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Soil bacteria spend significant periods in dormant or semi‐dormant states that are interrupted by resource pulses which can lead to periods of rapid growth and intense nutrient competition. Microbial populations have evolved diverse strategies to circumvent competitive interactions and facilitate coexistence. Here, we show that nutrient use of soilborne Streptomyces is temporally partitioned during experimental resource pulses, leading to reduced niche overlap, and potential coexistence. Streptomyces grew rapidly on the majority of distinct 95 carbon sources but varied in which individual resources were utilized in the first 24 h. Only a handful of carbon sources (19 out of 95) were consistently utilized (>95% of isolates) most rapidly in the first 24 h. These consistently utilized carbon sources also generated the majority of biomass accumulated by isolates. Our results shed new light on a novel mechanism microbes may employ to alleviate competitive interactions by temporally partitioning the consumption of carbon resources. As competitive interactions have been proposed to drive the suppression of disease‐causing microbes in agronomic soils, our findings may hold widespread implications for soil management for plant health. [ABSTRACT FROM AUTHOR]

To engage sustainable forest management, understanding the impact of disturbances on the stability of soil microorganisms is important. This study reported the immediate effects of two-level thinning intensities on the soil microbial population, community composition and functions of a plantation forest over two years. Results showed that the thinning of Cryptomeria japonica forest significantly increased viable counts of soil bacteria from 7.7 × 106 to 1.4 × 107 or 1.6 × 107 in the 3rd month and the effect subsided in the 6th month post-thinning. The counts of actinobacteria, cellulolytic, nitrogen-fixing and phosphate-solubilizing bacteria groups maintained stable populations in the forest soils. Denaturing gradient gel electrophoresis profiles indicated that soil bacterial communities significantly differed among 25% thinning, 50% thinning and control treatment from the 12th to 18th month post-thinning, with no significant differences after 22 months. The community level physiological profiles were significantly different between control and thinning treatments in the 12th month post-thinning, the impacts of thinning then subsided by the 22nd month post-thinning as well. Soil bacteria were sensitive to thinning disturbances, but with resilience, their community and function approached to the control status in 2 years. This study demonstrates that the soil microbes of Taiwanese C. japonica forests are very sensitive to thinning disturbances, but recover stability after a relatively short period of time. [ABSTRACT FROM AUTHOR]

Sour cherry (Prunus cerasus L.) is one of the most important fruit crops in Poland and 'Łutówka' is the dominant cultivar in commercial orchards. The experiment was carried out in 2007–2013 in three orchards; in each of them, three levels of fertilization were applied: 0 N kg ha−1, 60 kg N ha−1, and 120 kg N ha−1. The activity of dehydrogenase and protease in the soil was studied depending on nitrogen fertilization. The abundance of soil microorganisms was assessed: bacteria, fungi, actinomycetes, and nitrogenous bacteria (Azospirillum and Azotobacter) in the years during the experiments carried out with fertilization of 60 kg N ha−1 in all orchards. The enzyme activity of dehydrogenases increased after the use of 60 kg N ha−1 from 3.8 to 6.7 (cm3 H2 24 h−1 kg−1 DW soil), but a further increase in the dose to 120 kg N ha−1 caused a decrease in activity to 5.1 (cm3 H2 24 h−1 kg−1 DW soil). The activity of proteases was dependent on nitrogen fertilization, but to a large extent it was related to the course of climatic conditions. There is no relationship between the growth and the activity of proteases. The yield and selected quality parameters of the cherry fruits were associated with both dehydrogenases and proteases. The use of lower doses of nitrogen fertilizers allows for maintaining biological balance in the soil and a more efficient use of nutrients, contributing to less environmental pollution. [ABSTRACT FROM AUTHOR]

Root-knot nematode, Meloidogyne incognita is one of the most important nematodes affecting ginger crop. Rhodopseudomonas palustris PSB-06, as effective microbial fertilizer in increasing plant growth and suppressing soil-borne disease of many crops has been reported. The combination of R. palustris PSB-06 and dazomet treatments had been proved to inhibit root-knot nematode on ginger and increase ginger yield in our preliminary study. The field experiments were conducted to elucidate the reasons behind this finding, and followed by next-generation sequencing to determine the microbial population structures in ginger root rhizosphere. The results showed that combination of R. palustris PSB-06 and dazomet treatment had a synergetic effect by achieving of 80.00% reduction in root-knot nematode numbers less than soil without treatment, and also could increase 37.37% of ginger yield through increasing the contents of chlorophyll and total protein in ginger leaves. Microbiota composition and alpha diversity varied with treatments and growth stages, soil bacterial diversity rapidly increased after planting ginger. In addition, the combined treatment could increase diversity and community composition of probiotic bacteria, and decrease those of soil-borne pathogenic fungi comparing to the soil treated with dazomet alone. Meanwhile, it could also effectively increase soil organic matter, available phosphorus and available potassium. Analysis of correlation between soil microorganisms and physicochemical properties indicated that the soil pH value and available phosphorus content were important factors that could affect soil microorganisms structure at the harvest stage. The bacterial family was more closely correlated with the soil physicochemical properties than the fungal family. Therefore, the combination of R. palustris PSB-06 and dazomet was considered as an effective method to control root-knot nematode disease and improve ginger soil conditions. [ABSTRACT FROM AUTHOR]

The big hole planting system for oil palm is one of the efforts to control the infection of Ganoderma boninense. The big hole method can also improve physical and chemical soil properties that affect the soil microbes population and in turn suppress the soil pathogens. However, the information about soil microbes population under the big hole planting method is still limited. This study aimed to compare the population of soil bacteria and fungi in soil samples from oil palm plantations that applied the big hole for 15 years and non big hole (standard) planting method. The population of bacteria and fungi was analyzed using the dilution plate method, while the calculation was based on the total plate count. Based on the results of statistical analysis (P-Value = 0.05), it is known that the mean population of bacteria is significantly different but the mean population of fungi is not significantly different between the big hole and non-big hole planting systems. The population of soil bacteria under the big hole and standard method was 1.6 x 106 cfu/g and 1.1 x 106 cfu/g, respectively. Meanwhile, the population of soil fungi under the big hole method was 9.7 x 104 cfu/g and 7.2 x 104 cfu/g under the standard planting method. Microorganisms in soil are considered important for maintaining soil health and quality, because various microorganisms are involved in important soil functions. In addition, high soil microbial populations will contribute to reducing soil base disease or suppression of soil pathogens. [ABSTRACT FROM AUTHOR]

Understanding mechanisms shaping distributions and interactions of soil microbes is essential for determining their impact on large scale ecosystem services, such as carbon sequestration, climate regulation, waste decomposition, and nutrient cycling. As the functional unit of soil ecosystems, we focus our attention on the spatial structure of soil macroaggregates. Emulating this complex physico-chemical environment as a patchy habitat landscape we investigate on-chip the effect of changing the connectivity features of this landscape as Escherichia coli forms a metapopulation. We analyze the distributions of E. coli occupancy using Taylor's law, an empirical law in ecology which asserts that the fluctuations in populations is a power law function of the mean. We provide experimental evidence that bacterial metapopulations in patchy habitat landscapes on microchips follow this law. Furthermore, we find that increased variance of patch-corridor connectivity leads to a qualitative transition in the fluctuation scaling. We discuss these results in the context of the spatial ecology of microbes in soil. [ABSTRACT FROM AUTHOR]

The flavor profile of tea is influenced not only by different tea varieties but also by the surrounding soil environment. Recent studies have indicated the regulatory role of soil microbes residing in plant roots in nutrient uptake and metabolism. However, the impact of this regulatory mechanism on tea quality remains unclear. In this study, we showed that a consortium of microbes isolated from tea roots enhanced ammonia uptake and facilitated the synthesis of theanine, a key determinant of tea taste. Variations were observed in the composition of microbial populations colonizing tea roots and the rhizosphere across different seasons and tea varieties. By comparing the root microorganisms of the high-theanine tea variety Rougui with the low-theanine variety Maoxie, we identified a specific group of microbes that potentially modulate nitrogen metabolism, subsequently influencing the theanine levels in tea. Furthermore, we constructed a synthetic microbial community (SynCom) mirroring the microbe population composition found in Rougui roots. Remarkably, applying SynCom resulted in a significant increase in the theanine content of tea plants and imparted greater tolerance to nitrogen deficiency in Arabidopsis. Our study provides compelling evidence supporting the use of root microorganisms as functional microbial fertilizers to enhance tea quality. [Display omitted] • Tea-plant root microbial populations vary across seasons and tea varieties • Nitrogen-metabolizing taxa are abundant in the roots of Rougui with high theanine • A synthetic community from Rougui roots, SynCom, was reconstituted • SynCom promotes NH 4 + homeostasis and theanine synthesis Xin et al. show that a synthetic microbial community mirroring the native microbial population found in Rougui tea-plant roots enhanced ammonia uptake and facilitated the synthesis of theanine, a key determinant of tea taste. [ABSTRACT FROM AUTHOR]

Purpose: This study was purposely designed to understand the effects of intercropping banana and sweet potato on soil microbial community. The research question addressed was what were the differences in population number, population diversity and dominant population of soil microorganisms between interplant bananas with sweet potatoes and banana monoculture. Methods: The Illumina MiSeq high-throughput sequencing technology was used to detect and analyse the population composition and structure of soil microorganisms in banana field. Results: The results showed that from May to September, the number of soil bacterial population in intercropping sweet potato was 5.54-28.67% higher than that in monoculture, and the richness and diversity of the population were significantly or extremely significantly higher than that in monoculture. The number of dominant bacterial population was less than that in monoculture, and the relative abundance of non dominant population was 10.58 - 58.81% higher than that in monoculture. The number, abundance and diversity of soil fungal populations in intercropping were higher than those in monoculture. Conclusions: The intercropping of banana and sweet potato has a significant effect on regulating the composition structure of soil microbial population and improving the abundance and diversity of microbial population. There has a great significance to improve the micro ecological environment of banana root soil and promote the stable and sustainable development of banana industry. [ABSTRACT FROM AUTHOR]

Soil burial processes create large pools of soil organic carbon that have been sequestered in the deep for long periods of time. This buried organic carbon is generally thought to be stable and resistant to decomposition, consisting of the remains of past plants and soil microbes. As a result, there is a lack of research on the role of microbiomes in the carbon transformation processes that may occur in the deep buried soil layers. In this study, we characterized the microbiomes and their metabolic potentials in organic soil layers buried following the volcanic eruption approximately 300 and 1,640 years ago, using bacterial and archaeal 16S rRNA gene sequencing. Both buried layers had comparable or even larger carbon and nitrogen contents and a microbial population as abundant and diverse as that of the surface layer. However, the organic soil layer buried 1,640 years ago showed a distinct microbiome from the surface layer, with a higher proportion of chemolithotrophic taxa, such as methanogens and NH 3 -oxidizing archaea. Additionally, this buried layer had a higher metabolic potential for fixing CO 2 and synthesizing organic matter, while the surface community had a higher potential for degrading organic matter. These findings suggest that the buried organic soil in the deep may not simply be an accumulation of past organisms, but rather an active carbon sink driven by a chemolithotrophic microbiome that differs from the organotrophic microbiome of the surface soil. • Volcanic eruptions buried surface soil, forming deep soil layers. • Buried soil layer has comparable/larger C, N and microbial population than surface soil. • Buried soil layer contains a high proportion of chemolithotrophs. • Buried soil layer could be a large active carbon sink. [ABSTRACT FROM AUTHOR]

Rhizoremediation is acknowledged as a green technology for removing polychlorinated biphenyls (PCBs) in soil. However, rhizoremediation is limited because most soil microorganisms enter into a viable but non-culturable (VBNC) state under PCBs stress. This work was to study the effect of resuscitation-promoting factor (Rpf) on rhizoremediation efficiency of PCBs in alfalfa and rhizosphere microbiological communities. Results suggested that Rpf promoted alfalfa growth in PCB-contaminated soil by improving antioxidant enzymes and detoxification metabolites in alfalfa. After 40 d Rpf treatment, removal rate for five selected PCBs significantly increased by 0.5–2.2 times. Rpf enhanced relative abundances of bphA and bphC responsible for degrading PCBs, and enzymatic activities of metabolizing exogenous compounds in rhizosphere soil. High-throughput sequencing showed that Rpf did not change the dominant microbial population at phyla and genera levels, but caused variation of the bacterial community structures. The promoting function of Rpf was linked to the shift of various key populations having different functions depending on Rpf concentrations. Pseudomonas and Rhizobium spp. enrichment might stimulate PCB degradation and Streptomyces and Bacillus spp. primarily contributed to alfalfa growth. Predicted functions in rhizosphere soil bacterial community indicated Rpf facilitated soil nutrient cycling and environmental adaptation. This study indicated that Rpf was an active additive for strengthening rhizoremediation efficiency of PCB-contaminated soil and enhancing their in-situ remediation. [Display omitted] • Rpf enhanced the efficiency of PCBs degradation in rhizosphere soil. • Rpf promoted alfalfa growth by increasing PGPB growth and plant metabolism. • Rpf modulated various beneficial microbial populations in rhizosphere soil. [ABSTRACT FROM AUTHOR]

The green development of agriculture, the rational use of pesticides, and soil health are closely related. However, our understanding of them is still limited. Pyraclostrobin (PYRA) is one of the most popular strobilurin fungicides due to its broad-spectrum control of fungal diseases. However, PYRA has been shown to have negative effects on bacterial communities and soil enzyme activities under laboratory conditions. The effects of PYRA on soil microbes (mainly bacteria) in actual field environments still need to be addressed. In the present study, after applying PYRA in a wheat/maize rotation field for 2 years, we determined the level of residual PYRA and assessed the soil bacterial community structure, soil enzyme activity, and ammonia-oxidizing functional gene expression. The results show that the DT 50 of PYRA in agricultural soil was 2.16–38.93 days. The final residual levels of PYRA in wheat/maize grain were less than 0.01 mg kg−1, which is lower than the maximum residue limit (MRL) recommended (0.2 mg kg−1) by China and the European Union. The culturable fungi and bacteria populations were significantly reduced after applying PYRA. The genera's abundance (Sphingomonas and Lysobacter) and urease activity associated with phosphorus cycle were inhibited. The amoA genes abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) showed that the N-cycle function of soil microbes was inhibited. Overall, applying PYRA for 2 years did not increase the negative response of soil microbes. However, in some indicators, such as culturable microorganism populations, more significant reductions in populations were observed in the double recommended dose group than in the recommended dose group. The results obtained in this study reflect the response of soil microbes subjected to pyraclostrobin in an actual field and provide new insights into how agricultural development influences soil health. [Display omitted] • Pyraclostrobin formulation was applied to a wheat/maize rotation field for 2 years. • Soil functions sustaining microbial life and cycling nutrients were negatively affected. • Negative effects of pyraclostrobin on soil fungi and bacteria were observed. • The genus abundance and urease activity associated with P cycle were inhibited. • Expression of functional genes associated with N cycle was downregulated. [ABSTRACT FROM AUTHOR]

Tea tree pruning, an essential agronomic practice for maintaining the plant's table height, leads to the gradual accumulation of allelochemicals and accompanying changes in the physicochemical and biological properties of tea garden soils. The accumulated allelochemicals coupled with disturbance in the soil properties including soil microbiota gradually lead to 'soil-sickness' impeding the establishment of newly-planted tea saplings (replanting) and tea crop productivity. Although pruning is an essential and regular practice in tea management, its effect on the soil properties and the microbial populations is less understood. We used a metagenomics approach to decipher and compare the microbial community structure and functional characteristics in tea soils under pruning and non-pruning practices. Principal component analysis indicated the metagenomes of the two sample plots to be unique with key microbial taxa and metabolic pathways. The plot with pruned crops had significantly lesser microbial abundances and richness, but it harbored a relatively higher proportion of biologically important soil bacteria such as Pseudomonas , Candidatus Solibacter , Rhodopseudomonas and Nitrobacter. This indicated that a specific population and its associated soil functions play a significant role in plant growth and survival under stress conditions. The metabolic functions related to microbial growth and reproduction were prevalent in both metagenomes as revealed through the Kyoto Encyclopedia of Genes and Genomes (KEGGs) and Cluster of Orthologous Groups (COGs) analyses. The pruned-plot-metagenome contained six metabolic pathways linked to different stress-responsive metabolisms (starch, arginine and proline, pyrimidine, ribosome, and peroxisome). Although long-term pruning in tea plantations can decrease the microbial abundance, richness, and functions in soil, plants under these stress conditions may selectively encourage the growth and colonization of functionally-important microorganisms to aid in their survivability. [Display omitted] • Pruning increases the accumulation of allelochemicals and inhibitory compounds in tea plantation soils • The inhibitory compounds influence the soil physicochemical properties and soil biological processes • Tea soils under pruning practice harbored lesser microbial abundance as compared to native tea plantation soils • Niche microbial population is important for the survival of tea plants under pruning practice • Tea plants under such abiotic stress encourage the growth and colonization of functionally-important microorganisms [ABSTRACT FROM AUTHOR]

Biochar is a promising novel material for mitigating phosphorus (P) loss and enhancing P retention in chemical-amended agricultural soils. However, the optimal application rate for aforesaid effectiveness and potential drivers of the process are not well understood. Herein, a column-based pot experiment was carried out to investigate how and to what extent reed-biochar is effective in positively triggering P loss and availability in paddy soils treated by chemical fertilizer. Compared with chemical-only treatment, the accumulated leakage of total P, dissoluble P, and particulate P in chemical fertilizer coupled with 1–4% reed-biochar treatment decreased by 5.3–13.3%, 8.3–10.4%, and 3.0–15.4%, respectively. The accumulated leakage of total P and dissoluble P in 6–8% rate treatments was increased by 5.6–7.5% and 18.3–32.9%, respectively. Increasing reed-biochar rate from 1% to 8% caused an enhancement in soil total P and available P content and P activation coefficient, and the 4% rate achieved a similar effectiveness to the higher rate. Reed-biochar application increased the abundance and diversty of soil phoD-harboring microbes (P < 0.05), while the increment had little to do with the application rate. Soil phoD-harboring community composition and total C content were the main predictors of the P leaching losses, and meanwhile, the total C content was the dominated predictor of soil P retention and availability. These results suggest that adding 1–4% reed-biochar was more beneficial to mitigate paddy P loss and to enhance soil P availability. This study highlights the importance of understanding how microbial populations mediate P transformation to decipher the biochar-driven improvement of soil P utilization. [Display omitted] • Phosphorus loss and retention of paddy soil were related to reed-biochar addition rate. • 1–4% application rate was more beneficial to reduce P loss and enhance P availability. • Biochar addition notably increased abundance and diversty of phoD-harboring microbes. • Soil phoD community composition and total C content were mian predictors of P leakage. • Soil total C content was a dominated predictor of soil P retention and availability. [ABSTRACT FROM AUTHOR]

This study assesses the effects of the herbicide oxyfluorfen on the activities of enzymes and on the populations of soil microorganisms by considering experiments on soil samples maintained in both laboratory and in field conditions. Furthermore, the molecular docking approach was used to evaluate the interactions of oxyfluorfen with enzymes found in soil. There was a dose dependent inhibitory effect of oxyfluorfen against the activities of dehydrogenase, phosphatase, protease and urease. The enzymes activities obtained for the soil samples maintained under field conditions usually reflected a different trend than those obtained under laboratory conditions, emphasizing the influence of the soil physicochemical properties. For soil samples maintained in field conditions and for the normal dose of oxyfluorfen, dehydrogenase activity recovered after 14 days and a minimum of 21 days was necessary for the recovery of phosphatase, urease and protease activity, respectively. The most important parameters of soil influencing the activities of enzymes and the populations of microorganisms were the pH, N-NO3 and N-NH4 contents. A dose dependent behavior of populations of microorganisms found in soil treated with oxyfluorfen has been shown. There was a slight grows of the colonies of microorganisms when oxyfluorfen was applied, but this growth decreased with increasing the oxyfluorfen concentration. [ABSTRACT FROM AUTHOR]