Microbial Community Structures in Terrestrial Subsurface Sediments from the Southern Kanto Plain,Japan

Abstract

Microbial community structure reflects the surrounding natural environment and changes to that environment. Although the subsurface at 5–100?m depth is important for human activities and there are potential risks of environmental pollution in this region, there have been only a few reports of subsurface microbial community structures in terrestrial areas. We investigated the diversity and community compositions of Bacteria and Archaea in boring cores collected from various depths at three different sites in the southern Kanto Plain, Japan. The results of 16S rRNA gene amplicon sequencing using MiSeq showed that the microbial community composition varied with the geological unit. Proteobacteria (Alphaproteobacteria and Gammaproteobacteria) were dominant members within sediments accumulated during the Pleistocene in the Musashino Upland. In contrast, Acidobacteria and Chloroflexi characteristically appeared in the Holocene layers of the Arakawa Lowland. These data suggest that the subsurface microbial composition is controlled by the geological features of the sediments.     

马里亚纳海沟可培养水生细菌的多样性

[目的]马里亚纳海沟是地球表面最深的海沟,环境极端多样,如高压、低温及无光,拥有独特的微生物资源.本研究旨在探究马里亚纳海沟不同深度水生细菌形态特征并挖掘可培养细菌资源.[方法]采集马里亚纳海沟7个层位海水(2-8727 m),利用原子力显微镜与扫描电镜观察水生微生物的形态特征;采用2种常规培养基(1/5×2216E和...     

马里亚纳海沟沉积物可培养异养细菌的多样性及其DMSP降解能力

[目的]马里亚纳海沟是地球上最深的海沟,具有超高静水压力、低温、无光等生境特征,蕴含独特的微生物资源.二甲基巯基丙酸内盐(dimethylsulphoniopropionate,DMSP)是海洋环境中最丰富的有机硫分子之一,海洋异养微生物可裂解DMSP产生"冷室气体"二甲基硫(dimethyl sulfide,DMS)...     

马里亚纳海沟共培养细菌多样性动态变化及潜在微生物互作关系

马里亚纳海沟是世界已知最深的海沟,其寡营养、高压、低温、低氧等极端的深海环境孕育出独特的细菌群落结构及多样性特征。选取寡营养培养基对马里亚纳海沟海水及表层沉积物分别进行液体共培养,并在不同培养阶段取样进行高通量测序,分析细菌群落结构组成及其多样性的动态变化,探讨微生物之间可能的互作关系。研究结果表明：液体共培养样品中一共检测到19个门、34个纲、76个目、131个科、227个属的细菌,其中变形菌门（Proteobacteria）和拟杆菌门（Bacteroidetes）为优势菌群,其次为厚壁菌门（Firmicutes）;与其他样品相比,1000米海水样品中细菌群落的多样性最高,并且蓝细菌门（Cyanobacteria）具有更高的相对丰度。共培养样品中细菌丰富度、多样性、群落结构均随培养时间而改变,其中共培养中期样品的细菌多样性较高;表层沉积物样本中,盐单胞菌属（Halomonas）可能由于较强的竞争能力在共培养后期占据优势地位。基因功能预测与代谢通路富集结果显示,随着共培养时间的增加,微生物生长相关的代谢通路丰度明显下降,而与互作相关的代谢通路丰度明显增加。共培养样品检测到的细菌多样性远高于单独分离培养的多样性,仅有少量菌属为单独分离培养与共培养样品均检测到的共有属。综上所述,马里亚纳海沟细菌群落中存在竞争、互利共生的相互作用,共培养法有利于揭示细菌间的互作关系。研究为深渊及深海等极端环境下微生物生态系统组成及维持奠定了理论基础,也为进一步研究极端微生物的生存策略提供了科学指导。     

Developing a Novel Approach of rpoB Gene as a Powerful Biomarker for the Environmental Microbial Diversity

Use of the rpoB gene (the encoding the β-subunit of RNA Polymerase gene), a potential alternative biomarker to the 16S rRNA gene, has been limited to environmental microbial investigation for a long time because of the lack of effective primers. Here we developed a novel rpoB gene-based approach using a newly designed primer pair and tested it in three different environmental water samples with the traditional library method. The results showed that our novel approach presented different microbial diversity patterns from the different environmental samples. Compared to previous rpoB gene based reports, the first retrieved groups in our approach included mainly α-Proteobacteria, δ-Proteobacteria, Planctomycetes, Verrucomicrobia, Firmicutes, Chlorofexi and Actinobacteria, which greatly expanded the potential ability of the rpoB gene approach for environmental surveys. Most importantly, the use of the traditional clone library approach with the novel rpoB gene primers greatly supplement the microbial diversity based on the 16S rRNA gene approach with the universal primer pair (27f and 1492r), at all phylum, class, order, family and genus levels, indicating a powerful complementary method and a potential alternative biomarker of the current popular NGS (next-generation sequences) technologies for the environmental microbial investigation.     

Fungal Diversity in Deep Sea Sediments from East Yap Trench and Their Denitrification Potential

Abstract

In recent years, the hadal trenches have been recognized as biological hot spots for deep sea researchers. Due to high hydrostatic pressure, low temperatures, high salinity and low nutrients, the microorganisms in hadal trenches may have unique community structure with potential for biotechnical application. Compared with bacteria and archaea, the diversity and ecological roles of fungi in hadal trenches remain largely unknown. The purpose of this study was to explore fungal diversity in deep-sea sediments of the Yap trench and their denitrification potential. In the present study, a total of 106 fungal strains were isolated from six sediment samples collected in the East Yap Trench. These fungi belonged to five classes (Dothideomycetes, Eurotiomycetes, Sordariomycetes, Cystobasidiomycetes, and Microbotryomycetes), thirteen genera (Acremonium, Alternaria, Aureobasidium, Aspergillus, Cladosporium, Cystobasidium, Engyodontium, Gliomastix, Lecanicillium, Penicillium, Phoma, Rhodotorula and Trichoderma) and eighteen species, based on morphological identification and ITS-rDNA sequence analysis. Among them, the dominant genus is Cladosporium, which accounting for 42.45% of the total fungal strains. Meanwhile, the denitrification potential of the fungal strains was also examined with two different denitrifying media (nitrate and nitrite as sole substrate, respectively). Two fungal strains (Acremonium sp. and Aspergillus versicolor), were found to be able to produce N₂O ex situ in the presence of nitrite. No fungus was found to produce N₂O by using nitrate. Our results suggest that fungi in hadal sediments, play important roles in nitrogen cycles.     

Geochemistry and Microbial Populations in Sediments of the Northern Baffin Bay,Arctic

The Northern Baffin Bay between Greenland and Canada is a remote Arctic area restricted in primary production by seasonal ice cover, with presumably low sedimentation rates, carbon content and microbial activities in its sediments. Our aim was to study the so far unknown subseafloor geochemistry and microbial populations driving seafloor ecosystems. Shelf sediments had the highest organic carbon content, numbers of Bacteria and Archaea, and microcosms inoculated from Shelf sediments showed highest sulfate reduction and methane production rates. Sediments in the central deep area and on the southern slope contained less organic carbon and overall lower microbial numbers. Similar 16S rRNA gene copy numbers of Archaea and Bacteria were found for the majority of the sites investigated. Sulfate in pore water correlated with dsrA copy numbers of sulfate-reducing prokaryotes and differed between sites. No methane was found as free gas in the sediments, and mcrA copy numbers of methanogenic Archaea were low. Methanogenic and sulfate-reducing cultures were enriched on a variety of substrates including hydrocarbons. In summary, the Greenlandic shelf sediments contain vital microbial communities adapted to their specific environmental conditions.     

Microbial quality of soil from the Pampa biome in response to different grazing pressures

The aim of this study was to evaluate the impact of different grazing pressures on the activity and diversity of soil bacteria. We performed a long-term experiment in Eldorado do Sul, southern Brazil, that assessed three levels of grazing pressure: high pressure (HP), with 4% herbage allowance (HA), moderate pressure (MP), with 12% HA, and low pressure (LP), with 16% HA. Two reference areas were also assessed, one of never-grazed native vegetation (NG) and another of regenerated vegetation after two years of grazing (RG). Soil samples were evaluated for microbial biomass and enzymatic (β-glucosidase, arylsulfatase and urease) activities. The structure of the bacterial community and the population of diazotrophic bacteria were evaluated by RFLP of the 16S rRNA and nifH genes, respectively. The diversity of diazotrophic bacteria was assessed by partial sequencing of the 16S rDNA gene. The presence of grazing animals increased soil microbial biomass in MP and HP. The structures of the bacterial community and the populations of diazotrophic bacteria were altered by the different grazing managements, with a greater diversity of diazotrophic bacteria in the LP treatment. Based on the characteristics evaluated, the MP treatment was the most appropriate for animal production and conservation of the Pampa biome.     

Isolation and Characterization of Antimony-Reducing Bacteria from Sediments Collected in the Vicinity of an Antimony Factory

To date, there is very little information available on the oxidation and reduction of antimony by bacteria. An antimonate-respiring bacterium was isolated from sediment samples collected in the vicinity of an antimony oxide-producing factory in Korea. This bacterium was isolated by application of the Hungate standard anaerobic culture technique. Temporarily named strain JUK-1, it was found to be a rod-shaped bacterium and occurred individually or in pairs. Antimonate (pentavalent antimony) was reduced to antimonite (trivalent antimony) in the presence of JUK-1 in an anoxic minimal medium containing 5 mM antimonate and 10 mM acetate. The organism grew optimally at an initial pH of 7.7 and a temperature of 30°C. A part of the antimonite which was produced in medium precipitated as a bio-mineral containing approximately 50.0% antimony, 33.5% oxygen, 12.7% carbon, 2.0% sodium and 1.9% magnesium by weight. Based on the phylogenetics of 16S rRNA gene sequence and DNA G+C content, JUK-1 appears to be a new strain of the Sinorhizobium genus. The results suggest that bacteria may play a significant role in changing the redox state of antimony in the environment.     

南海西沙海槽表层沉积物微生物多样性

利用非培养的分子技术研究了西沙海槽表层沉积物中的微生物群落.沉积物中扩增的古菌16S rDNA 序列分属两个大类:泉古生菌(Crenarchaeota)和广古生菌(Euryarchaeota).以Marine Crenarchaeotic GroupⅠ (古菌16S rDNA文库的49.2%)和Terrestrial Miscellaneous Euryarchaeotal Group (16.9%)为主要类群;其余为Marine Benthic Group B (9.7%)、 Marine Benthic Group A (4%)、 Marine Benthic Group D (1.6%)、Novel Euryarchaeotic Group (0.8%)和 C3(0.8%).细菌克隆子多样性明显高于古菌,16S rDNA序列分别来自变形杆菌(Proteobacteria)(细菌16S rDNA文库的30.5%)、浮霉菌(Planctomycetes)(20.3%)、放线菌(Actinobacteria)(14.4%)、厚壁菌(Firmicutes)(15.3%)、屈桡杆菌(Chloroflexi)(8.5%)、酸杆菌(Acidobacteria)(3.4%)、candidate division OP8 (2.5%)、拟杆菌/绿菌(Bacterioidetes/Chlorobi)(1.7%)和疣微菌(Verrucomicrobia)(1.7%).变形杆菌为优势类群(包括Alpha-和Delta-Proteobacteria亚群).多数克隆子为未培养细菌和古菌.结果表明南海表层沉积物中蕴含大量未知的微生物资源.     

Microbial diversity in surface sediments of the Xisha Trough, the South China Sea

Microbial communities were obtained from the surface sediments of the Xisha Trough using the culture-independent technique. The characteristics of the 16S rDNA gene amplified from the sediments indicated that archaeal clones could be grouped into Euryarchaeota and Crenarchaeota, respectively. Two archaeal groups, Marine Crenarchaeotic GroupI and Terrestrial Miscellaneous Euryarchaeotal Group, were the most dominant archaeal 16S rDNA gene components in the sediments. The remaining components were related to the members of Marine Benthic Group B, Marine Benthic Group A, Marine Benthic Group D, Novel Euryarchaeotic Group and C3. The bacterial clones exhibited greater diversity than the archaeal clones with the 16S rDNA gene sequences from the members of Proteobacteria, Planctomycetes, Actinobacteria, Firmicutes, Chloroflexi, Acidobacteria, candidate division OP8, Bacterioidetes/Chlorobi and Verrucomicrobia. Most of these lineages represented uncultured microorganisms. The result suggests that a vast amount of microbial resource in the surface sediments of the South China Sea has not been known.     

Microbial Diversity in the Deep Marine Sediments from the Qiongdongnan Basin in South China Sea

The continental shelf and slope in the northern South China Sea is well known for its prospect of oil/gas/gas-hydrate resources. To study microbial communities and their roles in carbon cycling, a 4.9-m sediment core was collected from the Qiongdongnan Basin on the continental slope of the South China Sea during our cruise HY4-2005-5 in 2005. Geochemical, mineralogical, and molecular phylogenetic analyses were carried out. Sulfate concentration in pore water decreased with depth. Abundant authigenic carbonates and pyrite were observed in the sediments. The bacterial community was dominated by aerobic and facultative organisms. Bacterial clone sequences belonged to the Gamma-, Alpha-, Deltaproteobacteria and Firmicutes group, and they were related to Fe(III) and/or Mn(IV) reducers, sulfate reducers, aromatic hydrocarbon degraders, thiosulfate/sulfite oxidizers, and denitrifiers. Archaeal clone sequences exhibited greater overall diversity than the bacterial clones with most sequences related to Deep-Sea Archaeal Group (DSAG), Miscellaneous Crenarchaeotic Group (MCG), and Uncultured Euryarchaeotic Clusters (UECs). Archaeal sequences related to Methanosarcinales, South African Gold Mine Euryarchaeotic Group (SAGMEG), Marine Benthic Group-D (MBG-D) were also present. Most of these groups are commonly present in deep-sea sediments, particularly in methane/organic-rich or putative methane hydrate-bearing sediments.     

Microbial Diversity in Ngari,Hentak and Tungtap,Fermented Fish Products of North-East India

Ngari, hentak and tungtap are traditional fermented fish products of North-East India. Eighteen samples of ngari, hentak and tungtap were collected and were analysed for microbial load. Lactic acid bacteria, endospore-forming rods, yeasts and aerobic mesophilic counts ranged from 4.0 to 7.2, 3.3–4.6, <1–3.5 and 4.3–7.3 log c.f.u./g, respectively. Lactic acid bacteria were identified as Lactococcus lactis subsp. cremoris, Lactococcus plantarum, Enterococcus faecium, Lactobacillus fructosus, Lactobacillus amylophilus, Lactobacillus coryniformis subsp. torquens and Lactobacillus plantarum. Endospore-forming rods were identified as Bacillus subtilis and Bacillus pumilus, aerobic coccal strains were identified as Micrococcus. Yeasts were identified as species of Candida and Saccharomycopsis. Pathogenic contaminants were detected in all samples, however, none of the sample contained more than 10² c.f.u./g of Bacillus cereus, 10³ c.f.u./g of Staphylococcus aureus and enterobacteriaceae population, respectively. Enzymatic and antimicrobial activities of the isolates were tested. None of the strains produced biogenic amines in the method applied. Most strains of LAB had a high degree of hydrophobicity, indicating their ‘probiotic’ characters. This study has demonstrated the microbial diversity within the species of lactic acid bacteria, Bacillus and yeasts. This revised version was published online in July 2006 with corrections to the Cover Date.     

南海冷泉区深海沉积物中细菌的分离培养及多样性分析

为了认识南海深海冷泉区沉积物中可培养微生物的多样性,本文以冷泉区与非冷泉区两个站点的深海沉积物为样品,通过两种培养基(R2A海水培养基和2216E培养基)直接涂布或富集后平板分离纯化,从9个样品中共得到395株菌株,并通过16SrRNA基因鉴定,分属10个属。发现产芽胞细菌分布最广、丰度最大,包括3个属、15个种。其中芽胞杆菌(Bacillus)无论是在数量还是在种类上都分布最多。并且,随着水深和沉积物深度的增加,分离到的可培养微生物丰富度降低。本研究表明,即使在冷泉区,南海深海沉积物中产芽胞细菌也比较丰富。     

南海Formosa冷泉区沉积物微生物多样性与分布规律研究

【目的】当前对全球冷泉生态系统微生物生态学研究显示，冷泉生态系统中主要微生物类群为参与甲烷代谢的微生物，它们的分布差异与所处冷泉区生物地球化学环境密切相关。但在冷泉区内也存在环境因子截然不同的生境，尚缺乏比较冷泉区内小尺度生境间微生物多样性和分布规律的研究。本研究旨在分析南海Formosa冷泉区内不同生境间微生物多样性差异，完善和理解不同环境因子对冷泉内微生物群落结构的影响。【方法】对采集自南海Formosa冷泉区不同生境(黑色菌席区、白色菌席区和碳酸盐岩区)沉积物样本中古菌和细菌16S rRNA基因进行测序，结合环境因子，比较微生物多样性差异，分析环境因子对微生物分布的影响。【结果】发现在Formosa冷泉内的不同生境中，甲烷厌氧氧化古菌(anaerobic methanotrophic archaea,ANME)是主要古菌类群，占古菌总体相对丰度超过70%；在菌席区ANME-1b和ANME-2a/b是主要ANME亚群，碳酸盐岩区则是ANME-1b。硫酸盐还原菌(sulfate-reducing bacteria,SRB)和硫氧化菌(sulfur-oxidizing bacteria...     

Microbial Diversity in High Arsenic Groundwater in Hetao Basin of Inner Mongolia,China

The microbial diversity and community structure in twenty-one groundwater samples from high arsenic shallow aquifers of Hetao Basin, Inner Mongolia, China was investigated with an integrated approach including polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) and 16S rRNA gene phylogenetic analyses. A total of 25 bacterial and 32 archaeal DGGE bands were exercised for sequencing. Phylogenetic analyses showed that the bacterial DGGE bands were dominated by Proteobacteria, and the archaeal bands were dominated by Thaumarchaeota and Euryarchaeota. Based on arsenic concentrations, three samples (corresponding to low, medium, and high level of arsenic, respectively) were selected for construction of 16S rRNA gene clone libraries. A total of 912 (468 and 444 for bacteria and archaea, respectively) 16S rRNA gene clone sequences were obtained and subjected to phylogenetic analyses. The results showed that bacterial communities of these samples were dominated by Acinetobacter, Pseudomonas, Massilia, Dietzia, Planococcus, Brevundimonas, Aquabacterium and Geobacter, and archaeal communities by Nitrosophaera, Thermoprotei and Methanosaeta. The relative abundance of major groups varied as a function of changes in groundwater geochemistry. Acinetobacter, Brevundimonas, Geobacter, Thermoprotei and Methanosaeta dominated in high arsenic samples with high concentrations of methane and Fe(II), and low concentrations of SO^2? ₄ and NO^? ₃, while Pseudomonas and Nitrosophaera were abundant in low arsenic groundwater. These results imply that microbes play an important role in arsenic mobilization in the shallow aquifers of Hetao Basin, Inner Mongolia.     

先锋牧草-香根草联合固氮菌多样性研究

摘要：【目的】香根草（Vetiver zizanioides）是一种多年生禾本科草本植物,具有极强的生态适应性和抗逆能力,可作饲料和水土保持用。通过研究香根草联合固氮菌多样性,为进一步研究和应用打下基础。【方法】采用无氮培养基,首次从香根草中分离到47株联合固氮菌,分别应用SDS-PAGE全细胞蛋白质电泳、DNA指纹图谱、唯一碳源和16S rDNA全序列测定等方法,进行聚类和多样性分析。【结果】SDS-PAGE、IS-PCR和Bio-BIQA碳源利用的聚类结果基本一致,将供试菌株分为6个类群和4个单菌株;     

Abundance of Naked Amoebae in Sediments of Hiroshima Bay, Seto Inland Sea of Japan

ABSTRACT The present paper provides the first data on naked amoebae from sediments of Hiroshima Bay. Three stations in the inner part of the bay were sampled over a three-month period. Abundance of naked amoebae ranged from 1,019 to 45,561 cells/g dry sediment. Results indicate: (i) surface sediment populations in most cases were higher than subsurface populations; (ii) there was some evidence of temporal variation with counts generally increasing from March to May: and (iii) the site located near Hiroshima City had fewer amoebae on several occasions than the other two sites. There was a negative exponential relationship between acid-volatile sulfide concentration and abundance of amoebae. Most amoebae were small with the average size ranging from 6.6–14 μm. Morphotype 1, amoebae that extend lobose pseudopodia or subpseudopodia during normal locomotion, were dominant (40–100% of enumerated amoebae). Morphotypes 2 and 3 (limax amoebae) were found in lower numbers than the other two morphotypes. The proportion of amoebae occupied by Morphotype 4 (fan-shaped or discoidal-flattened amoebae) was higher at a lower total abundance.     

Microbial Communities Inhabiting a Rare Earth Element Enriched Birnessite-Type Manganese Deposit in the Ytterby Mine,Sweden

The dominant initial phase formed during microbially mediated manganese oxidation is a poorly crystalline birnessite-type phyllomanganate. The occurrence of manganese deposits containing this mineral is of interest for increased understanding of microbial involvement in the manganese cycle. A culture independent molecular approach is used as a first step to investigate the role of microorganisms in forming rare earth element enriched birnessite-type manganese oxides, associated with water bearing rock fractures in a tunnel of the Ytterby mine, Sweden. 16S rRNA gene results show that the chemotrophic bacterial communities are diverse and include a high percentage of uncultured unclassified bacteria while archaeal diversity is low with Thaumarchaeota almost exclusively dominating the population. Ytterby clones are frequently most similar to clones isolated from subsurface environments, low temperature milieus and/or settings rich in metals. Overall, bacteria are dominant compared to archaea. Both bacterial and archaeal abundances are up to four orders of magnitude higher in manganese samples than in fracture water. Potential players in the manganese cycling are mainly found within the ferromanganese genera Hyphomicrobium and Pedomicrobium, and a group of Bacteroidetes sequences that cluster within an uncultured novel genus most closely related to the Terrimonas. This study strongly suggest that the production of the YBS deposit is microbially mediated.