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.     

Effects of soil invertebrates on the survival of some genetically engineered bacteria in leaf litter and soil

Seven bacterial strains, most of them bearing natural or recombinant plasmids, were introduced in oak leaf litter or soddy-podzolic soil. In these substrata, which contained litter-dwelling diplopods and isopods, or endogenic earthworms, bacteria survival was followed. In the absence of the animals, the numbers of introduced strains gradually decreased. In the presence of the animals, plasmid-bearing strains of Pseudomonas putida survived at 10⁵–10⁷ CFUs g^-1 up to 1.5 months in both leaves and soil. The total numbers of bacteria found in excrements from the soil macrofauna were 5–15 times higher than in the food. The numbers of P. putida in the excrements were equal to or higher than in the food. The numbers of Pseudomonas stutzeri JM302 (pLV1013) and Azospirillum brasiliense ATCC29710 (pFACII) in the excrements were always 2–10 times lower than in the food. The digestive fluid taken from the middle part of the gut of the diplopod Pachyiulus flavipes showed a strong antibacterial activity. Those bacteria with lower survival in the gut appeared to be more sensitive to digestion by the midgut fluid. In contrast, the hindgut fluid did not suppress the viability of P. stutzeri JM302 (pLV1013). We postulate that the introduced bacteria partially survive the midgut passage and then multiply with a high growth rate in the hindgut of the animals. The environmental consequences of the interactions between soil invertebrates and the released bacteria are discussed.Dedicated to Professor J. C. G. Ottow on the occasion of his 60th birthday     

Screening of soil bacteria for plasmids carrying antibiotic resistance

Summary To evaluate the role of plasmids in soil communities antibiotic-resistant bacteria have been isolated from soil. Among them, 419 l-aminopeptidase positive strains (Gram-negative) and 28 l-aminopeptidase negative strains (Gram-positive) were screened for the presence of plasmids. None of the Gram-negative organisms contained plasmids. Among the Gram-positive bacteria plasmid-harboring strains were detected.     

沼泽红假单胞菌与枯草芽孢杆菌混施对水稻根域细菌多样性与功能的影响

[目的]微生物菌肥作为一种绿色环保的生物肥料,可以改善土壤质量,促进作物生长.以水稻根际和根表微生物为对象,探究不同微生物菌肥单施和混施对其群落多样性和功能的影响.[方法]采用盆栽试验,设单施沼泽红假单胞菌(Rhodopseudomonas palustris)、单施枯草芽孢杆菌(Bacillus subtilis)及...     

Growth rate of bacteria is affected by soil texture and extraction procedure

Effects of soil texture on the extraction efficiency of bacteria from soils and on biosynthetic activity of the extracted bacteria were studied. Bacterial extracts were prepared from three soils of different texture by homogenization (ultrasonication and mixing) or by homogenization-centrifugation at different speeds. Bacterial biosynthetic activity was estimated using thymidine and leucine incorporation techniques. In each step of the extraction procedure, a higher extractability of bacteria was obtained in finer soils than in coarse soil. Also cell-specific growth rates of bacteria were higher in the finer soils than in the coarse soil. However, in all soils, the extracted bacteria always had significantly lower cell-specific thymidine and leucine incorporation rates than the bacteria in soil slurries and thus did not represent so well the bacterial growth in the original soils. The total declines in cell-specific incorporation rates caused by the extraction were larger in fine soil (96-98%) than in coarse soil (90%), but bacteria in the coarse soil were more responsive to only minor intervention. The homogenization-centrifugation method eliminated the differences in bacterial biosynthesis found when working with soil slurries. Therefore, we recommend using of soil slurries or, optionally, soil suspensions to compare bacterial biosynthetic activity among soils of different textures.     

复垦土壤细菌群落结构及其与土壤肥力的关系

为了解两淮煤矿区复垦状况及其对土壤微生物的影响机制,合理人工干预,快速有效提高复垦土壤生产力,本研究以煤矸石充填复垦土壤为研究对象,通过野外调查与采样分析,采用Illumina MiSeq 高通量测序分析土壤细菌特定基因片段V4 区域,基于非度量多维尺度分析、冗余分析、方差分析、肥力指数、回归模型方法,对矸石充填土壤不同复垦方向的土壤细菌优势群落和生物多样性进行了探索,明晰土壤细菌群落及其与土壤肥力的响应作用。研究结果表明：细菌群落组成上,不同复垦方向对细菌优势群落分布并无显著性影响,变形菌门、酸杆菌门和放线菌门菌群为主要优势菌群。土壤微生物多样性层面上,表层土壤微生物有较高的丰富度和多样性,均匀度并无显著性差异。微生物多样性在不同复垦方向不存在显著性差异,Shannon_Wiener指数介于5.23～6.91之间,Chao1指数为867.1～5436,Pielou指数介于0.79～0.84之间,表中层同深层土壤的细菌群落结构具有差异性。TN、SOM、AP和AK是影响土壤细菌群落的主要肥力因子,土壤肥力质量指数与奇古菌门相对丰度呈显著正相关（P＜0.01）,同链霉菌属呈显著负相关（P＜0.05）,在一定程度上可将二者的相对丰度作为评价复垦土壤肥力状况的重要生物指标。研究成果可为两淮矿区矸石充填复垦土壤在微生物层面提高肥力质量提供理论支持。     

Isolation of culturable phosphobacteria with both phytate-mineralization and phosphate-solubilization activity from the rhizosphere of plants grown in a volcanic soil

Chilean volcanic soils contain large amounts of total and organic phosphorus, but P availability is low. Phosphobacteria [phytate-mineralizing bacteria (PMB) and phosphate-solubilizing bacteria (PSB)] were isolated from the rhizosphere of perennial ryegrass (Lolium perenne), white clover (Trifolium repens), wheat (Triticum aestivum), oat (Avena sativa), and yellow lupin (Lupinus luteus) growing in volcanic soil. Six phosphobacteria were selected, based on their capacity to utilize both Na-phytate and Ca-phosphate on agar media (denoted as PMPSB), and characterized. The capacity of selected PMPSB to release inorganic P (Pi) from Na-phytate in broth was also assayed. The results showed that from 300 colonies randomly chosen on Luria–Bertani agar, phosphobacteria represented from 44% to 54% in perennial ryegrass, white clover, oat, and wheat rhizospheres. In contrast, phosphobacteria represented only 17% of colonies chosen from yellow lupin rhizosphere. This study also revealed that pasture plants (perennial ryegrass and white clover) have predominantly PMB in their rhizosphere, whereas PSB dominated in the rhizosphere of crops (oat and wheat). Selected PMPSB were genetically characterized as Pseudomonas, Enterobacter, and Pantoea; all showed the production of phosphoric hydrolases (alkaline phosphatase, acid phosphatase, and naphthol phosphohydrolase). Assays with PMPSB resulted in a higher Pi liberation compared with uninoculated controls and revealed also that the addition of glucose influenced the Pi-liberation capacity of some of the PMPSB assayed.     

脱硫废弃物改良宁夏盐渍化土壤对细菌和氨氧化微生物丰度的影响

为探明脱硫废弃物改良盐渍化土壤对微生物群落的影响效果,在2009~2010年,采用田间试验,施用不同量的脱硫废弃物(0、0.74、1.49、2.25、3.00 kg·m-2),研究了脱硫废弃物对盐渍化土壤细菌、氨氧化细菌和氨氧化古菌的影响。试验结果表明:0~20 cm土层,Ca2+和NO-3-N含量随着施用量增加而增加;土壤p H值、电导率值显著下降。实时荧光定量PCR(q PCR)分析结果表明,微生物丰度随着脱硫废弃物的施用发生变化,但这种变化并不与脱硫废弃物的施用量呈线性关系。在0~20 cm土壤层,施脱硫废弃物使得细菌16S rRNA基因拷贝数处理组显著高于对照组。氨氧化古菌与氨氧化细菌基因拷贝数在T2和T4处理高于其它处理。20~40 cm土层各处理间微生物群落没有显著变化,或没有出现规律的变化趋势。因此,脱硫废弃物增加了土壤细菌和氨氧化功能基因丰度,且对上层土壤影响更为显著。本研究中施用脱硫废弃物1.49 kg·m-2(T2)是引起细菌和氨氧化功能基因丰度增加的施用量。     

Copper and temperature modify microbial communities,ammonium and sulfate release in soil

Recent studies suggest an important role of thermophilic bacterial communities of the Phylum Firmicutes on soil C, N and S cycling, and a positive effect on crop productivity through the production of sulfate (SO $ _4^{2 - } $ ) and ammonium (NH $ _4^+ $ ), essential plant nutrients. Copper (Cu) is commonly supplemented to soils as a fungicide in phytosanitary treatments although its consequences to the bacterial communities is frequently overlooked. Herein, we report on the influence of temperature and Cu on the microbial communities, namely those of the Phylum Firmicutes, from a soil collected at an olive orchard in S Portugal. Community fingerprints and band identification through sequencing was combined with measurement of SO $ _4^{2 - } $ and NH $ _4^+ $ production at different supplemented amounts of Cu and at moderate and high temperatures (30°C and 50°C, respectively). Both temperature and Cu induced changes in these communities, selecting for specific bacteria. Temperature induced the dominance of Brevibacillus, and Cu addition to soil caused a reduction of SO $ _4^{2 - } $ release by soil bacteria. Ammonium production during bacterial growth at moderate and high temperatures was not affected by Cu addition. A Cu‐tolerant thermophilic isolate, belonging to the Bacillus genus, showed significant inhibition by high Cu concentrations and a reduction of NH $ _4^+ $ release during growth; genera Brevibacillus and Bacillus have been previously reported as high NH $ _4^+ $ and SO $ _4^{2 - } $ producers of the Firmicutes phylum. Results indicate that Cu treatments select specific tolerant bacterial strains which could influence natural soil fertilization in Cu‐treated orchards.     

光合细菌和有机肥对土壤主要微生物类群的影响

将光合细菌菌液和发酵有机肥施入农田土壤，研究表层土壤中微生物区系变化。结果表明，光合细菌和有机肥显著增加土壤中放线菌、异养细菌、固氮菌、氨化细菌和硝化细菌数量，减少反硝化细菌数量，改善土壤微生物区系，光合细菌作用比有机肥更稳定和持久。光合细菌还能明显降低真菌数量，提高放线菌／真菌比值，促进土壤健康。     

几株产荚膜细菌在土壤水稳性团聚体形成中的作用

试验研究几株产荚膜细菌在土壤水稳定性团聚体形成中的作用结果表明,菌株次生代谢产物即发酵物在土壤水稳定性团聚体形成中起作用,而菌体本身不起作用。细菌能够显著促进>0.25mm土壤水稳定性团聚体的形成,其效果随加入C源物质而异,蔗糖效果优于小麦秸秆和玉米秸秆,风化煤几乎不起作用。加入不同C源物质时,菌株之间表现出明显差异。     

选用解磷菌剂改善缺磷土壤磷素的有效性

山西省大部分土壤为石灰性土壤,耕地土壤缺磷较严重,施入土壤的化学磷肥极易被固定,为了提高缺磷土壤磷素的有效性,分离筛选的B2和B67菌株研制的解磷菌剂(后称菌剂),首先接种到以磷酸三钙为唯一磷源的培养基中,液体速效磷含量比CK提高12.92倍和9.18倍,然后又接种到其它典型缺磷土壤中,可使土壤速效磷含量较CK增加1.35~3.04倍,且发现其溶磷效果和液体的pH值有关,也与土壤磷酸酶活性和有效活菌数相关,而且菌剂在提高土壤速效磷含量的同时,也提高了土壤速效钾的含量。另外菌剂在缺磷的盆栽和大田试验中取得相同效果,除显著提高土壤速效磷含量,培肥土壤外,同时还有改善作物农艺性状,提高作物产量的功效。     

Low soil C:N ratio results in accumulation and leaching of nitrite and nitrate in agricultural soils under heavy rainfall

Nitrate (NO^-₃) and nitrite (NO₂^-) leaching threatens groundwater quality.Soil C:N ratio,i.e.,the ratio of soil organic carbon to total nitrogen,affects mineralization,nitrification,and denitrification;however,its mechanism for driving soil NO^-₃ and NO^-₂ accumulation and leaching remains unclear.Here,a field investigation in a fluvo-aquic soil and a soil column experiment were performed to explore the relation...     

Grouping of soil bacteria by analysis of colony formation on agar plates

Summary The colony formation of soil bacteria was studied in relation to incubation time. The process was simulated by a colony-forming curve (CFC) which was a superposition of several component curves (cCFC) given theoretically by the first-order reaction (FOR) model. This model had been previously proposed to define the colony formation of cells of a single culture. Soil bacteria were divided into several groups by these cCFC, as different types of bacteria produced their own colonies. Bacteria belonging to a single group grew at a similar rate on the plating medium and each group was characterized by a different growth rate. Most copiotrophic bacteria were fast growers and most oligotrophic bacteria slow growers.     

Long-time precipitation reduction and nitrogen deposition increase alter soil nitrogen dynamic by influencing soil bacterial communities and functional groups

The effects of precipitation reduction and nitrogen deposition increase on soil bacterial communities and functions impact soil nitrogen cycling. Seasonal changes could modify the effects of precipitation reduction and nitrogen deposition increase on bacterial communities and functions by changing soil environments and properties. Understanding soil microbial communities and the seasonal response of functions to precipitation reduction and nitrogen deposition increase may be important for the accurate prediction of changes in the soil nitrogen dynamics. Thus, a long-term field simulation experiment of nitrogen deposition increase and throughfall exclusion was established to investigate soil bacterial communities’ response to nitrogen deposition increase and/or precipitation reduction, with no nitrogen deposition increase and no precipation reduction as a control, in a temperate forest. We examined soil bacterial communities (Illumina sequencing) under different treatments during the winter, freezing-thawing cycle periods (FTCs), and growing season. The bacterial functional groups were predicted by the FAPROTAX database. The results showed that nitrogen deposition increase, precipitation reduction, the combined effect of nitrogen deposition increase and precipitation reduction, and seasonal changes significantly altered the soil bacterial community composition. Interestingly, by combining the result of a previous study in which nitrogen deposition increase increased the nitrous oxide flux in the same experimental system, the loss of soil nitrogen was increased by the decrease in denitrification and increase of nitrification bacteria under nitrogen deposition increase, while ammonification bacteria significantly increased and N-fixing bacteria significantly decreased with precipitation reduction compared to the control. In relation to seasonal changes, the aromatic-degrading, cellulolytic, and ureolytic bacteria were lowest during FTCs, which indicated that FTCs might inhibit biodegradation. Nitrification and nitrite-oxidizing bacteria increased with nitrogen deposition increase or precipitation reduction and in FTCs compared to the control or other seasons. The interaction between treatment and season significantly changed the soil bacterial communities and functions. These results highlight that nitrogen deposition increase, precipitation reduction, seasonal changes, and their interactions might directly alter bacterial communities and indirectly alter the dynamics of soil N.     

再生水灌溉水平对土壤盐分累积与细菌群落组成的影响

为探明再生水不同灌水水平下土壤盐分、氮素、磷素与细菌群落组成动态变化效应,采用室内土柱灌水试验,研究再生水、自来水不同灌水水平对土壤盐分、氮素、磷素及细菌群落组成结构的影响。结果表明:1)再生水灌溉相比自来水显著提高了0~60 cm土层盐分含量、磷素及0~30 cm土层氮素含量也有所提高,降低了土壤细菌群落多样性和OTU数量;充分灌溉相比非充分灌溉提高了深层土壤盐分含量,降低了深层土壤细菌群落多样性和种类数。2)不同处理土壤细菌类群以放线菌门(24.5%~40.6%)和变形菌门(22.4%~30.3%)为主。非充分灌溉下,再生水灌溉相比自来水提高了土壤放线菌门、绿弯菌门、厚壁菌门及酸杆菌门比例,降低了变形菌门比例;充分灌溉下,再生水灌溉相比自来水大幅度提高了土壤放线菌门和硝化螺旋菌门比例,降低了土壤变形菌门、绿弯菌门、酸杆菌门及厚壁菌门比例。无论是在充分灌溉还是非充分灌溉下,再生水灌溉均对土壤放线菌门表现为促进作用,对变形菌门表现为抑制作用。再生水充分灌溉相比非充分灌溉对土壤放线菌门和变形菌门具有促进作用,对土壤绿弯菌门、酸杆菌门和厚壁菌门具有抑制作用;再生水灌水水平越高,越有利于土壤中优势菌群的生长。3)各处理土壤细菌代谢通路丰度占比最大的为膜转运、碳水化合物代谢及氨基酸代谢,再生水辅以较高灌水水平能够显著促进表层土壤微生物膜转运、碳水化合物代谢及氨基酸代谢过程。因此,再生水较高灌水水平可促进土壤物质能量循环,且对土壤细菌代谢繁殖过程也可起到积极的调节作用。研究可为再生水灌溉下的土壤生态环境效应研究提供依据。     

Effect of soil bacteria on the ability of polycyclic aromatic hydrocarbons (PAHs) removal by Trametes versicolor and Irpex lacteus from contaminated soil

The effect of bacteria represented by indigenous soil microflora or a mixture of soil bacteria Pseudomonas aeruginosa and Rhodococcus erythropolis on fungal growth, extracellular enzyme production and polycyclic aromatic hydrocarbons (PAHs) biodegradation efficiency in soil of white-rot fungi Trametes versicolor and Irpex lacteus was investigated. Both fungi were able to colonize soil. The growth yields measured by ergosterol were about two-fold in I. lacteus after 10 weeks. Laccase was produced in T. versicolor cultures in the presence or absence of bacteria but live bacteria reduced the laccase levels in soil about 5 times. Manganese-dependent peroxidase (MnP) was not detected in T. versicolor cultures. The amounts of MnP and laccase in I. lacteus cultures were not affected by the presence of bacteria. T. versicolor was more efficient in PAH removal for all PAHs tested although its capacity to colonize soil was lower. The removal rates of PAHs by T. versicolor in sterile soil were 1.5-fold, 5.8-fold and 1.8-fold for 2-3-ring, 4-ring and 5-6-ring PAHs, compared to I. lacteus, respectively. I. lacteus showed a low efficiency of removal of pyrene, benzo[a]anthracene and benzo[k]fluoranthene, compared to T. versicolor, whereas chrysene and benzo[b]fluoranthene were degraded by neither fungus. The main effect of the presence of the indigenous microflora or R. erythropolis and P. aeruginosa was a significant decrease of degradation of total PAHs by both T. versicolor and I. lacteus. Weak fungal/bacterial synergistic effects were observed in the case of removal of acenapthylene, benzo[a]pyrene, dibenzo[a,h]anthracene and benzo[g,h,i]perylene by I. lacteus and acenapthylene by T. versicolor. However, the bacterial effects were different in the two fungi. PAH abiotic losses represented 15 and 21% of the total PAHs after 5 and 10 weeks, respectively; naphthalene and acenaphthene were removed from the soil due to volatilization.     

Pine sawdust as stimulator of the microbial community in post-arable afforested soil

Sawdust and wood residues are considered to be stimulators of microbiological change in soil and could be used in post-arable sites designed for afforestation. In this study, we discuss changes in bacteria numbers within selected groups in relation to soil type (arable and forest) and method of sawdust application. Sawdust was spread along planting rows and mixed with the soil or put directly under roots of planted seedlings. Applying sawdust under the roots increased the number of cellulolytic bacteria in all experimental treatments. On post-arable soil, adding sawdust in rows increased the number of copiotrophic bacteria and reduced the number of fluorescent bacteria and actinomycetes (ACT). In control forest soils, the number of copiotrophic, oligotrophic and spore-forming bacteria decreased simultaneously with increased ACT in all treatments. The number of fluorescent bacteria increased when sawdust was applied on forest sites under planted trees and decreased when sawdust was spread in planting rows. Oligotrophic bacteria also decreased in the latter case. We present a list of bacteria identified by DNA – 16S rRNA gene sequences. Adding sawdust to arable soils significantly changed the quantitative and qualitative composition of microbial communities.