The phylogenetic composition and structure of soil microbial communities shifts in response to elevated carbon dioxide

One of the major factors associated with global change is the ever-increasing concentration of atmospheric CO₂. Although the stimulating effects of elevated CO₂ (eCO₂) on plant growth and primary productivity have been established, its impacts on the diversity and function of soil microbial communities are poorly understood. In this study, phylogenetic microarrays (PhyloChip) were used to comprehensively survey the richness, composition and structure of soil microbial communities in a grassland experiment subjected to two CO₂ conditions (ambient, 368 p.p.m., versus elevated, 560 p.p.m.) for 10 years. The richness based on the detected number of operational taxonomic units (OTUs) significantly decreased under eCO₂. PhyloChip detected 2269 OTUs derived from 45 phyla (including two from Archaea), 55 classes, 99 orders, 164 families and 190 subfamilies. Also, the signal intensity of five phyla (Crenarchaeota, Chloroflexi, OP10, OP9/JS1, Verrucomicrobia) significantly decreased at eCO₂, and such significant effects of eCO₂ on microbial composition were also observed at the class or lower taxonomic levels for most abundant phyla, such as Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes and Acidobacteria, suggesting a shift in microbial community composition at eCO₂. Additionally, statistical analyses showed that the overall taxonomic structure of soil microbial communities was altered at eCO₂. Mantel tests indicated that such changes in species richness, composition and structure of soil microbial communities were closely correlated with soil and plant properties. This study provides insights into our understanding of shifts in the richness, composition and structure of soil microbial communities under eCO₂ and environmental factors shaping the microbial community structure.     

2,4-D impact on bacterial communities, and the activity and genetic potential of 2,4-D degrading communities in soil

The key role of telluric microorganisms in pesticide degradation is well recognized but the possible relationships between the biodiversity of soil microbial communities and their functions still remain poorly documented. If microorganisms influence the fate of pesticides, pesticide application may reciprocally affect soil microorganisms. The objective of our work was to estimate the impact of 2,4-D application on the genetic structure of bacterial communities and the 2,4-D-degrading genetic potential in relation to 2,4-D mineralization. Experiments combined isotope measurements with molecular analyses. The impact of 2,4-D on soil bacterial populations was followed with ribosomal intergenic spacer analysis. The 2,4-D degrading genetic potential was estimated by real-time PCR targeted on tfdA sequences coding an enzyme specifically involved in 2,4-D mineralization. The genetic structure of bacterial communities was significantly modified in response to 2,4-D application, but only during the intense phase of 2,4-D biodegradation. This effect disappeared 7 days after the treatment. The 2,4-D degrading genetic potential increased rapidly following 2,4-D application. There was a concomitant increase between the tfdA copy number and the 14C microbial biomass. The maximum of tfdA sequences corresponded to the maximum rate of 2,4-D mineralization. In this soil, 2,4-D degrading microbial communities seem preferentially to use the tfd pathway to degrade 2,4-D.     

2,4—D在玉米幼叶培养中的歧义作用

本文报道,在玉米幼苗第二片叶的组织培养中:1.接近叶基的细胞对2,4-D敏感性强,而离叶基较远的细胞对2,4-D敏感性则相对弱;2.在0.02—6mg/L浓度下,2,4-D能刺激细胞进行分裂,而在20—40mg/L浓度时,2,4-D则起抑制作用;3.离叶基21mm以上的叶细胞失去对各种浓度2,4-D的反应能力;4.2,4-D诱导的愈伤组织,大多是由一些原先处于抑制状态的根原基形成的。     

Response of soil nematode communities to long-term application of inorganic fertilizers in the black soil of Northeast China

The effects of inorganic fertilizers on soil nematode communities were studied in a long-term fertilization experimental field in the Black Soil Region of Northeast China, where no fertilizer (CK), N fertilizer (N), combined application of N and P (NP), combined application of N and K (NK), and combined application of N, P and K (NPK) were compared. The results showed that the total nematode abundance was not affected significantly by inorganic fertilizers in the long-term field experiment. The numbers of bacterivores increased significantly in the NP treatment compared to the CK treatment, and those of fungivores and plant-parasites were inhibited in the NPK treatment. The similarity between CK and NPK treatment and the nematode diversity were higher than in other treatments. The stability of the soil ecosystem was disturbed by the inorganic fertilizers, as indicated by the change in MI values under different treatments. The response of soil nematodes mainly depended on the types of inorganic fertilizers applied.     

Response of soil nematode communities to long-term application of inorganic fertilizers in the black soil of Northeast China

The effects of inorganic fertilizers on soil nematode communities were studied in a long-term fertilization experimental field in the Black Soil Region of Northeast China,where no fertilizer (CK),N fertilizer (N),combined application of N and P (NP),combined application of N and K (NK),and combined application of N,P and K (NPK) were compared.The results showed that the total nematode abundance was not affected significantly by inorganic fertilizers in the long-term field experiment.The numbers of bacterivores increased significantly in the NP treatment compared to the CK treatment,and those of fungivores and plant-parasites were inhibited in the NPK treatment.The similarity between CK and NPK treatment and the nematode diversity were higher than in other treatments.The stability of the soil ecosystem was disturbed by the inorganic fertilizers,as indicated by the change in MI values under different treatments.The response of soil nematodes mainly depended on the types of inorganic fertilizers applied.     

Functional response of the soil microbial community to biochar applications

Biochar has the potential to mitigate the impacts of climate change and soil degradation by simultaneously sequestering C in soil and improving soil quality. However, the mechanism of biochar's effect on soil microbial communities remains unclear. Therefore, we conducted a global meta‐analysis, where we collected 2,110 paired observations from 107 published papers and used structural equation modeling (SEM) to analyze the effects of biochar on microbial community structure and function. Our result indicated that arbuscular mycorrhizal fungal abundance, microbial biomass C, and functional richness increased with biochar addition regardless of loads, time since application, and experiment types. Results from mixed linear model analysis suggested that soil respiration and actinomycetes (ACT) abundance decreased with biochar application. With the increase of soil pH, the effect of biochar on fungal abundance and C metabolic ability was lessened. Higher biochar pH associated with higher pyrolysis temperatures reduced the abundance of bacteria, fungi, ACT, and soil microbes feeding on miscellaneous C from Biolog Eco‐plate experiments. SEM that examined the effect of biochar properties, load, and soil properties on microbial community indicated that fungal abundance was the dominant factor affecting the response of the bacterial abundance to biochar. The response of bacterial abundance to biochar addition was soil dependent, whereas fungi abundance was mostly related to biochar load and pyrolysis temperature. Based on soil conditions, controlling biochar load and production conditions would be a direct way to regulate the effect of biochar application on soil microbial function and increase the capacity to sequester C.     

A rapid,cost-effective procedure for the extraction of microbial DNA from soil

Here we describe a DNA extraction method that is based on a simple, rapid polyvinylpolypyrrolidone–calcium chloride precipitation to release microorganisms from the soil combined with lysozyme–proteinase–SDS lysis of the microbial community. The extracted DNA is of high quality and allows direct detection of specific genes by the polymerase chain reaction (PCR) as well as cloning of indigenous microbial DNA. This method facilitates the extraction of 36 500-mg soil samples simultaneously in a 2-h period by one person. The procedure is safe, inexpensive, and does not require specialized equipment or generate hazardous wastes.     

转基因水稻对土壤微生物群落结构及功能的影响

以非转基因水稻为对照,以变性梯度凝胶电泳(DGGE)和Biolog技术为手段,研究了2种转基因水稻对土壤微生物群落结构及功能的影响。结果显示:转基因水稻仅在生长发育旺盛期对土壤细菌数量有显著影响;且不同品种转基因水稻土壤微生物间的遗传距离大于转基因水稻与对照间土壤微生物的距离,即2个转基因水稻品种对土壤微生物群落遗传多样性的影响均不显著;在水稻抽穗期,2种转基因水稻与其对照的土壤微生物群落在72h时的平均光密度呈现显著差异,而到了成熟期则差异不显著。土壤微生物群落多样性指数和均匀度指数也表现出类似趋势。本试验证明,在水稻生长发育旺盛时期,Mclntosh指数(u)是一个有效区分转基因水稻和非转基因水稻土壤微生物群落多样性的指标。     

Distinct responses of soil microbial communities to elevated CO2 and O3 in a soybean agro-ecosystem

The concentrations of atmospheric carbon dioxide (CO₂) and tropospheric ozone (O₃) have been rising due to human activities. However, little is known about how such increases influence soil microbial communities. We hypothesized that elevated CO₂ (eCO₂) and elevated O₃ (eO₃) would significantly affect the functional composition, structure and metabolic potential of soil microbial communities, and that various functional groups would respond to such atmospheric changes differentially. To test these hypotheses, we analyzed 96 soil samples from a soybean free-air CO₂ enrichment (SoyFACE) experimental site using a comprehensive functional gene microarray (GeoChip 3.0). The results showed the overall functional composition and structure of soil microbial communities shifted under eCO₂, eO₃ or eCO₂+eO₃. Key functional genes involved in carbon fixation and degradation, nitrogen fixation, denitrification and methane metabolism were stimulated under eCO₂, whereas those involved in N fixation, denitrification and N mineralization were suppressed under eO₃, resulting in the fact that the abundance of some eO₃-supressed genes was promoted to ambient, or eCO₂-induced levels by the interaction of eCO₂+eO₃. Such effects appeared distinct for each treatment and significantly correlated with soil properties and soybean yield. Overall, our analysis suggests possible mechanisms of microbial responses to global atmospheric change factors through the stimulation of C and N cycling by eCO₂, the inhibition of N functional processes by eO₃ and the interaction by eCO₂ and eO₃. This study provides new insights into our understanding of microbial functional processes in response to global atmospheric change in soybean agro-ecosystems.     

Elevated carbon dioxide accelerates the spatial turnover of soil microbial communities

Although elevated CO₂ (eCO₂) significantly affects the α‐diversity, composition, function, interaction and dynamics of soil microbial communities at the local scale, little is known about eCO₂ impacts on the geographic distribution of micro‐organisms regionally or globally. Here, we examined the β‐diversity of 110 soil microbial communities across six free air CO₂ enrichment (FACE) experimental sites using a high‐throughput functional gene array. The β‐diversity of soil microbial communities was significantly (P < 0.05) correlated with geographic distance under both CO₂ conditions, but declined significantly (P < 0.05) faster at eCO₂ with a slope of ?0.0250 than at ambient CO₂ (aCO₂) with a slope of ?0.0231 although it varied within each individual site, indicating that the spatial turnover rate of soil microbial communities was accelerated under eCO₂ at a larger geographic scale (e.g. regionally). Both distance and soil properties significantly (P < 0.05) contributed to the observed microbial β‐diversity. This study provides new hypotheses for further understanding their assembly mechanisms that may be especially important as global CO₂ continues to increase.     

三江平原土壤动物群落多样性对CO2浓度升高的响应

为研究大气CO₂浓度升高条件下土壤动物的响应, 本文采用开顶式气室(OTC)控制大气CO₂浓度, 设置了3个梯度, 分别为低浓度370 ppm背景CO₂ (AC)、中浓度550 ppm CO₂ (EC1)和高浓度700 ppm CO₂ (EC2)。于2017年秋季取样并用改良Tullgren干漏斗法和Baermann湿漏斗分离土壤动物。结果表明: (1)共捕获土壤动物6,268头, 隶属于7纲15目, 优势类群为甲螨亚目, 占捕获量的88.13%; 常见类群为弹尾目和双翅目幼虫, 合计占捕获量的9%。不同CO₂浓度水平下, 优势类群(甲螨亚目)和常见类群(弹尾目、双翅目幼虫)相同, 但是稀有类群存在一定差异。(2) CO₂浓度升高显著增加了甲螨亚目的类群数和个体密度, 显著降低了弹尾目的类群数和个体密度, 对其他土壤动物无显著影响。(3)三江平原不同浓度条件下土壤动物的Shannon-Wiener多样性指数、Pielou均匀度指数均为AC > EC1 > EC2, 而优势度指数为EC2 > EC1 > AC, 丰富度指数为AC > EC2 > EC1。研究表明, 气候变化有可能影响土壤动物的群落结构以及土壤动物的多样性。     

Ranking the magnitude of crop and farming system effects on soil microbial biomass and genetic structure of bacterial communities

Biological soil characteristics such as microbial biomass, community structures, activities, and functions may provide important information on environmental and anthropogenic influences on agricultural soils. Diagnostic tools and detailed statistical approaches need to be developed for a reliable evaluation of these parameters, in order to allow classification and quantification of the magnitude of such effects. The DOK long-term agricultural field experiment was initiated in 1978 in Switzerland for the evaluation of organic and conventional farming practices. It includes three representative Swiss farming systems with biodynamic, bio-organic and conventional fertilization and plant protection schemes along with minerally fertilized and unfertilized controls. Effects on microbial soil characteristics induced by the long-term management at two different stages in the crop rotation, i.e. winter wheat after potato or corn, were investigated by analyzing soil bacterial community structures using analysis of PCR-amplified rRNA genes by terminal restriction fragment length polymorphism and ribosomal intergenic spacer analysis. Application of farmyard manure consistently revealed the strongest influence on bacterial community structures and biomass contents. Effects of management and plant protection regimes occurred on an intermediate level, while the two stages in the crop rotation had a marginal influence that was not significant.     

The responses of soil organic carbon mineralization and microbial communities to fresh and aged biochar soil amendments

While biochar soil amendment has been widely proposed as a soil organic carbon (SOC) sequestration strategy to mitigate detrimental climate changes in global agriculture, the SOC sequestration was still not clearly understood for the different effects of fresh and aged biochar on SOC mineralization. In the present study of a two‐factorial experiment, topsoil samples from a rice paddy were laboratory‐incubated with and without fresh or aged biochar pyrolyzed of wheat residue and with and without crop residue‐derived dissolved organic matter (CRM) for monitoring soil organic matter decomposition under controlled conditions. The six treatments included soil with no biochar, with fresh biochar and with aged biochar treated with CRM, respectively. For fresh biochar treatment, the topsoil of a same rice paddy was amended with wheat biochar directly from a pyrolysis wheat straw, the soil with aged biochar was collected from the same soil 6 years following a single amendment of same biochar. Total CO₂ emission from the soil was monitored over a 64 day time span of laboratory incubation, while microbial biomass carbon and phospholipid fatty acid (PLFA) were determined at the end of incubation period. Without CRM, total organic carbon mineralization was significantly decreased by 38.8% with aged biochar but increased by 28.9% with fresh biochar, compared to no biochar. With CRM, however, the significantly highest net carbon mineralization occurred in the soil without biochar compared to the biochar‐amended soil. Compared to aged biochar, fresh biochar addition significantly increased the total PLFA concentration by 20.3%–33.8% and altered the microbial community structure by increasing 17:1ω8c (Gram‐negative bacteria) and i17:0 (Gram‐positive bacteria) mole percentages and by decreasing the ratio of fungi/bacteria. Furthermore, biochar amendment significantly lowered the metabolic quotient of SOC decomposition, thereby becoming greater with aged biochar than with fresh biochar. The finding here suggests that biochar amendment could improve carbon utilization efficiency by soil microbial community and SOC sequestration potential in paddy soil can be enhanced by the presence of biochar in soil over the long run.     

利用PLFA、CLPPs和ARDRA标记分析甲胺磷对土壤微生物群落的影响

利用磷脂脂肪酸(PLFA)、群落水平生理活性(CLPPs)和扩增核糖体DNA限制性分析(ARDRA)标记,综合评估低浓度和高浓度甲胺磷连续施用2和4 yr后对土壤微生物群落结构、功能和遗传多样性的影响。结果表明,甲胺磷胁迫使土壤微生物生物量减少而细菌(革兰氏阴性菌)数量增加,同时使微生物群落功能多样性下降而遗传多样性提高;处理2 yr后高浓度甲胺磷胁迫对微生物群落的影响较低浓度胁迫更为明显,处理4 yr后两个浓度胁迫则具有相似的显著影响,表明不同浓度甲胺磷的长期胁迫均能对微生物群落造成严重破坏。     

土壤微生物群落结构对中亚热带三种典型阔叶树种凋落物分解过程的响应

通过小盆模拟试验研究了南方红壤丘陵区典型阔叶树种香樟、白栎和青冈的凋落物分解过程中土壤微生物群落结构的异同。结果表明:(1)凋落物含氮量:白栎>香樟>青冈;碳、木质素的含量以及碳/氮比、木质素/氮比:青冈>香樟>白栎;分解速率:白栎>香樟>青冈;(2)随着凋落物分解的进程,土壤微生物群落16 ∶ 0、15 ∶ 0、i16 ∶ 0、a17 ∶ 0、17 ∶ 0、18 ∶ 2ω6,9c和10Me18 ∶ 0的含量上升,18 ∶ 0、14 ∶ 0、16 ∶ 1ω7c、18 ∶ 1ω7c、cy19 ∶ 0、i19 ∶ 0和10Me19 ∶ 0的含量下降,饱和直链脂肪酸/单不饱和脂肪酸、革兰氏阳性菌/革兰氏阴性菌以及cy19 ∶ 0/18 ∶ 1ω7c的比值都显著上升。(3)两个时期白栎凋落物处理土壤16 ∶ 0、15 ∶ 0、a15 ∶ 0、i16 ∶ 0、a17 ∶ 0、 17 ∶ 0、cy19 ∶ 0、18 ∶ 2ω6,9c、18 ∶ 1ω9c和10Me18 ∶ 0的含量显著高于香樟和青冈凋落物处理的土壤,细菌、真菌的磷脂脂肪酸含量以及磷脂脂肪酸总量显著高于香樟和青冈凋落物处理的土壤。随着阔叶凋落物的分解,变化的土壤环境对土壤微生物群落的胁迫增强,土壤微生物群落结构发生显著变化。与香樟和青冈的凋落物相比,白栎凋落物碳/氮比和木质素/氮比低、分解快,能显著改善土壤微生物群落结构,更有利于土壤肥力提高和生态系统养分循环的改善。     

Partitioning of beta‐diversity reveals distinct assembly mechanisms of plant and soil microbial communities in response to nitrogen enrichment

Nitrogen (N) deposition poses a serious threat to terrestrial biodiversity and alters plant and soil microbial community composition. Species turnover and nestedness reflect the underlying mechanisms of variations in community composition. However, it remains unclear how species turnover and nestedness contribute to different responses of taxonomic groups (plants and soil microbes) to N enrichment. Here, based on a 13‐year consecutive multi‐level N addition experiment in a semiarid steppe, we partitioned community β‐diversity into species turnover and nestedness components and explored how and why plant and microbial communities reorganize via these two processes following N enrichment. We found that plant, soil bacterial, and fungal β‐diversity increased, but their two components showed different patterns with increasing N input. Plant β‐diversity was mainly driven by species turnover under lower N input but by nestedness under higher N input, which may be due to a reduction in forb species, with low tolerance to soil Mn²⁺, with increasing N input. However, turnover was the main contributor to differences in soil bacterial and fungal communities with increasing N input, indicating the phenomenon of microbial taxa replacement. The turnover of bacteria increased greatly whereas that of fungi remained within a narrow range with increasing N input. We further found that the increased soil Mn²⁺ concentration was the best predictor for increasing nestedness of plant communities under higher N input, whereas increasing N availability and acidification together contributed to the turnover of bacterial communities. However, environmental factors could explain neither fungal turnover nor nestedness. Our findings reflect two different pathways of community changes in plants, soil bacteria, and fungi, as well as their distinct community assembly in response to N enrichment. Disentangling the turnover and nestedness of plant and microbial β‐diversity would have important implications for understanding plant–soil microbe interactions and seeking conservation strategies for maintaining regional diversity.     

2,4-D诱导固氮螺菌和慢生型大豆根瘤菌在小麦上的结瘤作用及其效果

分别在水培和砂培条件下进行了2,4-D诱导固氮螺菌和慢生型大豆根瘤菌在小麦根上的结瘤试验,结果表明2,4-D能诱发它们在小麦根系上形成“类根瘤”,扫描电镜结果证明只有个别细菌进入小麦根瘤细胞内,在细胞间隙有较多的细菌。用乙炔还原法仅检测到接种大豆根瘤菌的小麦根瘤有微量的固氮酶活性,但在盆栽植株的生长方面,看不到2,4-D,2,4-D+固氮螺菌或2,4-D+根瘤菌对小麦生长的促进作用。     

大港孔店油田水驱油藏微生物群落的分子分析

通过多聚酶链式反应温度梯度凝胶电泳（PCRTGGE）和构建16S rRNA基因克隆文库两种方法对比研究了大港油田孔二北断块注水井和采油井的微生物群落结构。16S rDNA V3区PCR扩增产物的TGGE图谱分析表明,这两个油井的微生物群落结构差异很大。注水井样品的TGGE图谱中有6条主要条带,而采油井样品中只有一个条带占绝对优势。同时,建立了两个样品的16S rRNA基因克隆文库,从中分别挑选了108和50个克隆进行限制性酶切片段长度多样性分析（ARDRA）。注水井样品有33个操作分类单元（OUT）,其中6个OUT是优势类型;而采油井样品只有8个OUT,有1个OUT在文库中占绝对优势。克隆文库和TGGE的研究结果一致,均表明注水井样品的微生物多样性比采油井丰富很多。每个OUT的代表克隆序列分析结果表明,注水井样品中的细菌主要属于α、β、γ变形菌纲和放线菌纲,尤其是红细菌亚纲（47%）。采油井样品的细菌主要属于α、β、γ变形菌纲,尤其是假单胞菌属（62%）。油藏微生物多样性的分子分析可为开展微生物采油技术研究奠定基础。