Summer temperature increase has distinct effects on the ectomycorrhizal fungal communities of moist tussock and dry tundra in Arctic Alaska

Arctic regions are experiencing the greatest rates of climate warming on the planet and marked changes have already been observed in terrestrial arctic ecosystems. While most studies have focused on the effects of warming on arctic vegetation and nutrient cycling, little is known about how belowground communities, such as fungi root‐associated, respond to warming. Here, we investigate how long‐term summer warming affects ectomycorrhizal (ECM) fungal communities. We used Ion Torrent sequencing of the rDNA internal transcribed spacer 2 (ITS2) region to compare ECM fungal communities in plots with and without long‐term experimental warming in both dry and moist tussock tundra. Cortinarius was the most OTU‐rich genus in the moist tundra, while the most diverse genus in the dry tundra was Tomentella. On the diversity level, in the moist tundra we found significant differences in community composition, and a sharp decrease in the richness of ECM fungi due to warming. On the functional level, our results indicate that warming induces shifts in the extramatrical properties of the communities, where the species with medium‐distance exploration type seem to be favored with potential implications for the mobilization of different nutrient pools in the soil. In the dry tundra, neither community richness nor community composition was significantly altered by warming, similar to what had been observed in ECM host plants. There was, however, a marginally significant increase in OTUs identified as ECM fungi with the medium‐distance exploration type in the warmed plots. Linking our findings of decreasing richness with previous results of increasing ECM fungal biomass suggests that certain ECM species are favored by warming and may become more abundant, while many other species may go locally extinct due to direct or indirect effects of warming. Such compositional shifts in the community might affect nutrient cycling and soil organic C storage.     

水稻种子的细菌含量和群落结构及其影响因素分析

【目的】种子是植物微生物群代际传递的重要途径,但种子携带的微生物群落尚缺乏系统的研究。本研究以水稻种子为模型,定量分析种子的细菌含量、测定种子的细菌群落结构、探究地域与品种对细菌含量及群落结构的影响和鉴定水稻种子的核心菌群。【方法】选取18个水稻品种,每个品种分别来自中国海南和天津2个地域,共36组样本。每组样本包含5或10个DNA样本,每个DNA样本由3粒种子提取的总DNA构成。使用细菌特异性16S rDNA介导的荧光定量PCR技术测定种子的细菌含量,并分析影响因素;使用16S rDNA扩增子测序技术测定种子的细菌群落结构,并用生物信息学方法分析了影响因素和核心菌群。【结果】本研究测定了1 080粒水稻种子的细菌含量,发现经过表面除菌的水稻种子内部存在共栖细菌,平均每克种子的细菌含量为1.53×10⁶。水稻品种对种子的细菌含量有显著影响,而地域无影响。测定180个扩增子文库的细菌群落结构,发现水稻种子的菌群与水稻植株有相似之处,均以变形菌门为主要的细菌门类;地域对水稻种子的细菌群落结构有重要影响,不同地域的水稻种子在主坐标分析(principal co-ordinate analysis, PCoA)中有明显分离;而粳稻和籼稻之间无显著差异。还发现水稻种子存在核心菌群,且相对丰度高达总菌群的85.56%。【结论】本研究系统地揭示了水稻种子的细菌含量、群落结构及其影响因素,为利用种传微生物促进水稻健康提供了数据和方法支持。     

Bacterial community structure and activity in different Cd-treated forest soils

In this study we compared indicators of Cd bioavailability (water extracts, Lakanen extracts, free ions) and ecotoxicity in forest soils with contrasting physico-chemical characteristics. Soil samples were treated with CdCl(2) solutions (0, 0.1, 1, 10 and 100 mM) and incubated for 30 days. Microbial activity indexes (acid phosphatase, beta-glucosidase, basal respiration) and changes in bacterial community structure using terminal restriction fragment length polymorphism (T-RFLP) fingerprinting were investigated. The Cd concentrations measured ranged from 1% to 37% of the total additions in water extracts, to higher levels in Lakanen extracts. Effects of Cd were observed at bioavailable concentrations exceeding United Nations/European Economic Commission UN/ECE guidelines for total Cd in the soil solution. Basal respiration was the most affected index, while enzymatic activities showed variable responses to the Cd treatments. We also noticed that soils with pH higher than 6.7 and clay content higher than 50% showed inhibition of basal respiration but no marked shift in bacterial community structure. Soils with lower pH (pH <5.8) with less clay content (<50%) showed in addition strong changes in the bacterial community structure. Our results provide evidence for the importance of relating the effects of Cd on the soil communities to soil properties and to bioavailability.     

Soil parent material is a key determinant of the bacterial community structure in arable soils

The bacterial community composition in soil and rhizosphere taken from arable field sites, differing in soil parent material and soil texture, was analyzed using terminal restriction fragment length polymorphism (T-RFLP) of 16S rRNA genes. Nine sandy to silty soils from North-East Germany could clearly be distinguished from each other, with a relatively low heterogeneity in the community structure within the field replicates. There was a relationship between the soil parent material, i.e. different glacial and aeolian sediments, and the clustering of the profiles from different sites. A site-specific grouping of T-RFLP profiles was also found for the rhizosphere samples of the same field sites that were planted with potatoes. The branching of the rhizosphere profiles corresponded partly with the soil parent material, whereas the effect of the plant genotype was negligible. Selected terminal restriction fragments differing in their relative abundance within the nine soils were analyzed based on the cloning of the 16S rRNA genes of one soil sample. A high phylogenetic diversity observed to include Acidobacteria, Betaproteobacteria, Bacteroidetes, Verrucomicrobia, and Gemmatimonadetes. The assignment of three out of the seven selected terminal restriction fragments to members of Acidobacteria suggested that this group seems to participate frequently in the shifting of community structures that result from soil property changes.     

Fertilisation practice changes rhizosphere microbial community structure in the agroecosystem

Rhizosphere microbial community is important for the acquisition of soil nutrients and closely related to plant species. Fertilisation practice changed soil quality. With the hypothesis of stronger rhizosphere effect of plant on rhizosphere microbial community than fertilisation management, we designed this research based on a long‐term field experiment (1982–present). This study consists of no fertilisation (NF), mineral fertilisers (NPK), mineral fertilisers plus 7,500 kg/ha of wheat straw addition (WS) and mineral fertilisers plus 30,000 kg/ha of cow manure (CM). After analysing, we found that fertilisation management not only elevated crop yield but also affected crop rhizosphere microbial community structure. The influence of fertilisation practice on wheat rhizosphere microbial structure was stronger than that of wheat. For wheat rhizosphere bacterial community, it was significantly affected by soil water content (SWC), nitrogen (TN), phosphorus (TP), pH, available phosphorus (AVP) and nitrogen (AVN), dissolved organic nitrogen (DON) and carbon (DOC). Besides SWC, pH, AVP, AVN, TN, TP and DOC, the wheat rhizosphere fungi community was also significantly affected by soil organic matter (SOM) and available potassium (AVK). Moreover, compared to rhizosphere bacterial community, the influences of soil physiochemical properties on rhizosphere fungal community was stronger. In conclusion, fertilisation practice was the primary factor structuring rhizosphere microbial community by changing soil nutrients availabilities in the agroecosystem.     

Bacterial community structure in Apis florea larvae analyzed by denaturing gradient gel electrophoresis and 16S rRNA gene sequencing

This study characterizes the colonization and composition of bacterial flora in dwarf Asian honeybee (Apis florea) larvae and compares bacterial diversity and distribution among different sampling locations. A. florea larvae were collected from 3 locations in Chiang Mai province, Thailand. Bacterial DNA was extracted from each larva using the phenol–chloroform method. Denaturing gradient gel electrophoresis was performed, and the dominant bands were excised from the gels, cloned, and sequenced for bacterial species identification. The result revealed similarities of bacterial community profiles in each individual colony, but differences between colonies from the same and different locations. A. florea larvae harbor bacteria belonging to 2 phyla (Firmicutes and Proteobacteria), 5 classes (Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Bacilli, and Clostridia), 6 genera (Clostridium, Gilliamella, Melissococcus, Lactobacillus, Saccharibacter, and Snodgrassella), and an unknown genus from uncultured bacterial species. The classes with the highest abundance of bacteria were Alphaproteobacteria (34%), Bacilli (25%), Betaproteobacteria (11%), Gammaproteobacteria (10%), and Clostridia (8%), respectively. Similarly, uncultured bacterial species were identified (12%). Environmental bacterial species, such as Saccharibacter floricola, were also found. This is the first study in which sequences closely related to Melissococcus plutonius, the causal pathogen responsible for European foulbrood, have been identified in Thai A. florea larvae.     

Defining seasonal marine microbial community dynamics

Here we describe, the longest microbial time-series analyzed to date using high-resolution 16S rRNA tag pyrosequencing of samples taken monthly over 6 years at a temperate marine coastal site off Plymouth, UK. Data treatment effected the estimation of community richness over a 6-year period, whereby 8794 operational taxonomic units (OTUs) were identified using single-linkage preclustering and 21 130 OTUs were identified by denoising the data. The Alphaproteobacteria were the most abundant Class, and the most frequently recorded OTUs were members of the Rickettsiales (SAR 11) and Rhodobacteriales. This near-surface ocean bacterial community showed strong repeatable seasonal patterns, which were defined by winter peaks in diversity across all years. Environmental variables explained far more variation in seasonally predictable bacteria than did data on protists or metazoan biomass. Change in day length alone explains >65% of the variance in community diversity. The results suggested that seasonal changes in environmental variables are more important than trophic interactions. Interestingly, microbial association network analysis showed that correlations in abundance were stronger within bacterial taxa rather than between bacteria and eukaryotes, or between bacteria and environmental variables.     

5株北极微藻藻际环境的细菌多样性

对5株北极微藻,如脆杆藻(Fragilariopsis sp.)、微单胞藻(Micromonas sp.)、四棘藻(Attheya septentrionalis)、海链藻(Thalassiosira sp.)和小球藻(Chlorella sp.)的不同生长时期的粘附细菌和游离细菌的16S rRNA基因进行PCR-DGGE分析,研究藻际环境的细菌多样性。结果表明,5株微藻具有不同的藻际微生物群落结构组成,其中微单胞藻、脆杆藻、四棘藻和海链藻的藻际细菌主要由Cyanobacteria(藻蓝细菌)、α-Proteobacteria(α-变形菌纲)和γ-Proteobacteria(γ-变形菌纲)组成,仅微单胞藻和脆杆藻检测出CFB(Cytophaga-Flexibacter-Bacteroides,噬纤维菌-屈挠杆菌-拟杆菌)。小球藻由Cyanobacteria、CFB、α-Proteobacteria和β-Proteobacteria(β-变形菌纲)组成。微单胞藻的藻际菌群结构稳定,不同生长时期的游离细菌和粘附细菌组成差异不明显。3株硅藻-脆杆藻、四棘藻和海链藻的游离细菌主要由γ-Proteobacteria组成,小球藻的游离细菌主要为β-Proteobacteria,而5株微藻的粘附细菌主要由Cyanobacteria组成。从DGGE图谱来看,在脆杆藻生长的延滞期、指数期和稳定期,其藻际游离细菌和粘附细菌的16S rRNA基因扩增条带数量和位置均有明显差异,但优势扩增条带较稳定;其他4株藻粘附细菌和游离细菌的扩增条带比较稳定,说明藻际关联菌群结构较稳定。藻菌种间特异性关系为不同微藻藻株提供了重要的线索,同时也带来更多的隐藏在藻际环境中的信息。     

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 succession in a high‐altitude subarctic glacier foreland is a three‐stage process

Alpine glaciers are retreating rapidly, exposing foreland minerals, which develop into soils. Bacterial communities in glacier forelands exhibit high rates of turnover and undergo dramatic shifts in composition within the first 50 years after deglaciation, followed by relative stabilization and convergence. This period of microbial development occurs simultaneously with plant colonization in most systems; thus, it remains unclear whether the changes in the bacterial communities occur primarily as the result of edaphic, climatic or biotic factors. We examined bacterial community structure along two replicate chronosequences within the glacial foreland of Duke River Glacier, Yukon, Canada. This foreland is estimated to include >200 years of bare soils before an appreciable grassline, likely due to the high latitude and altitude of the glacier. This enabled us to examine bacterial community development prior to plant colonization over a longer period than previous studies. We observed three successional groups in the chronosequence: (i) an ‘early’ group in soils of less than approximately 50 years since deglaciation; (ii) an ‘intermediate’ group within bare soils, after the early period but before the grassline, containing communities with a relatively high degree of variability in composition; and (iii) a ‘grassline’ group in soils collected after plant colonization with higher diversity but lower age‐group variability in community composition. These findings suggest rapid replacement and addition of species better adapted to glacier foreland conditions followed by slower community shifts over the next 150 years and, finally, indications of a possible response to plant colonization.     

Temporal patterns of microbial community structure in the Mid-Atlantic Bight

Although open ocean time-series sites have been areas of microbial research for years, relatively little is known about the population dynamics of bacterioplankton communities in the coastal ocean on kilometer spatial and seasonal temporal scales. To gain a better understanding of microbial community variability, monthly samples of bacterial biomass were collected in 1995-1996 along a 34-km transect near the Long-Term Ecosystem Observatory (LEO-15) off the New Jersey coast. Surface and bottom sampling was performed at seven stations along a transect line with depths ranging from 1 to 35 m (n=178). Microbial populations were fingerprinted using ribosomal 16S rRNA genes and terminal restriction fragment length polymorphism analysis. Results from cluster analysis revealed distinct temporal patterns among the bacterioplankton communities in the Mid-Atlantic Bight rather than grouping by sample location or depth. Principal components analysis models supported the temporal patterns. In addition, partial least squares regression modeling could not discern a significant correlation from traditional oceanographic physical and phytoplankton nutrient parameters on overall bacterial community variability patterns at LEO-15. These results suggest factors not traditionally measured during oceanographic studies are structuring coastal microbial communities.     

Orchard floor management practices that maintain vegetative or biomass groundcover stimulate soil microbial activity and alter soil microbial community composition

Groundcover management systems (GMS) are important in managing fruit-tree orchards because of their effects on soil conditions, nutrient availability, tree growth and yields. We employed a polyphasic approach, incorporating measures of soil microbial abundance, activity and community composition, to study the long-term effects of different GMS on biotic and abiotic factors in an orchard soil. Four GMS treatments – Pre-emergence residual herbicides (Pre-H), post-emergence herbicide (Post-H), mowed-sod (Grass), and hardwood bark mulch (Mulch) – were established in 2-m-wide strips within tree rows in an apple orchard in 1992, and have been maintained and monitored annually until the present. We have measured soil water and nutrient availability, tree growth, and yields annually from 1993 to 2003. Soil nematode numbers and trophic groups were evaluated in July and Oct. 2001, and Sept. 2003. Numbers of culturable bacteria and fungi, soil respiratory activity, eubacterial and fungal community composition were determined in May and Sept. 2003. The Pre-H treatment soil had the fewest culturable bacteria, while the Grass treatment had the largest population of culturable fungi. Soil nematode population size and diversity were also affected by GMS treatments; the Pre-H treatment had the lowest ratio of (bacteriovores + fungivores) to plant parasitic nematodes. Soil respiration rates were higher in the Mulch than in other treatments during a 40-day incubation period. Hierarchical cluster dendrograms of denaturing gradient gel electrophoresis (DGGE) fingerprints for eubacterial community 16S rRNA genes indicated that Post-H and Grass treatments clustered together and separately from the Pre-H and Mulch treatments, which were also grouped together. The influence of GMSs on the fungal community, as assessed by PCR-DGGE of the internal transcribed spacer (ITS) region, was not as pronounced as that observed for bacteria. Soil fungal community composition under the Mulch differed from that under other treatments. The effects of GMS on soil microbial community abundance, activity, and composition were associated with observed differences in soil organic matter inputs and turnover, nutrient availability, and apple tree growth and yields under the different GMS treatments.     

利用小亚基核糖体RNA 技术分析温室黄瓜近根土壤古菌和真菌多样性

土壤古菌和真菌在温室生态系统是仅次于细菌的微生物,具有类似于细菌的重要生态功能。通过构建古菌16S rRNA和真菌18S rRNA基因克隆文库,分析温室黄瓜近根土壤古菌和真菌群落结构组成,为开发利用温室这一特殊的生态环境中丰富的微生物资源以及理解微生物与植物间的互作提供参考依据。采用研磨-冻融-溶菌酶-蛋白酶K-SDS热处理以及CTAB处理等理化方法,提取和纯化微生物总DNA,构建古菌16S rRNA和真菌18S rRNA基因克隆文库。利用DOTUR软件将古菌和真菌序列按照相似性97％的标准分成若干个可操作分类单元 (OTUs)。土壤古菌克隆文库主要包括泉古菌门和未分类的古菌两大类,并有少部分广域古菌类群,所有泉古菌均属于热变形菌纲,共45个OTUs;真菌克隆文库包括真菌门的大多数亚门真菌,共24个OTUs,未发现担子菌亚门真菌。古菌多样性比较丰富,且发现少量的广域古菌 (甲烷菌),这一情况可能与温室长期高温高湿,高有机质含量,土壤处于缺氧环境有关;土壤真菌的优势种群为子囊菌,占到土壤真菌的80％以上,这可能与绝大多数植物真菌性病害属于土传病害,通过菌丝体、菌核或子囊壳在土壤病残体中越冬有一定的关系。     

Bacterial community structure, compartmentalization and activity in a microbial fuel cell

AIMS: To characterize bacterial populations and their activities within a microbial fuel cell (MFC), using cultivation-independent and cultivation approaches. METHODS AND RESULTS: Electron microscopic observations showed that the fuel cell electrode had a microbial biofilm attached to its surface with loosely associated microbial clumps. Bacterial 16S rRNA gene libraries were constructed and analysed from each of four compartments within the fuel cell: the planktonic community; the membrane biofilm; bacterial clumps (BC) and the anode biofilm. Results showed that the bacterial community structure varied significantly between these compartments. It was observed that Gammaproteobacteria phylotypes were present at higher numbers within libraries from the BC and electrode biofilm compared with other parts of the fuel cell. Community structure of the MFC determined by analyses of bacterial 16S rRNA gene libraries and anaerobic cultivation showed excellent agreement with community profiles from denaturing gradient gel electrophoresis (DGGE) analysis. CONCLUSIONS: Members of the family Enterobacteriaceae, such as Klebsiella sp. and Enterobacter sp. and other Gammaproteobacteria with Fe(III)-reducing and electrochemical activity had a significant potential for energy generation in this system. SIGNIFICANCE AND IMPACT OF THE STUDY: This study has shown that electrochemically active bacteria can be enriched using an electrochemical fuel cell.     

Microbial diversity and community structure in Fynbos soil

The Fynbos biome in South Africa is renowned for its high plant diversity and the conservation of this area is particularly important for the region. This is especially true in the case of endangered vegetation types on the lowlands such as Sand Fynbos, of which only small fragments remain. The question is thus whether the diversity of the above‐ground flora is mirrored in the below‐ground microbial communities. In order to determine the relationship of the above‐ and below‐ground communities, the soil community composition of both fungal and bacterial groups in Sand Fynbos was characterized over space and time. A molecular approach was used based on the isolation of total soil genomic DNA and automated ribosomal intergenic spacer analysis of bacterial and fungal communities. Soil from four different sites was compared to resolve the microbial diversity of eubacterial and fungal groups on a local (alpha diversity) scale as well as a landscape scale (beta diversity). The community structures from different sites were compared and found to exhibit strong spatial patterns which remained stable over time. The plant community data were compared with the fungal and the bacterial communities. We concluded that the microbial communities in the Sand Fynbos are highly diverse and closely linked to the above‐ground floral communities.     

Landscape patterns of free amino acids in arctic tundra soils

Concentrations of free amino acids were measured in soils from four major ecosystem types in arctic Alaska. Total free amino acid concentrations were several-fold higher than ammonium (the major form of inorganic nitrogen) in water extracts of soils. The dominant free amino acids in these soils were glycine, aspartic acid, glutamic acid, serine, and arginine. Concentrations of total amino acids ranged 5-fold across communities, being highest in tussock tundra and lowest in wet meadows. Incubation experiments indicate that the turnover of amino acids is rapid, which suggests high rates of gross nitrogen mineralization in these soils. The high concentrations and dynamic nature of soil free amino acids suggest that this nitrogen pool is a significant component of nitrogen cycling in these tundra ecosystems.     

舟山群岛不同功能区划海域细菌群落结构分析

浮游细菌在海洋生态系统中不可或缺,在海洋生物地球化学循环过程中起着关键性作用。【目的】为了解舟山群岛不同功能区划海域细菌群落结构及丰度变化,探索海洋生态因子对细菌群落结构的影响。【方法】于2016年夏季(8月)在舟山群岛不同功能区划海域共设置8个典型站位采集表层海水,基于细菌16S rRNA基因进行高通量测序;利用流式细胞术揭示各海域细菌丰度;利用典范对应分析(Canonical correspondence analysis,CCA)探讨海洋生态因子与细菌多样性之间的关系。【结果】共获取到305487条原始序列,基于97%相似性水平进行OTU(Operational Taxonomic Units)聚类分析,共得到1088个OTUs,包括29个门、62个纲、138个目、239个科、416个属。细菌群落组成在各个站位之间不尽相同,但都主要包括Flavobacteria、Alphaproteobacteria、Gammaproteobacteria三大优势菌纲。CCA结果表明细菌群落结构和多样性情况与站位分布和所在站位的环境因子息息相关,Cyanobacteria受硝酸盐影响显著,Parcubacteria受温度影响最大,而磷酸盐对本实验海域菌群影响甚微。对海洋菌群潜在功能进行预测的结果显示,各海域菌群在氨基酸代谢、碳水化合物代谢、膜运输等方面功能较为突出,为今后舟山海洋微生物研究提供了新的方向。【结论】高通量测序分析可以更精确地揭示海洋菌群的群落结构信息。该研究为细菌群落结构与环境因素的关联提供参考。本研究所取得的大量数据既可以作为对舟山市海洋功能区划施行情况的响应,又将为舟山及其邻近海域浮游细菌群落结构的进一步研究奠定基础。     

土地利用变化对土壤真菌群落结构的影响

应用PCR-RFLP和测序分析对川西亚高山米亚罗林区不同土地利用类型的土壤真菌18S rDNA基因进行了多样性和系统发育研究,探讨了土地利用变化对土壤真菌群落结构的影响。在20a龄云杉(Picea likiandensis var balfourianan)人工林和菜地两种类型土壤中,共得到238个阳性克隆,限制性内切酶MspI和RsaI进行RFLP分析后得到56个不同的分类操作单元(OTUs),其中20a龄云杉人工林样地获得137个阳性克隆和37个OTUs,而菜地样地获得101个阳性克隆和19个OTUs。在两类样地中具有不同的优势种群,其中20a龄云杉人工林样地有1个明显优势种群,占总克隆数的20.4%;菜地样地有2个明显优势种群,分别占总克隆数的25.7%和21.8%。对14个克隆进行了序列测定,序列的相似性在86%~99%之间,与GenBank数据库中的序列进行比对,与已知序列的相似性在92%~100%之间。系统发育分析表明,所有的18SrDNA基因被分为3个主要的簇,其中20a龄云杉人工林样地的克隆都聚集在第一和第三簇中,而菜地样地的克隆都聚集在第二簇中。结果说明,两类土壤中具有较为丰富的真菌多样性,而土地利用变化引起了土壤真菌群落结构的明显变化。