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  • 刊频： Quarterly, <1998->
  • NLM标题： Microbes Environ
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共576条结果
  • 1.

    【2hr】Transient-rare Bacterial Taxa Are Assembled Neutrally across Temporal Scales

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    机译 瞬时稀有的细菌分类群在颞尺度上中性组装
    摘要：Despite the importance of microbial communities in ecosystem functions, the mechanisms underlying the assembly of rare taxa over time are poorly understood. It remains largely unknown whether rare taxa exhibit similar assembly processes to common taxa in local communities. We herein retrieved the 16S rRNA sequences of bacteria collected bimonthly for 2 years from the Pohang wastewater treatment plant. The transient-rare taxa showed different abundance distributions from the common taxa. Transient-rare taxon assemblages also exhibited higher temporal variations than common taxon assemblages, suggesting the distinct ecological patterns of the two assemblages. A multivariate analysis revealed that environmental parameters accounted for 25.3 and 61.6% of temporal variations in the transient-rare and common taxon assemblages, respectively. The fitting of all observed taxa to a neutral community model revealed that 96.4% of the transient-rare taxa (relative abundance, 71.4%) and 73.3% of the common taxa (relative abundance, 45.6%) followed the model, suggesting that stochastic mechanisms were more important than deterministic ones in the assembly of the transient-rare taxa. Collectively, the present results indicate that the transient-rare bacterial taxa at the Pohang wastewater treatment plant differed from the common taxa in ecological patterns, suggesting that dispersal is a key process in their assembly.
  • 2.

    【2hr】Growth Rate-dependent Cell Death of Diatoms due to Viral Infection and Their Subsequent Coexistence in a Semi-continuous Culture System

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    机译 由于病毒感染导致的硅藻的生长率依赖性细胞死亡及其随后在半连续培养系统中的共存
    摘要：Viral infections are a major factor in diatom cell death. However, the effects of viruses on diatom dynamics remain unclear. Based on laboratory studies, it is hypothesized that virus-induced diatom mortality is dependent on the diatom growth rate. The present study aimed to elucidate the relationship between the diatom growth rate and virus-induced mortality using model systems of the marine planktonic diatom, Chaetoceros tenuissimus and its infectious viruses. We also examined the fate of diatom populations in a semi-continuous dilution culture system, in which host growth rates were controlled at 0.69, 2.08, and 3.47 day–1. Diatom populations gradually decreased following the viral inoculation of each culture system, and virus-induced mortality inversely correlated with the diatom growth rate. Furthermore, the viral burst size was slightly higher in lower growth rate cultures. These results suggested that the host physiological status related to the growth rate affected viral infection and proliferation. Diatom populations were not completely lysed or washed out in any of the dilution systems; they showed steady growth in the presence of infectious viruses. This may be partially explained by defective interference particles from viruses and cell debris. The present results indicate that diatoms in dilution environments maintain their populations, even under viral pressure. Moreover, diatom populations with a low growth rate may partially sustain higher growth populations through nutrient recycling following virus-induced cell death. The results of the present study provide insights into diatom dynamics in natural environments in the presence of infectious viruses.
  • 3.

    【2hr】Ultrastructure of the

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    机译 超微结构的
    摘要：Mycobacterium avium subsp. hominissuis (MAH) is one of the most common nontuberculous mycobacterial pathogens responsible for chronic lung disease in humans. It is widely distributed in biofilms in natural and living environments. It is considered to be transmitted from the environment. Despite its importance in public health, the ultrastructure of the MAH biofilm remains largely unknown. The ultrastructure of a MAH-containing multispecies biofilm that formed naturally in a bathtub inlet was herein reported along with those of monoculture biofilms developed from microcolonies and pellicles formed in the laboratory. Scanning electron microscopy revealed an essentially multilayered bathtub biofilm that was packed with cocci and short and long rods connected by an extracellular matrix (ECM). Scattered mycobacterium-like rod-shaped cells were observed around biofilm chunks. The MAH monoculture biofilms that developed from microcolonies in vitro exhibited an assembly of flat layers covered with thin film-like ECM membranes. Numerous small bacterial cells (0.76±0.19‍ ‍μm in length) were observed, but not embedded in ECM. A glycopeptidolipid-deficient strain did not develop the layered ECM membrane architecture, suggesting its essential role in the development of biofilms. The pellicle biofilm also consisted of flat layered cells covered with an ECM membrane and small cells. MAH alone generated a flat layered biofilm covered with an ECM membrane. This unique structure may be suitable for resistance to water flow and disinfectants and the exclusion of fast-growing competitors, and small cells in biofilms may contribute to the formation and transmission of bioaerosols.
  • 4.

    【2hr】Soil Sample Preservation Strategy Affects the Microbial Community Structure

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    机译 土壤样品保存策略影响微生物群落结构
    摘要：Sample preservation is a critical procedure in any research that relies on molecular tools and is conducted in remote areas. Sample preservation options include low and room temperature storage, which require freezing equipment and specific buffering solutions, respectively. The aim of the present study was to investigate whether DNA/RNA Shield 1x from Zymo Research and DESS (Dimethyl sulfoxide, Ethylenediamine tetraacetic acid, Saturated Salt) solution performed similarly to snap freezing in liquid nitrogen. Soil samples were stored for 1 month in each of the buffers and without any solution at a range of temperatures: –20, +4, and +23°C. All treatments were compared to the “optimal treatment”, namely, snap freezing in liquid nitrogen. The quality and quantity of DNA were analyzed, and the microbial community structure was investigated in all samples. The results obtained indicated that the quantity and integrity of DNA was preserved well in all samples; however, the taxonomic distribution was skewed in samples stored without any solution at ambient temperatures, particularly when analyses were performed at lower taxonomic levels. Although both solutions performed equally well, sequencing output and OTU numbers in DESS-treated samples were closer to those snap frozen with liquid nitrogen. Furthermore, DNA/RNA Shield-stored samples performed better for the preservation of rare taxa.
  • 5.

    【2hr】Characterization and Distribution of Agar-degrading

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    机译 琼脂降解的特征和分布
    摘要：The environment of plant rhizosphere soil differs from that of non-rhizosphere soil due to the secretion of mucilage polysaccharides from the roots. This environment is regarded as one of the preferential habitats for agar-degrading bacteria. In a previous study, agar-degrading Steroidobacter agariperforans KA5-BT was isolated from agar-enriched agricultural soil using diffusible metabolites from Rhizobiales bacteria. Based on the hypothesis that similar characteristic bacteria still exist in the rhizosphere, isolation was performed using rhizosphere soils. Agar-degrading SA29-BT and YU21-B were isolated from onion and soybean rhizosphere soils. The 16S rRNA genes of these strains showed ≥98.7% identities with the most closely related strain KA5-BT. However, differences were noted in polysaccharide utilization, and average nucleotide identities were <95–96% against strain KA5-BT, indicating that they are different species from S. agariperforans KA5-BT. To investigate the distribution of bacterial sequences affiliated with novel strains, a primer set was designed and a meta-analysis of the 16S rRNA gene was performed. Sequences were widely distributed in rhizospheres throughout Japan, but varied in plant- and region-dependent manners. Regarding phenotypic characterization, distinguishable features were observed in growth temperatures, pH, and dominant fatty acids. SA29-BT and YU21-B grew at 15–40°C and pH 6.0–12 and contained C16:0 as the dominant cell fatty acid, whereas KA5-BT showed no growth at 40°C and pH 12 and contained a moderate amount of C16:0. Based on these characteristics, SA29-BT (JCM 333368T=KCTC 72223T) and YU21-B (JCM 333367=KCTC 72222) represent novel species in the genus Steroidobacter, for which the name Steroidobacter agaridevorans sp. nov. is proposed.
  • 6.

    【2hr】Marseilleviridae

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    机译 马赛维里迪夫
    摘要：
  • 7.

    【2hr】Distribution and Community Composition of Anammox Bacteria in Shallow Groundwater of the Kathmandu Valley Nepal

    包量

    机译 尼泊尔加德满都山谷浅地下水中厌氧菌细菌的分布与社区组成
    摘要：The abundance and diversity of anaerobic ammonium oxidation (anammox) bacteria were assessed in 152 groundwater samples in the Kathmandu Valley, Nepal. Anammox bacterial 16S rRNA genes were detected in 54% (37/68) of samples collected in the dry season at 1.6×105–8.8×106 copies L–1, and in 60% (50/84) of samples collected in the wet season at 4.3×104–1.2×107 copies L–1. The 16S rRNA genes of “Candidatus Brocadia”, “Candidatus Anammoxoglobus”, and five new deduced anammox bacterial phylotypes were detected in the shallow groundwater samples. Diverse anammox bacteria were broadly distributed in the shallow groundwater aquifer of the Kathmandu Valley.
  • 8.

    【2hr】Induction of Extracellular Aminopeptidase Production by Peptides in Some Marine Bacterial Species

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    机译 在一些海洋细菌种类中肽诱导细胞外氨基肽酶生产
    摘要：Bacterial extracellular aminopeptidases are key enzymes in protein processing in oligotrophic seawater. To the best of our knowledge, the regulation of aminopeptidase production in microbes inhabiting seawater has not yet been reported. The present study attempted to experimentally clarify which organic materials affect bacterial extracellular aminopeptidase production by nutrient-rich and starved cells growing in artificial seawater using Photobacterium, Alteromonas, Ruegeria, and Sulfitobacter. In all four species, we found that peptides induced bacterial extracellular aminopeptidase production. Amino acids led to cell growth with markedly lower aminopeptidase production by Photobacterium and Sulfitobacter, but not by Alteromonas and Ruegeria. These results suggest that the extracellular aminopeptidases of marine bacteria are primarily produced on demand in response to the presence of relevant substrates (peptides) in seawater. Peptidyl substances may be regulatory nutrients for marine bacterial growth in aquatic environments.
  • 9.

    【2hr】Fungal Carbonyl Sulfide Hydrolase of Trichoderma harzianum Strain THIF08 and Its Relationship with Clade D β-Carbonic Anhydrases

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    机译 Trichoderma Harzianum菌株ThIF08的真菌羰基硫化物水解酶及其与疏水性β-碳酸酐酶的关系
    摘要：
  • 10.

    【2hr】Community Analysis-based Screening of Plant Growth-promoting Bacteria for Sugar Beet

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    机译 基于社区分析的植物生长促进糖甜度细菌的筛查
    摘要：Clone libraries of bacterial 16S rRNA genes (a total of 1,980 clones) were constructed from the leaf blades, petioles, taproots, and lateral roots of sugar beet (Beta vulgaris L.) grown under different fertilization conditions. A principal coordinate analysis revealed that the structures of bacterial communities in above- and underground tissues were largely separated by PC1 (44.5%). The bacterial communities of above-ground tissues (leaf blades and petioles) were more tightly clustered regardless of differences in the tissue types and fertilization conditions than those of below-ground tissues (taproots and lateral roots). The bacterial communities of below-ground tissues were largely separated by PC2 (26.0%). To survey plant growth-promoting bacteria (PGPBs), isolate collections (a total of 665 isolates) were constructed from the lateral roots. As candidate PGPBs, 44 isolates were selected via clustering analyses with the combined 16S rRNA gene sequence data of clone libraries and isolate collections. The results of inoculation tests using sugar beet seedlings showed that eight isolates exhibited growth-promoting effects on the seedlings. Among them, seven isolates belonging to seven genera (Asticcacaulis, Mesorhizobium, Nocardioides, Sphingobium, Sphingomonas, Sphingopyxis, and Polaromonas) were newly identified as PGPBs for sugar beet at the genus level, and two isolates belonging to two genera (Asticcacaulis and Polaromonas) were revealed to exert growth-promoting effects on the plant at the genus level for the first time. These results suggest that a community analysis-based selection strategy will facilitate the isolation of novel PGPBs and extend the potential for the development of novel biofertilizers.
  • 11.

    【2hr】The Thermosynechococcus Genus: Wide Environmental Distribution but a Highly Conserved Genomic Core

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    机译 热梭科视野类：广泛的环境分布但高度保守的基因组核心
    摘要：Cyanobacteria thrive in diverse environments. However, questions remain about possible growth limitations in ancient environmental conditions. As a single genus, the Thermosynechococcus are cosmopolitan and live in chemically diverse habitats. To understand the genetic basis for this, we compared the protein coding component of Thermosynechococcus genomes. Supplementing the known genetic diversity of Thermosynechococcus, we report draft metagenome-assembled genomes of two Thermosynechococcus recovered from ferrous carbonate hot springs in Japan. We find that as a genus, Thermosynechococcus is genomically conserved, having a small pan-genome with few accessory genes per individual strain as well as few genes that are unique to the genus. Furthermore, by comparing orthologous protein groups, including an analysis of genes encoding proteins with an iron related function (uptake, storage or utilization), no clear differences in genetic content, or adaptive mechanisms could be detected between genus members, despite the range of environments they inhabit. Overall, our results highlight a seemingly innate ability for Thermosynechococcus to inhabit diverse habitats without having undergone substantial genomic adaptation to accommodate this. The finding of Thermosynechococcus in both hot and high iron environments without adaptation recognizable from the perspective of the proteome has implications for understanding the basis of thermophily within this clade, and also for understanding the possible genetic basis for high iron tolerance in cyanobacteria on early Earth. The conserved core genome may be indicative of an allopatric lifestyle—or reduced genetic complexity of hot spring habitats relative to other environments.
  • 12.

    【2hr】Changes in ATP Sulfurylase Activity in Response to Altered Cyanobacteria Growth Conditions

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    机译 响应于改变的蓝杆菌生长条件ATP硫脲酶活性的变化
    摘要：
  • 13.

    【2hr】RNA Viral Metagenome Analysis of Subnanogram dsRNA Using Fragmented and Primer Ligated dsRNA Sequencing (FLDS)

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    机译 使用碎片和引物连接的DsRNA测序（FLDS）的亚族图DsRNA的RNA病毒偏见分析
    摘要：
  • 14.

    【2hr】Genetic Diversity and Characterization of Symbiotic Bacteria Isolated from Endemic Phaseolus Cultivars Located in Contrasting Agroecosystems in Venezuela

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    机译 在委内瑞拉造影樟脑体内生殖中分离的共生细菌的遗传多样性与表征
    摘要：Phaseolus vulgaris is a grain cultivated in vast areas of different countries. It is an excellent alternative to the other legumes in the Venezuelan diet and is of great agronomic interest due to its resistance to soil acidity, drought, and high temperatures. Phaseolus establishes symbiosis primarily with Rhizobium and Ensifer species in most countries, and this rhizobia-legume interaction has been studied in Asia, Africa, and the Americas. However, there is currently no evidence to show that rhizobia nodulate the endemic cultivars of P. vulgaris in Venezuela. Therefore, we herein investigated the phylogenetic diversity of plant growth-promoting and N2-fixing nodulating bacteria isolated from the root nodules of P. vulgaris cultivars in a different agroecosystem in Venezuela. In comparisons with other countries, higher diversity was found in isolates from P. vulgaris nodules, ranging from α- and β-proteobacteria. Some isolates belonging to several new phylogenetic lineages within Bradyrhizobium, Ensifer, and Mesorhizobium species were also specifically isolated at some topographical regions. Additionally, some isolates exhibited tolerance to high temperature, acidity, alkaline pH, salinity stress, and high Al levels; some of these characteristics may be related to the origin of the isolates. Some isolates showed high tolerance to Al toxicity as well as strong plant growth-promoting and antifungal activities, thereby providing a promising agricultural resource for inoculating crops.
  • 15.

    【2hr】Bioelectrical Methane Production with an Ammonium Oxidative Reaction under the No Organic Substance Condition

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    机译 生物电解甲烷在无有机物质条件下产生氧化反应的氧化反应
    摘要：The present study investigated bioelectrical methane production from CO2 without organic substances. Even though microbial methane production has been reported at relatively high electric voltages, the amount of voltage required and the organisms contributing to the process currently remain unknown. Methane production using a biocathode was investigated in a microbial electrolysis cell coupled with an NH4+ oxidative reaction at an anode coated with platinum powder under a wide range of applied voltages and anaerobic conditions. A microbial community analysis revealed that methane production simultaneously occurred with biological denitrification at the biocathode. During denitrification, NO3– was produced by chemical NH4+ oxidation at the anode and was provided to the biocathode chamber. H2 was produced at the biocathode by the hydrogen-producing bacteria Petrimonas through the acceptance of electrons and protons. The H2 produced was biologically consumed by hydrogenotrophic methanogens of Methanobacterium and Methanobrevibacter with CO2 uptake and by hydrogenotrophic denitrifiers of Azonexus. This microbial community suggests that methane is indirectly produced without the use of electrons by methanogens. Furthermore, bioelectrical methane production occurred under experimental conditions even at a very low voltage of 0.05‍ ‍V coupled with NH4+ oxidation, which was thermodynamically feasible.
  • 16.

    【2hr】Microevolution of Vibrio parahaemolyticus Isolated from Clinical Acute Hepatopancreatic Necrosis Disease Infecting Shrimps and Aquatic Production in China

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    机译 从中国感染虾的急性肝胰腺坏死病和水产生产分离副溶血性弧菌的微进化
    摘要：is the leading cause of bacteria-associated foodborne diarrheal diseases and specifically causes early mortality syndrome (EMS), which is technically known as acute hepatopancreatic necrosis disease (AHPND), a serious threat to shrimp aquaculture. To investigate the genetic and evolutionary relationships of in China, 184 isolates from clinical samples (VPC, =40), AHPND-infected shrimp (VPE, =10), and various aquatic production sources (VPF, =134) were collected and evaluated by a multilocus sequence analysis (MLST). Furthermore, the presence of potential virulence factors ( , , and ) and single nucleotide polymorphisms (SNPs) in isolates was assessed using genomic sequencing. Analyses of virulence factors revealed that the majority of VPC isolates (97.5%) possessed the and/or genes, while most of the VPF isolates (83.58%) did not encode hemolysin genes. Therefore, we hypothesized that the environment is a potential reservoir that promotes horizontal DNA transfer, which drives evolutionary change that, in turn, leads to the emergence of novel, potentially pathogenic strains. Phylogenetic analyses identified VPF-112 as a non-pathogenic maternal strain isolated from aquatic products and showed that it had a relatively high evolutionary status. All VPE strains and some VPC strains were grouped into several small subgroups and evenly distributed on phylogenetic trees. Anthropogenic activities and environmental selective pressure may be important factors influencing the process of transforming strains from non-pathogenic to pathogenic bacteria.
  • 17.

    【2hr】dsRNA-seq Reveals Novel RNA Virus and Virus-Like Putative Complete Genome Sequences from Hymeniacidon sp. Sponge

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    机译 dsRNA-seq揭示了Hymeniacidon sp。的新型RNA病毒和类似病毒的推定完整基因组序列。海绵
    摘要：Invertebrates are a source of previously unknown RNA viruses that fill gaps in the viral phylogenetic tree. Although limited information is currently available on RNA viral diversity in the marine sponge, a primordial multicellular animal that belongs to the phylum , the marine sponge is one of the well-studied holobiont systems. In the present study, we elucidated the putative complete genome sequences of five novel RNA viruses from sponge using a combination of double-stranded RNA sequencing, called fragmented and primer ligated dsRNA sequencing, and a conventional transcriptome method targeting single-stranded RNA. We identified highly diverged RNA-dependent RNA polymerase sequences, including a potential novel RNA viral lineage, in the sponge and three viruses presumed to infect sponge cells.
  • 18.

    【2hr】Enumeration of Chemoorganotrophic Carbonyl Sulfide (COS)-degrading Microorganisms by the Most Probable Number Method

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    机译 用最可能数法枚举降解化学有机营养的羰基硫（COS）的微生物。
    摘要：Carbonyl sulfide (COS) is the most abundant sulfur compound in the atmosphere, and, thus, is important in the global sulfur cycle. Soil is a major sink of atmospheric COS and the numerical distribution of soil microorganisms that degrade COS is indispensable for estimating the COS-degrading potential of soil. However, difficulties are associated with counting COS-degrading microorganisms using culture-dependent approaches, such as the most probable number (MPN) method, because of the chemical hydrolysis of COS by water. We herein developed a two-step MPN method for COS-degrading microorganisms: the first step for chemoorganotrophic growth that supported a sufficient number of cells for COS degradation in the second step. Our new MPN analysis of various environmental samples revealed that the cell density of COS-degrading microorganisms in forest soils ranged between 10 and 10 MPN (g dry soil) , which was markedly higher than those in volcanic deposit and water samples, and strongly correlated with the rate of COS degradation in environmental samples. Numerically dominant COS degraders that were isolated from the MPN-positive culture were related to bacteria in the orders and . The present results provide numerical evidence for the ubiquity of COS-degrading microbes in natural environments.
  • 19.

    【2hr】Quantification and Phylogenetic Analysis of Ammonia Oxidizers on Biofilm Carriers in a Full-Scale Wastewater Treatment Plant

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    机译 大型废水处理厂生物膜载体上氨氧化装置的定量和系统发育分析
    摘要：Biofilm carriers have been used to remove ammonia in several wastewater treatment plants (WWTPs) in Japan. However, the abundance and species of ammonia oxidizers in the biofilms formed on the surface of carriers in full-scale operational WWTP tanks remain unclear. In the present study, we conducted quantitative PCR and PCR cloning of the genes of ammonia-oxidizing bacteria and archaea (AOB and AOA) and a complete ammonia oxidizer (comammox) in the biofilm formed on the carriers in a full-scale WWTP. The quantification of genes showed that the abundance of AOB and comammox was markedly greater in the biofilm than in the activated sludge suspended in a tank solution of the WWTP, while AOA was not detected in the biofilm or the activated sludge. A phylogenetic analysis of genes revealed that as-yet-uncultivated comammox and uncultured AOB were predominant in the biofilm. The present results suggest that the biofilm formed on the surface of carriers enable comammox and AOB to co-exist and remain in the full-scale WWTP tank surveyed in this study.
  • 20.

    【2hr】Impact of Atrazine Exposure on the Microbial Community Structure in a Brazilian Tropical Latosol Soil

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    机译 r去津暴露对巴西热带Latosol土壤微生物群落结构的影响
    摘要：Atrazine is a triazine herbicide that is widely used to control broadleaf weeds. Its widespread use over the last 50 years has led to the potential contamination of soils, groundwater, rivers, and lakes. Its main route of complete degradation is via biological means, which is carried out by soil microbiota using a 6-step pathway. The aim of the present study was to investigate whether application of atrazine to soil changes the soil bacterial community. We used 16S rRNA gene sequencing and qPCR to elucidate the microbial community structure and assess the abundance of the atrazine degradation genes A, D, and N in a Brazilian soil. The results obtained showed that the relative abundance of A and N, encoding triazine-initiating metabolism in Gram-negative and -positive bacteria, respectively, increased in soil during the first weeks following the application of atrazine. In contrast, the abundance of D, encoding cyanuric acid amidohydrolase—the fourth step in the pathway—was not related to the atrazine treatment. Moreover, the overall soil bacterial community showed no significant changes after the application of atrazine. Despite this, we observed increases in the relative abundance of bacterial families in the 4 and 8 weeks following the atrazine treatment, which may have been related to higher copy numbers of A and N, in part due to the release of nitrogen from the herbicide. The present results revealed that while the application of atrazine may temporarily increase the quantities of the and genes in a Brazilian Red Latosol soil, it does not lead to significant and long-term changes in the bacterial community structure.
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