Role of PhoPR in the response to stress of Mycobacterium bovis

PhoP is part of the two-component PhoPR system that regulates the expression of virulence genes of Mycobacteria. The goal of this work was to elucidate the role of PhoP in the mechanism that Mycobacterium bovis, the causative agent of bovine tuberculosis, displays upon stress. An analysis of gene expression and acidic growth curves indicated that M. bovis neutralized the external acidic environment by inducing and secreting ammonia. We found that PhoP is essential for ammonia production/secretion and its role in this process seems to be the induction of asparaginase and urease expression. We also demonstrated that the lack of PhoP negatively affected the synthesis of phthiocerol dimycocerosates. This finding is consistent with the role of the lipid anabolism in maintaining the redox environment upon stress in mycobacteria. Altogether the results of this study indicate that PhoP plays an important role in the response mechanisms to stress of M. bovis.     

酸性土壤中决明属牧草高效根瘤菌的分离及筛选

为提高豆科决明属（Chamaecrista spp.）牧草的结瘤能力和固氮效率，促进决明属牧草在酸性土壤中的应用及推广，本研究以圆叶决明（Chamaecrista rotundifolia）和羽叶决明（Chamaecrasta nictitans）为试验材料，通过分离、纯化、nodA基因鉴定等方法，从酸性土壤里决明属牧草的根瘤中分离到10株候选根瘤菌株系。16S rDNA测序及系统发育树分析表明，这10株根瘤菌均属于慢生型根瘤菌。回接试验表明，上述10株根瘤菌均能与圆叶决明共生，形成根瘤。与不接种的对照相比，其固氮酶活性为0.08~4.65 μmol·g^-1·h^-1，植株干重、SPAD值和氮含量分别提高了99.17%~372.14%，399.27%~789.05%，235.00%~1043.33%。其中，4株根瘤菌TXR2，TXN1，WYSR1，JYN6对圆叶决明氮营养贡献最大，并且TXN1与宿主共生形成的根瘤数目最多，而JYN6的固氮酶活性最高。说明本研究分离鉴定到4株决明高效根瘤菌，具有较好的应用前景。     

基于宏基因组学的酸性森林土壤氨氧化微生物群落特征研究

全球30%以上陆地面积是酸性土壤(pH5.5),而酸性土壤中氨氧化微生物群落特征研究是破译其硝化过程微生物学机理的基础。尤其随着完全硝化微生物(Complete ammonia oxidizer,comammox)的发现,亟需重新认知酸性土壤中氨氧化微生物类群。以酸性马尾松林为研究对象,综合利用荧光定量PCR(qPCR)、凝胶电泳半定量和宏基因组测序等技术研究土壤中氨氧化古菌(Ammonia-oxidizing archaea,AOA)、氨氧化细菌(Ammonia-oxidizing bacteria,AOB)和Comammox的相对丰度以及群落组成特征。研究发现AOA和AOB amoA基因丰度分别为2.61×106 copies·g~(-1)和1.45×106copies·g~(-1);而comammoxamoA基因qPCR结果存在显著的非特异性扩增,导致其丰度被高估,而经凝胶电泳半定量矫正后,约为(1.38～1.47)×106copies·g~(-1),该结果和土壤宏基因测序揭示的comammox相对丰度基本吻合。此外,宏基因组分析发现经典嗜酸group1.1a-associated仅占AOA总类群的12%,而group1.1b则占88%,尽管目前仍未有嗜酸group 1.1b AOA纯菌株的报道。AOB主要类群为Nitrosospira(约64%),而Nitrosomonas约占36%。Comammox主要类群为clade B(约64%),而clade A仅占36%且均隶属于clade A.1亚枝,这暗示clade B与已报道的嗜中性comammox clade A纯菌株有极大的生理代谢差异。总之,本研究提供了综合利用qPCR、半定量和宏基因组分析土壤氨氧化微生物群落的策略,并建议优化comammox的qPCR引物,同时本研究系统分析了酸性马尾松林土壤中氨氧化微生物的相对丰度和群落组成特征。     

乳山湾沉积物中酸挥发性硫化物(AVS)的分布变化特征

2005年12月和2006年3、6、9月,乳山湾滩涂底质环境调查中的16个站点的酸挥发性硫化物(AVS)含量的测定分析结果表明,表层沉积物中AVS具有明显的时、空变化。水平变化范围分别为:春季16·46~230·62mg/kg(干重,下同)、夏季33·65~568·48mg/kg、秋季23·49~350·69mg/kg、冬季15·77~190·96mg/kg,平均值分别为92·82、208·65、177·27和82·87mg/kg。对养殖区与非养殖区AVS含量进行比较,结果表明,养殖区明显高于非养殖区。在深度为0~20cm之间,AVS含量基本是随着深度的增加而增加。本文还就近几年乳山湾东流区表层底质中的AVS含量作了年际比较分析,结果表明,AVS含量年际变化不明显。     

土地利用方式对酸性红壤丛枝菌根真菌群落的影响

为了研究土地利用方式对酸性红壤丛枝菌根真菌(arbuscular mycorrhizal fungi, AMF)群落的影响,调查了酸性红壤4种土地利用方式(草地、玉米、花生和大豆)下非根际和根际土壤AMF群落多样性和组成结构。结果表明：土地利用方式显著影响了AMF群落优势属球囊霉属(Glomus)和巨孢囊霉属(Paraglomus)的相对丰度,但是根际作用影响不明显。土地利用方式而非根际作用显著影响了AMF群落香农指数和物种丰富度,其中大豆地表现出最低的香农指数和物种丰富度。土地利用方式和根际作用都显著影响AMF群落组成结构,但是土地利用方式的作用强度明显高于根际作用。球囊霉属主要解释了不同土地利用方式之间的AMF群落组成差异。土壤p H是影响土壤AMF群落结构的最关键因子。因此,土地利用方式比根际作用表现出对酸性红壤AMF群落更大的影响,展现了土地利用变化在影响土壤AMF群落方面的重要作用。     

Response of ammonia oxidizing microbes to the stresses of arsenic and copper in two acidic alfisols

Soil pollution by elevated heavy metals exhibits adverse effects on soil microorganisms. Ammonia oxidizing bacteria and ammonia oxidizing archaea perform ammonia oxidative processes in acidic soils. However, influence of heavy metal stress on soil ammonia oxidizers distribution and diversity is inadequately addressed. This study investigated the responses of ammonia oxidizing bacteria and archaea to heavy metals, Cu and As during short-term laboratory experiment. Two different acidic alfisols named as Rayka and Hangzhou spiked with different concentrations of As, Cu and As + Cu were incubated for 10 weeks. Significant reduction in copy numbers of archaeal-16S rRNA, bacterial-16S rRNA and functional amoA genes was observed along elevated heavy metal concentrations. Ammonia oxidizing archaea was found to be more abundant than ammonia oxidizing bacteria in all the heavy metal treatments. The potential nitrification rate significantly decreased with increasing As and Cu concentrations in the two soils examined. Denaturing gradient gel electrophoresis analysis revealed no apparent community shift for ammonia oxidizing archaea even at higher concentrations of As and Cu. Phylogenetic analysis of archaeal amoA gene from 4 clone libraries indicated that all the archaeal amoA sequences were placed within 3 distinct clusters from soil and sediment group 1.1b of Thaumarchaeota. Our results could be useful for the better understanding of the ecological effects of heavy metals on the abundance and diversity of soil ammonia oxidizers.     

Fire-vegetation interplay in a mosaic structure of Quercus suber woodlands and Mediterranean maquis under recurrent fires

We examined the effects of fire recurrence on a mosaic structure of Quercus suber and Erica-Cistus shrubland communities of Southeastern France in order to improve the understanding of fire-vegetation interplay. Plant communities that were similar in 1959 (woodlands on shrublands called maquis on acidic soils) were compared along a gradient of fire recurrence, from 0 to 4 fires, with different time intervals between fires. The results showed that understory cover increased roughly with fire recurrence, whereas tree height, cover, density, stand basal area and litter depth decreased. Different fire recurrences along the past decades led to different vegetation types. High fire recurrence corresponded to maquis and sparse cork-oak woodlands while pure oak woodlands established in the absence of fire during the same period. In all, the diversity of tree diameter decreased with fire recurrence. High fire recurrence (3 or 4 fires in 50 years) led to a simple vertical structure of vegetation with a mono-layered shrub cover and few Quercus suber trees. In contrast, spatial connections between plants were maximal at longer time intervals, leading to a multi-layered vegetation. We finally discuss the potential implications of past fires on the behavior of future fires in the perspective of a sustainable management of these Mediterranean ecosystems.     

Evaluation of elemental depletion weathering rate estimation methods on acid-sensitive soils of north-eastern Alberta, Canada

Immobile element-based weathering estimation methods assume that Zr (or Ti) is an immobile element, and that weathering rates of other elements can be estimated according to the enrichment of Zr in weathered horizons relative to an unweathered parent material. This approach was used to estimate base cation weathering rates for 33 soil profiles on acid-sensitive terrain in north-eastern Alberta. Zirconium generally showed enrichment within the rooting zone, but the deepest (subsoil) samples were not always associated with the lowest Zr concentrations. Weathering rates estimated with the Zr depletion and Pedological Mass Balance (PMB) methods were generally low (ranges: 0-51 and 0-58 mmol_c m^− 2 yr^− 1, respectively); however, low base cation oxide concentrations and heterogeneity within soil profiles complicated weathering rate calculations and net base cation gains were calculated for several (six) sites. Evaluation of the Zr depletion and PMB weathering estimates against those calculated with the process-oriented PROFILE model at a subset (n = 9) of the sites indicated the estimates were poorly related, with PROFILE rates typically being higher. The effects-based emissions management strategy for acid precursors in this region requires spatial coverage of soil properties (including weathering rates) across a large area, but the apparent limitations associated with the immobile element based methods in this region: identifying representative parent soils and deriving weathering rate estimates comparable to more robust methods are arguments against their candidacy for future use.     

不同酸性物质对石灰性土壤的酸化效果研究

采用室内模拟试验研究了酸性物质对石灰性土壤的酸化效果。结果表明,磷酸能有效地降低石灰性土壤的pH,要使土壤pH由8.89降至6.0左右,最佳酸用量为3.27g/100g土。对于pH较高的石灰性土壤,只用低pH(pH=5.5)的酸水溶液在短时间内降低土壤pH是不切实际的。磷酸二氢铵不仅具有很好的酸化效果,且具有很好的缓冲性能,每100g土壤加入2.3g磷酸二氢铵可使石灰性土壤pH从8.89降低到6.39,并能维持较长的酸性环境。施用5%的硫磺可在30d内使土壤pH降低到7.0～7.5之间。     

碳酸钙和根际作用对酸性红壤解磷微生物丰度的影响

选用玉米品种郑单958为试验材料,设置不添加碳酸钙(CK)、每千克土添加0.3g碳酸钙(Ca-0.3)和0.5g碳酸钙(Ca-0.5)3个碳酸钙处理,以相应处理未种植物土壤为非根际对照土壤,研究了碳酸钙和根际作用对酸性红壤磷酸酶活性及解磷微生物相关功能基因phoC和phoD丰度的影响。结果表明:碳酸钙添加能有效改善玉米生长,促进地上部氮、磷、钾和钙的吸收。土壤酸性磷酸酶(ACP)活性显著高于碱性磷酸酶(ALP)活性,表明酸性土壤中ACP在矿化有机磷方面占主导地位。根际土壤ACP、ALP活性和phoD基因拷贝数均显著高于非根际,而仅Ca-0.5处理ALP活性和phoD基因拷贝数显著高于CK,说明根际效应强于碳酸钙处理。phoC基因拷贝数与土壤铵态氮、硝态氮含量存在显著相关性,ALP活性和phoD基因拷贝数与土壤pH及铵态氮、硝态氮、有效磷、交换性钙含量均存在显著相关性。可见,碳酸钙和根际作用均影响酸性土壤解磷微生物功能和丰度,但根际效应更加明显,这些作用与土壤理化因子的改变密切相关。