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  • 刊频： Monthly, 1993-
  • NLM标题： FEMS Microbiol Ecol
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  • 1.

    【2hr】Molecular Characterization and In Situ Quantification of Anoxic Arsenite Oxidizing Denitrifying Enrichment Cultures

    包量

    机译 缺氧亚砷酸氧化反硝化富集培养物的分子表征和原位定量
    摘要：To explore bacteria involved in the oxidation of arsenite (As(III)) under denitrifying conditions, three enrichment cultures (ECs) and one mixed culture (MC) were characterized that originated from anaerobic environmental samples. The oxidation of As(III) (0.5 mM) was dependent on NO3− addition and N2-formation was dependent on As(III) addition. The ratio of N2-N formed to As(III) fed approximated the expected stoichiometry of 2.5. A 16S rRNA gene clone library analysis revealed three predominant phylotypes. The first, related to the genus Azoarcus from the division β-Proteobacteria, was found in the three ECs. The other two predominant phylotypes were closely related to the genera Acidovorax and Diaphorobacter within the Comamonadaceae family of β-Proteobacteria and one of these was present in all of the cultures examined. Fluorescent in situ hybridization (FISH) confirmed that Azoarcus accounted for a large fraction of bacteria present in the ECs. The Azoarcus clones had 96% sequence homology with Azoarcus sp. strain DAO1, an isolate previously reported to oxidize As(III) with nitrate. FISH analysis also confirmed that Comamonadaceae were present in all cultures. Pure cultures of Azoarcus and Diaphorobacter were isolated and shown to be responsible for nitrate-dependent As(III) oxidation. These results taken as a whole suggest that bacteria within the genus Azoarcus and the family Comamonadaceae are involved in the observed anoxic oxidation of As(III).
  • 2.

    【2hr】Potential core species and satellite species in the bacterial community within the rabbit caecum

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    机译 兔盲肠细菌群落中潜在的核心物种和卫星物种
    摘要：A bacteria library was constructed from the caecum of a rabbit maintained under standard conditions. The complete gene 16S rRNA gene was sequenced. The 228 clones obtained were distributed in 70 operational taxonomic units (OTUs). The large majority of the OTUs were composed of one or two clones and seven OTUs contained half of the sequences. Fourteen sequences had high similarity to the sequence already registered in databases (threshold of 97%). Only one of these sequences has been identified as Variovorax sp. (99% identity). Units were distributed mainly (94%) in the Firmicutes phylum. Three sequences were related to Bacteroidetes. Nine clusters were defined in the phylogenic tree. A great diversity of caecal bacteria of the rabbit was shown. Half of the sequences generated in this library were distributed in the phylogenetic tree near the sequences characterized previously in rabbit caecum (potential core species), and the other half of the sequences were well separated (satellite species).
  • 3.

    【2hr】Role of hydrogen peroxidein competition and cooperation between Streptococcus gordonii and Actinomyces naeslundii

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    机译 过氧化氢在戈登链球菌与内氏放线菌竞争与合作中的作用
    摘要：In dental plaque α-haemolytic streptococci, including Streptococcus gordonii, are considered beneficial for oral health. These organisms produce hydrogen peroxide (H2O2) at concentrations sufficient to kill many oral bacteria. Streptococci do not produce catalase yet tolerate H2O2. We recently demonstrated that coaggregation with Actinomyces naeslundii stabilizes arginine biosynthesis in S. gordonii. Protein arginine residues are sensitive to oxidation by H2O2. Here, the ability of A. naeslundii to protect S. gordonii against self-produced H2O2 was investigated. Coaggregation with A. naeslundii enabled S. gordonii to grow in the absence of arginine, and promoted survival of S. gordonii following growth with or without added arginine. Arginine-replete S. gordonii monocultures contained 20–30 μM H2O2 throughout exponential growth. Actinomyces naeslundii did not produce H2O2 but synthesized catalase, removed H2O2 from coaggregate cultures and decreased protein oxidation in S. gordonii. On solid medium, S. gordonii inhibited growth of A. naeslundii; exogenous catalase overcame this inhibition. In coaggregate cultures, A. naeslundii cell numbers were >90% lower than in monocultures after 24 h. These results indicate that coaggregation with A. naeslundii protects S. gordonii from oxidative damage. However, high cell densities of S. gordonii inhibit A. naeslundii. Therefore, H2O2 may drive these organisms towards an ecologically balanced community in natural dental plaque.
  • 4.

    【2hr】Construction of an artificial symbiotic community using a Chlorella–symbiont association as a model

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    机译 以小球藻-共生菌为模型构建人工共生群落
    摘要：Chlorella sorokiniana IAM C-212 produces a polysaccharide gel, termed a sheath, under photoautotrophic conditions. The C. sorokiniana sheath is a suitable habitat for several symbiotic microorganisms because it ensures close proximity between the C. sorokiniana and symbionts. In this study, we established a method for increasing the volume of the sheath produced by C. sorokiniana, and proposed a method for constructing artificial communities of Chlorella and symbiotic microorganisms. The C. sorokiniana sheath was increased by addition of calcium chloride solution. The sheath resulted in coflocculation of C. sorokiniana and the associated symbiotic bacteria, thus strengthening the bacterial–Chlorella symbiotic association. An application of this technique was demonstrated by constructing a complex of C. sorokiniana and a propionate-degrading bacterium (PDS1). Although propionate inhibited the growth of axenic C. sorokiniana, the C. sorokiniana–PDS1 complex showed good growth in a medium containing a high concentration of propionate.
  • 5.

    【2hr】Multivariate analyses in microbial ecology

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    机译 微生物生态学的多元分析
    • 作者：Alban Ramette
    • 刊名：FEMS Microbiology Ecology
    • -1年第2期
    摘要：Environmental microbiology is undergoing a dramatic revolution due to the increasing accumulation of biological information and contextual environmental parameters. This will not only enable a better identification of diversity patterns, but will also shed more light on the associated environmental conditions, spatial locations, and seasonal fluctuations, which could explain such patterns. Complex ecological questions may now be addressed using multivariate statistical analyses, which represent a vast potential of techniques that are still underexploited. Here, well-established exploratory and hypothesis-driven approaches are reviewed, so as to foster their addition to the microbial ecologist toolbox. Because such tools aim at reducing data set complexity, at identifying major patterns and putative causal factors, they will certainly find many applications in microbial ecology.
  • 6.

    【2hr】The reductive dechlorination of 2345-tetrachlorobiphenyl in three different sediment cultures: evidence for the involvement of phylogenetically similar Dehalococcoides-like bacterial populations

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    机译 2345-四氯联苯在三种不同沉积物中的还原性脱氯作用：系统发育相似的类似Dehalococcoides类细菌种群的证据
    摘要：Anaerobic cultures capable of reductively dechlorinating 2,3,4,5-tetrachlorobiphenyl (CB) were enriched from three different sediments, one estuarine, one marine and one riverine. Two different electron donors were used in enrichments with the estuarine sediment (elemental iron or a mixture of fatty acids). The removal of doubly flanked meta and para chlorines to form 2,3,5-CB and 2,4,5-CB was observed in all cultures. Bacterial community analysis of PCR-amplified 16S rRNA gene fragments revealed different communities in these cultures, with the exception of one common population that showed a high phylogentic relatedness to Dehalococcoides species. No Dehalococcoides-like populations were ever detected in control cultures to which no PCBs were added. In addition, the dynamics of this Dehalococcoides-like population were strongly correlated with dechlorination. Subcultures of the estuarine sediment culture demonstrated that the Dehalococcoides-like population disappeared when dechlorination was inhibited with 2-bromoethanesulfonate or when 2,3,4,5-CB had been consumed. These results provide evidence that Dehalococcoides-like populations were involved in the removal of doubly flanked chlorines from 2,3,4,5-CB. Furthermore, the successful enrichment of these populations from geographically distant and geochemically distinct environments indicates the widespread presence of these PCB-dechlorinating, Dehalococcoides-like organisms.
  • 7.

    【2hr】Biofilms: hot spots of horizontal gene transfer (HGT) in aquatic environments with a focus on a new HGT mechanism

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    机译 生物膜：水生环境中水平基因转移（HGT）的热点重点是新的HGT机制
    摘要：Biofilms in water environments are thought to be hot spots for horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs). ARGs can be spread via HGT, though mechanisms are known and have been shown to depend on the environment, bacterial communities and mobile genetic elements. Classically, HGT mechanisms include conjugation, transformation and transduction; more recently, membrane vesicles (MVs) have been reported as DNA reservoirs implicated in interspecies HGT. Here, we review the current knowledge on the HGT mechanisms with a focus on the role of MVs and the methodological innovations in the HGT research.
  • 8.

    【2hr】Metagenome-assembled genome distribution and key functionality highlight importance of aerobic metabolism in Svalbard permafrost

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    机译 由基因组组装的基因组分布和关键功能突出了有氧代谢在斯瓦尔巴多年冻土中的重要性
    摘要：Permafrost underlies a large portion of the land in the Northern Hemisphere. It is proposed to be an extreme habitat and home for cold-adaptive microbial communities. Upon thaw permafrost is predicted to exacerbate increasing global temperature trend, where awakening microbes decompose millennia old carbon stocks. Yet our knowledge on composition, functional potential and variance of permafrost microbiome remains limited. In this study, we conducted a deep comparative metagenomic analysis through a 2 m permafrost core from Svalbard, Norway to determine key permafrost microbiome in this climate sensitive island ecosystem. To do so, we developed comparative metagenomics methods on metagenomic-assembled genomes (MAG). We found that community composition in Svalbard soil horizons shifted markedly with depth: the dominant phylum switched from and in top soils (active layer) to , , and in permafrost layers. Key metabolic potential propagated through permafrost depths revealed aerobic respiration and soil organic matter decomposition as key metabolic traits. We also found that Svalbard MAGs were enriched in genes involved in regulation of ammonium, sulfur and phosphate. Here, we provide a new perspective on how permafrost microbiome is shaped to acquire resources in competitive and limited resource conditions of deep Svalbard soils.
  • 9.

    【2hr】Weekly variations of viruses and heterotrophic nanoflagellates and their potential impact on bacterioplankton in shallow waters of the central Red Sea

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    机译 病毒和异养纳米鞭毛的每周变化及其对红海中部浅水区浮游细菌的潜在影响
    摘要：Bacterioplankton play a pivotal role in marine ecosystems. However, their temporal dynamics and underlying control mechanisms are poorly understood in tropical regions such as the Red Sea. Here, we assessed the impact of bottom-up (resource availability) and top-down (viruses and heterotrophic nanoflagellates) controls on bacterioplankton abundances by weekly sampling a coastal central Red Sea site in 2017. We monitored microbial abundances by flow cytometry together with a set of environmental variables including temperature, salinity, dissolved organic and inorganic nutrients and chlorophyll . We distinguished five groups of heterotrophic bacteria depending on their physiological properties relative nucleic acid content, membrane integrity and cell-specific respiratory activity, two groups of cyanobacteria and three groups of viruses. Viruses controlled heterotrophic bacteria for most of the year, as supported by a negative correlation between their respective abundances and a positive one between bacterial mortality rates and mean viral abundances. On the contrary, heterotrophic nanoflagellates abundance covaried with that of heterotrophic bacteria. Heterotrophic nanoflagellates showed preference for larger bacteria from both the high and low nucleic acid content groups. Our results demonstrate that top-down control is fundamental in keeping heterotrophic bacterioplankton abundances low (< 5 × 10 cells mL ) in Red Sea coastal waters.
  • 10.

    【2hr】Methanogenic response to long-term permafrost thaw is determined by paleoenvironment

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    机译 长期多年冻土融化的产甲烷响应取决于古环境
    摘要：Methane production in thawing permafrost can be substantial, yet often evolves after long lag phases or is even lacking. A central question is to which extent the production of methane after permafrost thaw is determined by the initial methanogenic community. We quantified the production of methane relative to carbon dioxide (CO ) and enumerated methanogenic ( ) gene copies in long-term (2–7 years) anoxic incubations at 4 °C using interglacial and glacial permafrost samples of Holocene and Pleistocene, including Eemian, origin. Changes in archaeal community composition were determined by sequencing of the archaeal 16S rRNA gene. Long-term thaw stimulated methanogenesis where methanogens initially dominated the archaeal community. Deposits of interstadial and interglacial (Eemian) origin, formed under higher temperatures and precipitation, displayed the greatest response to thaw. At the end of the incubations, a substantial shift in methanogenic community composition and a relative increase in hydrogenotrophic methanogens had occurred except for Eemian deposits in which a high abundance of potential acetoclastic methanogens were present. This study shows that only anaerobic CO production but not methane production correlates significantly with carbon and nitrogen content and that the methanogenic response to permafrost thaw is mainly constrained by the paleoenvironmental conditions during soil formation.
  • 11.

    【2hr】Total RNA sequencing reveals multilevel microbial community changes and functional responses to wood ash application in agricultural and forest soil

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    机译 总RNA测序揭示了农业和森林土壤中多级微生物群落的变化以及对木灰施用的功能响应
    摘要：Recycling of wood ash from energy production may counteract soil acidification and return essential nutrients to soils. However, wood ash amendment affects soil physicochemical parameters that control composition and functional expression of the soil microbial community. Here, we applied total RNA sequencing to simultaneously assess the impact of wood ash amendment on the active soil microbial communities and the expression of functional genes from all microbial taxa. Wood ash significantly affected the taxonomic (rRNA) as well as functional (mRNA) profiles of both agricultural and forest soil. Increase in pH, electrical conductivity, dissolved organic carbon and phosphate were the most important physicochemical drivers for the observed changes. Wood ash amendment increased the relative abundance of the copiotrophic groups Chitinonophagaceae (Bacteroidetes) and Rhizobiales (Alphaproteobacteria) and resulted in higher expression of genes involved in metabolism and cell growth. Finally, total RNA sequencing allowed us to show that some groups of bacterial feeding protozoa increased concomitantly to the enhanced bacterial growth, which shows their pivotal role in the regulation of bacterial abundance in soil.
  • 12.

    【2hr】The distribution and relative ecological roles of autotrophic and heterotrophic diazotrophs in the McMurdo Dry Valleys Antarctica

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    机译 南极麦克默多干旱谷自养和异养重氮营养菌的分布及其相对生态作用
    摘要：
  • 13.

    【2hr】Cell Architecture of the Giant Sulfur Bacterium Achromatium oxaliferum: Extra-cytoplasmic Localization of Calcium Carbonate Bodies

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    机译 巨型硫细菌草酸铬的细胞结构：碳酸钙体的胞质外定位。
    摘要：is a large sulfur bacterium easily recognized by large intracellular calcium carbonate bodies. Although these bodies often fill major parts of the cells’ volume, their role and specific intracellular location are unclear. In this study, we used various microscopy and staining techniques to identify the cell compartment harboring the calcium carbonate bodies. We observed that cells often lost their calcium carbonate bodies, either naturally or induced by treatments with diluted acids, ethanol, sodium bicarbonate and UV radiation which did not visibly affect the overall shape and motility of the cells (except for UV radiation). The water-soluble fluorescent dye fluorescein easily diffused into empty cavities remaining after calcium carbonate loss. Membranes (stained with Nile Red) formed a network stretching throughout the cell and surrounding empty or filled calcium carbonate cavities. The cytoplasm (stained with FITC and SYBR Green for nucleic acids) appeared highly condensed and showed spots of dissolved Ca (stained with Fura-2). From our observations, we conclude that the calcium carbonate bodies are located in the periplasm, in extra-cytoplasmic pockets of the cytoplasmic membrane and are thus kept separate from the cell's cytoplasm. This periplasmic localization of the carbonate bodies might explain their dynamic formation and release upon environmental changes.
  • 14.

    【2hr】Antibiotic-induced gut metabolome and microbiome alterations increase the susceptibility to Candida albicans colonization in the gastrointestinal tract

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    机译 抗生素诱导的肠道代谢组和微生物组改变增加了胃肠道中白色念珠菌定植的敏感性
    摘要：Antibiotic-induced alterations in the gut ecosystem increases the susceptibility to , yet the mechanisms involved remains poorly understood. Here we show that mice treated with the broad-spectrum antibiotic cefoperazone promoted the growth, morphogenesis and gastrointestinal (GI) colonization of . Using metabolomics, we revealed that the cecal metabolic environment of the mice treated with cefoperazone showed a significant alteration in intestinal metabolites. Levels of carbohydrates, sugar alcohols and primary bile acids increased, whereas carboxylic acids and secondary bile acids decreased in antibiotic treated mice susceptible to . Furthermore, using assays, we confirmed that carbohydrates, sugar alcohols and primary bile acids promote, whereas carboxylic acids and secondary bile acids inhibit the growth and morphogenesis of . In addition, in this study we report changes in the levels of gut metabolites correlated with shifts in the gut microbiota. Taken together, our and results indicate that cefoperazone-induced metabolome and microbiome alterations favor the growth and morphogenesis of , and potentially play an important role in the GI colonization of .
  • 15.

    【2hr】Distinctive microbial communities in subzero hypersaline brines from Arctic coastal sea ice and rarely sampled cryopegs

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    机译 来自北极沿海海冰的零度以下高盐盐水中的独特微生物群落且很少采样冷冻龙虾
    摘要：Hypersaline aqueous environments at subzero temperatures are known to be inhabited by microorganisms, yet information on community structure in subzero brines is very limited. Near Utqiaġvik, Alaska, we sampled subzero brines (–6°C, 115–140 ppt) from cryopegs, i.e. unfrozen sediments within permafrost that contain relic (late Pleistocene) seawater brine, as well as nearby sea-ice brines to examine microbial community composition and diversity using 16S rRNA gene amplicon sequencing. We also quantified the communities microscopically and assessed environmental parameters as possible determinants of community structure. The cryopeg brines harbored surprisingly dense bacterial communities (up to 10 cells mL ) and millimolar levels of dissolved and particulate organic matter, extracellular polysaccharides and ammonia. Community composition and diversity differed between the two brine environments by alpha- and beta-diversity indices, with cryopeg brine communities appearing less diverse and dominated by one strain of the genus , also detected in other cold, hypersaline environments, including sea ice. The higher density and trend toward lower diversity in the cryopeg communities suggest that long-term stability and other features of a subzero brine are more important selective forces than temperature or salinity, even when the latter are extreme.
  • 16.

    【2hr】Differential interaction of the dark septate endophyte Cadophora sp. and fungal pathogens in vitro and in planta

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    机译 黑暗的分隔的内生植物Cadophora sp。和植物体内的真菌和病原体
    摘要：Dark septate endophytes (DSEs) present a group of widespread root-colonizing fungi. The role of these endophytes in ecosystems and their interactions with plant pathogens are not well understood. In the current study, we assessed the antagonistic potential of the model DSE sp. against the tomato soilborne pathogens , and . To investigate their interactions, we conducted assays followed by a greenhouse experiments in which tomato plants were inoculated with different combinations of the DSE and pathogens. RNA accumulation of selected tomato pathogenesis-related genes and of sp. genes with putative antifungal function was analyzed. sp. inhibited the growth of the fungal pathogens and vice versa; a negative impact of the pathogens on the growth of the DSE was also detected. In roots, however, this mutual negative interaction could not be observed. Expression analyses of plant genes could not explain this differential effect, but among the sp. genes analyzed, a gene coding for a chalcone synthase was downregulated . The data indicate that plants can change the interaction between fungi and, therefore, detected antagonism does not necessarily reflect the situation inside the plant.
  • 17.

    【2hr】Distribution patterns of fungal taxa and inferred functional traits reflect the non-uniform vertical stratification of soil microhabitats in a coastal pine forest

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    机译 真菌类群的分布模式和推断的功能性状反映了沿海松树林中土壤微生境的垂直分层不均匀
    摘要：In boreal systems, soil profiles typically consist of distinct stratified horizons, with organic layers at the surface overlying deeper mineral horizons providing microhabitat variation along a depth gradient, and vertical stratification of fungal communities along such soil profiles is commonly observed. We studied fungal community structure in a coastal pine forest along a gradient of decreasing influence from the coast. In this system, the vertical stratification pattern of soil microhabitats (defined here as organic, mineral with roots and mineral without roots: O, MR and MN, respectively) is non-uniform; organic horizons are sometimes buried under drifting sand dunes. Our results show that soil microhabitats are distinct with respect to physiochemical characteristics, community composition and OTU richness. While community composition was partly related to depth and distance from the coastal forest edge, microhabitat appeared to have the strongest influence. A closer inspection of the OTUs with the highest relative sequence abundance within each microhabitat revealed that microhabitats support functionally distinct fungal communities with respect to trophic mode and growth morphology. These results suggest that in coastal pine forests, variation in soil microhabitats contributes to the high fungal diversity found belowground and may play an important role in optimizing nutrient cycling.
  • 18.

    【2hr】Bacterial colonization and antimicrobial resistance genes in neonatal enteral feeding tubes

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    机译 新生儿肠内饲管中的细菌定植和抗菌素耐药基因
    摘要：
  • 19.

    【2hr】Seasonal sub-seasonal and diurnal variation of soil bacterial community composition in a temperate deciduous forest

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    机译 温带落叶林土壤细菌群落组成的季节性季节变化和昼夜变化
    摘要：The temporal dynamics of soil bacterial communities are understudied, but such understanding is critical to elucidating the drivers of community variation. The goal of this study was to characterize how soil bacterial communities vary across diurnal, sub-seasonal and seasonal time-scales in a 5.8 m plot and test the hypothesis that bacterial diversity varies on each of these scales. We used 16S rDNA gene amplicon sequencing to quantify the alpha and beta diversity of soil bacteria as well as the Net Relatedness Index and Nearest Taxon Indices to assess the degree of phylogenetic clustering, and the extent to which community shifts were driven by stochastic vs. deterministic limitation. We found that species richness was highest in winter, lowest in fall and that communities were compositionally distinct across seasons. There was no evidence of diurnal-scale shifts; the finest temporal scale over which community shifts were detected using our DNA-based analysis was between sampling dates separated by 6 weeks. Phylogenetic analyses suggested that seasonal-scale differences in community composition were the result of environmental filtering and homogeneous selection. Our findings provide insight into temporal variation of soil bacterial communities across the hourly to seasonal scales while minimizing the potential confounding effect of spatial variation.
  • 20.

    【2hr】Primer set 2.0 for highly parallel qPCR array targeting antibiotic resistance genes and mobile genetic elements

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    机译 用于针对抗生素抗性基因和移动遗传元件的高度平行qPCR阵列的Primer Set 2.0
    摘要：
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