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Studies have shown that a diverse and metabolically active microbiota exists throughout different stages of coffee processing, from pre- to post-harvest. This microbiota originates from both the cultivation and processing environments. Additionally, microorganisms from the soil can be found on the fruit due to the transfer between them. This study reviews the microbiota present in Arabica coffee fruits and the soils where the plants are grown. It examines how microbial profiles are related to coffee variety, altitude, cultivation region, and processing method, and establishes a connection between the microbiota in soil and fruit. A diverse microbiota was observed in both coffee fruits and soils, with similar microorganisms identified across different growing regions, processing methods, and coffee varieties. However, exclusive detections of some microorganisms were also observed. These differences highlight the influence of terroir on coffee's microbial composition, confirming that environmental conditions, genetic factors, and processing methods shape coffee microbiota. Since microbial development during coffee fermentation can affect the beverage's quality, the data presented in this review offer valuable insights for researchers and producers. Understanding the influence of processing methods, coffee varieties, and cultivation regions on coffee microbiota enables the selection of specific fermentation conditions or starter cultures to enhance terroir characteristics or adjust microbial populations to favor or introduce microorganisms beneficial for coffee quality. [ABSTRACT FROM AUTHOR]

Introduction: Panax notoginseng, a medicinal herb in China, is attacked by several pathogens during its cultivation. Dazomet (DZ) is a soil fumigant that is effective in controlling soil-borne pathogens, but its long-term effects on P. notoginseng growth and soil properties are unknown. Methods: We conducted field experiments over two consecutive years to assess the impact of three concentrations of DZ fumigation (35 kg/666.7 m2, 40 kg/666.7 m2, and 45 kg/666.7 m2) on soil physicochemical properties, microbial diversity, and P. notoginseng growth. Correlation analyses were performed between microbial community changes and soil properties, and functional predictions for soil microorganisms were conducted. Results: DZ fumigation increased total nitrogen, total phosphorus, total potassium, available phosphorus, available potassium, and ammonia nitrogen levels in the soil. DZ fumigation promoted the nutrient accumulation and improvement of agronomic traits of P. notoginseng, resulted in a 2.83-3.81X yield increase, with the highest total saponin content increasing by 24.06%. And the 40 kg/666.7 m2 treatment had the most favorable impact on P. notoginseng growth and saponin accumulation. After DZ fumigation, there was a decrease in the relative abundance of pathogenic fungi such as Fusarium, Plectosphaerella, and Ilyonectria, while beneficial bacteria such as Ramlibacter, Burkholderia, and Rhodanobacteria increased. The effects of fumigation on soil microorganisms and soil physicochemical properties persisted for 18 months post-fumigation. DZ fumigation enhanced the relative abundance of bacteria involved in the biosynthesis of secondary metabolites and arbuscular mycorrhizal fungi, reduced the relative abundance of plant-animal pathogenic fungi, reduced the occurrence of soil-borne diseases. Conclusion: In conclusion, DZ fumigation enhanced soil physicochemical properties, increased the proportion of beneficial bacteria in the soil, and rebalanced soil microorganism populations, consequently improving the growth environment of P. notoginseng and enhancing its growth, yield, and quality. This study offers a theoretical foundation for DZ fumigation as a potential solution to the continuous cropping issue in perennial medicinal plants such as P. notoginseng. [ABSTRACT FROM AUTHOR]

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]

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]

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]

• Repeated metalaxyl persistence and effects on soil microbes were assessed in field. • Metalaxyl degradation was independent of increasing application frequency and dose. • Variations of cultivable microbial populations were related to application frequency. • Repeated applications of metalaxyl influenced the structure of bacterial communities. Metalaxyl, a chiral fungicide, was widely used to control mold fungi and oomycetes in many plants. However, studies are insufficient on the effects of successive metalaxyl applications on soil microorganisms and the residue dynamics. In the present study, metalaxyl was applied in field at two different doses (the recommended field rate, and twice of the recommended field rate) for 2 and 3 times, respectively. The soil samples were collected on days 0, 1, 3, 7, 14, 28 and 45 after the second and third treatment to determine the residue dynamics and were collected on days 7, 14, 28 and 56 to assess the effects of successive metalaxyl application on soil cultivable microbial populations and microbial community structure. The results revealed the degradation rate slightly accelerated with the increasing applied times of metalaxyl. The second application of metalaxyl increased soil bacteria populations, inhibited soil fungi, and had a transient stimulated effect on actinomycetes. No distinct differences were observed in soil bacterial, actinomycic and fungal populations except for fungi population on day 14 after the third treatment. The analysis of terminal restriction fragment length polymorphism (T-RFLP) and denaturing gradient gel electrophoresis (DGGE) revealed soil microbial community structure could be affected by metalaxyl at all experimental doses. These obtained results could provide basic data for evaluating the ecological toxicity of metalaxyl. [ABSTRACT FROM AUTHOR]

Sensitive models of climate change impacts would require a better integration of multi-omics approaches that connect the abundance and activity of microbial populations. Here, we show that climate is a fundamental driver of the protein abundance of Actinobacteria, Planctomycetes and Proteobacteria, supporting the hypothesis that metabolic activity of some dominant phyla may be closely linked to climate. These results may improve our capacity to construct microbial models that better predict the impact of climate change in ecosystem processes. [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]

To gain a better understanding of the biological effect on the water-gas-carbonate interaction, 15 sample plots from five ecotypes (grass land, ecological demonstration, artificial forest, tree-shrub, and forest community) in three experimental sites of SW China due to the absence of time-series succession ecotypes at the same karst site were selected to discuss the relationship between soil microbial populations, carbonic anhydrase (CA) and limestone dissolution rate. The results show that the soil microbial populations and soil CA activities within different ecotypes have the significantly positive correlation ( r = 0.968), which vary significantly and tend to decrease along the ecological succession process. In view of moist character and water-holding capacity in the evergreen forest, which can fleetly participate in water-gas-carbonate interaction, the limestone dissolution rate is not matching to the total microbial population and CA activity in forest community. If the ecotype for forest community was removed, the correlative coefficient between CA and the limestone dissolution rate is 0.950, the correlative coefficient between CA and total microbial population is 0.999 and the correlative coefficient between limestone dissolution rate and total microbial population is 0.952. It can be inferred that soil CA secreted by the soil microorganisms has the important role to promote the production of bicarbonate ions which affects limestone dissolution rate. [ABSTRACT FROM AUTHOR]

Endosulfan, an organochlorine pesticide, has been applied ubiquitously worldwide. However, endosulfan has been identified as a type of persistent organic pollutants (POPs), and its ecotoxicity has drawn attentions from scientists. The present study was implemented to examine the effects of endosulfan on the diversity and structure of soil microorganism communities. A control treatment and three concentrations (0.1, 1.0, and 10.0 mg/kg) were set up in laboratory experiments and sampled on days 7, 14, 21, and 28. The results revealed that the populations of bacteria and actinomycetes decreased significantly after 1.0 and 10.0 mg/kg treatments and that the soil microbial biomass carbon (MBC) was increased by endosulfan compared with the control. Terminal restriction fragment length polymorphism (T-RFLP) results revealed that the soil bacterial diversity was decreased by endosulfan and that the soil microbial community structure became unstable after endosulfan application. Moreover, the results of a 16S rRNA clone library revealed that the phyla Proteobacteria, Actinobacteria, Bacteroidetes, Spirochaetes, and Firmicutes showed an obvious advantage and closely relative. In conclusion, the results of the present study indicated that 0.1-10.0 mg/kg endosulfan showed obvious influences on the diversity and structure of the soil microbial community. [ABSTRACT FROM AUTHOR]

Aim To explore large-scale patterns and the drivers of carbon:nitrogen:phosphorus (C:N:P) stoichiometry in heterotrophic microbes. Location A 3500-km grassland transect on the Tibetan Plateau. Methods We investigated large-scale C:N:P stoichiometry patterns in the soil microbial biomass and their relationships with abiotic factors and soil microbial community structures by obtaining soil samples from 173 sites across the Tibetan alpine grasslands. Results C:N:P ratios in the soil microbial biomass varied widely among grassland types, with higher microbial C:N, C:P and N:P ratios in the alpine steppe than the alpine meadow. The soil microbial C:N:P ratio (81:6:1) in the alpine steppe was significantly wider than the global average (42:6:1). Combined stepwise regression and generalized additive models revealed that variations in the microbial C:N ratio were primarily related to abiotic variables, with the microbial C:N ratio exhibiting a decreasing trend along the precipitation gradient. In contrast, variations in microbial C:P and N:P ratios were primarily associated with shifts in the community structure of soil microbes. The microbial C:P and N:P ratios were both negatively associated with all components of the soil microbial communities. However, the fungi to bacteria ratio only regulated the microbial C:P ratio. Main conclusions These results demonstrate that microbial C:N:P stoichiometry exhibits significant flexibility across various ecosystem types. This flexibility is partly induced by shifts in microbial community structure and variations in environmental conditions. [ABSTRACT FROM AUTHOR]

Tillage practices are critical for sustaining soil quality necessary for successful crop growth and productivity. A three-year study (2012–2014) was carried out to evaluate the influence of strip and conventional tillage practices and three water status levels [T1 = 100% of evapotranspiration (ET) demands, T2 = 0.75T1and T3 = 0.5T1] on plant morphology, physiology, yield and quality of triploid (seedless) watermelon ( Citrullus lanatus cv. Magestic). Soil chemical and biological properties were also assessed at the end of the experimental study. Tillage practices (strip or ST and conventional or CT) started in 2009 and are being carried out to the present date of 2016. Irrigation was established using a center pivot system. Photosynthesis rate ( Pn ), stomatal conductance ( gs ), and chlorophyll content index (SPAD) were measured at flowering, fruit development and harvest stage and vine length measured at the harvest stage. Total marketable yield and fruit quality (firmness and sugar content) were determined during the harvest period. Soil chemical and microbial analysis were conducted at the end of the experimental period (March 2015). No significant differences ( P = 0.05) were found between water deficit treatments in vine length, SPAD, Pn , gs , fruit firmness, and sugar content during the three-year study, except for vine length in 2013. But, marketable yield from T1 treatment was significantly higher ( P = 0.03) than T3 in 2013. Vine length and SPAD measured from the ST plots were higher than CT, especially in 2012. Interestingly, marketable yield from ST was 8.6, 9.7 and 14.9 t ha −1 higher than CT in 2012, 2013 and 2014, respectively. Additionally, fruit sugar content under ST was statistically higher ( P = 0.05) than those from CT. After 6 years of tillage practices (2009–2015) in the same site, ST increased total bacteria by 49%, active bacteria by 27%, active and total fungi by 37%, nematodes by 275%, and electrical conductivity by 14% compared to CT. However, ST significantly increased root-feeding nematodes (harmful to plant roots) and reduced phosphorus and nitrate-N compared to CT. Although long-term studies aimed at assessing soil quality and cumulative yield are required to further validate our results, yield and fruit quality (sugar content) responses were consistent across three years and with promising abundance of soil microbial activities. [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]

Landfills are always the most important part of solid waste management and bear diverse metabolic activities involved in element biogeochemical cycling. There is an increasing interest in understanding the microbial community and activities in landfill cover soils. To improve our knowledge of landfill ecosystems, we determined the microbial physiological profiles and communities in three landfill cover soils (Ninghai: NH, Xiangshan: XS, and Fenghua: FH) of different ages using the MicroResp, phospholipid fatty acid (PLFA), and high-throughput sequencing techniques. Both total PLFAs and glucose-induced respiration suggested more active microorganisms occurred in intermediate cover soils. Microorganisms in all landfill cover soils favored l-malic acid, ketoglutarate, and citric acid. Gram-negative bacterial PLFAs predominated in all samples with the representation of 16:1ω7, 18:1ω7, and cy19:0 in XS and NH sites. Proteobacteria dominated soil microbial phyla across different sites, soil layers, and season samples. Canonical correspondence analysis showed soil pH, dissolved organic C (DOC), As, and total nitrogen (TN) contents significantly influenced the microbial community but TN affected the microbial physiological activities in both summer and winter landfill cover soils. [ABSTRACT FROM AUTHOR]

Many studies have investigated whether microbiota has been adapted to decompose a given litter type but we have limited information about the specific role of microarthropods in litter decaying processes. This experiment studied functional redundancy of microarthropods in a litter decomposition system by interchanging mesofauna among three different litter types. The study hypothesized that total microarthropod densities would be lower in foreign litter type than in original (‘home’) litter; and litter with foreign mesofauna would decompose slower than with native one. Scotch pine ( Pinus sylvestris ), Turkey oak ( Quercus cerris ) and black locust ( Robinia pseudoacacia ) litter were stored in microcosms with original microbiota. Microarthropods from the same (‘home’) or different (‘foreign’) type of litter were inoculated to microcosms. Litter mass loss and total density of collembolans, oribatid and other mites were recorded at the end of incubation (3 and 12 months). Litter quality determined total density of microarthropods irrespective of the origin of animals. Litter mass loss values differed in the three litter types. For pine litter, the origin of microarthropods had significant effects on litter mass loss. In oak litter, mainly microarthropod density influenced decomposition. Neither the origin nor the density of animals influenced the decomposition rate of black locust litter. Litter quality may have determined the different patterns of decaying. Mesofauna may enhance litter decomposition stronger in recalcitrant litter than in high-quality litter. [ABSTRACT FROM AUTHOR]

Soil microbial communities are sensitive to carbon amendments and largely control the decomposition and accumulation of soil organic matter. In this study, we evaluated whether the type of carbon amendment applied to wheat-cropped or fallow soil imparted lasting effects on the microbial community with detectable differences in activity, population size, or community structure after a period of seven years post-amendment. The microbial communities from the top 10 cm of soil were analyzed for activity related to C-cycling (glucosidase, galactosidase), P-cycling (acid phosphatase), S-cycling (arylsulfatase), and N-cycling (β-glucosaminidase, arylamidase), in addition to fungal and bacterial abundance and structure. The amendments were applied at similar carbon rates for five years under annual wheat or continuous fallow and included cotton linters, sucrose, wheat residue, composted wheat residue, brassica residue, wood sawdust, alfalfa feed pellets, manure, biosolid and a no treatment control. Two crops, brassica and grass, were in the fallow treatments. The majority of the communities in the amended soils were not distinguishable from the no-treatment control. For amendments and crops that produced changes, significant differences in the population size and community structure were observable for fungi but not bacteria. Wood, sugar, and grass cropping produced the most pronounced effects on enzyme activity, fungal abundance and structure. Overall, the species of the planted crop had a significant effect on the soil enzyme activity and population size of fungi, with the greatest values under grass compared to wheat or brassica. The microbial communities were differentially affected by C source amendments in which the persistency of change and the aspect of the community affected (i.e. function, size, structure, kingdom) were dependent on amendment type. [ABSTRACT FROM AUTHOR]

Recent developments in modelling soil organic carbon decomposition include the explicit incorporation of enzyme and microbial dynamics. A characteristic of these models is a positive feedback between substrate and consumers, which is absent in traditional first-order decay models. With sufficiently large substrate, this feedback allows an unconstrained growth of microbial biomass. We explore mechanisms that curb unrestricted microbial growth by including finite potential sites where enzymes can bind and by allowing microbial scavenging for enzymes. We further developed a model where enzyme synthesis is not scaled to microbial biomass but associated with a respiratory cost and microbial population adjusts enzyme production in order to optimise their growth. We then tested short- and long-term responses of these models to a step increase in temperature and find that these models differ in the long-term when shortterm responses are harmonised. We show that several mechanisms, including substrate limitation, variable production of microbial enzymes, and microbes feeding on extracellular enzymes eliminate oscillations arising from a positive feedback between microbial biomass and depolymerisation. The model where enzyme production is optimised to yield maximum microbial growth shows the strongest reduction in soil organic carbon in response to warming, and the trajectory of soil carbon largely follows that of a first-order decomposition model. Modifications to separate growth and maintenance respiration generally yield short-term differences, but results converge over time because microbial biomass approaches a quasi-equilibrium with the new conditions of carbon supply and temperature. [ABSTRACT FROM AUTHOR]

Although reductive soil disinfestation (RSD) is increasingly used for the control of soil-borne diseases, its impact on the soil microbial community during and after RSD remains poorly understood. MiSeq pyrosequencing, real-time PCR and denaturing gradient gel electrophoresis were performed to investigate the changes of microbial community in the Fusarium oxysporum f. sp. cubense (FOC) infected soil during RSD and at the simulative banana cultivation after RSD. The results showed that RSD significantly increased soil microbial populations and a different microbial community with the pathogenic soil was established after RSD. Specifically, the number of Firmicutes mainly containing Ruminococcus and Coprococcus followed by a small part of Clostridium which were the dominant bacterial genera significantly increased during RSD. In contrast, Symbiobacterium and Flavisolibacter were the dominant genera in the flooding soil. When the soils were recovered under aerobic condition, the relative abundances of the bacteria belonging to the phylum Bacteroidetes , Acidobacteria , Planctomycetes increased as alternatives to the reducing Firmicutes . For fungi, the population of F. oxysporum significantly decreased during RSD accompanied with the pH decline, which resulted in the significant decrease of relative abundance in the phylum Ascomycota . Alternatively, the relative abundances of some other fungal species increased, such as Chaetomium spp. and Penicillium spp. belonging to Ascomycota and the family Clavulinaceae belonging to Basidiomycota . Then, the relative abundance of Ascomycota re-increased after RSD with Podospora and Zopfiella as dominant genera, whereas the relative abundance of Fusarium further decreased. Overall, the microbial populations and community re-established by RSD made the soil more disease-suppressive and beneficial to the soil nutrient cycling and plant growth compared with the previous pathogenic soil. [ABSTRACT FROM AUTHOR]

Forest floor mineral soil mix (FMM) and peat mineral soil mix (PMM) are cover soils commonly used for upland reclamation post open-pit oil sands mining in northern Alberta, Canada. Coarse woody debris (CWD) can be used to regulate soil temperature and water content, to increase organic matter content, and to create microsites for the establishment of microorganisms and vegetation in upland reclamation. We studied the effects of CWD on soil microbial community level physiological profile (CLPP) and soil enzyme activities in FMM and PMM in a reclaimed landscape in the oil sands. This experiment was conducted with a 2 (FMM vs PMM) × 2 (near CWD vs away from CWD) factorial design with 6 replications. The study plots were established with Populus tremuloides (trembling aspen) CWD placed on each plot between November 2007 and February 2008. Soil samples were collected within 5 cm from CWD and more than 100 cm away from CWD in July, August and September 2013 and 2014. Microbial biomass was greater (p<0.05) in FMM than in PMM, in July, and August 2013 and July 2014, and greater (p<0.05) near CWD than away from CWD in FMM in July and August samplings. Soil microbial CLPP differed between FMM and PMM (p<0.01) according to a principal component analysis and CWD changed microbial CLPP in FMM (p<0.05) but not in PMM. Coarse woody debris increased microbial community functional diversity (average well color development in Biolog Ecoplates) in both cover soils (p<0.05) in August and September 2014. Carbon degrading soil enzyme activities were greater in FMM than in PMM (p<0.05) regardless of distance from CWD but were not affected by CWD. Greater microbial biomass and enzyme activities in FMM than in PMM will increase organic matter decomposition and nutrient cycling, improving plant growth. Enhanced microbial community functional diversity by CWD application in upland reclamation has implications for accelerating upland reclamation after oil sands mining. [ABSTRACT FROM AUTHOR]

Livestock grazing is a global land-use activity with multiple social, cultural, and environmental impacts. However, it is expected to decrease progressively in the Cantabrian Mountain areas as notable changes in livestock management systems have been observed, such as shorter stay in mountain, lower stocking rates, and less shepherd control. This study aimed to evaluate the effect of grazing abandonment on microbial function and diversity through changes promoted in aboveground vegetation and soil properties. In 2005, we erected permanent fences around two 50 × 50-m plots (excluded plots) in a temperate mountain grassland that has historically supported livestock managed by an extensive grazing system. A grazed plot was defined around each excluded plot. After 5 years, grazing abandonment induced shifts in floristic composition, decreased soil compaction at 0–10 cm soil depth, and reduced soil temperature in the summer due to a thicker plant layer. Consequently, microorganisms reduced soil enzymatic activity and microbial biomass, and increased CO 2 emissions and metabolic quotient, which indicated a lower metabolic efficiency of soil processes in excluded plots. These results suggest that soil microbial community function was very sensitive to the impacts of livestock grazing exclusion. The bacterial community was more diverse compared to the fungal community, but no significant difference in bacterial species richness was found between excluded and grazed plots. Microbial genetic diversity was not directly correlated with aboveground vegetation diversity and no clear pattern emerged as a response to grazing abandonment, probably because soil microbial diversity depends on site attributes that operate at a very fine spatial scale. [ABSTRACT FROM AUTHOR]

Oxygen is considered as a limiting factor for nitrification in rice paddy soil. However, little is known about how the nitrifying microbial community responds to different oxygen concentrations at community and transcript level. In this study, soil and roots were harvested from 50-day-old rice microcosms and were incubated for up to 45 days under two oxygen concentrations: 2 % O and 20 % O (ambient air). Nitrification rates were measured from the accumulation of nitrite plus nitrate. The population dynamics of bacterial (AOB) and archaeal (AOA) ammonia oxidizers was determined from the abundance (using quantitative PCR (qPCR)) and composition (using terminal restriction fragment length polymorphism and cloning/sequencing) of their amoA genes, that of nitrite oxidizers (NOB) by quantifying the nxrA gene of Nitrobacter spp. and the 16S rRNA gene of Nitrospira spp. The activity of the nitrifiers was determined by quantifying the copy numbers of amoA and nxrA transcripts (using RT-qPCR). Different oxygen concentrations did not affect the community compositions of AOB, AOA, and NOB, which however were different between surface soil, bottom soil, and rice roots. However, nitrification rates were higher under ambient air than 2 % O, and abundance and transcript activities of AOB, but not of AOA, were also higher. Abundance and transcript copy numbers of Nitrobacter were also higher at ambient air. These results indicate that AOB and NOB, but not AOA, were sensitive to oxygen availability. [ABSTRACT FROM AUTHOR]

Dimethylsulphide (DMS) has an important role in the global sulphur cycle and atmospheric chemistry. Microorganisms using DMS as sole carbon, sulphur or energy source, contribute to the cycling of DMS in a wide variety of ecosystems. The diversity of microbial populations degrading DMS in terrestrial environments is poorly understood. Based on cultivation studies, a wide range of bacteria isolated from terrestrial ecosystems were shown to be able to degrade DMS, yet it remains unknown whether any of these have important roles in situ. In this study, we identified bacteria using DMS as a carbon and energy source in terrestrial environments, an agricultural soil and a lake sediment, by DNA stable isotope probing (SIP). Microbial communities involved in DMS degradation were analysed by denaturing gradient gel electrophoresis, high-throughput sequencing of SIP gradient fractions and metagenomic sequencing of phi29-amplified community DNA. Labelling patterns of time course SIP experiments identified members of the Methylophilaceae family, not previously implicated in DMS degradation, as dominant DMS-degrading populations in soil and lake sediment. Thiobacillus spp. were also detected in 13C-DNA from SIP incubations. Metagenomic sequencing also suggested involvement of Methylophilaceae in DMS degradation and further indicated shifts in the functional profile of the DMS-assimilating communities in line with methylotrophy and oxidation of inorganic sulphur compounds. Overall, these data suggest that unlike in the marine environment where gammaproteobacterial populations were identified by SIP as DMS degraders, betaproteobacterial Methylophilaceae may have a key role in DMS cycling in terrestrial environments. [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]

Soil from Trhové Dušníky (Příbram, Czech Republic) is characterized by its high polymetallic accumulations in Pb–Ag–Zn due to mining and smelting activities. In previous studies performed in our research group, we have evaluated the potential use of amendments that would reduce the mobility and availability of metals such as Hg. We have observed that the application of digestate and fly ash in metal-polluted soil has an impact in immobilizing these metals. However, until now we have lacked information about the effect of these amendments on soil microbial functionality and communities. The multi-contaminated soil was used to grow wheat in a pot experiment to evaluate the impact of digestate and fly ash application in soil microbial communities. Soil samples were collected after 30 and 60 days of treatment. The digestate application improved chemical attributes such as the content in total organic carbon (TOC), water soluble carbon (WSOC), total soluble carbon (C), total soluble nitrogen (N), and inorganic N forms ( NO 3 − ) as consequence of high content in C and N which is contained in digestate. Likewise, microbial activity was greatly enhanced by digestate application, as was physiological diversity. Bacterial and fungal communities were increased, and the microbial biomass was highly enhanced. These effects were evident after 30 and 60 days of treatment. In contrast, fly ash did not have a remarkable effect when compared to digestate, but soil microbial biomass was positively affected as a consequence of macro- and micro-nutrient sources applied by the addition of fly ash. This study indicates that digestate can be used successfully in the remediation of metal-contaminated soil. [ABSTRACT FROM AUTHOR]

Nitrogen (N) and phosphorus (P) additions to forest ecosystems are known to influence various above-ground properties, such as plant productivity and composition, and below-ground properties, such as soil nutrient cycling. However, our understanding of how soil microbial communities and their functions respond to nutrient additions in subtropical plantations is still not complete. In this study, we added N and P to Chinese fir plantations in subtropical China to examine how nutrient additions influenced soil microbial community composition and enzyme activities. The results showed that most soil microbial properties were responsive to N and/or P additions, but responses often varied depending on the nutrient added and the quantity added. For instance, there were more than 30% greater increases in the activities of β-glucosidase (βG) and N-acetyl-β-D-glucosaminidase (NAG) in the treatments that received nutrient additions compared to the control plot, whereas acid phosphatase (aP) activity was always higher (57 and 71%, respectively) in the P treatment. N and P additions greatly enhanced the phospholipid fatty acids (PLFAs) abundance especially in the N2P (100 kg ha-1 yr-1 of N C50 kg ha-1 yr-1 of P) treatment; the bacterial PLFAs (bacPLFAs), fungal PLFAs (funPLFAs) and actinomycic PLFAs (actPLFAs) were about 2.5, 3 and 4 times higher, respectively, than in the CK (control). Soil enzyme activities were noticeably higher in November than in July, mainly due to seasonal differences in soil moisture content (SMC). βG or NAG activities were significantly and positively correlated with microbial PLFAs. These findings indicate that βG and NAG would be useful tools for assessing the biogeochemical transformation and metabolic activity of soil microbes. We recommend combined additions of N and P fertilizer to promote soil fertility and microbial activity in this kind of plantation. [ABSTRACT FROM AUTHOR]

Salt stress has been increasingly constraining crop productivity in arid and semiarid lands of the world. In a previous study, salt stress was alleviated and maize productivity improved remarkably with soil amendment with biochar poultry-manure compost (BPC) in conjunction with pyroligneous solution (PS) in a saline soil from Central China Plain. In 2010, before maize sowing, BPC was incorporated into topsoil at 12 t ha −1 following surface spray of diluted PS solution at 0.15 t ha −1 one week in advance (BPC-PS2). Such an experiment was repeated in adjacent fields in 2011 (BPC-PS1). Both bulk and rhizosphere samples of these experiment plots were collected at the vegetative growth stage of maize in 2012. Microbial biomass carbon (C mic ) and nitrogen (N mic ), and soil enzyme activity were measured. Based on 16S rRNA and 18S rRNA gene, bacterial and fungal community structure and abundance were respectively characterized using denaturing gradient gel electrophoresis (DGGE) and quantitative real-time PCR (qPCR). With the amendment, C mic and N mic , and bacterial gene abundance were significantly and greatly increased in both bulk and rhizosphere samples, being greater under BPC-PS2 than under BPC-PS1. On contrast, smaller increase in fungal gene abundance was observed, along with a significant reduction in fungal diversity under BPC-PS2. In addition, two single bands belonging respectively to Alphaproteobacteria and Deltaproteobacteria emerged in the amended soil. Meanwhile, activities of urease, invertase and phosphatase in both bulk soils and rhizosphere soils were increased by 19–44% with the amendment except of urease in rhizosphere soils. Therefore, with the great enhancement of microbial growth and enzyme activities, combined use of biochar and poultry manure with pyroligneous solution could be a practical option to alleviate salt stresses on plant and soil microbial community in order to improve crop production in saline soils. [ABSTRACT FROM AUTHOR]

Soil microorganisms are critical to ecosystem functioning and the maintenance of soil fertility. However, despite global increases in the inputs of nitrogen (N) and phosphorus (P) to ecosystems due to human activities, we lack a predictive understanding of how microbial communities respond to elevated nutrient inputs across environmental gradients. Here we used high-throughput sequencing of marker genes to elucidate the responses of soil fungal, archaeal, and bacterial communities using an N and P addition experiment replicated at 25 globally distributed grassland sites. We also sequenced metagenomes from a subset of the sites to determine how the functional attributes of bacterial communities change in response to elevated nutrients. Despite strong compositional differences across sites, microbial communities shifted in a consistent manner with N or P additions, and the magnitude of these shifts was related to the magnitude of plant community responses to nutrient inputs. Mycorrhizal fungi and methanogenic archaea decreased in relative abundance with nutrient additions, as did the relative abundances of oligotrophic bacterial taxa. The metagenomic data provided additional evidence for this shift in bacterial life history strategies because nutrient additions decreased the average genome sizes of the bacterial community members and elicited changes in the relative abundances of representative functional genes. Our results suggest that elevated N and P inputs lead to predictable shifts in the taxonomic and functional traits of soil microbial communities, including increases in the relative abundances of fastergrowing, copiotrophic bacterial taxa, with these shifts likely to impact belowground ecosystems worldwide. [ABSTRACT FROM AUTHOR]

We tested a method of estimating the activity of detectable individual bacterial and archaeal OTUs within a community by calculating ratios of absolute 16S rRNA to rDNA copy numbers. We investigated phylogenetically coherent patterns of activity among soil prokaryotes in non-growing soil communities. ‘Activity ratios’ were calculated for bacteria and archaea in soil sampled from a tropical rainforest and temperate agricultural field and incubated for one year at two levels of moisture availability and with and without carbon additions. Prior to calculating activity ratios, we corrected the relative abundances of OTUs to account for multiple copies of the 16S gene per genome. Although necessary to ensure accurate activity ratios, this correction did not change our interpretation of differences in microbial community composition across treatments. Activity ratios in this study were lower than those previously published (0.0003–210, logarithmic mean = 0.24), suggesting significant extracellular DNA preservation. After controlling for the influence of individual incubation jars, significant differences in activity ratios between all members of each phylum were observed. Planctomycetes and Firmicutes had the highest activity ratios and Crenarchaeota had the lowest activity overall. Our results suggest that greater caution should be taken in interpreting soil microbial community data derived from extracted DNA. Indirect extraction methods may be useful in ensuring that microbes identified from extracellular DNA are not erroneously interpreted as components of an active microbial community. [ABSTRACT FROM AUTHOR]

This study investigated how microbial community structure and diversity varied with depth and topography in ice wedge polygons of wet tundra of the Arctic Coastal Plain in northern Alaska and what soil variables explain these patterns. We observed strong changes in community structure and diversity with depth, and more subtle changes between areas of high and low topography, with the largest differences apparent near the soil surface. These patterns are most strongly correlated with redox gradients (measured using the ratio of reduced Fe to total Fe in acid extracts as a proxy): conditions grew more reducing with depth and were most oxidized in shallow regions of polygon rims. Organic matter and pH also changed with depth and topography but were less effective predictors of the microbial community structure and relative abundance of specific taxa. Of all other measured variables, lactic acid concentration was the best, in combination with redox, for describing the microbial community. We conclude that redox conditions are the dominant force in shaping microbial communities in this landscape. Oxygen and other electron acceptors allowed for the greatest diversity of microbes: at depth the community was reduced to a simpler core of anaerobes, dominated by fermenters ( Bacteroidetes and Firmicutes). [ABSTRACT FROM AUTHOR]

X-ray Microfocused Computed Tomography (X-ray µ-CT) allows a non-destructive and three-dimensional observation of microbial habitats (i.e. pore space) in soil. A major premise for microbiological studies integrating X-ray µ-CT is that soil microorganisms are not affected by irradiation dose in terms of physiology and composition. However, the compatibility of X-ray µ-CT and soil biological experiments has been evaluated controversially. We performed an incubation experiment with packed microcosms to assess the effect of X-ray µ-CT on native microbial populations with emphasis on soil archaea and bacteria. Before (14 days) and after (1 and 14 days) scanning we analyzed (i) respiration, (ii) enzyme activity, (iii) microbial biomass, (iv) abundance and (v) community structure in scanned and control treatments. None of the microbial parameters exhibited significant differences among scanned and unscanned soil samples at all sampling times with the exception of lower archaeal cell numbers subsequent to X-ray µ-CT. Incubation time was the main factor that induced a significant alteration of microbial soil populations while irradiation had no or only very little effect thereupon. Taken together, three-dimensional in situ data obtained via X-ray µ-CT may well be combined with microbiological analyses in soil. [ABSTRACT FROM AUTHOR]

An original integral structural-functional method has been proposed for characterizing microbial communities. The novelty of the approach is the in situ study of microorganisms based on the growth kinetics of microbial associations in liquid nutrient broth media under selective conditions rather than on the level of taxa or large functional groups. The method involves the analysis of the integral growth model of a periodic culture. The kinetic parameters of such associations reflect their capacity of growing on different media, i.e., their physiological diversity, and the metabolic capacity of the microorganisms for growth on a nutrient medium. Therefore, the obtained parameters are determined by the features of the microbial ecological strategies. The inoculation of a dense medium from the original inoculate allows characterizing the taxonomic composition of the dominants in the soil community. The inoculation from the associations developed on selective media characterizes the composition of syntrophic groups, which fulfill a specific function in nature. This method is of greater information value than the classical methods of inoculation on selective media. [ABSTRACT FROM AUTHOR]

Spatial patterns of microbial communities have been extensively surveyed in well-developed soils, but few studies investigated the vertical distribution of micro-organisms in newly developed soils after glacier retreat. We used 454-pyrosequencing to assess whether bacterial and fungal community structures differed between stages of soil development ( SSD) characterized by an increasing vegetation cover from barren (vegetation cover: 0%/age: 10 years), sparsely vegetated (13%/60 years), transient (60%/80 years) to vegetated (95%/110 years) and depths (surface, 5 and 20 cm) along the Damma glacier forefield (Switzerland). The SSD significantly influenced the bacterial and fungal communities. Based on indicator species analyses, metabolically versatile bacteria (e.g. Geobacter) and psychrophilic yeasts (e.g. Mrakia) characterized the barren soils. Vegetated soils with higher C, N and root biomass consisted of bacteria able to degrade complex organic compounds (e.g. Candidatus Solibacter), lignocellulolytic Ascomycota (e.g. Geoglossum) and ectomycorrhizal Basidiomycota (e.g. Laccaria). Soil depth only influenced bacterial and fungal communities in barren and sparsely vegetated soils. These changes were partly due to more silt and higher soil moisture in the surface. In both soil ages, the surface was characterized by OTUs affiliated to Phormidium and Sphingobacteriales. In lower depths, however, bacterial and fungal communities differed between SSD. Lower depths of sparsely vegetated soils consisted of OTUs affiliated to Acidobacteria and Geoglossum, whereas depths of barren soils were characterized by OTUs related to Gemmatimonadetes. Overall, plant establishment drives the soil microbiota along the successional gradient but does not influence the vertical distribution of microbiota in recently deglaciated soils. [ABSTRACT FROM AUTHOR]

Effects of extremely high carbon dioxide (CO2) concentrations on soil microbial communities and associated processes are largely unknown. We studied a wetland area affected by spots of subcrustal CO2 degassing (mofettes) with focus on anaerobic autotrophic methanogenesis and acetogenesis because the pore gas phase was largely hypoxic. Compared with a reference soil, the mofette was more acidic (ΔpH ∼0.8), strongly enriched in organic carbon (up to 10 times), and exhibited lower prokaryotic diversity. It was dominated by methanogens and subdivision 1 Acidobacteria, which likely thrived under stable hypoxia and acidic pH. Anoxic incubations revealed enhanced formation of acetate and methane (CH4) from hydrogen (H2) and CO2 consistent with elevated CH4 and acetate levels in the mofette soil. 13CO2 mofette soil incubations showed high label incorporations with ∼512 ng 13C g (dry weight (dw)) soil−1 d−1 into the bulk soil and up to 10.7 ng 13C g (dw) soil−1 d−1 into almost all analyzed bacterial lipids. Incorporation of CO2-derived carbon into archaeal lipids was much lower and restricted to the first 10 cm of the soil. DNA-SIP analysis revealed that acidophilic methanogens affiliated with Methanoregulaceae and hitherto unknown acetogens appeared to be involved in the chemolithoautotrophic utilization of 13CO2. Subdivision 1 Acidobacteriaceae assimilated 13CO2 likely via anaplerotic reactions because Acidobacteriaceae are not known to harbor enzymatic pathways for autotrophic CO2 assimilation. We conclude that CO2-induced geochemical changes promoted anaerobic and acidophilic organisms and altered carbon turnover in affected soils. [ABSTRACT FROM AUTHOR]

We examined the influence of sand burial of 0.5-mm and 10-mm depths on micro-fungal communities inhabiting moss-dominated and mixed biocrusts in the vicinity of the Shapotou Research Station in the Tengger Desert, China. The buried communities were compared with those in unburied crusts, as well as with the sandy below-crust and topsoil communities. We isolated 65 fungal species belonging to 43 genera using the soil dilution plate method. Compared to the unburied communities, the buried crust communities were characterized by lower abundance of melanin containing species, especially those with large many-celled conidia, but higher abundance of species producing small light-colored and one-celled conidia, mainly mesophilic Penicillium spp. Sand deposition also caused reduction of isolate density that was more pronounced in the mixed crusts. Diversity characteristics of micro-fungal communities and isolate densities varied in the two crust types in response to the same level of sand burial. This difference between the mixed and moss-dominated crusts was less expressed when the communities had been subjected to the deep sand burial. Below-crust sandy communities showed a more significant decrease both in isolate density and species richness compared to buried crust communities, which was accompanied by the substitution of dominant species – the thermotolerant Aspergillus fumigatus in the subcrust sandy layers instead of melanized species with large multicellular conidia in the crusts. On the whole, the influence of sand burial on crust micro-fungal communities was likely associated with the shielding effect of sand layer which might protect the crust layer from evaporation and UV-radiation. Whereas sand deposition in the crusts partly changed the substrate quality and microclimatic conditions for soil micro-fungi, transition from the crust to the below-crust sandy layer much more substantially altered the environmental situation (mainly in nutrient status, from the comparatively rich organic crust layer to the poor mineral sandy layer) thus leading to the more significant changes in the micro-fungal communities. [ABSTRACT FROM AUTHOR]

Microeukaryotes play many different functional roles in soil ecosystems, but the environmental factors that shape their community composition are poorly understood. Here we studied the impact of chemical and organic fertilizers on the microeukaryotic soil communities of rice field plots under long-term (82 years) fertilizer management. Terminal restriction fragment polymorphism (T-RFLP) and clone library analyses of 18S rRNA genes and their transcripts obtained from soils subjected to five different fertilizer treatments showed that fertilizer management strongly influenced microeukaryotic community composition in the soils and that its impact was greater than that of water management or seasonality. Among the different chemical fertilizers, the effects of phosphorus fertilizer on community composition were more pronounced than those of either nitrogen or potassium. Soils without phosphorus fertilizer were characterized by a high relative abundance of diatoms and algivorous nematodes whereas in phosphorus-fertilized soils green algae predominated. Different rates of organic fertilizer (rice straw compost) application had distinctive effects on the DNA-based microeukaryotic community, especially its algal composition. Thus, protistan grazers were the largest group in the potentially active community from soils with a higher amount of organic fertilizer application. Our findings provide evidence that long-term fertilization shapes the microeukaryotic community composition of rice field soils. The results imply that fertilizer management of rice field soils is an important determinant of the structure and function of the microbial food web. [ABSTRACT FROM AUTHOR]

Biochar application to soils has received much attention due to the potential for dual benefits of improved fertility and carbon (C) sequestration. Whilst its effect on C and nitrogen (N) cycling in soils has been investigated previously, this has usually either focussed on the bulk soil organic matter, or a single compound such as glucose. Five low molecular weight dissolved organic C (LMWDOC) substrates (three sugars, one amino acid, one organic acid) were selected for a 14C-CLPP experiment from which turnover rate (t1/2) and immediate carbon use efficiency (CUE) of the substrate were estimated. We demonstrated that whilst soil type had the greatest effect on soil microbial function, the addition of biochar also influenced microbial turnover and CUE of the substrates, most notably in the lowest fertility soil. We also identified that the relationship between turnover and CUE of the five substrates differed substantially, and the effect of biochar and soil type was more pronounced in the amino acid than the organic acid. This effect tended to be greatest in biochars produced at 450 °C, and less pronounced with the addition of biochars produced at 550 °C, though these trends were not consistent for all compounds in all soils tested. We conclude biochars and soils interact to manifest non-systematic differences in turnover rates of LMWDOCs, and thus a variety of mechanisms are likely responsible for this observation. As these compounds are most commonly found in the rhizosphere and can contribute a significant portion of photosynthetically-fixed C, and plant roots have been observed to grow preferentially around biochar particles, it is apparent that biochar may significantly affect the flow of LMWDOC through the microbial community in soils. [ABSTRACT FROM AUTHOR]

To evaluate the relationship between the potassium (K) status in the microbial community and the exchangeable K concentration in soils, the effects of K addition on microbial activity were assessed in cultivated Andisols not having received K fertilizer. Potassium limitation was not observed in the microbial community, even in a soil amended with only nitrogen (N) and phosphorus (P) but not K since 1938, though crop plants in this soil showed severe K deficiency symptoms. Furthermore, in a soil amended with NP + compost, microbial activity was limited by K only after limitation of carbon (C) and N. These results suggest that soil microorganisms demand more C and N than K, even in soils with low K availability, and also that the soil microbial community is less susceptible to K deficiency than are crop plants. [ABSTRACT FROM AUTHOR]

Secondary succession studies have mainly focused on plants, but little is known about the fate of soil microbial communities and their relationship with plant succession after disturbance, particularly in dry ecosystems. We examined changes in soil properties and of plant and soil microbial communities across a chronosequence of abandoned arable fields that included five successional stages according to time of abandonment stretching near a century. We hypothesized the existence of a parallel secondary succession above- and below-ground and explored the possible linkages between plant and microbial communities as well as the role of changes in soil properties over the successional gradient. Soil microbial communities were characterized by PLFAs analysis, enzymatic activities, and pyrosequencing of the 16S rDNA. We found clear patterns of plant and microbial secondary succession characterized by an increase in organic C, NH4+, and silt content as well as in soil microbial biomass and activity along the successional stages, linked to an increase in plant productivity and diversity. Plant and microbial composition were significantly different among successional stages, although no distinct microbial communities were observed in the two initial stages, suggesting that microbial succession may lag behind plant succession. However, the degree of change in the composition of soil microbial communities and plant communities across our chronosequence evidenced that above- and below-ground secondary succession developed with similar patterns and correlated with changes in multiple ecosystem functions such as increases in above-and below-ground productivity, diversity and nutrient accumulation as plant and microbial succession progressed. [ABSTRACT FROM AUTHOR]

Factors affecting community structure and connectivity within systems are crucial for provision of microbial ecosystem-services (e.g., soil nitrogen cycling), but what these factors are and how they are affected by land-use and management is poorly understood. Biogeochemical cycles are disrupted in agricultural-systems, providing an excellent opportunity to investigate the roles of management and land-use in shaping microbial communities and ecosystem function. We investigated soil ammonia oxidisers under different cropping practices and within a nearby grassy woodland; representing a gradient of physical/chemical disturbance. Land-use and management practices resulted in significant differences in community structure. Major differences in system connectivity were observed between land-uses, but not within management practices, indicating that land-use change is the major driver of ecosystem change, rather than management within land-uses. Agricultural ammonia oxidiser communities appeared to be less well connected and rely less on biotic interactions than those in natural systems, perhaps a reflection of the extent to which natural feedback loops are disturbed in managed systems. Smaller, but significant, differences were also evident between management treatments. Despite differences in community structure and connectivity there was, however, no significant effect on potential N-cycle rates, indicating that although land-use and management impacts may drive community changes, these do not necessarily translate into changes in functional capacity. [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]

Data on soil microbial community distribution at large scales are limited despite the important information that could be drawn with regard to their function and the influence of environmental factors on nutrient cycling and ecosystem services. This study investigates the distribution of Archaea, Bacteria and Fungi as well as the dominant bacterial phyla ( Acidobacteria, Actinobacteria, Bacteroidetes, Firmicutes) , and classes of Proteobacteria ( Alpha- and Betaproteobacteria) across the Koiliaris watershed by qPCR and associate them with environmental variables. Predictive maps of microorganisms distribution at watershed scale were generated by co-kriging, using the most significant predictors. Our findings showed that 31-79% of the spatial variation in microbial taxa abundance could be explained by the parameters measured, with total organic carbon and pH being identified as the most important. Moreover, strong correlations were set between microbial groups and their inclusion on variance explanation improved the prediction power of the models. The spatial autocorrelation of microbial groups ranged from 309 to 2.226 m, and geographic distance, by itself, could explain a high proportion of their variation. Our findings shed light on the factors shaping microbial communities at a high taxonomic level and provide evidence for ecological coherence and syntrophic interactions at the watershed scale. [ABSTRACT FROM AUTHOR]

Large amounts of veterinary antibiotics are applied worldwide to farm animals and reach agricultural fields by manure fertilization, where they might lead to an increased abundance and transferability of antibiotic-resistance determinants. In this review we discuss recent advances, limitations, and research needs in determining the fate of veterinary antibiotics and resistant bacteria applied with manure to soil, and their effects on the structure and function of soil microbial communities in bulk soils and the rhizosphere. The increased abundance and mobilization of antibiotic-resistance genes (ARGs) might contribute to the emergence of multi-resistant human pathogens that increasingly threaten the successful antibiotic treatment of bacterial infections. [ABSTRACT FROM AUTHOR]

Decabromodiphenyl ether (BDE209) and tetrabromobisphenol A (TBBPA) are the main contaminants at e-waste recycling sites, and their potential toxicological effects have received extensive attention. However, the impact on soil culturable microbial population and enzyme activity of joint exposure to the two chemicals remains almost unknown. Therefore, indoor incubation tests were performed on control and contaminated soil samples to determine the eco-toxicological response in the joint presence of BDE209 and TBBPA for the first time. The results have demonstrated some notable toxic effects due to long-term exposure to either or both contaminants. The inhibition ratios of microbial populations increased with incubation time and increasing concentrations of BDE209 or TBBPA following certain dose–response relationships and time-effect trends. The response sensitivity sequence was fungi > bacteria > actinomycete. The influence of the two chemicals on soil enzymes reached peak values on day 7, and highly significant differences ( P < 0.01) were observed compared to the controls. Urease was more susceptive to the two chemicals than catalase and saccharase activities. Generally, the joint toxicity of both contaminants on soil microbes, catalase or saccharase activities indicated antagonistic effects, while, as for urease activity, addition role was dominant. Such observations have provided the useful information of potential ecological effects of brominated flame retardants contamination in the environment. [ABSTRACT FROM AUTHOR]