N2O emission associated with shifts of bacterial communities in riparian wetland during the spring thawing periods

Soil freeze–thaw processes lead to high nitrous oxide (N₂O) emissions and exacerbate the greenhouse effect. The wetlands of the Inner Mongolia Plateau are in the pronounced seasonal freeze–thaw zone, but the effect of spring thaw on N₂O emissions and related microbial mechanisms is still unclear. We investigated the effects of different periods (freeze, freeze–thaw, and thaw) on soil bacterial community diversity and composition and greenhouse gas emissions during the spring freeze–thaw in the XiLin River riparian wetlands in China by amplicon sequencing and static dark box methods. The results showed that the freeze–thaw periods predominantly impact on the diversity and composition of the bacterial communities. The phyla composition of the soil bacteria communities of the three periods is similar in level, with Proteobacteria, Chloroflexi, Actinobacteria, and Acidobacteria dominating the microbial communities. The alpha‐diversity of bacterial communities in different periods varies that the freezing period is higher than that of the freeze–thaw period (p < .05). Soil total carbon, soil water content, and microbial biomass carbon were the primary factors regulating the abundance and compositions of the bacterial communities during spring thawing periods. Based on functional predictions, the relative abundance of nitrification and denitrification genes was higher in the freezing period than in the thawing period, while the abundance was lowest in the freeze–thawing period. The correlation results found that N₂O emissions were significantly correlated with amoA and amoB in nitrification genes, indicating that nitrification may be the main process of N₂O production during spring thaw. This study reveals potential microbial mechanisms of N₂O emission during spring thaw and provides data support and theoretical basis for further insight into the mechanism of N₂O emission during spring thaw.     

Shifts of tundra bacterial and archaeal communities along a permafrost thaw gradient in Alaska

Understanding the response of permafrost microbial communities to climate warming is crucial for evaluating ecosystem feedbacks to global change. This study investigated soil bacterial and archaeal communities by Illumina MiSeq sequencing of 16S rRNA gene amplicons across a permafrost thaw gradient at different depths in Alaska with thaw progression for over three decades. Over 4.6 million passing 16S rRNA gene sequences were obtained from a total of 97 samples, corresponding to 61 known classes and 470 genera. Soil depth and the associated soil physical–chemical properties had predominant impacts on the diversity and composition of the microbial communities. Both richness and evenness of the microbial communities decreased with soil depth. Acidobacteria, Verrucomicrobia, Alpha‐ and Gamma‐Proteobacteria dominated the microbial communities in the upper horizon, whereas abundances of Bacteroidetes, Delta‐Proteobacteria and Firmicutes increased towards deeper soils. Effects of thaw progression were absent in microbial communities in the near‐surface organic soil, probably due to greater temperature variation. Thaw progression decreased the abundances of the majority of the associated taxa in the lower organic soil, but increased the abundances of those in the mineral soil, including groups potentially involved in recalcitrant C degradation (Actinomycetales, Chitinophaga, etc.). The changes in microbial communities may be related to altered soil C sources by thaw progression. Collectively, this study revealed different impacts of thaw in the organic and mineral horizons and suggests the importance of studying both the upper and deeper soils while evaluating microbial responses to permafrost thaw.     

Phylogenetic analysis of bacterial communities associated with larvae of the Atlantic halibut propose succession from a uniform normal flora

Halibut, the largest of all flatfishes is a valuable species with a great potential for aquaculture. Bacteria play an important role in regulating the health of the early life stages. The present article is the first broad-range molecular analysis of bacterial communities in larvae of the Atlantic halibut (Hippoglossus hippoglossus). DNA was extracted from larvae, water and silo biofilm from hatcheries in Norway, Scotland, Iceland and Canada. Eubacterial 16S rRNA gene fragments were amplified by polymerase chain reaction (PCR) with broad-range primers. Sequences spanning the hyper variable V3 region representing individual bacterial species were separated into community profiles by denaturing gradient gel electrophoresis (DGGE). The profiles revealed simple communities after hatching and bacterial succession following growth. Sequencing and phylogenetic analysis of excised DGGE bands suggested aerobic heterotrophs related to groups of Pseudomonas, Janthinobacterium and possibly Marinomonas to be the primary colonisers of the larvae. After onset of feeding, fermentative species (Vibrio) were detected as well. Comparative analysis of bacterial communities from different geographical regions indicated that larvae of the Atlantic halibut possess a distinct and specific normal flora.     

Bacterial communities in the initial stage of marine biofilm formation on artificial surfaces

Succession of bacterial communities during the first 36 h of biofilm formation in coastal water was investigated at 3 approximately 15 h intervals. Three kinds of surfaces (i.e., acryl, glass, and steel substratum) were submerged in situ at Sacheon harbor, Korea. Biofilms were harvested by scraping the surfaces, and the compositions of bacterial communities were analyzed by terminal restriction fragment length polymorphism (T-RFLP), and cloning and sequencing of 16S rRNA genes. While community structure based on T-RFLP analysis showed slight differences by substratum, dramatic changes were commonly observed for all substrata between 9 and 24 h. Identification of major populations by 16S rRNA gene sequences indicated that gamma-Proteobacteria (Pseudomonas, Acinetobacter, Alteromonas, and uncultured gamma-Proteobacteria) were predominant in the community during 0 approximately 9 h, while the ratio of alpha-Proteobacteria (Loktanella, Methylobacterium, Pelagibacter, and uncultured alpha-Proteobacteria) increased 2.6 approximately 4.8 folds during 24 approximately 36 h of the biofilm formation, emerging as the most predominant group. Previously, alpha-Proteobacteria were recognized as the pioneering organisms in marine biofilm formation. However, results of this study, which revealed the bacterial succession with finer temporal resolution, indicated some species of gamma-Proteobacteria were more important as the pioneering population. Measures to control pioneering activities of these species can be useful in prevention of marine biofilm formation.     

Hydrolytic Enzymes Producing Bacterial Endophytes of Some Poaceae Plants

Endophytic bacteria represent microorganisms that live during the whole life cycle within the tissues of healthy plants without causing any obvious signs of disease. In this study, the ability of 128 endophyte bacterial isolates from some cultivated and wild grain plants (Poaceae family) in Van, Turkey, were investigated in terms of producing several extracellular hydrolytic enzymes. It was demonstrated that lipases, proteases, amylases, cellulases, pectinases, and xylanases were produced by the bacteria with relative frequencies of 74.2%, 65.6%, 55.4%, 32%, 21.8%, and 7.8%, respectively. In addition, molecular identification of a certain number of isolates selected according to their enzyme-producing capabilities was performed by 16S rRNA gene sequencing using a next-generation sequencing platform. As a result of the analysis, the isolates yielded certain strains belonging to Pseudomonas, Micrococcus, Paenibacillus, Streptococcus, Curtobacterium, Chryseobacterium, and Bacillus genera. Also, the strain G117Y1T was evaluated as a member of potential novel species based on 16S rRNA sequencing results.     

Phylogenetic analysis of bacteria associated with Laminaria saccharina

Bacterial communities associated with the brown alga Laminaria saccharina from the Baltic Sea and from the North Sea were investigated using denaturing gradient gel electrophoresis and 16S rRNA gene clone libraries. The rhizoid, cauloid, meristem and phyloid revealed different 16S rRNA gene denaturing gradient gel electrophoresis banding patterns indicating a specific association of bacterial communities with different parts of the alga. Associations with cauloid and meristem were more specific, while less specific associations were obtained from the old phyloid. In addition, seasonal and geographical differences in the associated communities were observed. Results from 16S rRNA gene libraries supported these findings. Bacterial phylotypes associated with the alga were affiliated with the Alphaproteobacteria (nine phylotypes), Gammaproteobacteria (nine phylotypes) and the Bacteroidetes group (four phylotypes). A number of bacteria associated with other algae and other marine macroorganisms were among the closest relatives of phylotypes associated with L. saccharina.     

河南宝天曼不同林龄与林型森林土壤的细菌群落结构与多样性

采用高通量16S rRNA标签测序法,比较了地处北亚热带与暖温带过渡带的宝天曼自然保护区不同林龄与林分类型的土壤细菌群落结构及多样性.结果表明： 宝天曼森林土壤细菌以变形菌门(29%)、酸杆菌门(18.5%)、疣微菌门(10%)等为主,共检测到60门1209属,优势属主要有疣微菌门的DA101(6.3%)、酸杆菌门的Acidobacteria 2(5.9%)和Candidatus Solibacter(2.9%)、泉古菌门的Candidatus Nitrososphaera(2.6%)等.不同林龄和林分类型土壤分别具有特有的种属组成及高丰度和低丰度种属.林龄与林分类型都对土壤微生物群落结构影响显著,且林分类型的影响大于林龄.80年林龄的锐齿栎土壤菌群多样性在不同林龄和林分类型中均最低.pH、土壤全氮、有机碳等是不同林龄及林分类型下土壤菌群结构变化的重要影响因子.     

Bacterial community composition over a dry winter in meso- and eutrophic Portuguese water bodies

In order to investigate the bacterial diversity in a number of rivers, reservoirs and lakes in northern and central Portugal during the winter of 2004/5 (atypically dry), we applied molecular methodologies, namely denaturing gradient gel electrophoresis with primers targeting fractions of the bacterial 16S rRNA gene. Environmental parameters such as pH, conductivity, inorganic nutrients, total suspended solids and chlorophyll a were determined in order to characterize the trophic status of the studied water bodies. We found water bodies with oligotrophic to hypereutrophic characteristics. Organisms belonging to the Bacteroidetes and Alphaproteobacteria were found at the highest pH environment. Bacteroidetes were also related to high nutrient concentrations. Verrucomicrobia were associated with the most oligotrophic reservoir and low pH values. Actinobacteria were present in all samples from lakes and reservoirs, indicating its preference for lentic water bodies. Cyanobacteria dominance was related to high pH and conductivity levels. In general the conductivity values recorded in winter 2005 were the highest over recent years and chlorophyll a also reached very high levels. The data emphasize an enhanced risk of eutrophication for the studied water bodies, especially in the subsequent months when the temperature rises.     

Denaturing gradient gel electrophoresis analysis with different primers of subgingival bacterial communities under mechanical debridement

DGGE of 16S rDNA is one of the most frequently used methods to study microbial communities. In this study, the DGGE profiles of different 16S rDNA regions of the periodontal pathogens Porphyromonas gingivalis, Fusobacterium nucleatum, and Prevotella nigrescens were investigated. The results suggested that V3-V5 and V6-V8 fragments may be suitable for community analysis of subgingival bacteria. Further analysis of subgingival samples with V3-V5 and V6-V8 regions as target fragments suggested that, in chronic periodontitis, re-colonization by periodontal bacteria with a population very similar to the baseline may occur by 6 weeks after mechanical debridement.     

Bacterial Diversity and Community Structure in High Arsenic Aquifers in Hetao Plain of Inner Mongolia,China

The bacterial diversity and community structure of high arsenic (As) aquifers was investigated using an integrated approach adopting both geochemistry and molecular biology (polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) and 16S rRNA gene clone library analyses). Nine borehole sediments and one groundwater sample from the living place of a villager (affected by arseniasis) and 12 sediments from a control borehole in Hetao Plain were investigated. The As concentrations ranged from 33.6 to 77.6 mg/kg in high As borehole sediments and 1.5 to 5.8 mg/kg in those samples from the control. The As concentration in the groundwater was 744.8 μg/L. Ratios between As(III) and total As in high As sediments increased gradually with depth and ranged from 0.02 to 0.34. Similarly, the Fe(II)/total Fe presented the same increasing trend with depth. The correlation between TOC contents and total As was positive. High concentrations of total As, S, Fe and TOC were found in clay and low in sand samples. Phylogenetic analysis showed significantly different bacterial communities among high As sediments, control sediments and the high As groundwater. Both DGGE and 16S rRNA gene clone library results showed that the high As sediments were dominated by Thiobacillus, Pseudomonas, Brevundimonas, and Hydrogenophaga, with Thiobacillus being distinctly dominant (63.5%). Whereas the low As sediments were dominated by some other genera including Psychrobacter, Massilia and Desulfotalea. The bacterial populations in the high As groundwater mainly included Pseudomonas, Acinetobacter and Aquabacterium. These results improve our understanding of the bacterial diversity in high As aquifers in Hetao Plain and suggest how specific bacterial populations help mediate the mobilization of As into high As groundwaters.     

利用PCR-DGGE未培养技术对中国白酒高温和中温大曲细菌群落结构的分析

采用聚合酶链式反应-变性梯度凝胶电泳(PCR-DGGE)技术,研究了5种高温和中温白酒大曲细菌群落结构,通过优势条带切胶鉴定确定了大曲中优势细菌种属信息。结果表明,Weissella cibaria、Lactobacillus helveticus、L.fermentum、L.panis等乳酸菌普遍存在于5种大曲中,Ther-moactinomyces sanguinis仅存在于高温曲酱曲中,同时DGGE检测到了传统方法未能分离鉴定的Staphylococcus xylosus、Klebsiella oxytoca。不同工艺大曲细菌群落结构存在明显差异,随着制曲温度的升高,大曲细菌多样性指数有下降趋势。PCR-DGGE技术是一种能够快速有效地研究白酒大曲细菌群落结构的技术。     

南京玄武湖底泥微生物群落结构研究

采用变性梯度凝胶电泳(DGGE)的方法研究了南京玄武湖底泥中的微生物群落结构分布。此外,我们还采用了典范对应分析(CCA)的方法研究了底泥中一些环境因子对微生物群落结构的影响。在玄武湖三个不同湖区共选取八个采样点采集底泥样品,测定不同底泥样品中的总氮(TN)、总磷(TP)、有机质(OM)、pH和氧化还原电位(Eh),发现不同采样点的环境参数存在差异。其中,采样点S2底泥样品的总氮和有机质含量最高,氧化还原电位水平最低。对DGGE分离的DNA条带进行测序,测序结果利用BLAST与GenBank数据库中的菌种进行对比,运用MEGA 3.0软件构建了系统进化树。结果表明:玄武湖底泥中分离出的微生物属于Proteobacteria, Actinobacteria, Verrucomicrobia 和 Nitrospira,它们都属于富营养化湖泊中常见的微生物类群。典范对应分析(CCA)的结果表明: 底泥样品的pH值和氧化还原电位水平对底泥当中的微生物群落结构有显著影响。     

Diversity of endophytic bacterial communities in poplar grown under field conditions

Bacterial endophytes may be important for plant health and other ecologically relevant functions of poplar trees. The composition of endophytic bacteria colonizing the aerial parts of poplar was studied using a multiphasic approach. The terminal restriction fragment length polymorphism analysis of 16S rRNA genes demonstrated the impact of different hybrid poplar clones on the endophytic community structure. Detailed analysis of endophytic bacteria using cultivation methods in combination with cloning of 16S rRNA genes amplified from plant tissue revealed a high phylogenetic diversity of endophytic bacteria with a total of 53 taxa at the genus level that included Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes. The community structure displayed clear differences in terms of the presence and relative proportions of bacterial taxa between the four poplar clones studied. The results showed that the genetic background of the hybrid poplar clones corresponded well with the endophytic community structure. Out of the 513 isolates and 209 clones identified, Actinobacteria, in particular the family Microbacteriaceae, made up the largest fraction of the isolates, whereas the clone library was dominated by Alpha- and Betaproteobacteria. The most abundant genera among the isolates were Pseudomonas and Curtobacterium, while Sphingomonas prevailed among the clones.     

宁夏地区春季奶牛场牛舍土壤细菌群落特征

【背景】现代规模化生产模式下,牛舍环境管理是影响奶牛高效健康生产的重要因素。【目的】探讨牛场不同牛舍土壤细菌群落特征,为奶牛健康生产提供理论依据。【方法】采集宁夏某规模化奶牛场的哺乳犊牛岛、断奶犊牛舍、育成牛舍、低产泌乳牛舍、高产头胎泌乳牛舍、高产经产泌乳牛舍、干奶牛舍和病牛舍这8个不同牛舍的土样,每个牛舍6个重复,共48份土样。利用16S rRNA基因扩增子测序分析细菌群落结构与多样性,并对细菌群落的功能进行预测。【结果】不同牛舍土样细菌群落组成存在差异,并且8个牛舍中高产头胎泌乳牛舍土样的细菌群落多样性最高。哺乳犊牛岛土壤与其他牛舍土壤细菌群落在门水平上差异较大;泌乳期牛舍土样之间的细菌群落结构相似度较高。在门的水平上,拟杆菌门(Bacteroidetes)、变形菌门(Proteobacteria)、放线菌门(Actinobacteria)和厚壁菌门(Firmicutes)是这8个牛舍土样共有的优势菌门。在属的水平上,嗜盐碱的盐单胞菌属(Halomonas)、具有潜在降解特性的Fermentimonas和栖海面菌属(Aequorivita)及致病菌的鸟杆菌属(Ornithobacterium)是犊牛期牛舍土样的优势菌属;嗜盐碱的Truepera是育成牛舍土样的优势菌属;致病菌的不动杆菌属(Acinetobacter)和Parapedobacter、耐药菌的Pedobacter是泌乳期牛舍土样的优势菌属。【结论】致病菌和参与硝酸盐呼吸的细菌主要分布在哺乳犊牛岛,嗜盐碱菌主要分布在断奶犊牛舍和育成牛舍,产甲烷的细菌主要分布在高产头胎泌乳牛舍。本研究分析了不同牛舍土壤细菌群落多样性,为奶牛健康生产提供理论依据。     

The microbiota in spider mite feces potentially reflects intestinal bacterial communities in the host

Microorganisms provide many physiological functions to herbivorous hosts. Spider mites (genus Tetranychus) are important agricultural pests throughout the world; however, the composition of the spider mite microbial community, especially gut microbiome, remains unclear. Here, we investigated the bacterial community in five spider mite species and their associated feces by deep sequencing of the 16S rRNA gene. The composition of the bacterial community was significantly different among the five prevalent spider mite species, and some bacterial symbionts showed host‐species specificity. Moreover, the abundance of the bacterial community in spider mite feces was significantly higher than that in the corresponding spider mite samples. However, Flavobacterium was detected in all samples, and represent a “core microbiome”. Remarkably, the maternally inherited endosymbiont Wolbachia was detected in both spider mite and feces. Overall, these results offer insight into the complex community of symbionts in spider mites, and give a new direction for future studies.     

Two cultivated legume plants reveal the enrichment process of the microbiome in the rhizocompartments

The microbiomes of rhizocompartments (nodule endophytes, root endophytes, rhizosphere and root zone) in soya bean and alfalfa were analysed using high‐throughput sequencing to investigate the interactions among legume species, microorganisms and soil types. A clear hierarchical filtration of microbiota by plants was observed in the four rhizocompartments – the nodule endosphere, root endosphere, rhizosphere and root zone – as demonstrated by significant variations in the composition of the microbial community in the different compartments. The rhizosphere and root zone microbial communities were largely influenced by soil type, and the nodule and root endophytes were primarily determined by plant species. Diverse microbes inhabited the root nodule endosphere, and the corresponding dominant symbiotic rhizobia belonged to Ensifer for alfalfa and Ensifer–Bradyrhizobium for soya bean. The nonsymbiotic nodule endophytes were mainly Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes. The variation in root microbial communities was also affected by the plant growth stage. In summary, this study demonstrated that the enrichment process of nodule endophytes follows a hierarchical filtration and that the bacterial communities in nodule endophytes vary according to the plant species.     

Bacterial community composition of a shallow hypertrophic freshwater lake in China, revealed by 16S rRNA gene sequences

The phylogenetic composition of a bacterial community from a hypertrophic freshwater lake in China was investigated by sequencing cloned 16S rRNA genes. Three hundred and thirty-six bacterial clones from four clone libraries in different months (March, May, July and September in 2004) were classified into 142 operational taxonomic units, most of which were affiliated with bacterial divisions commonly found in freshwater ecosystem, e.g. Alpha-, Beta-, Gamma- and Deltaproteobacteria, Bacteriodetes and Actinobacteria. The results showed that the composition of bacterial community in the July library was the most diverse one. Actinobacteria was the most significant lineage in Lake Taihu, with dominant numbers of operational taxonomic units in the May, July and September libraries. Phylogenetic analysis suggested that 53 sequences were grouped into six novel clusters which may represent specific populations indigenous to the environment. Coverage analyses indicated that the clone libraries could provide a fine inventory of bacterial diversity in the lake.     

Midgut bacterial communities in the giant Asian honeybee (Apis dorsata) across 4 developmental stages: A comparative study

Bacterial communities are known to play important roles during the developmental stages of insects, but current knowledge of bacteria associated with the midgut of Apis dorsata, the giant Asian honeybee, is limited. Using polymerase chain reaction‐denaturing gradient gel electrophoresis analysis (PCR‐DGGE) and 16S rRNA sequencing, the aim of this study was to determine the dynamics of bacterial community structure across four A. dorsata life stages in different geographical locations. The results reveal that bacterial diversity increased as the bee progressed through larval stage to newly emerged worker and old worker. However, in the pupal stage, no bands identified as bacteria could be observed. Overall, 2 bacterial phyla (Proteobacteria and Firmicutes) and 4 classes (Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, and Bacilli) were identified, but the frequency varied among the different stages and locations. The classes of Gammaproteobacteria and Bacilli dominated among larval, newly emerged worker and old worker developmental stages.     

种植体周围炎生物膜的微生物群落多样性研究进展

种植体周围炎是发生在骨性结合种植体周围组织的炎症,是由微生物引发的感染性疾病,可引起种植体周围支持组织丧失而导致种植失败。阐明种植体周围炎生物膜的微生物学基础,可为制定相应防治策略提供理论依据。随着测序技术的发展,基于16S rRNA基因的测序分析技术逐渐应用于与口腔种植体相关的微生物学研究,使人们对种植体周围炎生物膜的微生物群落多样性有了更全面的了解,也进一步认识到种植体周围炎和牙周炎菌斑生物膜的微生物结构存在显著差别。本文根据基于16S rRN基因A序列分析技术的最新研究成果,对种植体周围炎菌斑生物膜的微生物学研究进展作一综述。