不同土壤母质黄棕壤剖面细菌的生物多样性及其对钾矿物风化作用的研究
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摘要
土壤微生物多样性是指土壤微生物群落的结构与组成的差异,一般可包括物种多样性、遗传多样性、生态多样性和功能多样性。研究土壤微生物的多样性,不仅有助于对微生物资源及生物多样性的深入认识,丰富微生物资源库和基因库,揭示微生物多样性与土壤理化因子之间的关系,还可以筛选高效分解钾矿物的细菌,为研究细菌对矿物的风化及在土壤形成过程中的作用提供理论依据和实验材料。
采用16S rDNA克隆文库构建法及变性梯度凝胶电泳法(DGGE)对小龙山(A)和后汉路(B)两个土壤剖面不同深度样品的细菌生物多样性进行了研究。结果表明,小龙山土壤剖面中细菌菌群归属于13大类群,分别为α-,β-,γ-和δ-Proteobacteria(变形菌门)、Acidobacteria(酸杆菌门)、Actinobacteria(放线菌门)、Chloroflexi(绿弯菌门)、Firmicutes(厚壁菌门)、Verrucomicrobia(疣微菌门)、Bacteroidetes(拟杆菌门)、Gemmatimonadetes、Ktedonobacteria和OP10。其中优势菌群为y-Proteobacteria、 Acidobacteria、Actinobacteria、Firmicutes和Chloroflexi;在后汉路土壤剖面中细菌菌群归属于9大类群,分别为α-,β-,γ-和δ-Proteobacteria、Acidobacteria、Actinobacteria、 Verrucomicrobia、Bacteroidetes和Ktedonobacteria,其中菌群Proteobacteria、 Actinobacteria、Acidobacteria为优势菌群。菌群Actinobacteria、Acidobacteria和y-Peoteobacteria是两个土壤剖面中共有的优势菌群。某些优势菌群随着土壤剖面深度的变化而变化。小龙山土壤剖面中,菌群y-Proteobacteria中的克隆子主要分布于剖面L2中；菌群Acidobacteria中的克隆子数量随着深度的增加而逐渐降低；菌群Actinobacteria中的克隆子主要分布于剖面Ll和L2中,而在L3中克隆子数量则有显著降低；而菌群Chloroflexi和Firmicutes中的克隆子则主要分布于剖面L3中。后汉路土壤剖面中,菌群Acidobacteria和Verrucomicrobia中的克隆子数量随着土壤剖面深度的增加有降低的趋势；菌群Actinobacteria中克隆子则在H2层数量最多；y-Proteobacteria中的克隆子主要分布剖面H3及H4中。DGGE分析结果表明,小龙山土壤剖面中的优势种群为Proteobacteria、Actinobacteria、Bacteroidetes、Acidobacteria、 Firmicutes和Chloroflexi,其中Rhodoplanes、Pseudomonas、Serratia和Arthrobacter为优势菌属。后汉路土壤剖面中的优势种群为γ-Proteobacteria、Bacteroidetes、Actinobactcria和Acidobacteria,其中Pseudomonas、Serratia、Arlhrobacter为优势菌属。
主成分分析(PCA)表明,土壤pH、有机质、有效性Fe和Al、土壤有效磷以及速效钾能够影响土壤细菌群落结构。典型相关分析(CCA)分析表明,小龙山土壤剖面中菌群y-Proteobacteria易受到土壤中活性铝的影响(r=-0.8,P<0.05)；Acidobacteria与土壤中有效磷含量呈显著正相关(r=0.99,P<0.05)。后汉路土壤剖面中y-Proteobacteria与土壤有效磷和速效钾存在明显的正相关(r=0.94,P<0.05；r=0.99,P<0.05)。优势菌属Arthrobacter在土壤矿物风化的进程中可能起了重要的作用。
采用缺钾培养基通过稀释平板法从上述土壤剖面中分离筛选到36株钾矿物分解细菌,16S rDNA序列分析结果表明,36株细菌隶属于菌群Firmicutes、Proteobacteria和Actinobacteria中的的9个菌属,分别为Bacillus(芽孢杆菌属)、Paenibacillus(类芽孢杆菌属),Dyella、Pantoea(泛菌属)、Burkholderia(伯克霍尔德菌属),Nocardioides(类诺卡氏菌属)、Isoptericola(白蚁菌属)、Microbacterium(微杆菌属)、Arthrobacter节杆菌属)。其中Bacillus、Paenibacillus、Arthrobacter和Burkholderia为两个土壤剖面的共有菌属,表现出较丰富的物种多样性。
菌株H17与Isoptericola属的亲缘关系最近,与同属的6株模式菌株的16S rRNA基因序列的同源性为97.8%-99.6%。菌株H17细胞壁肽聚糖为L-Lys-D-Asp,细胞壁糖为半乳糖、木糖和甘露糖,脂肪酸主要为anteiso-C15:0和iso-C15:0'主要极性脂为diphosphatidylglycerol、phosphatidylglycerol、phospholipids、phosphatidylinositol、 phosphoglycolipid、glycolipid和lipid,主要萘醌为MK9(H4),未检测到分枝菌酸,其G+C mo1%为72.4%,与6株模式菌株的DNA-DNA杂交同源性为15.2%-45.6%。综合这些结果,我们建议菌株H17为Isoptericola属的一个新种,命名为Isoptericola nanjingensis sp. nov.。
摇瓶条件下,对来源于供试菌株L11(Bacillus),H5(Burkholderia), H15(Arthrobacter)的矿物分解能力进行了研究。结果表明,培养30d后接菌处理的发酵液中Fe、Si、Al含量分别比接灭活菌对照增加27.5-115、1.5-2.2和13-35倍。扫描电镜(SEM)结果表明,接菌处理的钾长石矿物表面形成腐蚀坑,同时在钾长石表面形成了球形物和较小的颗粒状物质,对照处理的钾长石矿物表面比较平整；能谱(EDX)分析发现,上述球形物和较小的颗粒状物质是Fe和Ca的氧化物,推测是在钾长石矿物表面形成的次生矿物。另外,还研究了菌株Q12对云母(黑云母、白云母和金云母)的风化效应。ICP测定表明,接菌处理的溶液中Fe、Si、Al和K含量分别比对照增加9-173%、9-18%、10-310%和9-29%；SEM分析发现,菌株Q12在云母表面形成生物膜,云母表面形成了絮状、颗粒状和针状的物质,EDX分析表明,这些物质可能是形成的方解石、赤铁矿等次生矿物；X衍射(XRD)结果表明,接菌处理可以使黑云母形成赤铁矿和富镁蒙脱石等次生矿物。另外,透射电镜(TEM)观察发现,在菌株Q12细胞表面可以吸附一些矿物颗粒。
砂培试验表明,菌株L11和H5能够促进钾矿物的溶解,促进水稻植株的生长并提高水稻植株对钾素的利用。SEM分析表明,菌株能够在矿物表面和水稻植株根际定殖。在矿物表面或根表面形成圆球形、簇状、多面体、针状等物质。结合EDX分析,推测主要形成了方解石、草酸钙石、赤铁矿、磁铁矿等次生矿物。
Soil microbial diversity is the difference related to microbial communities and species, including species diversity, genetic diversity, ecological diversity and functional diversity. Researches on bacterial diversity will further understand microbial resource and biodiversity, enrich pool of microbial resource and gene, clarify the relationship between biodiversity and soil physicochemical factors, obtain efficient strains to weather mineral, and offer the theoretical and experimental basis for mineral weathering and soil formation.
16S rRNA gene sequence clone library and denaturing gradient gel electrophoresis (DGGE) were used to analyze bacterial biodiversity of two soil profiles sampled at site A (Longshan) and site B (Houhan Road). The results showed that there were13bacterial communities in site A and the major communities were γ-Proteobacteria, Acidobacteria, Actinobacteria, Firmicutes and Chloroflexi; while at site B, there were9bacterial communities, and the dominant communities were y-Proteobacteria, Actinobacteria, Acidobacteria. Actinobacteria, Acidobacteria and γ-Peoteobacteria were the same dominant phyla in both profiles. The major bacterial communities varied with soil depth. In profile A, clones of y-Proteobacteria mainly distributed layer-L2, and clones affiliated to Acidobacteria decreased with soil depth. The numbers of clone of Chloroflexi and Firmicutes mainly distributes in layer-L3. In profile B, the proportion of Acidobacteria and Verrucomicrobia decreased with soil depth, and the most abundant Actinobacteria was in profile B-H2, while clones of y-Peoteobacteria mainly distributed in H3and H4. The major communities were Proteobacteria, Actinobacteria, Bacteroidetes, Acidobacteria, Firmicutes and Chloroflexi at site A by DGGE, and the dominant genera were Rhodoplanes, Pseudomonas、Serratia and Arthrobacter. While at site B, the major phyla were y-Proteobacteria, Bacteroidetes, Actinobacteria and Acidobacteria, and the dominant genera were Pseudomonas, Serralia and Arthrobacter. Principal component analysis (PCA) suggested soil bacterial biodiversity was affected by soil physical and chemical factors such as soil pH, organic matter, effective Fe and Al, soil rapidly available phosphorus and available potassium. Canonical Correlation Analysis indicated bacteria affiliated to y-Proteobacteria were sensitive to soil available Al (r=-0.8, P<0.05), and bacteria affiliated to Acidobacteria were positive related to effective phosphorus significantly (r=0.99, P<0.05) at site A. At site B, bacteria affiliated to y-Proteobacteria were positive related to effective phosphorus and available potassium significantly (r=0.94, P<0.05; r=0.99, P<0.05). Arthrobacter affiliated to Actinobacteria were reported to have the ability to weather minerals in soil.
Thirty-six strains were separated from the two soil profiles by dilution plate method using potassium-limited medium.16S rRNA gene sequences revealed that36strains were grouped to9genera affiliated to3phyla, that is Bacillus, Paenibacillus, Dyella, Pantoea, Burkholderia, Nocardioides, Isoptericola, Microbacterium and Arthrobacter. Bacillus, Paenibacillus, Arthrobacter and Burkholderia were the common genera in both profiles, which showed abundant species diversity.
Strain H17had the highest similarities with Isoptericola spp., and showed97.8%-99.6%sequence similarities with the other strains. The cell-wall peptidoglycan type of strain H17is L-Lys-D-Asp. The whole-cell sugars are galactose, xylose and mannose. The major fatty acids (>10%of total) are anteiso-C15:0and iso-C15:0.The total polar lipids are diphosphatidylglycerol, phosphatidylglycerol, phospholipids, phosphatidylinositol, phosphoglycolipid, one unidentified glycolipid and one unidentified lipid. The menaquinone of strain H17T is MK9(H4). Mycolic acids were not detected. The DNA-DNA relatedness studies showed relatively low rates with the type strains of I. variabilis MX5T (45.6%), I. hypogeus HKI0342T(37.9%), I. jiangsuensis CLGT (33.4%), I. dokdonensis DS-3T (33.4%), I. halotolerans YIM70177T (40.9%) and I.chiayiensis06182M-1T (15.2%). The DNA G+C content of the type strain is72.4mol%. These results indicated that strain H17T represents a novel species of the genus Isoptericola, for which the name Isoptericola nanjingensis sp. nov. is proposed.
Strains Lll, H5and H15derived from different species were tested to weather potassium feldspar by shaking culture. The concentration of Fe, Si and Al increased27.5-115,1.5-2.2and13-35times than controls, respectively, by inductively coupled plasma optical emission spectrometry (ICP-OES). Scanning electron microscope (SEM) analisis showed that there were many corrosion pits in the surface of potassium feldspar, and spherical and small graininess around the mineral, while there was nothing around controls. These spherical and small graininess were the oxide of Fe and Ca, and were speculated to be secondary minerals. In addition, weathering effects of the strain Q12to micas (biotite, muscovite and phlogopite) were also studied. The concentration of Fe, Si, Al and K increased9-173%,9-18%,10-310%and9-29%compared to the controls according to ICP-AES, respectively. Biofilms were formed in the surface of micas after interactions with strain Q12by SEM. Some cotton-shaped, graininess and acicular materials were found around micas, which were identified to calcite and hematite by X-ray energy dispersive spectrum (EDS). X-ray diffraction (XRD) demonstrated that haematite and Mg-bearing turface were formed after interaction between the strain Q12and biotite. Transmission electron microscope (TEM) revealed small grains were adsorbed by bacterial cells.
Sand culture experiment showed the strains L11and H5could accelerate weathering of potassium feldspar, promote the growth of rice plants and increase utilization of potassium by rice plants. SEM indicated strain L11, H5and H15could colonize the surfaces of potassium feldspar and the rhizosphere of rice plants, and spheroidal, cluster-shaped, polyhedron and acicular materials were also found. These materials were speculated to be calcite, calcium oxalate, hematite and magnetite by EDS.
采用16S rDNA克隆文库构建法及变性梯度凝胶电泳法(DGGE)对小龙山(A)和后汉路(B)两个土壤剖面不同深度样品的细菌生物多样性进行了研究。结果表明,小龙山土壤剖面中细菌菌群归属于13大类群,分别为α-,β-,γ-和δ-Proteobacteria(变形菌门)、Acidobacteria(酸杆菌门)、Actinobacteria(放线菌门)、Chloroflexi(绿弯菌门)、Firmicutes(厚壁菌门)、Verrucomicrobia(疣微菌门)、Bacteroidetes(拟杆菌门)、Gemmatimonadetes、Ktedonobacteria和OP10。其中优势菌群为y-Proteobacteria、 Acidobacteria、Actinobacteria、Firmicutes和Chloroflexi;在后汉路土壤剖面中细菌菌群归属于9大类群,分别为α-,β-,γ-和δ-Proteobacteria、Acidobacteria、Actinobacteria、 Verrucomicrobia、Bacteroidetes和Ktedonobacteria,其中菌群Proteobacteria、 Actinobacteria、Acidobacteria为优势菌群。菌群Actinobacteria、Acidobacteria和y-Peoteobacteria是两个土壤剖面中共有的优势菌群。某些优势菌群随着土壤剖面深度的变化而变化。小龙山土壤剖面中,菌群y-Proteobacteria中的克隆子主要分布于剖面L2中；菌群Acidobacteria中的克隆子数量随着深度的增加而逐渐降低；菌群Actinobacteria中的克隆子主要分布于剖面Ll和L2中,而在L3中克隆子数量则有显著降低；而菌群Chloroflexi和Firmicutes中的克隆子则主要分布于剖面L3中。后汉路土壤剖面中,菌群Acidobacteria和Verrucomicrobia中的克隆子数量随着土壤剖面深度的增加有降低的趋势；菌群Actinobacteria中克隆子则在H2层数量最多；y-Proteobacteria中的克隆子主要分布剖面H3及H4中。DGGE分析结果表明,小龙山土壤剖面中的优势种群为Proteobacteria、Actinobacteria、Bacteroidetes、Acidobacteria、 Firmicutes和Chloroflexi,其中Rhodoplanes、Pseudomonas、Serratia和Arthrobacter为优势菌属。后汉路土壤剖面中的优势种群为γ-Proteobacteria、Bacteroidetes、Actinobactcria和Acidobacteria,其中Pseudomonas、Serratia、Arlhrobacter为优势菌属。
主成分分析(PCA)表明,土壤pH、有机质、有效性Fe和Al、土壤有效磷以及速效钾能够影响土壤细菌群落结构。典型相关分析(CCA)分析表明,小龙山土壤剖面中菌群y-Proteobacteria易受到土壤中活性铝的影响(r=-0.8,P<0.05)；Acidobacteria与土壤中有效磷含量呈显著正相关(r=0.99,P<0.05)。后汉路土壤剖面中y-Proteobacteria与土壤有效磷和速效钾存在明显的正相关(r=0.94,P<0.05；r=0.99,P<0.05)。优势菌属Arthrobacter在土壤矿物风化的进程中可能起了重要的作用。
采用缺钾培养基通过稀释平板法从上述土壤剖面中分离筛选到36株钾矿物分解细菌,16S rDNA序列分析结果表明,36株细菌隶属于菌群Firmicutes、Proteobacteria和Actinobacteria中的的9个菌属,分别为Bacillus(芽孢杆菌属)、Paenibacillus(类芽孢杆菌属),Dyella、Pantoea(泛菌属)、Burkholderia(伯克霍尔德菌属),Nocardioides(类诺卡氏菌属)、Isoptericola(白蚁菌属)、Microbacterium(微杆菌属)、Arthrobacter节杆菌属)。其中Bacillus、Paenibacillus、Arthrobacter和Burkholderia为两个土壤剖面的共有菌属,表现出较丰富的物种多样性。
菌株H17与Isoptericola属的亲缘关系最近,与同属的6株模式菌株的16S rRNA基因序列的同源性为97.8%-99.6%。菌株H17细胞壁肽聚糖为L-Lys-D-Asp,细胞壁糖为半乳糖、木糖和甘露糖,脂肪酸主要为anteiso-C15:0和iso-C15:0'主要极性脂为diphosphatidylglycerol、phosphatidylglycerol、phospholipids、phosphatidylinositol、 phosphoglycolipid、glycolipid和lipid,主要萘醌为MK9(H4),未检测到分枝菌酸,其G+C mo1%为72.4%,与6株模式菌株的DNA-DNA杂交同源性为15.2%-45.6%。综合这些结果,我们建议菌株H17为Isoptericola属的一个新种,命名为Isoptericola nanjingensis sp. nov.。
摇瓶条件下,对来源于供试菌株L11(Bacillus),H5(Burkholderia), H15(Arthrobacter)的矿物分解能力进行了研究。结果表明,培养30d后接菌处理的发酵液中Fe、Si、Al含量分别比接灭活菌对照增加27.5-115、1.5-2.2和13-35倍。扫描电镜(SEM)结果表明,接菌处理的钾长石矿物表面形成腐蚀坑,同时在钾长石表面形成了球形物和较小的颗粒状物质,对照处理的钾长石矿物表面比较平整；能谱(EDX)分析发现,上述球形物和较小的颗粒状物质是Fe和Ca的氧化物,推测是在钾长石矿物表面形成的次生矿物。另外,还研究了菌株Q12对云母(黑云母、白云母和金云母)的风化效应。ICP测定表明,接菌处理的溶液中Fe、Si、Al和K含量分别比对照增加9-173%、9-18%、10-310%和9-29%；SEM分析发现,菌株Q12在云母表面形成生物膜,云母表面形成了絮状、颗粒状和针状的物质,EDX分析表明,这些物质可能是形成的方解石、赤铁矿等次生矿物；X衍射(XRD)结果表明,接菌处理可以使黑云母形成赤铁矿和富镁蒙脱石等次生矿物。另外,透射电镜(TEM)观察发现,在菌株Q12细胞表面可以吸附一些矿物颗粒。
砂培试验表明,菌株L11和H5能够促进钾矿物的溶解,促进水稻植株的生长并提高水稻植株对钾素的利用。SEM分析表明,菌株能够在矿物表面和水稻植株根际定殖。在矿物表面或根表面形成圆球形、簇状、多面体、针状等物质。结合EDX分析,推测主要形成了方解石、草酸钙石、赤铁矿、磁铁矿等次生矿物。
Soil microbial diversity is the difference related to microbial communities and species, including species diversity, genetic diversity, ecological diversity and functional diversity. Researches on bacterial diversity will further understand microbial resource and biodiversity, enrich pool of microbial resource and gene, clarify the relationship between biodiversity and soil physicochemical factors, obtain efficient strains to weather mineral, and offer the theoretical and experimental basis for mineral weathering and soil formation.
16S rRNA gene sequence clone library and denaturing gradient gel electrophoresis (DGGE) were used to analyze bacterial biodiversity of two soil profiles sampled at site A (Longshan) and site B (Houhan Road). The results showed that there were13bacterial communities in site A and the major communities were γ-Proteobacteria, Acidobacteria, Actinobacteria, Firmicutes and Chloroflexi; while at site B, there were9bacterial communities, and the dominant communities were y-Proteobacteria, Actinobacteria, Acidobacteria. Actinobacteria, Acidobacteria and γ-Peoteobacteria were the same dominant phyla in both profiles. The major bacterial communities varied with soil depth. In profile A, clones of y-Proteobacteria mainly distributed layer-L2, and clones affiliated to Acidobacteria decreased with soil depth. The numbers of clone of Chloroflexi and Firmicutes mainly distributes in layer-L3. In profile B, the proportion of Acidobacteria and Verrucomicrobia decreased with soil depth, and the most abundant Actinobacteria was in profile B-H2, while clones of y-Peoteobacteria mainly distributed in H3and H4. The major communities were Proteobacteria, Actinobacteria, Bacteroidetes, Acidobacteria, Firmicutes and Chloroflexi at site A by DGGE, and the dominant genera were Rhodoplanes, Pseudomonas、Serratia and Arthrobacter. While at site B, the major phyla were y-Proteobacteria, Bacteroidetes, Actinobacteria and Acidobacteria, and the dominant genera were Pseudomonas, Serralia and Arthrobacter. Principal component analysis (PCA) suggested soil bacterial biodiversity was affected by soil physical and chemical factors such as soil pH, organic matter, effective Fe and Al, soil rapidly available phosphorus and available potassium. Canonical Correlation Analysis indicated bacteria affiliated to y-Proteobacteria were sensitive to soil available Al (r=-0.8, P<0.05), and bacteria affiliated to Acidobacteria were positive related to effective phosphorus significantly (r=0.99, P<0.05) at site A. At site B, bacteria affiliated to y-Proteobacteria were positive related to effective phosphorus and available potassium significantly (r=0.94, P<0.05; r=0.99, P<0.05). Arthrobacter affiliated to Actinobacteria were reported to have the ability to weather minerals in soil.
Thirty-six strains were separated from the two soil profiles by dilution plate method using potassium-limited medium.16S rRNA gene sequences revealed that36strains were grouped to9genera affiliated to3phyla, that is Bacillus, Paenibacillus, Dyella, Pantoea, Burkholderia, Nocardioides, Isoptericola, Microbacterium and Arthrobacter. Bacillus, Paenibacillus, Arthrobacter and Burkholderia were the common genera in both profiles, which showed abundant species diversity.
Strain H17had the highest similarities with Isoptericola spp., and showed97.8%-99.6%sequence similarities with the other strains. The cell-wall peptidoglycan type of strain H17is L-Lys-D-Asp. The whole-cell sugars are galactose, xylose and mannose. The major fatty acids (>10%of total) are anteiso-C15:0and iso-C15:0.The total polar lipids are diphosphatidylglycerol, phosphatidylglycerol, phospholipids, phosphatidylinositol, phosphoglycolipid, one unidentified glycolipid and one unidentified lipid. The menaquinone of strain H17T is MK9(H4). Mycolic acids were not detected. The DNA-DNA relatedness studies showed relatively low rates with the type strains of I. variabilis MX5T (45.6%), I. hypogeus HKI0342T(37.9%), I. jiangsuensis CLGT (33.4%), I. dokdonensis DS-3T (33.4%), I. halotolerans YIM70177T (40.9%) and I.chiayiensis06182M-1T (15.2%). The DNA G+C content of the type strain is72.4mol%. These results indicated that strain H17T represents a novel species of the genus Isoptericola, for which the name Isoptericola nanjingensis sp. nov. is proposed.
Strains Lll, H5and H15derived from different species were tested to weather potassium feldspar by shaking culture. The concentration of Fe, Si and Al increased27.5-115,1.5-2.2and13-35times than controls, respectively, by inductively coupled plasma optical emission spectrometry (ICP-OES). Scanning electron microscope (SEM) analisis showed that there were many corrosion pits in the surface of potassium feldspar, and spherical and small graininess around the mineral, while there was nothing around controls. These spherical and small graininess were the oxide of Fe and Ca, and were speculated to be secondary minerals. In addition, weathering effects of the strain Q12to micas (biotite, muscovite and phlogopite) were also studied. The concentration of Fe, Si, Al and K increased9-173%,9-18%,10-310%and9-29%compared to the controls according to ICP-AES, respectively. Biofilms were formed in the surface of micas after interactions with strain Q12by SEM. Some cotton-shaped, graininess and acicular materials were found around micas, which were identified to calcite and hematite by X-ray energy dispersive spectrum (EDS). X-ray diffraction (XRD) demonstrated that haematite and Mg-bearing turface were formed after interaction between the strain Q12and biotite. Transmission electron microscope (TEM) revealed small grains were adsorbed by bacterial cells.
Sand culture experiment showed the strains L11and H5could accelerate weathering of potassium feldspar, promote the growth of rice plants and increase utilization of potassium by rice plants. SEM indicated strain L11, H5and H15could colonize the surfaces of potassium feldspar and the rhizosphere of rice plants, and spheroidal, cluster-shaped, polyhedron and acicular materials were also found. These materials were speculated to be calcite, calcium oxalate, hematite and magnetite by EDS.
引文
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