Longitudinal changes in the bacterial community composition of the Danube River: a whole-river approach

The Danube River is the second longest river in Europe, and its bacterial community composition has never been studied before over its entire length. In this study, bacterial community composition was determined by denaturing gradient gel electrophoresis (DGGE) analysis of PCR-amplified portions of the bacterial 16S rRNA gene from a total of 98 stations on the Danube River (73 stations) and its major tributaries (25 stations), covering a distance of 2,581 km. Shifts in the bacterial community composition were related to changes in environmental conditions found by comparison with physicochemical parameters (e.g., temperature and concentration of nutrients) and the concentration of chlorophyll a (Chl a). In total, 43 distinct DGGE bands were detected. Sequencing of selected bands revealed that the phylotypes were associated with typical freshwater bacteria. Apparent bacterial richness in the Danube varied between 18 and 32 bands and correlated positively with the concentration of P-PO(4) (r = 0.56) and negatively with Chl a (r = -0.52). An artificial neural network-based model explained 90% of the variation of apparent bacterial richness using the concentrations of N-NO(2) and P-PO(4) and the distance to the Black Sea as input parameters. Between the cities of Budapest and Belgrade, apparent bacterial richness was significantly lower than that of other regions of the river, and Chl a showed a pronounced peak. Generally, the bacterial community composition developed gradually; however, an abrupt and clear shift was detected in the section of the phytoplankton bloom. Large impoundments did not have a discernible effect on the bacterial community of the water column. In conclusion, the riverine bacterial community was largely influenced by intrinsic factors.     

The influence of habitat heterogeneity on freshwater bacterial community composition and dynamics

Multiple forces structure natural microbial communities, but the relative roles and interactions of these drivers are poorly understood. Gradients of physical and chemical parameters can be especially influential. In traditional ecological theory, variability in environmental conditions across space and time represents habitat heterogeneity, which may shape communities. Here we used aquatic microbial communities as a model to investigate the relationship between habitat heterogeneity and community composition and dynamics. We defined spatial habitat heterogeneity as vertical temperature and dissolved oxygen (DO) gradients in the water column, and temporal habitat heterogeneity as variation throughout the open-water season in these environmental parameters. Seasonal lake mixing events contribute to temporal habitat heterogeneity by destroying and re-creating these gradients. Because of this, we selected three lakes along a range of annual mixing frequency (polymictic, dimictic, meromictic) for our study. We found that bacterial community composition (BCC) was distinct between the epilimnion and hypolimnion within stratified lakes, and also more variable within the epilimnia through time. We found stark differences in patterns of epilimnion and hypolimnion dynamics over time and across lakes, suggesting that specific drivers have distinct relative importance for each community.     

不同草田轮作模式土壤养分及细菌群落组成特征

为研究不同草田轮作模式下土壤养分及细菌群落的组成特征,以5年紫花苜蓿-1年小麦(A5W1)、5年紫花苜蓿-1年玉米(A5C1)、5年紫花苜蓿-2年小麦(A5W2)和5年紫花苜蓿-2年玉米(A5C2)草田轮作模式为对象,测定了土壤有机质、全氮、全磷、全钾、碱解氮、速效磷和速效钾含量,在此基础上,基于16S rRNA基因序列扩增子测序研究了4种轮作模式下耕层土壤细菌群落组成特征。结果表明:轮作第2年各土壤养分含量较第1年显著下降。细菌组成研究结果显示,4种轮作模式下占优势的菌门为变形菌门、放线菌门和厚壁菌门。土壤细菌群落优势属以丙酸杆菌属(Propionibacterium)、芽孢杆菌属(Bacillus)、链球菌属(Streptococcus)以及奈瑟氏球菌属(Neisseria)为主。土壤细菌多样性以A5C2轮作处理最高,A5C1最低;聚类分析显示A5W1和A5C1的组成最接近,其次是A5C2,A5W2的组成与前两者相差较大。土壤养分含量与几种优势属之间呈显著相关性(P<0.05 or P<0.01)。研究结果揭示了河西走廊灌溉区种植紫花苜蓿多年后轮作小麦和玉米改善土壤肥力...     

Effect of different carbon sources on community composition of bacterial enrichments from soil

Soil is a highly heterogeneous matrix, which can contain thousands of different bacterial species per gram. Only a small component of this diversity (maybe <1%) is commonly captured using standard isolation techniques, although indications are that a larger proportion of the soil community is in fact culturable. Better isolation techniques yielding greater bacterial diversity would be of benefit for understanding the metabolic activity and capability of many soil microorganisms. We studied the response of soil bacterial communities to carbon source enrichment in small matrices by means of terminal restriction fragment length polymorphism (TRFLP) analysis. The community composition of replicate enrichments from soil displayed high variability, likely attributable to soil heterogeneity. An analysis of TRFLP data indicated that enrichment on structurally similar carbon sources selected for similar bacterial communities. The same analysis indicated that communities first enriched on glucose or benzoate and subsequently transferred into medium containing an alternate carbon source retained a distinct community signature induced by the carbon source used in the primary enrichment. Enrichment on leucine presented a selective challenge that was able to override the imprint left by primary enrichment on acetate. In a time series experiment community change was most rapid 18 hours after inoculation, corresponding to exponential growth. Community composition did not stabilize even 4 days after secondary enrichment. Four different soil types were enriched on four different carbon sources. TRFLP analysis indicated that in three out of four cases communities enriched on the same carbon source were more similar regardless of which soil type was used. Conversely, the garden soil samples yielded similar enrichment communities regardless of the enrichment carbon source. Our results indicate that in order to maximize the diversity of bacteria recovered from the environment, multiple enrichments should be performed using a chemically diverse set of carbon sources.     

矿区高硫煤覆盖对土壤细菌群落组成和多样性的影响

【背景】土壤微生物生态研究对于矿区污染生态影响调查和矿区生态恢复都具有非常重要的意义,高硫煤覆盖对其下方土壤微生物群落的影响目前尚不清楚。【目的】探究煤矿区长期高硫煤覆盖对其下方土壤细菌群落组成和多样性产生的影响。【方法】从高硫煤矿附近煤场采集3种类型土壤样品(高硫煤覆盖层、高硫煤下方土壤、对照土壤),通过测定土壤理化性质和运用高通量测序技术研究高硫煤覆盖对土壤性质和细菌群落产生的影响。【结果】与对照土壤相比,高硫煤覆盖使其下方土壤pH值降低,硫酸盐、有机质、有效氮、有效磷含量升高。高硫煤覆盖使其下方土壤中细菌的多样性指数降低,细菌群落组成发生了较大改变。在属水平上,与对照土壤相比,高硫煤下方土壤中Bacillus的相对丰度较高;Acidiphilium与Sulfobacillus在3个样本组中的相对丰度呈现为高硫煤覆盖层>高硫煤下方土壤>对照土壤,硫氧化菌在高硫煤中的优势地位及其对下方土壤的影响由此可以得到证实。共现性网络分析表明,Acidiphilium和Sulfobacillus在高硫煤覆盖区域的土壤细菌群落中占有重要地位,对其他细菌类群影响非常大。【结论】高硫煤覆盖及硫氧化菌的优势存在,对高硫煤下方土壤的理化性质及细菌群落产生明显影响。研究结果有助于增进对矿区土壤微生物生态的认识,为高硫煤矿区生态恢复治理提供微生物学理论基础。     

玉米秸秆还田对土壤线虫数量动态与群落结构的影响

通过大田玉米秸秆还田试验研究了其对农田土壤线虫数量动态、属的种类及群落结构等的影响。结果表明:2013—2014连续两年试验期间,蠡玉35玉米秸秆还田(CR)与不还田对照处理(CK)共鉴定到土壤线虫36个属(CR 36个属,CK 30个属);其中,植食性线虫12个属(CR 12属,CK 10属),食细菌线虫15个属(CR 15属,CK 14属),食真菌线虫5个属(CR 5属,CK4属),捕/杂食线虫4个属(CR 4属,CK 2属)。秸秆还田处理与不还田处理相比,植食线虫和食真菌线虫的相对丰度降低,而食细菌线虫和杂/捕食线虫的相对丰度提高,且食细菌线虫的相对丰度显著提高达42.95%。此外,秸秆还田处理土壤线虫总数高于不还田对照处理,但差异不显著;而秸秆还田处理可显著增加食细菌线虫数量,增幅高达16.3%—125.6%。与不还田处理对照相比,秸秆还田处理可显著提高土壤线虫群落多样性指数(H')、属类丰富度(S)和线虫通路指数(NCR),但对群落均匀度(J)、瓦斯乐斯卡指数(WI)和总成熟指数(∑MI)的影响不显著。可见,玉米秸秆还田具有重要的生态学意义,可在一定程度上增加土壤线虫数量和种类多样性,进而使土壤生态系统向稳定健康的方向发展。     

炭基肥对植烟黄壤细菌、真菌群落结构和多样性的影响

【目的】探究施用炭基肥对植烟黄壤质量影响的微生物学机制,为应用炭基肥培育植烟黄壤肥力提供科学依据。【方法】2016年,以烤烟品种云烟87和贵州黄壤为供试材料,通过大田试验,设置不施肥(NF)、常规肥(CF,条施有机肥和烤烟专用基肥,穴施烤烟专用追肥)和炭基肥(BF,条施炭基有机肥和炭基复混肥,穴施烤烟专用追肥) 3个处理,2年后采集样品,采用Illumina Miseq高通量测序技术,剖析土壤细菌、真菌群落结构和多样性的响应差异,揭示影响微生物的主要土壤因子。【结果】与NF处理和CF处理比较,BF处理烤烟产量提高,土壤碱解氮和有效磷含量显著提高。BF处理土壤细菌OTUs数量最大(1592),显著大于其余两处理;土壤细菌丰富度和多样性指数最高。BF处理土壤真菌OTUs数量最小(280);土壤真菌丰富度和多样性指数最低。BF处理土壤细菌群落物种最多样,属于25个门,CF处理属于23个门,NF处理仅属于22个门。细菌门水平,BF处理拟杆菌门(Bacteroidetes)相对丰度(1.50%)提高,Latescibacteria相对丰度(0.11%)降低;与NF处理比较,拟杆菌门、Latesc...     

Shrub encroachment is associated with changes in soil bacterial community composition in a temperate grassland ecosystem

Plant and Soil - The growth and root morphology responses to soil phosphorus (P) fertility by five cultivars of Trifolium subterraneum (a temperate annual pasture legume) were examined to assess...     

Exploring the bovine rumen bacterial community from birth to adulthood

The mammalian gut microbiota is essential in shaping many of its host''s functional attributes. One such microbiota resides in the bovine digestive tract in a compartment termed as the rumen. The rumen microbiota is necessary for the proper physiological development of the rumen and for the animal''s ability to digest and convert plant mass into food products, making it highly significant to humans. The establishment of this microbial population and the changes occurring with the host''s age are important for understanding this key microbial community. Despite its importance, little information about colonization of the microbial populations in newborn animals, and the gradual changes occurring thereafter, exists. Here, we characterized the overall bovine ruminal bacterial populations of five age groups, from 1-day-old calves to 2-year-old cows. We describe the changes occurring in the rumen ecosystem after birth, reflected by a decline in aerobic and facultative anaerobic taxa and an increase in anaerobic ones. Some rumen bacteria that are essential for mature rumen function could be detected as early as 1 day after birth, long before the rumen is active or even before ingestion of plant material occurs. The diversity and within-group similarity increased with age, suggesting a more diverse but homogeneous and specific mature community, compared with the more heterogeneous and less diverse primary community. In addition, a convergence toward a mature bacterial arrangement with age was observed. These findings have also been reported for human gut microbiota, suggesting that similar forces drive the establishment of gut microbiotas in these two distinct mammalian digestive systems.     

Microbial community composition affects soil fungistasis

Most soils inhibit fungal germination and growth to a certain extent, a phenomenon known as soil fungistasis. Previous observations have implicated microorganisms as the causal agents of fungistasis, with their action mediated either by available carbon limitation (nutrient deprivation hypothesis) or production of antifungal compounds (antibiosis hypothesis). To obtain evidence for either of these hypotheses, we measured soil respiration and microbial numbers (as indicators of nutrient stress) and bacterial community composition (as an indicator of potential differences in the composition of antifungal components) during the development of fungistasis. This was done for two fungistatic dune soils in which fungistasis was initially fully or partly relieved by partial sterilization treatment or nutrient addition. Fungistasis development was measured as restriction of the ability of the fungi Chaetomium globosum, Fusarium culmorum, Fusarium oxysporum, and Trichoderma harzianum to colonize soils. Fungistasis did not always reappear after soil treatments despite intense competition for carbon, suggesting that microbial community composition is important in the development of fungistasis. Both microbial community analysis and in vitro antagonism tests indicated that the presence of pseudomonads might be essential for the development of fungistasis. Overall, the results lend support to the antibiosis hypothesis.     

Temporal dynamics of soil bacterial network regulate soil resistomes

Soil bacteria are diverse and form complicated ecological networks through various microbial interactions, which play important roles in soil multi-functionality. However, the seasonal effects on the bacterial network, especially the relationship between bacterial network topological features and soil resistomes remains underexplored, which impedes our ability to unveil the mechanisms of the temporal-dynamics of antibiotic resistance genes (ARGs). Here, a field investigation was conducted across four seasons at the watershed scale. We observed significant seasonal variation in bacterial networks, with lower complexity and stability in autumn, and a wider bacterial community niche in summer. Similar to bacterial communities, the co-occurrence networks among ARGs also shift with seasonal change, particularly with respect to the topological features of the node degree, which on average was higher in summer than in the other seasons. Furthermore, the nodes with higher betweenness, stress, degree, and closeness centrality in the bacterial network showed strong relationships with the 10 major classes of ARGs. These findings highlighted the changes in the topological properties of bacterial networks that could further alter antibiotic resistance in soil. Together, our results reveal the temporal dynamics of bacterial ecological networks at the watershed scale, and provide new insights into antibiotic resistance management under environmental changes.     

16S rDNA克隆文库法探索转基因香石竹对土壤细菌群落的影响

【目的】通过研究转基因香石竹对土壤细菌群落的影响,为转基因香石竹的环境安全性评价提供依据。【方法】通过构建16S rDNA克隆文库,分析种植转基因和非转基因香石竹的土壤中细菌的群落结构组成。【结果】转基因和非转基因香石竹土壤中,共有的菌群有变形菌门(Proteobacteria)、浮霉菌门(Planctomycetes)、酸杆菌门(Acidobacteria),其中α-变形菌门、β-变形菌门、浮霉菌门为优势菌群;而在放线菌门(Actinobacteria)、疣微菌门(Verrucomicrobia)及未培养菌(Uncultured bacterium clone)等菌群存在部分差异。【结论】通过16S rDNA克隆文库方法揭示了转基因香石竹的土壤中细菌多样性十分丰富,其栽培对土壤细菌群落结构影响有限。     

Land use alters bacterial growth dynamics in soil

Microbial growth and mortality are major determinants of soil carbon cycling. We measured in situ growth dynamics of individual bacterial taxa in cropped and successional soils in response to a resource pulse. We hypothesized that land use imposes selection pressures on growth characteristics. We estimated growth and death for 453 and 73 taxa, respectively. The average generation time was 5.04 ± 6.28 (SD; range 0.7–63.5) days. Lag times were shorter in cultivated than successional soils and resource amendment decreased lag times. Taxa exhibiting the greatest growth response also exhibited the greatest mortality, indicative of boom-and-bust dynamics. We observed a bimodal growth rate distribution, representing fast- and slow-growing clusters. Both clusters grew more rapidly in successional soils, which had more organic matter, than cultivated soils. Resource amendment increased the growth rate of the slower growing but not the faster-growing cluster via a mixture of increased growth rates and species turnover, indicating that competitive dynamics constrain growth rates in situ. These two clusters show that copiotrophic bacteria in soils may be subdivided into different life history groups and that these subgroups respond independently to land use and resource availability.     

Effect of decabromodiphenyl ether (BDE 209) on soil microbial activity and bacterial community composition

In many areas of the world, polybrominated diphenyl ethers are ubiquitous due to their use as fire retardants. It is known that the hydrophobic characteristics of PBDEs cause them to sink in soil and sediment, yet their effect on microbes within the soil is not well understood. In this study, soil was treated with 1, 10, and 100 mg kg⁻¹ BDE 209 for up to 45 days. Treatment effects on soil enzymatic activities for urease and catalase were evaluated. The impact on the microbe community structure was estimated using denaturing gradient gel electrophoresis after polymerase chain reaction amplification of total genomic DNA, using bacterial variable V3 region targeted primers. The effects on the soil microbial community size and major bacterial groups were evaluated using fluorescence in situ hybridization analysis. Forty-five days after the addition of BDE 209, urease activity was suppressed by BDE 209, even at a concentration of 1 mg kg⁻¹. Catalase activity increased in the samples containing lower concentrations of BDE 209, but was suppressed in samples containing higher concentrations. The bacterial community also varied in response to the addition of BDE 209, and the variation of community composition differed among treatments. In addition, α, β and γ subclass proteobacteria decreased in the group of 100 mg kg⁻¹ BDE 209 spiked soil after 45 days of treatment. Throughout the experiment, no BDE 209 degradation was detected under darkness. These observations demonstrated that BDE 209 in soil, although of low bioavailability, had an adverse impact on the structure and function of the soil microbial community and microbial processes.