Archaeal populations in biological soil crusts from arid lands in North America

Archaea are common and abundant members of biological soil crust communities across large-scale biogeographic provinces of arid North America. Regardless of microbial community development, archaeal populations averaged 2 × 10⁷ 16S rRNA gene copies per gram of soil, representing around 5% of the prokaryotic (total calculated bacterial and archaeal) numbers assessed by quantitative-PCR. In contrast, archaeal diversity, determined by denaturing gradient gel electrophoresis fingerprinting and clone libraries of 16S rRNA genes, was very restricted. Only six different phylotypes (all Crenarchaea) were detected, three of which were very dominant. Some phylotypes were widespread, while others were typical of Southern desert areas.     

Phylogenetic characterization of dwarf archaea and bacteria from a semiarid soil

Microscopic studies have shown that most microbes exist in soils as dwarf cells that are thought to be an adaptation to nutrient limitation. Most dwarfs are uncultured by current approaches and have not been identified phylogenetically. Only a few dwarf bacteria have been isolated in culture and dwarf archaea have received little study. We selected a semiarid creosotebush shrubland site for studying dwarf microorganisms because arid and semiarid soils are generally nutrient-poor. Soils were collected beneath creosotebush canopies and in open areas between shrubs. Cells were eluted in sodium pyrophosphate and filtered with a 0.45-μm pore-size filter. Filtrate DNA was extracted, PCR-amplified using universal bacterial and archaeal 16S rDNA primers, cloned, RFLP-screened, and sequenced. The eluted cell filtrates were also inoculated into R2B medium. After incubation, cultures were filtered to select against populations of dwarfs that formed large cells in the presence of nutrients (pleomorphic dwarfs) and to select for populations that retained dwarf size (intrinsic dwarfs). Dwarf archaea and bacteria were present in the initial filtrate and in the cultures. A single dwarf archaeon (SevArch-01) that is related to other soil Crenarchaeota sequences was found in the initial filtrates and in subsequent filtrate cultures, indicating an intrinsically dwarf archaeon. Dwarf bacteria fell into four bacterial phyla: Proteobacteria, Firmicutes, Actinobacteria, and the TM-7 group. Intrinsically dwarf bacteria in enrichment cultures were identified as α- and β-Proteobacteria. Dwarf bacteria related to Arthrobacter, Propionibacterium, and other actinobacteria were detected. Several sequences showed no close relationships to any microorganisms that have been grown in culture.     

一个红壤剖面微生物群落的焦磷酸测序法研究

利用定量PCR和454焦磷酸测序法,研究了湖南湘阴县一典型红壤剖面微生物相关基因的多度及微生物(古菌、细菌、真菌)群落结构.结果显示,随剖面深度增加,土壤黏粒含量增多,有机质和全氮含量、碳氮比则下降.每克干土微生物基因拷贝数也趋于下降,其值为:10 7.09～ 109.30(古菌16S rDNA),108.10～109.70(细菌16S rDNA),106.54～107.95(真菌18S rDNA),10 7.24～108.61(古菌amoA基因),104.76～106.25(细菌amoA基因),105.94～ 107.88(nirK基因),106.81～109.21(nirS基因),107.03～ 109.46(nosZ基因).焦磷酸测序得到了6 459条古菌16S rRNA基因序列,平均长度为496 bp;28 626条细菌16S rRNA基因序列,平均长度为448 bp;4 683条真菌18S rRNA基因序列,平均长度为534 bp.OTU(97％相似度)分析表明,微生物群落d-多样性与所测土壤理化性质均无显著相关.Jaccard差异度分析表明同一剖面各土壤层次间微生物群落结构更为相似,而不同位点的三个表层土之间的差异较大;Mantel检验发现,与微生物群落变化相关的主要土壤因子是黏粒含量.在所有土样中,古菌以泉古菌门中的热变形菌纲(89％)为主,其分布与土壤黏粒含量相关.细菌的主要类群为酸杆菌门(33％)、变形菌门(17％)、绿弯菌门(12％)、厚壁菌门(10％)和放线菌门(7％),分类地位不明确的细菌约占11％.其中,酸杆菌门和变形菌门的相对多度在表层土中高于非表层土;而绿弯菌门和厚壁菌门的相对多度则在非表层土中更高,与土壤深度呈显著正相关.所有真菌序列分属于三个门,即子囊菌门(87％)、担子菌门(9％)和球囊菌门(4％),在纲一级的分类水平上,各样品间群落结构无明显差异.     

一株产碱性磷酸酶菌株的鉴定及酶的纯化

[目标]筛选分离自硝尔库勒盐湖产碱性磷酸酶菌株,对菌株进行多项分类鉴定,分离纯化碱性磷酸酶。[方法]利用微孔板法,筛选碱性磷酸酶产生菌。通过形态特征观察、生理生化测定、利用硫酸铵沉淀、阴离子交换层析和分子筛层析得到电泳纯的酶16S rRNA序列分析等实验,确定菌株的分类地位。[结果]从我国硝尔库勒盐湖样品中分离得到一株产碱性磷酸酶酶的菌株tarim4,经过多项分类鉴定显示它是与Natrinema pellirubrum不同的新菌株。[结论]多项分类结果鉴定,菌株为Natrinema pellirubrum tarim 4。该菌株产生的碱性磷酸酶有进一步的研究价值。     

Temporal and seasonal change in microbial community structure of an undisturbed,disturbed, and carbon-amended pasture soil

Disturbance and change to C inputs can alter microbial community structure and impact ecosystem function. Particularly in temperate regions, seasonal change also has an effect on microbial communities both directly through climate and indirectly through plant function. The temporal change in microbial communities of an undisturbed pasture, disturbed pasture (similar to a single tillage event) and pasture soil amended with two forms of particulate carbon were monitored over eight consecutive seasons after grass was reestablished. The soil microbial community was assessed by a DNA fingerprinting technique (terminal restriction fragment length polymorphism, TRFLP) of bacterial, fungal and archaeal communities, and also from phospholipid fatty acid (PLFA) analysis. The single disturbance had a significant effect on fungal microbial community structure (by TRFLP) and significantly decreased the fungal:bacterial ratio. Though the change was relatively small, it persisted throughout the sampling period. Nitrate was also higher on the disturbed treatment providing evidence for the theory that changes to fungal:bacterial ratios can alter nutrient cycling and retention. Fungal communities were the most altered by the C amendments, and while bacteria were also affected by the C amendments, seasonal change was a greater cause of variation. Correlation to soil and climatic variables explained more of the total variability for PLFA (78% for all treatments) than bacterial (50%), fungal (35%) and archaeal (14%) restriction fragments. Most climate and soil variables explained significant variation for seasonal patterns in the multivariate community structures but measurements of soil moisture were important for all communities while pH was relatively more important for bacteria, temperature for fungi, and soil C:N ratio for archaea. Autumn was particularly distinct from other seasons for bacteria (less so for the fungal community) and although there was seasonal change in pH suggesting pasture management was a factor, the significant correlation of other soil characteristics suggests that plant physiological changes (most probably root exudates) also played a significant role. The large change in the saprotrophic fungal community due to the particulate C addition but minor seasonal change would tend to suggest that the fungal community may be more responsive to changes in litter inputs rather than root exudates while the reverse is true for bacteria.