Assessing effects of earthworm cast on methanotrophic community in a soil biocover by concurrent use of microarray and quantitative real-time PCR

Effects of earthworm cast (EC) on the methanotrophic community in a soil biocover were evaluated using microarray and quantitative real-time PCR (qRT-PCR). Soil was collected from a biocover with either soil alone or a mixture of soil and EC (3:1, w/w). The microarray results showed a more diverse methanotrophic community in the EC biocover than that in the soil biocover (p < 0.05). A principal component analysis result confirmed a substantial change in the methanotrophic community structure due to the added EC. Type I methanotrophs dominated both biocovers, with Methylobacter being most abundant. The qRT-PCR results showed that EC greatly increased the methanotrophic population levels (p < 0.05) up to 100 fold. In conclusion, EC can increase the population density of methanotrophs as well as their diversity, resulting in a substantial shift in the community structure. The results confirmed the promising potential of EC as a bed material for enhancing the biocover performance.     

Estimation of soil texture from the sample density

Abstract

Soil texture often plays an important role in the interpretation of soil analytical data for fertilizer advisory purposes. A reliable and inexpensive method of clay content estimation is, therefore, a requirement of most advisory laboratories. This note discusses the use of sample density (i.e. the mass of a scooped volume of soil) as an index of clay content. A strong relationship was found to exist between sample density and clay content, and such estimates of clay content were superior to those obtained by experienced pedologists using the “finger test” procedure. The use of this quick and simple procedure is considered to be ideally suited to soil testing laboratories handling large numbers of samples.     

Balanced fertilization improved soil ammonia-oxidizing bacterial community in latosolic red soil

Abstract

We investigated the impact of nitrogen (N), phosphorus (P), potassium (K) (NPK) and NPK plus glucose-balanced fertilization compared with N-only fertilization on the soil pH, NH₄ ⁺, NO₃ ^?, ammonia-oxidizing bacterial community, bacterial community and function during microcosm incubation. The NPK and NPK plus glucose treatments resulted in significantly reducing soil acidification and NO₃ ^? accumulation compared with the N-only fertilization. The terminal restriction fragment size measuring 283 (Nitrosospira) and 54 bp (unidentified) were predominant in the soil ammonia-oxidizing bacterial composition for all treatments. The N-only fertilization did not change the ammonia-oxidizing bacterial community, the bacterial community composition based on terminal restriction fragment length polymorphism analysis, and the bacterial functional diversity based on Biolog EcoPlate^TM incubation. The NPK and NPK plus glucose treatments resulted in a shift in the soil ammonia-oxidizing bacterial community and bacterial community composition, and significantly increased the bacterial functional diversity (average well colour development, Richness and Shannon index). Nitrosomonas species were detected in the soil upon NPK and NPK plus glucose treatment on incubation day 9 but not on days 1 and 31. The effect of NPK treatment on the bacterial community composition was transient; a new 116 bp fragment was present on incubation day 9, but the data returned to their original values by day 31. In contrast, treatment with NPK plus glucose resulted in the appearance of a new 116 bp fragment that remained until incubation day 31. These results demonstrated that the balanced fertilization of N, P, K and glucose, plays an important role in regulating ammonia-oxidizing bacterial community quickly, and promoting nitrification functions. The results also showed the importance of balanced fertilization in reducing acidification, improving bacterial community structure and function in latosolic red soil. Therefore, optimizing the ammonia oxidation process by balanced fertilization may be helpful to reduce the loss of soil nitrogen.     

均腐土不同亚纲典型土系土壤细菌群落多样性研究

为研究中国土壤系统分类(CST)体系下均腐土不同亚纲土壤细菌群落结构的多样性,以 4个干润均腐土[富牧西系(DFm)、春雷南系(DCl)、保国系(DBg)、明水系(DMs)]和 4个湿润均腐土[大西江系(MDx)、新发北系(MXf)、卫星农场系(MWx)、裴德系(MPd)]的腐殖质层(Ah层)为研究对象,采用高通量测序技术研究细菌群落多样性,分析细菌群落结构与环境因子间的关系,以探讨影响均腐土不同亚纲群落结构的主要环境因子。结果表明:均腐土 8个土系样品共获得 1 674 634条基因序列,Shannon指数和 Chao1指数表现为:干润均腐土 >湿润均腐土。均腐土 8个土系细菌群落主要包括 10个门类,其中变形菌门(Proteobacteria)、放线菌门(Actinobacteria)、酸杆菌门(Acidobacteria)为富牧西系、春雷南系、保国系、大西江系、新发北系、卫星农场系、裴德系优势菌门,明水系以绿湾菌门(Chloroflexi)、变形菌门(Proteobacteria)、放线菌门(Actinobacteria)为优势菌门;属水平上,均腐土各土系的群落差异较大。样品热图分析将 8个土系细菌群落聚为 2类,其中干润均腐土聚为一类,湿润均腐土聚为一类。pH、交换性 Ca、CEC、交换性 Mg、SOC和 TP是影响均腐土细菌群落结构发生变化的主要因子( P<0.05)。此外,RDA分析发现,土壤 pH为影响均腐土细菌群落结构的主导因子,而 pH、交换性 Ca、CEC为驱动干润均腐土细菌群落结构发生变化的主要影响因素,交换性 Mg、SOC、TP为驱动湿润均腐土细菌群落发生变化的主要影响因素。     

Vermicompost and humic fertilizer improve coastal saline soil by regulating soil aggregates and the bacterial community

Soil salinity, poor soil structure and macronutrient deficiencies are three important limitations responsible for poor crop yields in coastal saline soils. Here we used humic fertilizer and vermicompost to ameliorate salt-induced stress by regulating the soil bacterial community and aggregates in different growth stages of winter wheat. Soil salinity, aggregates, nutrient availability, the soil bacterial community from next-generation high-throughput sequencing, and wheat yield were determined in this study. The results indicated that humic fertilizer and vermicompost could efficiently alleviate salt accumulation (by 16.8–41.1 and 13.3–42.7%, respectively) in topsoil by inhibiting resalinization and increase the proportion of soil macroaggregates (by 26.7–85.9 and 31.6–105.5%, respectively) in the wheat growth stages. Skermanella, Arthrobacter and Sphingomonas were the dominant genera in the study soil. Humic fertilizer and vermicompost could improve soil total N (by 4.7–15.6 and 2.4–25.2%, respectively), available P (by 15.9 and 7.3–64.4%, respectively), and exchangeable K (by 3.9–18.4 and 0.7–12.1%, respectively) by increasing the abundance of Arthrobacter and Pedobacter, consequently improving shoot biomass (by 41.1 and 52.8%, respectively) and grain yield (by 45.1 and 60.2%, respectively) of wheat. Therefore, vermicompost and humic fertilizer ameliorate salt-induced stress in coastal saline soil through the integrated improvement of soil physical, chemical and biological properties.     

Detection and quantification of the nematophagous fungus Hirsutella minnesotensis in soil with real-time PCR

A real-time PCR assay was developed to quantify in soil the fungus Hirsutella minnesotensis, an important parasite of secondary-stage juvenile (J2) of the soybean cyst nematode. A primer pair 5′-GGGAGGCCCGGTGGA-3′ and 5′-TGATCCGAGGTCAACTTCTGAA-3′ and a TaqMan probe 5′-CGTCCGCCGTAAAACGCCCAAC-3′ were designed based on the sequence of the ITS region of the rRNA gene. The primers were highly species-specific. The PCR reaction system was very sensitive and able to detect as few as 4 conidia g^?1 soil. Regression analysis showed similar slopes and efficiency on DNA from pure culture (y = ?3.587x + 41.017, R² = 0.9971, E = 0.9055) and from Log conidia g^?1 soil (y = ?3.855x + 37.669, R² = 0.9139, E = 0.8172), indicating that the real-time PCR protocol can reliably quantify H. minnesotensis in the soil. The real-time PCR assay was applied to 20 soil samples from soybean fields, and compared with a parasitism assay. The real-time PCR assay detected H. minnesotensis in six of the soils, whereas the parasitism assay detected H. minnesotensis in the same six soils and three additional soils. The real-time PCR assay was weakly correlated (R² = 0.49) with the percentage of parasitized J2 in the six soils, indicating that different types of soil may interfere the efficiency of the real-time PCR assay, possibly due to the effect of soil types on efficacy of DNA extraction. The parasitism assay appeared to be more sensitive than real-time PCR in detecting presence of H. minnesotensis, but real-time PCR was much faster and less costly and provided a direct assessment of fungal biomass. Using the two assays in combination can obtain more complete information about the fungus in soil than either assay alone. Hirsutella parasitism was widespread and detected in 13 of the 20 field soils, indicating that these fungi may contribute to suppressiveness of soybean cyst nematode in nature and likely have high biological control potential for the nematode.     

毒死蜱对棉花根际土细菌群落多样性和结构的影响

通过室内盆栽试验模拟自然环境条件,采用高效液相色谱(HPLC)和末端限制性片段长度多态性(T-RFLP)技术,研究了土壤使用推荐剂量(5 mg·kg~(-1))及推荐剂量的2倍、3倍和4倍(10 mg·kg~(-1)、15 mg·kg~(-1)、20 mg·kg~(-1))毒死蜱对棉花根际土壤细菌群落多样性和结构的影响,以不施用毒死蜱的土壤为对照。结果表明,5 mg·kg~(-1)、10 mg·kg~(-1)、15 mg·kg~(-1)和20 mg·kg~(-1)毒死蜱在土壤中的半衰期分别为10.04 d、11.36 d、11.55 d和12.16 d,60 d时基本完全降解。毒死蜱处理60 d后,棉花生物量显著降低;毒死蜱浓度越高,棉花生物量越低。无毒死蜱条件下不同取样时间根际细菌多样性无显著差异,毒死蜱处理组前30 d细菌多样性均显著降低,60 d时毒死蜱处理组细菌多样性恢复到正常水平。研究发现毒死蜱浓度越高对细菌多样性抑制作用越显著,恢复越缓慢。主成分分析结果发现,第10 d、30 d和60 d毒死蜱处理组与对照组细菌群落结构差异显著,其中60 d时20 mg·kg~(-1)毒死蜱处理组差异最显著,即使土壤中毒死蜱完全降解,根际细菌群落结构仍不会恢复到正常水平。60 d时,被毒死蜱抑制的细菌有硝化刺菌属(Nitrospina sp.)和Cellulophaga sp.等,被激活的有芽孢杆菌属(Bacillus sp.)和链霉菌属(Streptomyces sp.)等。可见,毒死蜱的引入,重新构建了土壤细菌群落结构,显著影响棉花生长,对棉花根际土壤微生态环境冲击较大,应对其生态安全性予以重视。     

土壤厌氧消毒对青枯病的控制及土壤细菌群落结构的影响

近年来,土壤厌氧消毒(Anaerobic soil disinfestation,ASD)作为一种非化学、环境友好型土壤消毒方法,在缓解连作障碍和防治土传病害方面具有显著效果,但其作用机理尚不完全清楚。本研究设置6个处理,即对照、添加米糠(DRB)、麦麸(DWB)、茶麸(DTB)、秸秆(DRS)和不添加物料(D)5种土壤厌氧消毒处理,分析不同处理对青枯病防控效果、土壤理化性质及土壤细菌群落结构组成及多样性的影响。结果表明,与CK相比,添加4种物料厌氧消毒处理对青枯病的防效均达100%,单纯厌氧处理防效为83.3%,且除了DRB外各厌氧处理均能大幅度促进番茄生长。各ASD能显著提高土壤温度、p H和电导率,降低Eh和土壤青枯菌数量。田间试验表明,与CK相比,ASD的番茄青枯病发病率降低29.4%~42.7%,产量增加2.5倍~4.7倍。利用16S r DNA对土壤测序表明,ASD降低了土壤细菌α多样性指数,不同处理间土壤细菌物种种类、丰富度及多样性均存在显著差异。添加不同有机物料的ASD厚壁菌门(Firmicutes)相对丰度大幅度提高,成为优势群落;该门中的厌氧型细菌梭菌科(Clostridiaceae)、瘤胃菌科(Ruminococcaceae)和耐受性细菌芽孢杆菌科(Bacillaceae)等相对丰度也大幅度提高。本研究表明,土壤厌氧消毒处理显著改变了土壤细菌群落结构组成及多样性,厌氧和耐受型细菌丰度大幅度增加,这可能是ASD防控土传病害青枯病的作用机理之一。     

Effects of grazing by sheep on the structure of methane-oxidizing bacterial community of steppe soil

Soils of three sites were studied in the Inner Mongolia steppe; one site non-grazed for 26 yr (NG26), another site non-grazed for 6 yr (NG6) and a third site freely grazed all along (FG). The composition of methantrophic communities was characterized by pmoA gene fragments (coding for a subunit of particulate methane monooxygenase) that were PCR amplified from total soil DNA extracts, using denaturing gradient gel electrophoresis (DGGE) method. Cluster analysis based on the DGGE band patterns indicated that the methanotrophic communities structure of NG6 and FG soils were similar to each other but different from that of NG26 soil. Sequence analysis showed that most bands belonged to the cluster of USCγ. This is the first report that USCγ cluster is dominated in the grassland soil.     

Characterization of copper-resistant bacterial community in rhizosphere of highly copper-contaminated soil

The characteristics of copper (Cu)-resistant bacterial communities in a rhizosphere and a non-rhizosphere of the ditch reed, Phragmites, in a highly Cu-contaminated area near a copper mine were investigated. The total Cu concentration was 720 μg·g^–1 in the rhizosphere soil and 5 680 μg·g^–1 in the non-rhizosphere soil. In the rhizosphere, the multiplication of bacteria, particularly non-resistant bacteria, was promoted as compared with the non-rhizosphere. The properties of the bacterial community in the rhizosphere were quite different from those in the non-rhizosphere in terms of Cu sorption ability, growth rate and exopolymer production. Both the Cu-resistant bacteria and non-resistant bacteria in the rhizosphere grew more rapidly in media than those in the non-rhizosphere. For almost all the isolated Cu-resistant bacteria, exopolymer production was prompted by Cu stimuli especially for the isolates from the rhizosphere. The adverse effect of Cu on the growth rate was found to be small for the Cu-resistant bacteria producing exopolymers in a large quantity, suggesting the involvement of exopolymers in the detoxification of Cu. The role of Cu resistance in the bacterial chemotactic migration in the Cu-contaminated soils was not evident.     

Fertilization management affects the alkaline phosphatase bacterial community in barley rhizosphere soil

There is increasing interest in good agriculture practices that address the issues of sustainability, reduction in inputs such as fertilizers and pesticides while maintaining crop yield and soil fertility. It is important that soil microbial diversity and function are not impaired by altered agricultural practice. In this study, as indicators of soil quality, the bacterial community structure was evaluated from a long-term field trial managed with conventional and low-input fertilization/pesticide regimes. The low-input plots under study received approximately one fifth less N fertilizer than the conventional-input plots, a maximum of half the recommended application rates of fungicides and pesticides and no externally added P source. A non-culturable approach was taken using polymerase chain reaction–denaturing gradient gel electrophoresis analysis of 16S rRNA and alkaline phosphomonoesterase [phosphatase] (ALP) genes in an attempt to relate bacterial community structure to respective field management regimes. To identify the ALP bacteria in these plots, randomly selected ALP clones were sequenced. The results based on Shannon diversity indices and community structure analysis of ALP genes suggest differences in community diversity and structure under conventional and low-input barley sites in most sampling seasons. We conclude that soil fertilization management affects the ALP bacteria in the barley rhizosphere, while the overall changes in bacterial community in these sites are prominently due to seasonal variation compared to crop or input regimes. The randomly selected ALP sequences identified from these sites were mostly from the Alpha and Gamma classes of Proteobacteria.     

Estimation of the effects of earthworms and initial substrates on the bacterial community in vermicomposts

The effects of earthworms and initial substrates on the structural and functional compositions of the bacterial community in vermicomposts have been estimated by the method of denaturing gradient gel electrophoresis (DGGE) of amplified bacterial 16S rRNA gene fragments and by the kinetic method for assessing the physiological state of bacterial communities. ANOVA of the data on structural characteristics of the community (DGGE data) has demonstrated that the nature of the composted substrate has the major effect on the structure of the bacterial community. The associated variance for this factor accounts for 53% and exceeds the effect of earthworms (29%). A functional characterization of the bacterial community (data on the physiological state of bacteria as judged from their growth on different organic compounds) suggests that the presence of earthworms activates the bacterial community by increasing the variable characterizing the physiological state of bacteria (r ₀). As has been shown, it is impossible to predict the effect of earthworms on the particular bacterial taxa, because the effects of similar signs (increase, decrease, or the absence of changes in all the variants) just for the three analyzed types of substrates have only been observed for 15% of the operational taxonomic units.     

From the micro-scale to the habitat: Assessment of soil bacterial community structure as shown by soil structure directed sampling

Natural structural units of a luvisol under maize crop were studied to assess if soil structure directed sampling could improve the understanding of arrangements of bacteria in spatially constraint location. Three habitats were defined: (i) soil around fine lateral roots (rhizo-aggregates), (ii) soil close to basal roots (core clods) and (iii) unplanted soil between rows (bare soil clods). These habitats were also investigated with maize plants resulting from Azospirillum lipoferum CRT1 inoculated seeds as a model of enhanced fine root system. Rhizo-aggregates were clearly separated from each other (disconnected habitat) in contrast to micro-samples (fragments) from clods, which belong to cohesive macro-structures. Genetic fingerprints on metagenomic extracts were used to characterize the structure of bacterial communities on 95 micro-samples from the three habitats. For eubacteria, automated RISA (Ribosomal Intergenic Spacer Analysis) of ITS (Internal Transcribed Spacer) profiles were performed. PCR-RFLP on nifH gene were used to describe the N-fixer guilds. Exploratory multivariate analyses (PCA and MDS) revealed bacterial community patterns in the sampled habitats. On the basis of ITS profiles, rhizo-aggregates harboured closely related communities, distant from those of the unplanted soil, and each sampled rhizo-aggregate could therefore be considered as a sub-unit of the whole macro-habitat, comprising all the fine roots. The observed low dissimilarity of disconnected rhizo-aggregates is likely to result from the direct influence of maize root tips on the recruitment of rhizosphere bacteria. Molecular fingerprints of nifH from basal root clods (core) were more similar to bare soil than to rhizo-aggregates, indicating similar ecological conditions without, or with, at least, poor maize exudating root influence. Although our study was performed on a limited number of situations, the distribution of bacteria was revealed to be patterned by soil structure units, which is a first step to improve the modelling of microbial ecology in soils.     

Dynamics of extracellular DNA decomposition and bacterial community composition in soil

Microbial necromass is an important source of stabilized organic matter in soil, yet the decomposition dynamics of necromass constituents have not been adequately characterized. This includes DNA, a nutrient-rich molecule that when released into the environment as extracellular DNA (eDNA) can be readily used by soil microorganisms. However, the ecological relevance of eDNA as a nutrient source for soil microorganisms is relatively unknown. To address these deficits, we performed a laboratory experiment wherein soils were amended with ¹³C-labeled eDNA and clay minerals known to interact with DNA (kaolinite and montmorillonite). The amount of eDNA-carbon remaining in the soil declined exponentially over time. Kaolinite amendment decreased eDNA decomposition rates and, after 30 days, retained a higher fraction of eDNA-carbon (∼70% remaining) than control or montmorillonite soils (∼40% remaining), indicating that clay mineral sorption can stabilize eDNA-derived carbon in soil. Sequencing of bacterial 16S rRNA genes showed that during the incubation the relative abundance of the added eDNA's sequence decreased by 98%, 92% and 99% in the control, montmorillonite, and kaolinite amended soils respectively. These results suggest that the fraction of eDNA-carbon that remained in the soil was incorporated into microbial biomass, firmly bound to soil constituents, or fragmented and no longer amenable to sequencing. In addition, the eDNA amendment affected the composition of the bacterial community. Specifically, the relative abundance of select phyla (Planctomycetes and TM7) and genera (e.g., Arthrobacter and Nocardioides) were elevated in soils that received eDNA, suggesting these groups may be particularly effective at degrading eDNA and using it for growth. Taken together, these results indicate that while eDNA is consumed by bacteria in soil, a fraction of eDNA material is resistant to decomposition, particularly when stabilized by soil minerals, suggesting a substantial amount of recalcitrant eDNA could accumulate over time.     

Rapid changes in the rhizosphere bacterial community structure during re-colonization of sterilized soil

Diversity has been shown to be pivotal in ecosystem stability and resilience. It is therefore important to increase our knowledge about the development of diversity. The aim of this study was to investigate the temporal dynamics of the bacterial community structure in the rhizosphere of wheat plants growing in a soil in which the initial conditions for bacterial re-colonization were modified by mixing different amounts of sterilized with native soil at ratios of 19:1, 9:1, 4:1 and 1:1. Additional treatments comprised sterilized soil or native soil. Plant dry weight at day 20 decreased with increasing percentage of native soil in the mix. The bacterial community structure in the rhizosphere was assessed by polymerase chain reaction-denaturing gradient gel electrophoresis (DGGE) at days 3, 14 and 20 after planting. The bacterial community in the sterilized soil had a lower diversity and evenness than the native soil. Both diversity and evenness increased with time in the sterilized soil. Community structure in the different mixes changed over time and the changes were mix-specific. Principal component analyses of the DGGE banding patterns showed clear differences between the treatments particularly at day 3 and day 14 and revealed changes in community structure within a few days in a given treatment. The results of the present study show that bacterial communities rapidly re-colonize sterilized soil. During re-colonization, the community structure changes rapidly with a general trend towards higher diversity and evenness. The changes in community structure over time are also affected by the amount of sterile substrate to be re-colonized.     

Estimation of the bacterial community diversity of soybean-nodulating bradyrhizobia isolated from Rj-genotype soybeans

Abstract

The diversities of communities of soybean-nodulating indigenous bradyrhizobia in Japan were estimated using mathematical ecology methods based on the results of polymerase chain reaction–restriction fragment length polymorphism analysis of the 16S–23S rDNA internal-transcribed spacer region. Polar ordination analysis indicated a significant correlation between the compositions of bradyrhizobial communities and northern latitudes in Japan. This result suggests that the composition and the geographical distribution of indigenous soybean-nodulating bradyrhizobia might be affected by soil temperature and the associated diversity of the host plants acclimatized to a particular climate. Furthermore, for estimation of the compositional difference in bacterial communities among three different Rj-genotype soybean cultivars, an analysis of the diversity indexes was conducted and this analysis indicated differences in the composition of the communities isolated from the Rj ₂ Rj ₃-genotype compared with those from the non-Rj- and Rj ₄-genotype cultivars. This result suggests that Rj ₂ Rj ₃-genotype soybeans might affect not only compatibility with particular bradyrhizobia, but also preference to bradyrhizobia for nodulation.     

不同深度土壤控水对稻田土壤微生物区系及细菌群落多样性的影响

为研究不同深度土壤控水对壤土稻田土壤水势、微生物区系和细菌群落多样性的影响,通过土培池栽试验,在水稻生育后期设置土壤深度0~5 cm（S05）、0~10 cm（S10）和0~15 cm（S15）控水处理,以保持水层为对照,分析了不同深度控水处理下5 cm、10 cm、15 cm深土壤水势与土壤微生物区系、细菌群落多样性的变化。结果表明：土壤5 cm、10 cm、15 cm深度的水势随着控水深度增加而降低,S05控水处理主要影响上层（5 cm）土壤水势,S10控水处理影响上、中层（10 cm）土壤水势,S15控水处理土壤水势随土层深度的增加而升高。花后8 d和32 d,S05控水处理上层土壤细菌数量显著高于S10、S15控水处理;花后16~24 d,S05控水处理中层、下层（15 cm）土壤细菌数量均显著高于S15控水处理;土壤水势与水稻生育后期中、下层土壤细菌数量呈极显著正相关关系。S05控水处理10 cm、15 cm土层的细菌丰富度Chao指数均显著高于S15控水处理及CK。3个控水处理中,5 cm土层细菌的多样性Shannon指数以S05控水处理最低。优势细菌菌群分析发现,优势群落主要为变形菌门、绿弯菌门、酸杆菌门、拟杆菌门,四者总相对丰度在80%以上;S15控水处理中层土壤变形菌门相对丰度低于S05和S10控水处理。3个控水处理土壤样品中优势纲（相对丰度大于2%）达15个,主要包括α-变形菌纲、β-变形菌纲、δ-变形菌纲、厌氧绳菌纲等,这4个纲的总相对丰度在47%以上,其中厌氧绳菌纲相对丰度最高;上层土壤中S05控水处理的β-变形菌纲相对丰度显著低于S10和S15控水处理。因此,不同深度土壤控水对壤土土壤水势、细菌数量存在影响,改变了细菌的多样性及丰富度,对土壤细菌优势菌种类无显著影响。     

The impact of iron oxide magnetic nanoparticles on the soil bacterial community

Purpose  

Iron oxide magnetic nanoparticles (IOMNPs) have numerous exciting applications due to their unique chemical and physical properties. With increased applications of engineered nanostructures, releases of such materials to soil are undoubtedly inevitable. Their potential environmental risks have attracted increasing concern. One area of concern is their effect on microorganisms, which are important components of ecosystems.     

Molecular approaches to investigate herbicide-induced bacterial community changes in soil microcosms

Since biochemical and microbiological methods used to study microbial community changes induced by anthropogenic activities can be biased, the impact of two herbicides on soil microorganisms was investigated by culture-independent molecular techniques. The effect of three different amounts (the recommended field dose, tenfold, and 100-fold the dose) of propanil or prometryne on the bacterial community of a clay soil, two modalities of incubation (soil moisture at 70% of the field capacity and a soil-herbicide suspension, 1:10, w:v), and time of incubation were investigated by denaturing gradient gel electrophoresis (DGGE) and amplified rDNA restriction analysis (ARDRA). Two sets of primers for 16S rDNA were used to amplify total soil DNA. Sterile and non-sterile samples were used to determine, by HPLC, the amounts of herbicides adsorbed on soil and transformed by soil microorganisms. Prometryne persisted in soil longer than propanil. Propanil was removed significantly more by non-sterile than by sterile samples, while for prometryne, slight differences were observed. 3,4-Dichloroaniline, a product of propanil hydrolysis, was detected in non-sterile samples and increased with incubation time. Propanil did not affect soil bacteria significantly as indicated by DGGE and ARDRA, with the only exception being the soil-herbicide suspension. Despite a lower utilization of prometryne by soil microorganisms, DGGE analysis showed a more diverse banding than with propanil. Some bands were also detected in the DNA sample extracted from the soil-prometryne suspension, and could be representative of bacterial species utilizing the herbicide as a carbon source, in two very different soil microcosms.     

Changes in soil bacterial community structure and microbial function caused by straw retention in the North China Plain

ABSTRACT

The effects of straw retention on soil bacterial community structure, microbial function, and biochemical properties were assessed. Terminal restriction fragment length polymorphism (T-RFLP) and community-level physiological profile (CLPP) assays were used to assess the bacteria community structure and microbial function respectively. Treatments included straw removal with conventional tillage (CT), straw retention with conventional tillage (SRCT) and straw retention with no tillage (SRNT). SRCT and SRNT significantly (p < 0.05) increased soil organic carbon by 8.9% and 9.7%, and microbial biomass carbon by 44.7% and 330.8%, respectively, compared with CT. T-RFLP analysis indicated that straw retention had no favourable effect on soil bacterial diversity, and SRCT significantly (p < 0.05) decreased bacterial diversity compared to CT. Among the three treatments, SRNT had the highest activity of urease, invertase, cellulase, and β-glucosidase. SRCT significantly (p < 0.05) increased the activity of invertase and β-glucosidase compared to CT treatment. CLPP analysis showed that microbial functional diversity was significantly (p < 0.05) increased by straw retention. Enzyme activity and microbial functional diversity were not correlated with bacterial diversity. Therefore, according to this study, SRNT is a better farming practice because it improves soil fertility and biological quality.