基于高通量测序的鄱阳湖典型湿地土壤细菌群落特征分析

采用高通量测序技术分析了鄱阳湖典型湿地土壤细菌群落特征。测序结果表明,不同植被土壤细菌群落丰度与多样性的排序相同:苔草带苔草-虉草带芦苇带泥滩带藜蒿带。沿湖面至坡地,空间位置相近的土壤细菌群落结构具有更大的相似性,苔草-虉草带、苔草带和芦苇带的细菌群落结构相近,泥滩带和藜蒿带的细菌群落结构差异较大。变形菌门(30.0%)是湿地土壤平均相对丰度最高的门,其次为酸杆菌门(16.7%)和绿弯菌门(16.5%);多数门分类细菌相对丰度沿湖面至坡地存在一定变化趋势。硝化螺菌属是第一大属分类水平细菌群落。在土壤化学指标中,与鄱阳湖湿地细菌群落相关性较大的是总磷、铵态氮和有机质含量。以上研究结果表明,鄱阳湖湿地不同植被土壤细菌群落具有结构性差异,但沿湖面至坡地存在规律性变化。     

健康与感染青枯病烟株根际土壤与茎秆细菌群落结构与多样性

【目的】了解健康烟株与感染青枯病烟株在根际土壤、茎杆发病部位、茎杆病健交界部位以及未发病茎杆的细菌群落结构与多样性。【方法】分别对土壤与茎杆样品中细菌的16S rRNA基因V3-V4区进行扩增,采用Illumina MiSeq测序技术对扩增片段进行高通量测序,然后对健康烟株与感染青枯病烟株不同部位细菌群落结构与多样性进行分析。【结果】感染青枯病烟株发病茎杆及根际土壤的细菌群落多样性高于健康烟株茎杆及其根际土壤样品,病健交界茎杆样品细菌群落多样性低于健康烟株。变形菌门(Proteobacteria)在所有样品中均为优势菌门;所有烟株根际土壤的优势菌门为拟杆菌门(Bacteroidetes)、酸杆菌门(Acidobacteria)、放线菌门(Actinobacteria)和绿弯菌门(Chloroflexi);健康烟株茎杆部位的优势菌门为蓝细菌门(Cyanobacteria);感染青枯病烟株发病茎杆和病健交界茎杆部位的优势菌门为蓝细菌门(Cyanobacteria)和厚壁菌门(Firmicutes)。所有根际土壤样品的优势菌属为劳尔氏菌属(Ralstonia)、假单胞菌属(Pseudomonas)、鞘脂单胞菌属(Sphingomonas)、黄杆菌属(Flavobacterium)和代尔夫特菌属(Delftia),而感染青枯病烟株根际土壤的劳尔氏菌属(Ralstonia)和假单胞菌属(Pseudomonas)相对丰度显著高于健康烟株根际土壤,鞘脂单胞菌属相对丰度显著低于健康烟株根际土壤。烟株茎杆的优势菌属为劳尔氏菌属和假单胞菌属等。感染青枯病烟株病健交界茎杆中劳尔氏菌属、肠杆菌属(Enterobacter)和泛菌属(Pantoea)相对丰度显著低于健康烟株样品。【结论】健康与感染青枯病烟株茎杆样品细菌群落的丰富度和多样性明显低于相应的根际土壤样品。较健康烟株而言,感染青枯病烟株根际土壤和茎杆样品细菌群落丰富度和多样性均表现出不同程度地增加,且根际土壤细菌群落结构变化较茎杆样品明显,而病健交界茎杆样品细菌群落丰富度和多样性降低。烟草青枯病为典型土传病害,其病原茄科劳尔氏菌尽管能在烟株维管束中蔓延扩增,但主要还是分布于土壤中;它的存在似乎对土壤细菌群落的影响大于茎杆样品的。该研究结果提示对于青枯病的防治不能局限于烟株本身,田间土壤也应加大防治力度。     

徐州权台煤矿井下700m水平微生物群落分布特征

煤矿井下与表生环境具有明显差异,研究其微生物群落分布及多样性对深入探讨井下水-岩-气-生作用机制具有重要意义。本研究在徐州权台煤矿井下700 m水平采集了8个沉积物样本,对样品进行了理化指标测试和Miseq高通量测序。结果表明,煤矿井下具有丰富的微生物多样性,8个样本共检测到35个细菌门类,其中变形菌门(Proteobacteria)、厚壁菌门(Firmicutes)和放线菌门(Actinobacteria)为优势菌门,其相对丰度之和占比超过80%;煤矿井下的优势菌属主要包括乳球菌属(Lactococcus)、假单胞菌属(Pseudomonas)、分枝杆菌属(Mycobacterium)和芽孢杆菌属(Bacillus)。从井下环境细菌群落分布来看,变形菌门和厚壁菌门主要分布在岩巷中,而放线菌门则主要分布在煤巷中。岩巷中的细菌多样性整体上高于煤巷。样本理化指标与微生物群落间的相关性分析表明,pH值是影响煤矿细菌群落门水平分布的主要因素(R2=0.766,P<0.05),其中放线菌、厚壁菌门和Latescibacteria与pH呈正相关,其他门类与pH呈负相关。TOC、总氮、总磷及硫酸盐对群落丰度分布也有一定的影响。因此,在煤矿污染机制及污染物迁移的研究中需充分考虑井下微生物的影响。     

不同水稻组织内生细菌的群落多样性

[目的]为详细了解水稻不同组织内生细菌群落多样性。[方法]对宁粳43号内生细菌的总DNA提取后,采用高通量测序技术对水稻内生细菌的16S rRNA基因进行了序列测定,分析了水稻不同组织部位内生细菌群落结构特征。[结果]叶部共获得内生细菌OTUs 610个,茎部411个,根部174个。物种分类显示,叶部内生细菌种类隶属于22门40纲103目198科399属,其中优势类群是红球菌属（Rhodococcus）和乳酸杆菌属（Lactobacillus）,它们的相对丰度分别为21.00%和9.19%;茎部内生细菌种类隶属于19门31纲85目169科306属,其中优势类群是红球菌属和罗尔斯通菌属（Ralstonia）,它们的相对丰度分别为19.25%和13.52%;根部内生细菌种类隶属于9门19纲44目82科140属,其中优势类群是肠杆菌属（Enterobacter）和埃希氏杆菌属（Escherichia）,它们的相对丰度分别为81.13%和10.89%。根茎叶中相同的OTU有78个,放线菌门（Actinobacteria）与大多数细菌具有相关性。根系内生细菌中具有调控各种代谢网络功能的物种丰度高于茎部和叶部。[结论]不同水稻组织内生细菌具有丰富的群落多样性,其中叶部的内生细菌物种最丰富,根系参与各种代谢调控的细菌丰度最高,各个组织部位的优势菌属各不相同,变形菌门是最重要的水稻内生细菌。     

基于宏基因组的茉莉花内生细菌多样性分析

为了解茉莉花(Jasminum sambac)的内生菌多样性,利用16S rDNA高通量测序技术对其内生细菌组成进行测定。结果表明,茉莉花的内生细菌有38门78纲150目257科434属,其中变形菌门、放线菌门、壁厚菌门、拟杆菌门和绿弯菌门的物种丰度较高。变形菌门在6-10月的丰度均最高(70.3%～85.7%)。7月份植株的细菌Shannon指数最高(3.14)、Simpson指数最小(0.13),表明细菌群落多样性最高,且高温有利于提高植株内生细菌多样性。聚类和主成分分析表明,7和8月、9和10月的植株内生细菌群落构成相似度高,6月与其他月份的差异大。冗余分析和热图分析表明,土壤营养成分影响植株内生群落组成,以全氮、全磷和有机质含量为主要。这为挖掘利用茉莉花有益的内生菌资源奠定基础。     

银北盐渍化土壤中6种耐盐植物根际细菌群落结构及其多样性

土壤微生物对土壤肥力的形成和植物营养的转化起着积极的作用。对盐渍化土壤中植物根际微生物群落组成和多样性进行研究,有助于发现新的重要微生物功能类群或者功能潜力,对于盐碱土壤的植被恢复和生态重建都具有十分重要的意义。通过高通量测序和分离培养方法,对宁夏银北地区盐渍化土壤中的6种耐盐植物根际细菌的群落结构和多样性进行了分析。结果表明:所有土壤样品共检测到31门(亚门) 67纲253科400属细菌类群,不同植物根际微生物群落组成相似,但丰度各有差异,厚壁菌门、变形菌门、放线菌门和拟杆菌门为主要优势类群;在纲水平芽孢杆菌纲相对丰度最高,其次为α-变形菌、γ-变形菌和梭菌纲;在属水平上,芽孢杆菌属以极高的丰度(15.57%—53.85%)占据绝对优势,其次是鞘氨醇单胞菌属、不动杆菌属和节杆菌属。6种植物根际细菌的群落结构组成表现为芨芨草和柽柳相似,柳枝稷、苜蓿与枸杞相似,苦豆子则与另外5种差别最大。分离培养出的110株根际细菌多数具有较强的盐碱耐受性和一种以上生物学活性,分别隶属于芽孢杆菌属、假单胞菌属、鞘氨醇杆菌属、节杆菌属和中华根瘤菌属,在属水平上多样性单一,其中芽孢杆菌属是优势属。传统的分离培养和高通量测序结果都反映出银北地区盐渍化土壤中定殖着许多有重要生态功能的微生物类群,可用于进一步筛选和利用根际微生物改良盐碱土壤。     

高通量测序技术解析中学校园细菌群落的特征组成

中小学校园是具有人口密度大、微生物传播和交流活跃等特点的特殊人居环境。校园微生物群落组成及其传播是影响青少年健康微生物组形成和发育的重要因素。以某中学校园为研究对象,探究校园不同场所的微生物群落结构,力图初步阐明校园微生物群落及其特征分布。采集教学楼扶手、实验楼扶手门和把手、体育馆扶手、食堂门把手等人体最易接触到的物体微生物样品,采用Illumina HiSeq平台对采集的样品进行细菌16S rRNA基因V4区高通量测序,分析各样品的细菌群落特征。结果显示,不同场所细菌群落存在着不同的特征组成。尽管各场所物体表面的微生物主要属于变形菌门(Proteobacteria),厚壁菌门(Firmicutes)和放线菌门(Actinobacteria)等的栖水菌属(Enhydrobacter),链球菌属(Streptococcus),葡萄球菌(Staphylococcus)等属,但其相对丰度存在着显著的差异。例如,从食堂样品中检测到的丰度较高的不动杆菌属(Acinetobacter)和气球菌属(Aerococcus),在教学区域场所中未发现这两类微生物。体育馆楼梯扶手表面物种多样性显著高于其他场所设施表面物种多样性。通过对校园不同场所细菌组成的初步分析,发现了细菌群落具有按场所用途进行区分的特征,推测这些特征分布应与不同类型教学与生活活动密切相关,为后续研究校园环境对青少年身体健康的影响提供了实践参考。     

鄂尔多斯台地盐沼滩涂湿地土壤细菌群落结构及特征

依据植被分类法将鄂尔多斯高原盐沼滩涂湿地划分为肉质耐盐草甸(B)、苔草草甸(C)、禾草草甸(D)和杂类草草甸(E)等4个植被亚型,并以盐沼裸地(A)为对照样地,共计5种盐沼滩涂湿地景观类型。运用高通量测序技术分别研究其土壤细菌群落结构特征、分布情况,以及土壤盐分与土壤细菌之间的关系。结果表明:(1) 5种盐沼滩涂湿地的土壤细菌样品共12213条OTUs,属于45个门,122个纲,365个目,663个科,1375个属,2882个种。(2)变形菌门(26.19%)是盐沼滩涂湿地平均相对丰度最高的门,其次为放线菌门(17.15%),绿弯菌门(12.62%),芽单胞菌门(Gemmatimonadetes,11.23%),拟杆菌门(Bacteroidetes,9.38%),酸杆菌门(Acidobacteria,8.83%)厚壁菌门(Firmicutes,2.96%);芽单胞菌纲中的未定细菌(norank＿c＿Gemmatimonadetes)是丰度最高的属,平均丰度为5.75%。(3)鄂尔多斯盐沼滩涂湿地自西南向东北,空间位置相近的土壤细菌群落结构具有更大的相似性,随着土壤盐分变化,变形菌门相对...     

4种抗生素对蚯蚓-污泥系统细菌群落结构的影响

蚯蚓可摄食污泥中的有机物,其肠道微生物群落在其分解过程中起着主要的作用。利用赤子爱胜蚓(Eisenia foetida)和人工湿地基质构建蚯蚓-污泥系统,添加氯霉素、四环素、链霉素和青霉素4种抗生素,研究不同抗生素对污泥和蚓粪的细菌群落结构的影响。采用高通量测序技术比较分析污泥和蚓粪的细菌多样性及群落结构变化。结果表明,外加抗生素能够导致污泥的Chao1和ACE指数降低,同时降低拟杆菌门和变形菌门的相对丰度,加入氯霉素和青霉素会增加厚壁菌门的相对丰度,降低酸杆菌门、放线菌门和绿弯菌门的相对丰度,加入四环素和链霉素则与之相反。蚓粪样品中,添加氯霉素和链霉素导致Chao1和ACE指数降低,而添加四环素和青霉素则导致Chao1和ACE指数升高,外加抗生素可降低拟杆菌门的相对丰度,增加放线菌门、变形菌门和疣微菌门的相对丰度。主成分分析(PCA)和聚类分析表明,氯霉素和青霉素对污泥细菌群落影响作用相似,四环素与链霉素效果类似;氯霉素对蚓粪群落结构的影响小于其他抗生素。研究结果显示,抗生素可影响污泥和蚓粪的细菌多样性及群落结构,不同抗生素对污泥和蚓粪的影响程度存在差异。     

药用植物刺山柑不同部位细菌群落结构及其多样性

【目的】研究传统药用植物刺山柑（Capparis spinosa L.）不同部位细菌群落结构、物种组成和多样性特征,为药用植物微生物资源的开发及微生物与宿主互作提供理论依据。【方法】本研究以刺山柑地上部植物组织（果实、茎）和地下部土壤（根际土壤、非根际土壤）为研究材料,采用高通量测序技术分析刺山柑不同部位细菌的16S rRNA基因多样性,比较其细菌群落结构和物种组成特征。【结果】刺山柑4种样本共获得的3 649个操作分类单元（operational taxonomic unit,OTU）,属于34门、88纲、248目、464科和1 051属。土壤样本的细菌多样性大于植物组织,细菌群落多样性以根际土壤、非根际土壤、茎和果实的顺序逐渐降低,果实内生细菌群落多样性始终最低,显著低于根际土壤。不同部位相对丰度较高的细菌门如下：植物组织中以变形菌门为主,根际土壤中为变形菌门和放线菌门,非根际土中为厚壁菌门和放线菌门。无色杆菌属（Achromobacter）、欧文氏菌属（Erwinia）、肠球菌属（Enterococcus）、微小杆菌属（Exiguobacterium）、乳杆菌属（Lactobacillus）和克雷伯氏菌属（Klebsiella）主要存在于刺山柑植物组织中。游动球菌属（Planomicrobium）、库克菌属（Kocuria）、类芽孢杆菌属（Paenibacillus）、链霉菌属（Streptomyces）、微枝形杆菌属（Microvirga）和节杆菌属（Arthrobacter）主要分布于土壤中。β多样性分析结果表明,刺山柑植物组织和土壤的细菌群落结构具有显著差异,同类型样本的细菌群落结构相似。【结论】刺山柑土壤样本中细菌群落的多样性和丰富度均高于植物组织,刺山柑不同部位的细菌群落组成不同。本研究对刺山柑不同部位细菌群落结构进行了初步分析,鉴定了各部位细菌群落中的核心菌群,为以后挖掘刺山柑的功能研究和利用提供了准确的微生物信息。     

Comparative analysis of salivary bacterial microbiome diversity in edentulous infants and their mothers or primary care givers using pyrosequencing

Bacterial contribution to oral disease has been studied in young children, but there is a lack of data addressing the developmental perspective in edentulous infants. Our primary objectives were to use pyrosequencing to phylogenetically characterize the salivary bacterial microbiome of edentulous infants and to make comparisons against their mothers. Saliva samples were collected from 5 edentulous infants (mean age?=?4.6±1.2 mo old) and their mothers or primary care givers (mean age?=?30.8±9.5 y old). Salivary DNA was extracted, used to generate DNA amplicons of the V4-V6 hypervariable region of the bacterial 16S rDNA gene, and subjected to 454-pyrosequencing. On average, over 80,000 sequences per sample were generated. High bacterial diversity was noted in the saliva of adults [1012 operational taxonomical units (OTU) at 3% divergence] and infants (578 OTU at 3% divergence). Firmicutes, Proteobacteria, Actinobacteria, and Fusobacteria were predominant bacterial phyla present in all samples. A total of 397 bacterial genera were present in our dataset. Of the 28 genera different (P<0.05) between infants and adults, 27 had a greater prevalence in adults. The exception was Streptococcus, which was the predominant genera in infant saliva (62.2% in infants vs. 20.4% in adults; P<0.05). Veillonella, Neisseria, Rothia, Haemophilus, Gemella, Granulicatella, Leptotrichia, and Fusobacterium were also predominant genera in infant samples, while Haemophilus, Neisseria, Veillonella, Fusobacterium, Oribacterium, Rothia, Treponema, and Actinomyces were predominant in adults. Our data demonstrate that although the adult saliva bacterial microbiome had a greater OTU count than infants, a rich bacterial community exists in the infant oral cavity prior to tooth eruption. Streptococcus, Veillonella, and Neisseria are the predominant bacterial genera present in infants. Further research is required to characterize the development of oral microbiota early in life and identify environmental factors that impact colonization and oral and gastrointestinal disease risk.     

Network Analysis Highlights Complex Interactions between Pathogen,Host and Commensal Microbiota

Interactions between bacteria and their host represent a full continuum from pathogenicity to mutualism. From an evolutionary perspective, host-bacteria relationships are no longer considered a two-component system but rather a complex network. In this study, we focused on the relationship between brook charr (Salvelinus fontinalis) and bacterial communities developing on skin mucus. We hypothesized that stressful conditions such as those occurring in aquaculture production induce shifts in the bacterial community of healthy fish, thus allowing pathogens to cause infections. The results showed that fish skin mucus microbiota taxonomical structure is highly specific, its diversity being partly influenced by the surrounding water bacterial community. Two types of taxonomic co-variation patterns emerged across 121 contrasted communities’ samples: one encompassing four genera well known for their probiotic properties, the other harboring five genera mostly associated with pathogen species. The homeostasis of fish bacterial community was extensively disturbed by induction of physiological stress in that both: 1) the abundance of probiotic-like bacteria decreased after stress exposure; and 2) pathogenic bacteria increased following stress exposure. This study provides further insights regarding the role of mutualistic bacteria as a primary host protection barrier.     

Characterization of the diversity and temporal stability of bacterial communities in human milk

Recent investigations have demonstrated that human milk contains a variety of bacterial genera; however, as of yet very little work has been done to characterize the full diversity of these milk bacterial communities and their relative stability over time. To more thoroughly investigate the human milk microbiome, we utilized microbial identification techniques based on pyrosequencing of the 16S ribosomal RNA gene. Specifically, we characterized the bacterial communities present in milk samples collected from 16 women at three time-points over four weeks. Results indicated that milk bacterial communities were generally complex; several genera represented greater than 5% of the relative community abundance, and the community was often, yet not always, stable over time within an individual. These results support the conclusion that human milk, which is recommended as the optimal nutrition source for almost all healthy infants, contains a collection of bacteria more diverse than previously reported. This finding begs the question as to what role this community plays in colonization of the infant gastrointestinal tract and maintaining mammary health.     

Molecular Comparison of Bacterial Communities on Peripheral Intravenous Catheters and Matched Skin Swabs

Skin bacteria at peripheral intravenous catheter (PIVC) insertion sites pose a serious risk of microbial migration and subsequent colonisation of PIVCs, and the development of catheter related bloodstream infections (CRBSIs). Common skin bacteria are often associated with CRBSIs, therefore the bacterial communities at PIVC skin sites are likely to have major implications for PIVC colonisation. This study aimed to determine the bacterial community structures on skin at PIVC insertion sites and to compare the diversity with associated PIVCs. A total of 10 PIVC skin site swabs and matching PIVC tips were collected by a research nurse from 10 hospitalised medical/surgical patients at catheter removal. All swabs and PIVCs underwent traditional culture and high-throughput sequencing. The bacterial communities on PIVC skin swabs and matching PIVCs were diverse and significantly associated (correlation coefficient = 0.7, p<0.001). Methylobacterium spp. was the dominant genus in all PIVC tip samples, but not so for skin swabs. Sixty-one percent of all reads from the PIVC tips and 36% of all reads from the skin swabs belonged to this genus. Staphylococcus spp., (26%), Pseudomonas spp., (10%) and Acinetobacter spp. (10%) were detected from skin swabs but not from PIVC tips. Most skin associated bacteria commonly associated with CRBSIs were observed on skin sites, but not on PIVCs. Diverse bacterial communities were observed at skin sites despite skin decolonization at PIVC insertion. The positive association of skin and PIVC tip communities provides further evidence that skin is a major source of PIVC colonisation via bacterial migration but microbes present may be different to those traditionally identified via culture methods. The results provide new insights into the colonisation of catheters and potential pathogenesis of bacteria associated with CRBSI, and may assist in developing new strategies designed to reduce the risk of CRBSI.     

Bacterial Community Composition in Central European Running Waters Examined by Temperature Gradient Gel Electrophoresis and Sequence Analysis of 16S rRNA Genes

The bacterial community composition in small streams and a river in central Germany was examined by temperature gradient gel electrophoresis (TGGE) with PCR products of 16S rRNA gene fragments and sequence analysis. Complex TGGE band patterns suggested high levels of diversity of bacterial species in all habitats of these environments. Cluster analyses demonstrated distinct differences among the communities in stream and spring water, sandy sediments, biofilms on stones, degrading leaves, and soil. The differences between stream water and sediment were more significant than those between sites within the same habitat along the stretch from the stream source to the mouth. TGGE data from an entire stream course suggest that, in the upper reach of the stream, a special suspended bacterial community is already established and changes only slightly downstream. The bacterial communities in water and sediment in an acidic headwater with a pH below 5 were highly similar to each other but deviated distinctly from the communities at the other sites. As ascertained by nucleotide sequence analysis, stream water communities were dominated by Betaproteobacteria (one-third of the total bacteria), whereas sediment communities were composed mainly of Betaproteobacteria and members of the Fibrobacteres/Acidobacteria group (each accounting for about 25% of bacteria). Sequences obtained from bacteria from water samples indicated the presence of typical cosmopolitan freshwater organisms. TGGE bands shared between stream and soil samples, as well as sequences found in bacteria from stream samples that were related to those of soil bacteria, demonstrated the occurrence of some species in both stream and soil habitats. Changes in bacterial community composition were correlated with geographic distance along a stream, but in comparisons of different streams and rivers, community composition was correlated only with environmental conditions.     

Colostrum of Healthy Slovenian Mothers: Microbiota Composition and Bacteriocin Gene Prevalence

Microbial communities inhabiting the breast milk microenvironment are essential in supporting mammary gland health in lactating women and in providing gut-colonizing bacterial ''inoculum'' for their infants’ gastro-intestinal development. Bacterial DNA was extracted from colostrum samples of 45 healthy Slovenian mothers. Characteristics of the communities in the samples were assessed by polymerase chain reaction (PCR) coupled with denaturing gradient gel electrophoresis (DGGE) and by quantitative real-time PCR (qPCR). PCR screening for the prevalence of bacteriocin genes was performed on DNA of culturable and total colostrum bacteria. DGGE profiling revealed the presence of Staphylococcus and Gemella in most of the samples and exposed 4 clusters based on the abundance of 3 bands: Staphylococcus epidermidis/Gemella, Streptococcus oralis/pneumonia and Streptococcus salivarius. Bacilli represented the largest proportion of the communities. High prevalence in samples at relatively low quantities was confirmed by qPCR for enterobacteria (100%), Clostridia (95.6%), Bacteroides-Prevotella group (62.2%) and bifidobacteria (53.3%). Bacterial quantities (genome equivalents ml^-1) varied greatly among the samples; Staphylococcus epidermidis and staphylococci varied in the range of 4 logs, streptococci and all bacteria varied in the range of 2 logs, and other researched groups varied in the range of 1 log. The quantity of most bacterial groups was correlated with the amount of all bacteria. The majority of the genus Staphylococcus was represented by the species Staphylococcus epidermidis (on average 61%), and their abundances were linearly correlated. Determinants of salivaricin A, salivaricin B, streptin and cytolysin were found in single samples. This work provides knowledge on the colostrum microbial community composition of healthy lactating Slovenian mothers and reports bacteriocin gene prevalence.     

Effect of streptomycin treatment on bacterial community structure in the apple phyllosphere

We studied the effect of many years of streptomycin use in apple orchards on the proportion of phyllosphere bacteria resistant to streptomycin and bacterial community structure. Leaf samples were collected during early July through early September from four orchards that had been sprayed with streptomycin during spring of most years for at least 10 years and four orchards that had not been sprayed. The percentage of cultured phyllosphere bacteria resistant to streptomycin at non-sprayed orchards (mean of 65%) was greater than at sprayed orchards (mean of 50%) (P?=?0.0271). For each orchard, a 16S rRNA gene clone library was constructed from leaf samples. Proteobacteria dominated the bacterial communities at all orchards, accounting for 71 of 104 OTUs (determined at 97% sequence similarity) and 93% of all sequences. The genera Massilia, Methylobacterium, Pantoea, Pseudomonas, and Sphingomonas were shared across all sites. Shannon and Simpson's diversity indices and Pielou's evenness index were similar among orchards regardless of streptomycin use. Analysis of Similarity (ANOSIM) indicated that long-term streptomycin treatment did not account for the observed variability in community structure among orchards (R?=?-0.104, P?=?0.655). Other variables, including time of summer, temperature and time at sampling, and relative distance of the orchards from each other, also had no significant effect on bacterial community structure. We conclude that factors other than streptomycin exposure drive both the proportion of streptomycin-resistant bacteria and phylogenetic makeup of bacterial communities in the apple phyllosphere in middle to late summer.     

Illumina sequencing of bacterial 16S rDNA and 16S rRNA reveals seasonal and species-specific variation in bacterial communities in four moss species

In order to better understand the factors that influence bacterial diversity and community composition in moss-associated bacteria, a study of bacterial communities in four moss species collected in three seasons was carried out via high-throughput sequencing of 16S rDNA and 16S rRNA. Moss species included Cratoneuron filicinum, Pylaisiella polyantha, Campyliadelphus polygamum, and Grimmia pilifera, with samples collected in May, July, and October 2015 from rocks at Beijing Songshan National Nature Reserve. In total, the bacterial richness and diversity were high regardless of moss species, sampling season, or data source (DNA vs. RNA). Bacterial sequences were assigned to a total of 558 OTUs and 279 genera in 16 phyla. Proteobacteria and Actinobacteria were the two most abundant phyla, and Cellvibrio, Lapillicoccus, Jatrophihabitans, Friedmanniella, Oligoflexus, and Bosea the most common genera in the samples. A clustering algorithm and principal coordinate analysis revealed that C. filicinum and C. polygamum had similar bacterial communities, as did P. polyantha and G. pilifera. Metabolically active bacteria showed the same pattern in addition to seasonal variation: bacterial communities were most similar in summer and autumn, looking at each moss species separately. In contrast, DNA profiles lacked obvious seasonal dynamics. A partial least squares discriminant analysis identified three groups of samples that correlated with differences in moss species resources. Although bacterial community composition did vary with the sampling season and data source, these were not the most important factors influencing bacterial communities. Previous reports exhibited that mosses have been widely used in biomonitoring of air pollution by enriching some substances or elements in the moss-tag technique and the abundant moss associated bacteria might also be important components involved in the related biological processes. Thus, this survey not only enhanced our understanding of the factors which influence microbial communities in mosses but also would be helpful for better use and development of the moss-tag technique in the environmental biomonitoring.     

Genetic variation of Batrachochytrium dendrobatidis is linked to skin bacterial diversity in the Pacific treefrog Hyliola regilla (hypochondriaca)

Symbiotic bacterial communities are crucial to combating infections and contribute to host health. The amphibian skin microbiome plays an important role in protecting their hosts against pathogens such as Batrachochytrium dendrobatidis (Bd), one of the causative agents of chytridiomycosis, which is responsible for dramatic amphibian population declines worldwide. Although symbiotic skin bacteria are known to inhibit Bd growth, an understanding of the relationship between Bd genetic variability, environmental conditions, and skin bacterial communities is limited. Therefore, we examined the associations between Bd infection load, Bd genetic diversity and skin bacterial communities in five populations of Hyliola regilla (hypochondriaca) from environmentally contrasting sites in Baja California, Mexico. We observed differences in Bd genetics and infection load among sites and environments. Genetic analysis of Bd isolates revealed patterns of spatial structure corresponding to the five sites sampled. Amphibian skin bacterial diversity and community structure differed among environments and sites. Bacterial community composition was correlated with Bd genetic differences and infection load, with specific bacterial taxa enriched on infected and un-infected frogs. Our results indicate that skin-associated bacteria and Bd strains likely interact on the host skin, with consequences for microbial community structure and Bd infection intensity.