regulate the fruiting body development of matsutake mushrooms. This study will provide a basis for the semi-artificial cultivation of matsutake. [ABSTRACT FROM AUTHOR]

The breeding of laying hens and broilers in China has increased tremendously. Wet organic fertilizer prepared from hen manure using high-temperature container fermentation preserves high levels of nutrients and a diverse microbial community. We applied low doses of organic fertilizer to peanuts in the black soil area of China's northeastern region. Based on the calculation of nitrogen content, treatments were set as follows: chemical fertilizer (PCF), organic fertilizer (POF, 4500 kg·ha−1), and replacement of 50% chemical fertilizer with organic fertilizer (PR, 2250 kg·ha−1). Compared to the plots with chemical fertilizers, the use of organic fertilizer and replacing 50% of the chemical fertilizers with organic fertilizer significantly increased peanut yields. Both the organic fertilizer and replacing 50% of the chemical fertilizers with organic fertilizer did not significantly affect the activities of the most tested soil enzymes related to carbon transformation and the absolute abundance of microorganisms. However, they did significantly enhance soil dehydrogenase and α-glucosidase. The community abundance ratio of fungi/bacteria trended downward, leading to soil with a high-fertility bacterial composition. The replacement of 50% chemical fertilizer with organic fertilizer significantly enhanced the species richness and diversity of the bacterial and fungal communities. Organic fertilizer treatment significantly increased the relative abundance of Gemmatimonas and Sphingomonas. The relative abundance of Mycobacterium in the treatment where 50% of the chemical fertilizers were replaced with organic fertilizer was significantly lower than that in the organic fertilizer treatment. PCoA results showed that the low-dose organic fertilizer treatment, replacing 50% of the chemical fertilizers with organic fertilizer, had a significant impact on the composition of soil bacterial communities. [ABSTRACT FROM AUTHOR]

Plastic film mulching, widely used in agriculture, leads to microplastic (MP) pollution in soils. While biodegradable polybutylene adipate terephthalate (PBAT) films may offer a solution, their impacts on subsurface soils and microorganisms remain unclear. To investigate the effects of conventional non-biodegradable polyethylene (PE) and biodegradable PBAT MPs on the properties of sub-surface soils and microbial communities, MPs were added at varying doses in a field experiment and incubated for 160 days. Physicochemical characteristics, nutrient dynamics, and microbial composition, diversity, and networks of soils were analyzed using standard techniques and 16S rRNA/ITS gene sequencing. Correlations between soil properties and microbes were assessed. Both MP types significantly altered soil characteristics, with PBAT-MP elevating pH and the levels of available phosphorus and potassium more than PE-MP. Microbial composition shifts occurred, with low-addition PBAT-MP promoting plastic-degrading genera. The assessment of α/β-diversity indicated that PBAT-MP predominantly influenced fungi while PE-MP impacted bacteria. An examination of microbial co-occurrence networks highlighted that PE-MP primarily disrupted fungal interactions, whereas PBAT-MP streamlined network complexity. Correlation analyses revealed that PBAT-MP promoted fungal diversity/network resilience correlating to nutrients. PE-MP and PBAT-MP significantly altered native soil/microbe relationships. PBAT-MP may exert greater, yet unknown, impacts over time through its biodegradation into newer and smaller fragments. Future research needs to integrate multi-omics and stable isotope science to elucidate the deep mechanistic impacts of degraded film-derived MPs on microbial ecological functions and biogeochemical cycles. Attention should also be paid to the long-term accumulation/transport of MPs in agricultural soils. Overall, this work deepens the impact and understanding of MPs from plastic film on sub-surface soil ecology. Furthermore, it provides a theoretical foundation for managing 'white pollution' in the film-covered farmlands of arid and semi-arid regions in China. [ABSTRACT FROM AUTHOR]

In modern agriculture, more and more attention is being paid to the use of microorganisms that can increase crop productivity and quality even under adverse weather conditions. Due to the declining biodiversity of crops and the occurrence of soil erosion and nutrient losses, the introduction of cover crops (CC) can be a positive crop management technique. In the field study presented here, the effect of growing spring barley with CCs applied simultaneously with bacterial consortia on the ratio of the total number of bacteria to actinobacteria (B/A) and the number of fungi in the soil was evaluated. The biomass yield of CCs and the subsequent effect on the yield of spelt wheat grown with the application of bacterial consortia were also evaluated. The bacterial consortia applied included consortium 1, comprising Bacillus subtilis, Bacillus amyloliquefaciens, and Pseudomonas fluorescens, and consortium 2, comprising Bacillus subtilis, Bacillus amyloliquefaciens, Pseudomonas fluorescens, and Azotobacter chroococcum. The CCs were red clover, red clover + Italian ryegrass, and Italian ryegrass. The most favorable B/A ratio and the highest number of fungi were obtained after growing spring barley with a CC consisting of a mixture of red clover and Italian ryegrass when using bacterial consortium 2. These conditions additionally had the most favorable influence on spelt wheat. The combination of such a forecrop with the application of bacterial consortium 2 resulted in the highest yields of spelt wheat. [ABSTRACT FROM AUTHOR]

Agricultural soil microorganisms play a crucial role in farmland ecosystems and are integral to the material cycle in these environments. The composition and abundance of soil microorganisms are influenced by agronomic measures that alter the soil microenvironment. These changes are pivotal to enhancing crop resistance, maximizing yield, and facilitating nutrient cycling in farmlands. Drawing on prior research advancements, this study systematically examined the functions of soil microorganisms, the effects of various agronomic measures on their populations, and the ways in which agronomic measures regulate soil microorganisms, and this article offers a comprehensive study of agricultural influences on microorganisms. Additionally, it outlines key areas for future research on soil microorganisms in farmlands, aiming to provide valuable insights for the sustainable development of farmland ecosystems. [ABSTRACT FROM AUTHOR]

Soil microorganisms play a critical role in shaping the biodiversity dynamics of plant communities. These microbial effects can arise through direct mediation of plant fitness by pathogens and mutualists, and over the past two decades, numerous studies have shined a spotlight on the role of dynamic feedbacks between plants and soil microorganisms as key determinants of plant species coexistence. Such feedbacks occur when plants modify the composition of the soil community, which in turn affects plant performance. Stimulated by a theoretical model developed in the 1990s, a bulk of the empirical evidence for microbial controls over plant coexistence comes from experiments that quantify plant growth in soil communities that were previously conditioned by conspecific or heterospecific plants. These studies have revealed that soil microbes can generate strong negative to positive frequency‐dependent dynamics among plants. Even as soil microbes have become recognized as a key player in determining plant coexistence outcomes, the past few years have seen a renewed interest in expanding the conceptual foundations of this field. New results include re‐interpretations of key metrics from classic two‐species models, extensions of plant–soil feedback theory to multispecies communities, and frameworks to integrate plant–soil feedbacks with processes like intra‐ and interspecific competition. Here, I review the implications of theoretical developments for interpreting existing empirical results and highlight proposed analyses and designs for future experiments that can enable a more complete understanding of microbial regulation of plant community dynamics. [ABSTRACT FROM AUTHOR]

Background and Aims The successful plant Fallopia  ×  bohemica presents interesting capacities for control of the soil nitrogen cycle at the adult stage, termed biological inhibition of denitrification (BDI). The BDI strategy allows the plant, via the production of secondary metabolites (procyanidins), to compete with the denitrifying microbial community and to divert nitrate from the soil for its benefit. In this study, we analysed whether seedlings of F.  ×  bohemica can implement BDI at the seedling stage. We also determined whether soil nitrogen availability influences the implementation of BDI and seedling growth. Methods We sowed achenes of F.  ×  bohemica in soils representing a nitrogen gradient (six treatments) and harvested seedlings after 20 or 40 days of growth. The denitrification and related microbial communities (i.e. functional gene abundances of nirK and nirS), soil parameters (nitrate content and humidity) and plant performance (biomass, growth and root morphology) were determined. Key Results On soil without addition of nitrogen, BDI was observed after 20 days of growth, whereas a stimulation of denitrification was found after 40 days. The increase of soil N content had few effects on the activity and structure of the soil denitrifying community and on the plant biomasses or the relative growth rates. Correlations between plant and microbial parameters were observed after 20 days of growth, reflecting early and strong chemical interactions between plants and the denitrifying community, which decreased with plant growth after 40 days. Conclusions This study shows that an early BDI enhances the efficiency of nitrogen acquisition in the first weeks of growth, allowing for a conservative root strategy after 40 days. This switch to a conservative strategy involved resource storage, an altered allocation to above- and below-ground parts and an investment in fine roots. It now seems clear that this storage strategy starts at a very young age with early establishment of BDI, giving this clonal plant exceptional capacities for storage and multiplication. [ABSTRACT FROM AUTHOR]

A total of 817 Lactobacillus-like isolates were obtained from different sources, including soil, ruminant gastric juice, and fermented foods. They were screened to select the best isolate for the production of 1,3-propanediol (1,3-PDO). The isolate SY235 was selected and designated as Lactobacillus reuteri based on the 16S rRNA gene sequence. It was then employed in fed-batch fermentation for producing 1,3-PDO. The highest titer of 1,3-PDO (52.6 ± 2.4 g/L) was attained at 60 h, corresponding to a yield of 0.55 ± 0.01 g/g glycerol and a productivity of 0.88 ± 0.04 g/L/h. No further production was observed after 60 h of incubation. These results demonstrate that the newly isolated strain L. reuteri SY235 can efficiently transform glycerol into 1,3-PDO. [ABSTRACT FROM AUTHOR]

Chemicals involved in plutonium uranium reduction extraction (PUREX) can be released from nuclear reprocessing facilities and accumulate in the environment. We exposed chemically diverse soils to a range of concentrations of key chemicals used in the PUREX process. The responses of soil microbial communities are dependent on soil type, and tributyl phosphate exposure generates the most reproducible changes in microbial communities. We reconstructed the genomes of key bacteria and find several phosphotriesterase genes found only in Rhizobiaceae. The abundance of phosphotriesterase genes is significantly higher in samples exposed to tributyl phosphate. These phosphotriesterase genes may be involved in breakdown of tributyl phosphate, and a means of accessing phosphate for these bacteria. [ABSTRACT FROM AUTHOR]

Introduction: Plastic pollution has surged due to increased human consumption and disposal of plastic products. Microbial communities capable of utilizing plastic as a carbon source may play a crucial role in degrading and consuming environmental plastic. In this study, we investigated the potential of a modified Winogradsky column (WC) to enrich Connecticut landfill soil for plastic-degrading bacteria and genes. Methods: By filling WCs with landfill soil and inorganic Bushnell Haas medium, and incorporating polyethylene (PE) strips at different soil layers, we aimed to identify bacterial taxa capable of degrading PE. We employed high-throughput 16S rRNA sequencing to identify the microbes cultivated on the plastic strips and the intervening landfill soil. We used PICRUSt2 to estimate the functional attributes of each community from 16S rRNA sequences. Results and discussion: After 12 months of incubation, distinct colors were observed along the WC layers, indicating successful cultivation. Sequencing revealed significant differences in bacterial communities between the plastic strips and the intervening landfill-soil habitats, including increased abundance of the phyla Verrucomicrobiota and Pseudomonadota (ne' e' Proteobacteria) on the strips. Based on inferred genomic content, the most highly abundant proteins in PE strip communities tended to be associated with plastic degradation pathways. Phylogenetic analysis of 16S rRNA sequences showed novel unclassified phyla and genera enriched on the plastic strips. Our findings suggest PE-supplemented Winogradsky columns can enrich for plastic-degrading microbes, offering insights into bioremediation strategies. [ABSTRACT FROM AUTHOR]

We report here the identification, characterization and three‐dimensional (3D) structure determination of NaNga, a newly identified β‐N‐acetylgalactosaminidase from the Gram‐negative soil bacterium Niabella aurantiaca DSM 17617. When recombinantly expressed in Escherichia coli, the enzyme selectively cleaved 4‐nitrophenyl‐N‐acetyl‐β‐d‐galactosamine (pNP‐β‐d‐GalpNAc). The X‐ray crystal structure of the protein was refined to 2.5 Å and consists of an N‐terminal β‐sandwich domain and a (β/α)8 barrel catalytic domain. Despite a mere 22% sequence identity, the 3D structure of NaNga is similar to those previously determined for family GH123 members, suggesting it also employs the same substrate‐assisted catalytic mechanism. Inhibition by N‐acetyl‐galactosamine thiazoline (GalNAc‐thiazoline) supports the suggested mechanism. A phylogenetic analysis of its proximal sequence space shows significant clustering of unknown sequences around NaNga with sufficient divergence with previously identified GH123 members to subdivide this family into distinct subfamilies. Although the actual biological substrate of our enzyme remains unknown, examination of the active site pocket suggests that it may be a β‐N‐acetylgalactosaminide substituted by a monosaccharide at O‐3. Analysis of the genomic context suggests, in turn, that this substituted β‐N‐acetylgalactosaminide may be appended to a d‐arabinan from an environmental Actinomycete. [ABSTRACT FROM AUTHOR]

Low‐carbon alkaline thermal hydrolysis of sewage sludge for the production of high‐quality plant‐growth‐promoting nutrients and biostimulants is a growing concern for sludge resource utilization in agriculture. Thus, this study aims to investigate functional characteristics and soil biochemical effects of sewage sludge‐derived nutrients and biostimulants (SS‐NB). The content of heavy metals in SS‐NB decreased by 47.39–100%, and an increase in soil protease, invertase, and soil nutrient utilization rates are observed in SS‐NB groups. SS‐NB substituted for chemical fertilizer increased the diversity and evenness of microbial community and reduced the abundance of the soil‐borne bacterial genus Arthrobacter. The dominant community of SS‐NB100 group is mainly enriched in Microvirga, Ensifer, Novosphingobium, Bosea and Ellin6055, which are principally beneficial symbiotic bacteria of plants and participated in C and N cycles. Moreover, SS‐NB reduced the accumulation of Ktedonobacteria and Nitrosospira, which are involved in the production of CO2 and N2O, and also enhanced the coordination of soil microorganisms with enzyme activities and nutrient utilization rate. In conclusion, the results suggest that SS‐NB exerts a positive effect on reducing greenhouse gas emissions and preventing soil‐borne diseases, and can further enhance collaboration with soil enzyme activity and soil nutrient utilization by stimulating soil microorganisms. [ABSTRACT FROM AUTHOR]

Background and aims: Male Populus cathayana individuals alleviate the stress-induced damage on females when both sexes of plant individuals grow together compared with the female-female competition relationship. However, it is still largely unknown how microbiota associated with roots are regulated by intra- and inter-sexual plant competition that affect the plant ecology, such as the ability to mitigate stressors. Methods: Bacterial communities in the rhizosphere and root endosphere were investigated in intra-sexual competition male-male, female-female and inter-sexual competition male-female of the dioecious species P. cathayana under different availabilities of water. Results: Female P. cathayana individuals were more strongly subjected to competition from a same sex neighbor and suffered more severe damage by drought compared with the males in male-male competition. More carbon deprived from roots was assimilated by soil microorganisms in female-female competition than male-female and male-male competitions under conditions of adequate water. Changes in neighbor effect were a driving force in regulating the bacterial community in the rhizosphere and endosphere. This study found that male-male, female-female and male-female competitions recruited large numbers of unique operational taxonomic units and largely influenced bacterial β-diversity. Moreover, the inter-sexual competition highly increased the association between species of the bacterial network. Male neighbors favored colonization of the female roots by the growth promoting taxa Streptomyces and Phyllobacterium. Conclusions: It was emphasized that the beneficial roles of males in alleviating the drought-induced damage on females was associated with root microbiota, which were impacted by the sexual identity of neighbor under drought. [ABSTRACT FROM AUTHOR]

Background and aims: The addition of functional soil microbes to the soil can enhance the utilization of soil phosphorus (P) for plants, but the mechanisms underlying this process are not fully understood. The study aimed to investigate the effects of inoculating phosphate-solubilizing microorganisms (PSMs), with or without arbuscular mycorrhizal fungi (AMF), on Phyllostachys edulis seedling growth in soils with varying P levels. Methods: The pot experiment was conducted on P. edulis seedings with inoculation treatments of a mixture of 15 PSMs from the P. edulis rhizosphere alone, or PSMs in cooperation with AMF. Plant mass and nutrient concentrations, soil properties and soil microbial communities were assessed when the seedlings had completed their first-year growth spurt (T1) and second-year growth spurt (T2). Results: The application of PSMs, particularly in combination with AMF, resulted in significant increases in seedling mass and nutrient content under P-deficient conditions, accomplished through modifications in soil nutrient concentrations and enzyme activities related to nitrogen, carbon, and P metabolism. The beneficial outcomes were accompanied by alterations in the composition and interactions within the constituents of the rhizosphere microbial community. Remarkably, the co-inoculation of AMF and PSMs led to a higher abundance of microorganisms that promote plant growth within the rhizosphere. Conclusion: The utilization of PSMs, especially in combination with AMF, proves to be an effective strategy for enhancing P. edulis seedlings growth during their second-year growth, particularly in P-deficient soil. This approach modifies the soil microenvironment, offering a promising avenue for improving soil P utilization by woody plants. [ABSTRACT FROM AUTHOR]

Aims: Soil organic carbon (SOC) stability greatly affects soil carbon sequestration capacity and carbon emissions, is related to soil bacterial communities, but it remains unclear whether such relationships exist in alpine wetland biogeomorphic succession. Methods: Here, we used a space-for-time approach across hydrological gradients, and alpine wetland succession can be divided into three types: "Swamp" (S), "Swamp Meadow" (SM), and "Meadow" (M) to examine the dynamics change of SOC fractions and bacterial communities. Results: The succession from S-SM-M resulted in decreased SOC stability (SM and M decreased by 18.65% and 31.88% compared to S). Furthermore, the decrease in SOC stability was primarily due to the decrease in soil moisture during succession and moisture-induced changes in bacterial community structure. e.g., the relative abundance of Proteobacteria decreased significantly by 40.99% and 52.87% in SM and M, while the relative abundance of Acidobacteria increased by 43.49% and 185.04% in SM and M compared to S. Co-occurrence network and random forest analyses further identified that changes in keystone taxa of bacteria, including Deltaproteobacteria, Acidimicrobiia, Bacteroidia and Gammaproteobacteria, were associated with SOC stability. Conclusions: In conclusion, bacteria shifted their community composition to reduce SOC stability in response to soil moisture variations during succession, and underscores the importance of identifying keystone taxa that are crucial for maintaining SOC stability. [ABSTRACT FROM AUTHOR]

Intercropping is a powerful practice to alter the allocation of photosynthetic carbon (C) to belowground ecosystems via promotion of diversified plant communities. The feedback of soil C stability to intercropping is controlled by microbial C use efficiency (CUE). Despite its significance, there is currently insufficient evidence to decipher how soil microbial CUE reacts to intercropping. By combining a 10-year-long intercropping experiment with a substrate-independent 18O-H2O labelling approach and high-throughput sequencing, we elucidated the performance of intercropping on soil C pool and microbial metabolic traits as well as their relationships with soil microbial communities. Compared with monoculture, maize intercropping with peanut and soybean significantly increased soil C storage, soil mineral-associated organic C (MAOC), soil dissolved organic (DOC), and soil microbial biomass (MBC) contents at maize four growth stages. Soil microbial CUE increased significantly, especially at maize flowering and mature stages, as a consequence of enhanced microbial growth and biomass turnover rate after maize intercropping with peanut and soybean. Soil C storage and accessibility indicators (e.g., MAOC, DOC, and MBC contents) could significantly predict the changes of soil microbial diversity and core taxa. Meanwhile, the beta-diversity (community composition) of soil bacteria, fungi, saprotroph and protists, as well as rare fungal taxa were positively correlated with soil microbial CUE, and these indicators showed a high prediction of the microbial CUE. Soil C storage and accessibility indicators directly and indirectly influenced soil microbial CUE by regulating microbial diversity and key taxa. Soil microbial diversity and core taxa directly and indirectly influenced microbial CUE by mediating microbial respiration, growth, biomass, and enzyme activity, which mediated by soil C storage and accessibility. These findings provide an evidence for the associations between microbial diversity, CUE, and soil C stability, highlighting the importance of intercropping-driven soil microbiome to enhance soil microbial CUE. [ABSTRACT FROM AUTHOR]

Microorganisms regulate soil organic matter (SOM) formation through accumulation and decomposition of microbial necromass, which is directly and indirectly affected by elevated CO2 and N fertilization. We investigated the role of microorganisms in SOM formation by analyzing 13C recovery in microorganisms and carbon pools in paddy soil under two CO2 levels, with and without N fertilization, after continuous 13CO2 labelling was stopped. Microbial turnover transferred 13C from living microbial biomass (determined by the decrease in phospholipid fatty acids) to necromass (determined by the increase in amino sugars). 13C incorporation in fungal living biomass and necromass was higher than that in bacteria. Bacterial turnover was faster than necromass decomposition, resulting in net necromass accumulation over time; fungal necromass remained stable. Elevated CO2 and N fertilization increased the net accumulation of bacterial, but not fungal, necromass. CO2 levels, but not N fertilization, significantly affected 13C incorporation in SOM pools. Elevated CO2 increased 13C in particulate organic matter via the roots, and in the mineral-associated organic matter (MAOM) via bacterial, but not fungal, necromass. Overall, bacterial necromass plays a dominant role in the MAOM formation response to elevated CO2 because bacteria are sensitive to elevated CO2. [ABSTRACT FROM AUTHOR]

Graphene (GR) has huge industrial and biomedical potential, and its adverse effect on soil microorganisms has been evaluated in ecotoxicological studies. These studies focused on single exposure to GR, but repeated exposures with low concentration are more likely to occur under actual exposure scenario. In this study, we compared the impact of single and repeated exposures of GR on structure, abundance and function of soil bacterial community based on soil enzyme activity and high-throughput sequencing. The results displayed that after 4 days of incubation the activities of urease and fluorescein diacetate esterase increased by approximately 12% and 4% upon repeated exposure to GR (biweekly 15 mg doses GR for the two-exposure experiment, 10 mg doses GR for the three-exposure experiment, resulting in the same final concentration of 300 mg/kg), respectively. Instead, the activities of urease and fluorescein diacetate esterase decreased by 13% and 6% upon single exposure (30 mg for the single-exposure experiment), respectively. As the incubation time increased to 60 days, these activities showed little difference. The alpha diversity of soil bacterial community under repeated exposures increased more than that under single exposure, demonstrating that a low concentration chronic exposure to GR increase the diversity within a specific bacterial community. The PCoA and sample level clustering tree showed single exposure to GR after 4 days alter the soil bacterial community to some extent. During the entire incubation process, no matter what kind of exposure scenarios to GR, the majority of bacterial phylotypes at the phylum level had no great change except for Proteobacteria and Actinobacteria according to the relative abundance of phylotypes. These results elucidated the repeated exposures to GR increased the metabolic activity and diversity of the soil microbial community as compared with single exposure. This study can provide a new perspective on the impact of carbon nanomaterials on soil microbial community. [ABSTRACT FROM AUTHOR]

Vanadium (V) pollution potentially threatens human health. Here, it is found that nsp1 and nsp2, Rhizobium symbiosis defective mutants of Medicago truncatula, are sensitive to V. Concentrations of phosphorus (P), iron (Fe), and sulfur (S) with V are negatively correlated in the shoots of wild‐type R108, but not in mutant nsp1 and nsp2 shoots. Mutations in the P transporter PHT1, PHO1, and VPT families, Fe transporter IRT1, and S transporter SULTR1/3/4 family confer varying degrees of V tolerance on plants. Among these gene families, MtPT1, MtZIP6, MtZIP9, and MtSULTR1; 1 in R108 roots are significantly inhibited by V stress, while MtPHO1; 2, MtVPT2, and MtVPT3 are significantly induced. Overexpression of Arabidopsis thaliana VPT1 or M. truncatula MtVPT3 increases plant V tolerance. However, the response of these genes to V is weakened in nsp1 or nsp2 and influenced by soil microorganisms. Mutations in NSPs reduce rhizobacterial diversity under V stress and simplify the V‐responsive operational taxonomic unit modules in co‐occurrence networks. Furthermore, R108 recruits more beneficial rhizobacteria related to V, P, Fe, and S than does nsp1 or nsp2. Thus, NSPs can modulate the accumulation and tolerance of legumes to V through P, Fe, and S transporters, ion homeostasis, and rhizobacterial community responses. [ABSTRACT FROM AUTHOR]

Insects lack acquired immunity and were thought to have no immune memory, but recent studies reported a phenomenon called immune priming, wherein sublethal dose of pathogens or nonpathogenic microbes stimulates immunity and prevents subsequential pathogen infection. Although the evidence for insect immune priming is accumulating, the underlying mechanisms are still unclear. The bean bug Riptortus pedestris acquires its gut microbiota from ambient soil and spatially structures them into a multispecies and variable community in the anterior midgut and a specific, monospecies Caballeronia symbiont population in the posterior region. We demonstrate that a particular Burkholderia strain colonizing the anterior midgut stimulates systemic immunity by penetrating gut epithelia and migrating into the hemolymph. The activated immunity, consisting of a humoral and a cellular response, had no negative effect on the host fitness, but on the contrary protected the insect from subsequent infection by pathogenic bacteria. Interruption of contact between the Burkholderia strain and epithelia of the gut weakened the host immunity back to preinfection levels and made the insects more vulnerable to microbial infection, demonstrating that persistent acquisition of environ- mental bacteria is important to maintain an efficient immunity. [ABSTRACT FROM AUTHOR]

Background: The fertile islands formed by shrubs are major drivers of the structure and function of desert ecosystems, affecting seedling establishment, plant–plant interactions, the diversity and productivity of plant communities, and microbial activity/diversity. Although an increasing number of studies have shown the critical importance of soil microbes in fertile island formation, how soil microbial community structure and function are affected by the different fertile island effect intensities is still unknown. As an endangered and dominant shrub species in the West Ordos Desert, Tetraena mongolica was selected for further exploration of its fertile island effect on the soil microbial community in the present study to test the following two hypotheses: (1) T. mongolica shrubs with different canopy sizes exert fertile island effects of different strengths; (2) the soil microbial community structure and function beneath the T. mongolica canopy are affected by the fertile island, and the strength of these effects varies depending on the shrub canopy size. Results: The contents of soil total nitrogen (TN) and available phosphorus (AVP) were significantly greater beneath T. mongolica shrub canopy than outside the shrub canopy. With increasing shrub canopy size, the enrichment of soil TN and AVP increased, indicating a stronger fertile island effect. The structure and function of soil microbial communities, including fungal, archaeal and bacterial communities, are affected by the fertile island effect. An increase in canopy size increased the relative abundance of Ascomycota (Fungi) and Thaumarchaeota (Archaea). For the soil microbial functional groups, the relative abundance of endophytes in the fungal functional groups; steroid hormone biosynthesis, sphingolipid metabolism, and steroid biosynthesis genes in the bacterial functional groups; and nonhomologous end-joining and bisphenol degradation functional genes in the archaeal functional groups increased significantly with increasing T. mongolica canopy size. Conclusions: These results revealed that T. mongolica had a fertile island effect, which affected the soil microbial community structure and functions, and that the fertile island effect might increase with increasing shrub canopy size. The fertile island effect may strengthen the interaction between T. mongolica shrubs and microbes, which may be beneficial to the growth and maintenance of T. mongolica. [ABSTRACT FROM AUTHOR]

Nitrogen (N) additions often decrease soil respiration and increase soil organic carbon (C) stock. However, it is unclear how microbial substrates may shift with N additions and increasing temperature. Leveraging 12 years of N fertilization experiments and the associated shift in the dominant vegetation from C4 to C3, we explored the δ13C‐CO2 and temperature sensitivities of respired CO2 and extracellular enzyme activities in control and fertilized soils. N additions increased cellulose‐decaying extracellular enzyme activity while respiration remained similar between the control and fertilized soils. Temperature sensitivity of cellulose‐decaying extracellular enzyme activity decreased with the N additions. The δ13C‐CO2 data reveal that, as temperature increased, microbes in fertilized soils changed their dominant substrate from bulk soil organic C to plant litterfall. Our results suggest that long‐term N fertilization imposed C limitation on microbes, leading to enhanced microbial efforts to acquire C. This study highlights how long‐term N additions can promote the relative preservation of organic C in mineral soil while litterfall, the precursor to mineral‐associated C, is increasingly decayed as temperatures increase. [ABSTRACT FROM AUTHOR]

The dynamic of plant-parasitic nematode populations in soil is closely related to soil microorganisms. Fungi from Heterodera zeae cysts were isolated to explore the phenomenon of decline in the H. zeae population in the soil. Phylogenetic study of partial ITS, BenA, CaM, and RPB2 gene sequences, in addition to morphological investigations, was utilized to identify a nematode-destroying fungus. The nematicidal activity of a novel strain GX1 against H. zeae was assessed in vitro and in the greenhouse. Our findings revealed that strain GX1 is a new species of Talaromyces, named Talaromyces cystophila. It has a strong parasitic and lethal effect on H. zeae cysts, with 91.11% parasitism on cysts at 3 days after treatment. The contents of second-stage juveniles (J2s) and eggs inside the cysts were degraded and formed dense vacuoles, and the damaged eggs could not hatch normally. The spore suspension exhibited high nematophagous activity against nematodes, and fermentation filtrate exhibited marked inhibition of egg hatching and nematicidal activities on J2s. The hatching inhibition rates of eggs exposed to 1 × 108 CFU/ml spore suspensions or 20% 1-week fermentation filtrate (1-WF) for 15 days were 98.56 and 100%, respectively. The mortality of J2s exposed to 1 × 108 CFU/ml spore suspension reached 100% at 24 h; exposure to 50% 2-WF was 98.65 and 100% at 24 and 48 h, respectively. Greenhouse experiments revealed that the spore suspension and fermentation broth considerably decreased H. zeae reproduction by 56.17 to 78.76%. T. cystophila is a potential biocontrol strain with nematophagous and nematicidal activity that deserves attention and application. [ABSTRACT FROM AUTHOR]

The rhizosphere is the soil environment where the plant root is available and is a zone of maximum microbial activity, resulting in a confined nutrient pool in which essential macro-and micronutrients are extracted. The microbial population in the rhizosphere is relatively different from that of its surroundings due to root exudates that function as a source of nutrients for microbial growth. Those resulting in symbiotic and non-symbiotic nitrogen fixation are considerably important among all these interactions. In recent years, the use of bacteria (rhizobacteria) to promote plant growth has increased in several regions of the world and has acquired relevant importance in developing countries that are the producers of raw materials for food. In the present study Rhizobacteria was isolated from the soil and the production of IAA and phosphate solubilisation was studied. The effect of PGPR was shown on mat seeds (matki) and black-eyed pea seeds (chawali) on the growth of plants. [ABSTRACT FROM AUTHOR]

Soil salinity is a serious problem facing many countries globally, especially those with semi-arid and arid climates. Soil salinity can have negative influences on soil microbial activity as well as many chemical and physical soil processes, all of which are crucial for soil health, fertility, and productivity. Soil salinity can negatively affect physiological, biochemical, and genetic attributes of cultivated plants as well. Plants have a wide variety of responses to salinity stress and are classified as sensitive (e.g., carrot and strawberry), moderately sensitive (grapevine), moderately tolerant (wheat) and tolerant (barley and date palm) to soil salinity depending on the salt content required to cause crop production problems. Salinity mitigation represents a critical global agricultural issue. This review highlights the properties and classification of salt-affected soils, plant damage from osmotic stress due to soil salinity, possible approaches for soil salinity mitigation (i.e., applied nutrients, microbial inoculations, organic amendments, physio-chemical approaches, biological approaches, and nano-management), and research gaps that are important for the future of food security. The strong relationship between soil salinity and different soil subdisciplines (mainly, soil biogeochemistry, soil microbiology, soil fertility and plant nutrition) are also discussed. [ABSTRACT FROM AUTHOR]

Arbuscular mycorrhizal (AM) fungi engage in symbiosis with more than 80% of terrestrial plants, enlarging root phosphorus (P) absorption volume by producing extensive extraradical hyphae (ERH) in the soil. In addition, AM fungi recruit and cooperate with soil bacteria to enhance soil organic P mobilization and improve fungal and plant fitness through hyphal exudates. However, the role of the dominant compounds in the hyphal exudates in enhancing organic P mobilization in the mycorrhizal pathway is still not well understood. In this study, we added sugars, i.e., glucose, fructose, and trehalose, which are detected in the hyphal exudates, to the hyphal compartments (HCs) that allowed the ERH of the AM fungus to grow or not. The results showed that in AM fungus-inoculated pots, adding three sugars at a concentration of 2 mmol C kg−1 soil significantly increased the phosphatase activity and facilitated the mobilization of organic P in the HCs. The addition of fructose at a concentration of 2 mmol C kg−1 soil was the most efficient in increasing the phosphatase activity and enhancing organic P mobilization. The released inorganic P was then absorbed by the ERH of the AM fungus. The enhanced mobilization of organic P was correlated with the increase in phoD gene number and the changing bacterial community in the presence of fungal hyphae. The sugar addition enriched the relative abundance of some bacterial taxa, e.g., Betaproteobacteriales. Our study suggested that the addition of the sugars by mycorrhizae could be a pivotal strategy in managing P uptake in agricultural production, potentially directing future practices to optimize plant–fungi–bacteria interactions for improved P use efficiency. [ABSTRACT FROM AUTHOR]

Subarctic ecosystems are subjected to increasing nitrogen (N) enrichment and disturbances that induce particularly strong effects on plant communities when occurring in combination. There is little experimental evidence on the longevity of these effects. We applied N-fertilization (40 kg urea-N ha−1 year−1 for 4 years) and disturbance (removal of vegetation and organic soil layer on one occasion) in two plant communities in a subarctic forest-tundra ecotone in northern Finland. Within the first four years, N-fertilization and disturbance increased the share of deciduous dwarf shrubs and graminoids at the expense of evergreen dwarf shrubs. Individual treatments intensified the other's effect resulting in the strongest increase in graminoids under combined N-fertilization and disturbance. The re-analysis of the plant communities 15 years after cessation of N-fertilization showed an even higher share of graminoids. 18 years after disturbance, the total vascular plant abundance was still substantially lower and the share of graminoids higher. At the same point, the plant community composition was the same under disturbance as under combined N-fertilization and disturbance, indicating that multiple perturbations no longer reinforced the other's effect. Yet, complex interactions between N-fertilization and disturbance were still detected in the soil. We found higher organic N under disturbance and lower microbial N under combined N-fertilization and disturbance, which suggests a lower bioavailability of N sources for soil microorganisms. Our findings support that the effects of enhanced nutrients and disturbance on subarctic vegetation persist over decadal timescales. However, they also highlight the complexity of plant–soil interactions that drive subarctic ecosystem responses to multiple perturbations across varying timescales. [ABSTRACT FROM AUTHOR]