三种耕作制度下密西西比州两种加入家禽垫料的土壤上磷动态研究

An experiment arranged in a randomized complete block design with three replications was conducted on a Lexington soil (fine-silty, mixed, active, thermic, Ultic Hapludalfs) and a Loring soil (fine-silty, mixed, active, thermic, Oxyaquic Fragiudalfs) in Mississippi from September 1997 to September 2000 on 18 runoff plots under natural rainfall condition to study the phosphorus (P) dynamics in poultry litter amended soils under three management systems combining tillage and planting date treatments to identify effective management practices in southern U. S. A. The management systems in the study were:1) tillage in the fall prior to litter application followed by a delayed planting of fall forages (CT-DP); 2) tillage followed by immediate planting of the fall forage with subsequent litter application (CT-IP); and 3) no-till with planting prior to litter application (NT-IP). The results indicated that there was significant increase in soil P after 3 years of poultry litter application for both Lexington and Loring soils (P <0.05). Based on P budget analysis, the majority of P from poultry litter application (> 90%), was accumulated in both soils. In Loring soil, soluble P mass in the runoff was significantly higher from NT-IP than from CT-DP and CT-IP over the entire study period (P <0.01). For both soils, there were no significant differences in sediment P mass between management systems. For Loring soil, CT-DP and CT-IP were effective management practices to mitigate negative effects due to poultry litter application.     

钙盐诱导下土壤锰和铁的释放及其对胡椒的生物有效性

Releases of manganese and iron ions from an albic soil (Albic-Udic Luvisol), a yellow-red soil (Hap-Udic Ferrisol) and a yellow-brown soil (Arp-Udic Luvisol) induced by calcium salt addition and their bioavailability to pepper (Capsicum frutescens L.) were studied in a pot experiment. Addition of Ca(NO₃)₂ decreased soil pH and increased both exchangeable and DTPA (diethylenetriamine pentaacetic acid)-extractable Mn and Fe in soils. Meanwhile, total Mn accumulation in the shoots of Capsicum frutescens L. on the salt-treated soils increased significantly (P< 0.01) compared with the control, suggesting that salt addition to soil induced Mn toxicity in Capsicum frutescens L. Although exchangeable and DTPA-extractable Fe increased also in the salt-treated soils, Fe uptake by the shoots of Capsicum frutescens L. decreased. The effect of added salts in soils on dry matter weight of pepper varied with the soil characteristics, showing different buffer capacities of the soils for salt toxicity in an order of yellow-brown soil > albic soil > yellow-red soil. Fe/Mn ratio in shoots of Capsicum frutescens L. decreased with increasing salt addition for all the soils, which was ascribed to the antagonistic effect of Mn on Fe accumulation. The ratio of Fe/Mn in the tissue was a better indicator of the appearance of Mn toxicity symptoms than Mn concentration alone.     

Phosphate Solubilizing Ability and Phylogenetic Diversity of Bacteria from P-Rich Soils Around Dianchi Lake Drainage Area of China

The phylogenetic diversity of phosphate solubilizing bacteria(PSB)distributed in P-rich soils in the Dianchi Lake drainage area of China was characterized,and the tricalcium phosphate(TCP)solubilizing activities of isolated PSB were determined.Among 1 328 bacteria isolated from 100 P-rich soil samples,377 isolates(28.39%of the total)that exhibited TCP solubilization activity were taken as PSB.These PSB showed different abilities to solubilize TCP,with the concentrations of solubilized P in bacterial cultures varying from 33.48 to 69.63 mg L^-1.A total of 123 PSB isolates,with relatively high TCP solubilization activity(>54.00 mg L^-1),were submitted for restriction fragment length polymorphism(RFLP)analysis,which revealed 32 unique RFLP patterns.Based on these patterns,62 representative isolates,one to three from each RFLP pattern,were seffected for 16S rRNA sequencing.Phylogenetic analysis placed the 123 PSB into three bacterial phyla,namely Proteobacteria,Actinobacteria and Firmicutes.Members of Proteobacteria were the dominant PSB,where 107 isolates represented by 26 RFLP patterns were associated with the genera of Burkholderia,Pseudomonas,Acinetobacter,Enterobacter,Pantoea,Serratia,Klebsiella,Leclercia,Raoultella and Cedecea.Firmicutes were the subdominant group,in which 13 isolates were affiliated with the genera of Bacillus and Brevibacterium.The remaining 3 isolates were identified as three species of the genus Arthrobacter.This research extends the knowledge on PSB in P-rich soils and broadens the spectrum of PSB for the development of environmentally friendly biophosphate fertilizers.     

Microbial Community Changes Along a Land-Use Gradient of Desert Soil Origin

Soil harbors remarkably stabilize bacterial communities at the phylum level.However,no two soils have exactly the same structure of bacterial phyla.The structure of microbial community is strongly influenced by the type of land-use through changes in soil attributes.Using high-throughput pyrosequencing and quantitative polymerase chain reaction techniques,soil microbial community structures were investigated along a land-use gradient of 100- and 27-year farmlands,a 33-year Pinus forest,a 28-year poplar forest,and a 21-year shrubland,as well as a native desert from which all cultivated systems were converted.The results revealed that the dominant phylotypes in the native soil comprised primarily of Alphaproteobacteria,Actinobacteria,Bacteroidetes,and Firmicutes,accounting for >71.4%of the total bacterial 16S rRNA sequence reads.Changes in land-use led to a significant decrease in these dominant phylotypes down to 33.4%.In contrast,the phylotypes with low abundance,such as Acidobacteria,Chloroflexi,Nitrospira,and Gammaproteobacteria,increased sharply from 4.5%-5.9%in the native soil to 20.9%-30.2%of the total 16S rRNA gene sequences in the cultivated soils except for the soil from the shrubland.These contrasting changes in the major taxa appear to be correlated with the changes in soil attributes.For instance,bacterial and archaeal amoA genes were found to be 960-and 3 800-fold more abundant in the soil from the 100-year farmland than the native soil.The changes in numerically less dominant nitrifying phylotypes are consistent with soil inorganic nitrogen dynamics.Quantification of the 16S rRNA genes demonstrated that bacteria and archaea were about two to three orders of magnitude more abundant in the cultivated soil than in the native soil.Hence,land-use type affects the soil bacterial community structure,which has profound consequences on ecosystem function.     

利用PCR-DGGE技术研究长期自然恢复、种植作物和裸地条件下黑土土壤细菌群落结构变化

Soil microbial biomass and community structures are commonly used as indicators for soil quality and fertility. A investigation was performed to study the effects of long-term natural restoration, cropping, and bare fallow managements on the soil microbial biomass and bacterial community structures in depths of 0--10, 20--30, and 40--50 cm in a black soil (Mollisol). Microbial biomass was estimated from chloroform fumigation-extraction, and bacterial community structures were determined by analysis of 16S rDNA using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). Experimental results showed that microbial biomass significantly declined with soil depth in the managements of restoration and cropping, but not in the bare fallow. DGGE profiles indicated that the band number in top 0--10 cm soils was less than that in depth of 20--30 or 40--50 cm. These suggested that the microbial population was high but the bacterial community structure was simple in the topsoil. Cluster and principle component analysis based on DGGE banding patterns showed that the bacterial community structure was affected by soil depth more primarily than by managements, and the succession of bacterial community as increase of soil depth has a similar tendency in the three managements. Fourteen predominating DGGE bands were excised and sequenced, in which 6 bands were identified as the taxa of Verrucomicrobia, 2 bands as Actinobacteria, 2 bands as α-Proteobacteria, and the other 4 bands as δ-Proteobacteria, Acidobacteria, Nitrospira, and unclassified bacteria. In addition, the sequences of 11 DGGE bands were closely related to uncultured bacteria. Thus, the bacterial community structure in black soil was stable, and the predominating bacterial groups were uncultured.     

不同细菌饲喂细菌线虫对土壤细菌数量、活性以及群落结构的影响

The effects of bacterial-feeding nematodes on bacterial number, activity, and community composition were studied through a microcosm experiment using sterilized soil inoculated with soil bacteria （soil suspension） and with bacteria and three species of bacterial-feeding nematodes （ Cephalobus persegnis, Protorhabditis filiformis, and Caenorhabditis elegans）. Catalyzed reporter deposition-fluorescence in situ hybridization, CO2 evolution, and denaturing gradient gel electrophoresis （DGGE） of PCR ampli- fied 16S rRNA gene fragments were used to investigate bacterial numbers, antivity, and community composition, respectively. Our results showed that bacterial numbers and activity significantly increased in the presence of bacterial-feeding nematodes, which indicated that bacterial-feeding nematodes had a significant positive effect on soil bacteria. The different nematode species had different effects on bacterial numbers and activity. C. persegnis and P. filiformis, isolated from native soil, increased the bacterial number and activity more than C. elegans. The DGGE analysis results showed that dominant bacterial species significantly differed among the treatments, which suggested that bacterial-feeding nematode species modified the bacterial community composition in soil. Further gene sequence analysis results showed that the dominant bacterial species in this study were gram-negative bacteria. Given the completely same conditions except nematode species, the varied selective feeding behavior of different nematode species was the most likely reason for the altered bacterial community composition. Overall, the alteration of bacterial numbers, activity and community composition resulting from the bacterial-feeding nematodes may ult!mately affect soil ecological functioning and processes.     

Genomic characterization of multidrug-resistant extraintestinal pathogenic Escherichia coli isolated from grain culture soils

Multidrug-resistant (MDR) Escherichia coli, mainly extraintestinal pathogenic E. coli (ExPEC), has been widely reported in infections worldwide. In agricultural soils, manure is a hotspot for the dissemination of antimicrobial resistance genes (ARGs) and pathogenic bacteria; however, MDR bacteria have also been reported in soils with no history of manure use. In addition, cross-resistance and co-resistance have been described as responsible for the metal-driven selection of bacteria resistant to antimicrobials. Therefore, the aim of this study was to analyze three MDR E. coli isolates obtained from Brazilian grain culture soil samples with no history of manure use by whole-genome sequencing. The MDR E. coli isolates were recovered from soils from corn and coffee fields, and presented resistance to β-lactams, quinolones, aminoglycosides, tetracyclines, sulphonamides, and dihydrofolate reductase inhibitor. Resistome analysis showed ARGs to several antimicrobials (i.e., β-lactams, tetracyclines, aminoglycosides, sulphonamides, trimethoprim, phenicols, fosfomycin, and macrolides) as well as several metal resistance genes and antibacterial biocide resistance genes. In addition, known mutations in quinolone-resistance-determining regions of GyrA (Ser83Leu and Asp87Asn), ParE (Ser458Thr), and ParC (Ser80Ile) were also detected. Virulome analysis showed the presence of virulence genes (lpfA, mcmA, gad, mchF, iroN, cma, and iss) associated with ExPEC. Multidrug-resistant ExPEC isolates were assigned to phylogenetic group B1. The presence of MDR B1-ExPEC in soil samples shows the ability of these isolates to survive in soils. This study reports for the first time some sequence types (i.e., ST345, ST448, and ST1146) of MDR E. coli in Brazilian soils. Therefore, these findings contribute to the monitoring of antimicrobial resistance and surveillance studies based on whole-genome sequencing worldwide.     

Effect of indaziflam on microbial activity and nitrogen cycling processes in an orchard soil

Indaziflam is a preemergent herbicide widely used for the control of weeds in pecan (Carya illinoinensis) orchards in the southwestern region of the United States. Given the paucity of data regarding the effect of indaziflam on the biochemical properties of soils supporting pecan production, this study was conducted to evaluate the effects of different application rates of indaziflam on soil microbial activity, diversity, and biochemical processes related to nitrogen (N) cycling. During two consecutive growing seasons (2015 and 2016), soil samples were obtained from experimental mesocosms consisting of soil-filled pots where pecan saplings were grown and treated with indaziflam applied at two different rates (25 and 50 g active ingredient (ai) ha^-1, with the higher rate being slightly lower than the recommended field application rate of 73.1 g ai ha^-1). Soil samples were collected approximately one week before and one week after herbicide application for determination of soil microbial biomass and diversity, N mineralization, and β-glucosaminidase activity. Soil samples collected from the control mesocosms without herbicide application were treated in the laboratory with two rates of indaziflam (75 and 150 g ai ha^-1) to determine the immediate effect on microbial activity. No significant effect of herbicide treatment on soil respiration and microbial biomass was detected. The results showed a slight to moderate decrease in microbial diversity (7% in 2015 and 44% in 2016). However, decreased β-glucosaminidase activity with herbicide treatment was observed in soils from the mesocosms (33%) and soils treated with indaziflam in the laboratory (45%). The mineral N pool was generally dominated by ammonium after indaziflam application, which was consistent with the drastic decrease (75%) in nitrification activity measured in the laboratory experiment. The results of this study indicate that indaziflam, even when applied at higher than recommended rates, has limited effects on soil microbial activity, but may affect N cycling processes.     

用熏蒸提取法校正酸性红壤的KEC值

Commonly used K_EC value (0.45) of the fumigation-extraction (FE) method was obtained on the basis of temperate neutral soils. To ascertain its applicability to acidic red soils widespread in southern China and other subtropical regions, the K_EC value was investigated based on 8 acidic red soils by in situ labelling of native soil microorganisms using ¹⁴C-labelled glucose. Realistic K_EC value for red soils could be obtained by in situ ¹⁴C-labelling as long as an incubation period of 72 h is adopted after addition of ¹⁴C glucose to soil. The single K_EC values for the eight red soils ranged from 0.27 to 0.35 and averaged 0.31. Lower K_EC value obtained in red soils probably resulted from different soil quality, compared with other types of soil, which causes possible changes in microbial community structure and extractability of cellular component. Microbial biomass C contents of the eight red soils measured using a unique and constant K_EC value of 0.45 decreased by 22.2%~40% in comparison to those using variable K_EC values. The results suggest that microbial biomass C would be significantly underestimated using the present K_EC value and a calibration of the K_EC value is necessary for red soils.     

镉胁迫下的实验室放线菌种群结构变化的DGGE分析

The actinomycete populations and functions in cadmium (Cd) contaminated soil were investigated by the cultivationindependent molecular methods. The genomic DNA was extracted and purified from soil adulterated with various concentrations of Cd in the laboratory. The partial 16S rDNA genes were amplified by polymerase chain reaction (PCR) using specific primers bound to evolutionarily conserved regions within these actinomycete genes. The diversity in PCRamplified products, as measured by denaturing gradient gel electrophoresis (EGGE), was used as a genetic fingerprint of the population. Principle component analysis and Shannon-Weaver diversity index (H) analyses were used to analyze the DGGE results. Results showed that the two principal components accounted for only a low level of the total variance. The value H in contaminated soil was lower than that in the control at later stages of cultivation, whereas at earlier stages it was higher. Among the six sampling time points, the first, fifth and sixth weeks had the highest values of H. Significantly negative correlations between bioavailable Cd concentration and H values existed in the samples from weeks 2 (R = 0.929, P < 0.05) and 4 (R =0.909, P < 0.05). These results may shed light on the effect of Cd on the soil environment and the chemical behavior and toxicity of Cd to actinomycetes.     

苏云金芽孢杆菌菌剂对棉花根际土壤细菌数量及多样性的影响

采用稀释平板培养法与PCR-DGGE技术, 以阿维菌素为阳性对照, 水为阴性对照, 研究了大田喷施推荐剂量(0.1 kg·hm^-2)和高剂量(10 kg·hm^-2)苏云金芽孢杆菌(Bt)菌剂对棉花根际土壤细菌种群数量及结构的影响。结果表明, 喷雾处理后1~3 d, 不同处理组土壤细菌数量间无显著性差异, 在3 d时细菌数量均值达到最大, 之后开始下降, 12 d后清水对照、推荐剂量Bt菌剂、高剂量Bt菌剂处理组土壤细菌数量均值维持在4.0×107 CFU·g^-1左右; 推荐剂量Bt菌剂处理样品土壤细菌数量在6 d时显著高于清水对照, 其余时间与清水对照间无显著性差异; 高剂量Bt菌剂处理与清水对照在整个试验期间均无显著性差异; 阿维菌素处理组土壤细菌数量在0~6 d内与清水对照无显著性差异, 而在12~45 d内显著低于其他3个处理组。DGGE图谱显示, Bt菌剂处理对棉花根际土壤17种细菌均无显著抑制作用。聚类分析结果表明, Bt菌剂对土壤细菌群落结构的扰动在12 d后得到恢复。与阴性对照组相比, Bt菌剂对土壤细菌多样性指数无显著影响, 而阳性对照阿维菌素对土壤细菌种群消长和多样性指数有较强的影响。对DGGE图谱中17条电泳条带的序列分析, 证明棉花根际土壤中存在起固氮作用的慢生根瘤菌属细菌和具有污染修复与净化活性的鞘脂菌属、鞘氨醇单胞菌属和红球菌属细菌。Bt菌剂与阿维菌素处理均对这些土壤有益菌群无明显不利影响。总体结果表明, Bt菌剂无论是在正常推荐剂量下还是在较高剂量(推荐剂量的100倍)下使用, 对棉花根际土壤微生态环境产生的冲击都较小, 是一种生态安全性较高的生物农药。     

Functional stability of the nitrate-reducing community in grassland soils towards high nitrate supply

To study the effects of short-term fluctuation of nitrate concentrations on the nitrate-reducing community, repacked soil cores were amended with 0, 100 and soil and incubated for 3, 7 and 14 days, respectively. The nitrate reductase activity was determined in a laboratory-based enzyme assay. In parallel, the community structure of nitrate-reducing microorganisms was characterised by RFLP-PCR using the functional gene narG, which encodes the catalytic site of the membrane-bound nitrate reductase. The community structure remained constant over the experimental period indicating that this functional community is characterised by a high resistance towards fluctuating nitrate concentrations. Decreases in nitrate concentration as well as increase in pH values indicated a very active nitrate-reducing community under nitrate addition. Surprisingly, inhibition of nitrite reductase by 2,4-dinitrophenol, which is a precondition for the measurement of nitrate reductase activity, could not be achieved in the treatment despite increased concentrations of the inhibitor. However, comparison of the nitrate reductase in the control and the treatment showed a significant increase in the latter at day 3. No further differences were observed at days 7 and 14, which suggests a high resilience of the nitrate reductase activity.     

Diversity and Characterization of Potential H2-Dependent Fe(Ⅲ)-Reducing Bacteria in Paddy Soils

Microbial ferric iron reduction, with organic carbon or hydrogen as the electron donor, is one of the most important biogeochemical processes in anoxic paddy soils; however, the diversity and community structure of hydrogen-dependent dissimilatory iron-reducers remain unknown. Potential H2-dependent Fe(III)-reducing bacteria in paddy soils were explored using enrichment cultures with ferrihydrite or goethite as the electron acceptor and hydrogen as the electron donor. Terminal restriction fragment length polymorphism (T-RFLP) analysis and cloning/sequencing were conducted to reveal bacterial community structure. Results showed that Geobacter and Clostridium were the dominant bacteria in the enrichment cultures. Fe(III) oxide mineral phases showed a strong effect on the community structure; Geobacter and Clostridium were dominant in the ferrihydrite treatment, while Clostridium spp. were dominant in the goethite treatment. These suggested that H2-dependent Fe(III)-reducing bacteria might be widely distributed in paddy soils and that besides Geobacter, Clostridium spp. might also be an important group of H2-dependent Fe(III)-reducing microorganisms.     

Distinctive fungal and bacterial communities are associated with mats formed by ectomycorrhizal fungi

The distinct rhizomorphic mats formed by ectomycorrhizal Piloderma fungi are common features of the organic soil horizons of coniferous forests of the Pacific Northwest. These mats have been found to cover 25-40% of the forest floor in some Douglas-fir stands, and are associated with physical and biochemical properties that distinguish them from the surrounding non-mat soils. In this study, we examined the fungal and bacterial communities associated with Piloderma mat and non-mat soils. Each mat and non-mat area was repeatedly sampled at four times throughout the year. Characterization of the mat activity and community was achieved using a combination of N-acetylglucosaminidase (NAGase) enzyme assays, and molecular analysis of fungal and bacterial communities using T-RFLP profiles, clone libraries, and quantitative PCR. Piloderma mats had consistently greater NAGase activity across all dates, although the magnitude of the difference varied by season. Furthermore, we found distinct fungal and bacterial communities associated with the Piloderma mats, yet the size of the microbial populations differed little between the mat and non-mat soils. Significant temporal variation was seen in the NAGase activity and in the sizes of the fungal and bacterial populations, but the community composition remained stable through time. Our results demonstrate the presence of two distinct microbial communities occupying the forest floor of Douglas-fir stands, whose populations and activities fluctuate seasonally but with little change in composition, which appears to be related to the physiochemical nature of mat and non-mat habitats.     

Influence of hydrological fluxes on the structure of nitrate-reducing bacteria communities in a peatland

Factors influencing nitrate dynamics and nitrate-reducing bacteria in peat soil in the field, were investigated in laboratory experiments. A previous study had indicated that the on-site effects of redox conditions and nutrient fluxes on microbial activity were influenced by hydrological conditions. However, the laboratory experiments indicated that peat samples from sites under different hydrological regimes exhibited different microbial activities independently of oxygenation conditions. The effects of redox conditions and nutrient fluxes (i.e. influence of NO₃⁻ and O₂ concentration) on the nitrate reducer community were therefore assessed. Microbial community structures in peat samples from sites under different hydrologic regimes were compared using Terminal-Restriction Fragment Length Polymorphism diversity signatures of the narG gene. This gene encodes the catalytic subunit of the nitrate reductase. Unexpectedly, the nitrate reducer communities were very similar at the beginning of the experiment whatever the peatland soil analysed. However, a strong structuration and divergence within the nitrate reducer communities, that was site-dependent, was evident after 76 h of incubation. These modifications within the microbial communities seemed to be due to differences in peat saturation at the sampling sites resulting from the different hydrological regimes. Of the forcing variables tested, oxygenation had a slight effect on the composition of the nitrate-reducers' community whereas nitrate addition had no effect. This study shows that a physical constraint such as hydrological regime might be considered important in microbial community composition.     

三种农田土壤中氨氧化细菌amoA基因多样性比较分析

比较分析中国东部不同季风气候区中海伦黑土(HL)、封丘潮土(FQ)和鹰潭红壤(YT)3种土壤氨氧化细菌amoA基因多样性。采用非培养方法直接从土壤中提取微生物总DNA,用氨氧化细菌amoA基因特异引物扩增总DNA,构建了3种土壤amoA基因文库,并对文库进行限制性长度多态性(RFLP)分析。HL、FQ和YT的amoA基因文库克隆数量分别为49、50和48个,相应的RFLP类型数为10、10和14个OTUs,其中有4个OTUs为三种土壤共有;YT中氨氧化细菌amoA基因多样性指数最高,FQ最低;HL和FQ群落的相似为70%,HL与YT的相似度为50%,而FQ和YT之间仅为42%,说明氨氧化细菌具有地理分布的规律:17个amoA基因序列可以被聚成6个cluster,分属Nitrosospira和Nitrosomonas两个属。三种农田土壤中均存在丰富的氨氧化细菌,表明氨氧化细菌在农田土壤氮素循环中具有重要作用。     

盐胁迫油菜根际中含假单胞菌（Pseudomonas spp.1）的氨基环丙烷-1-羧酸 (ACC) 脱氨基酶特征研究

When exposed to biotic or abiotic stress conditions,plants produce ethylene from its immediate precursor 1-aminocyclopropane-1-carboxylate(ACC),leading to retarded root growth and senescence.Many plant growth-promoting rhizobacteria contain the enzyme ACC deaminase and this enzyme can cleave ACC to form α-ketobutyrate and ammonium,thereby lowering levels of ethylene.The aim of this study was to isolate and characterize ACC deaminase-producing bacteria from the rhizosphere of salt-stressed canola(Brassica napus L.).Out of 105 random bacterial isolates,15 were able to utilize ACC as the sole source of nitrogen.These 15 isolates were also positive for indole acetic acid(IAA) production.Phylogenetic analysis based on partial 16 S rDNA sequences showed that all isolates belonged to fluorescent Pseudomonas spp.In the canola rhizosphere investigated in this study,Pseudomonas fluorescens was the dominant ACC deaminase-producing species.Cluster analysis based on BOX-A1R-based repetitive extragenic palindromic-polymerase chain reaction(BOX-PCR) patterns suggested a high degree of genetic variability in ACC deaminase-producing P.fluorescens strains.The presence of indigenous ACC-degrading bacteria in the rhizosphere of canola grown in saline soils indicates that these bacteria may contribute to salinity tolerance.     

The under-recognized dominance of Verrucomicrobia in soil bacterial communities

Verrucomicrobia are ubiquitous in soil, but members of this bacterial phylum are thought to be present at low frequency in soil, with few studies focusing specifically on verrucomicrobial abundance, diversity, and distribution. Here we used barcoded pyrosequencing to analyze verrucomicrobial communities in surface soils collected across a range of biomes in Antarctica, Europe, and the Americas (112 samples), as well as soils collected from pits dug in a montane coniferous forest (69 samples). Data collected from surface horizons indicate that Verrucomicrobia average 23% of bacterial sequences, making them far more abundant than had been estimated. We show that this underestimation is likely due to primer bias, as many of the commonly used PCR primers appear to exclude verrucomicrobial 16S rRNA genes during amplification. Verrucomicrobia were detected in 180 out of 181 soils examined, with members of the class Spartobacteria dominating verrucomicrobial communities in nearly all biomes and soil depths. The relative abundance of Verrucomicrobia was highest in grasslands and in subsurface soil horizons, where they were often the dominant bacterial phylum. Although their ecology remains poorly understood, Verrucomicrobia appear to be dominant in many soil bacterial communities across the globe, making additional research on their ecology clearly necessary.     

Bacterial diversity and community structure along different peat soils in boreal forest

Bacteria in peat forest soil play important role in global carbon cycling. The distribution of bacteria population in different peat soils as a whole and how forest management practices alter the bacterial populations are still poorly known. Using pyrosequencing analysis of 16S rRNA gene, we quantified the diversity and community structure of bacteria in eight peat forest soils (pristine and drained) and two mineral forest soils from Lakkasuo, Finland with either spruce-dominant or pine-dominant tree species. In total, 191,229 sequences which ranged from 15,710 to 22,730 per sample were obtained and affiliated to 13 phyla, 30 classes and 155 genera. The peat forest soils showed high bacterial diversity and species richness. The tree species seems to have more strong impact on the bacterial diversity than the type of peat soil, which drives the changes in bacterial community structure. The dominant taxonomic groups across all soils (>1% of all sequences) were Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, Planctomycetes and Verrucomicrobia. The relative abundance of bacteria phylum and genus differed between soil types and between vegetation. Significant differences in relative abundance of bacteria phyla were only found for Gemmatimonadetes and Cyanobacteria between the pristine and the drained peat forest soils. At genus level, the relative abundance of several genera differed significantly between the peat soils with same or different tree species, including Burkholderia, Caulobacter, Opitutus, Mucilanginibacter, Acidocella, Mycobacterium, Bradyrhizobium, Dyella and Rhodanobacter.