The microbial diversity and structure in peatland forest in Indonesia

The microbial community structure and function under forest in tropical peatlands are poorly understood. In this study, we investigated the microbial community structure and diversity in natural peat swamp forest soil, disturbed peat soil and mineral soil in Central Kalimantan, Indonesia, using 454 pyrosequencing. The results showed that the natural peat soil had the greatest fungal species richness (Chao1), which was significantly (p < .05) larger than that in the other two soils. Community structure of both fungi and bacteria in natural peat soil differed significantly from that in the disturbed peat soil (p = .039 and p = .045, respectively). Ascomycota (40.5%) was the most abundant phylum across the three soils followed by Basidiomycota (18.8%), Zygomycota (<0.1%) and Glomeromycota (<0.1%). The linear discriminant analysis with effect size (LEfSe) showed that Ascomycota (p < .05) and genus Gliocephalotrichum (p < .05) dominated in natural peat soil. Functionally, pathotrophs were more abundant in disturbed peat soil (p < .05). Proteobacteria (43.8%) were the most abundant phylum followed by Acidobacteria (32.6%), Actinobacteria (9.8%), Planctomycetes (1.7%). Methylocystis, Telmatospirillum, Syntrophobacter, Sorangium and Opitutus were the more abundant genera in disturbed peat soil, whereas Nevskia and Schlesneria were more abundant in mineral soil and natural peat soil, respectively. The natural peat forest soil supported a more diverse microbiology; however, the land use of such a soil can change its microbial community structure. The results provide evidence that the disturbance of tropical peat land could lead to the introduction and spread of a large number of fungal diseases     

Effect of cyclodextrin diallyl maleate on methane production, ruminal fermentation and microbes in vitro and in vivo

Effects of β‐cyclodextrin diallyl maleate (CD‐M) on methane production, ruminal fermentation and digestibility were studied both in vitro and in vivo. In in vitro study, diluted ruminal fluid (30 mL) was incubated anaerobically at 38°C for 6 and 24 h with or without CD‐M using hay plus concentrate (1.5:1) as a substrate. The CD‐M was added at different concentrations (0, 1.25, 2.5, 5.0 and 7.5 g/L). The pH of the medium and numbers of protozoa were not affected by the addition of CD‐M. Total volatile fatty acids were increased and ammonia‐N was decreased, molar proportion of acetate was decreased and propionate was increased (P < 0.05) by CD‐M. Methane was inhibited (P < 0.05) by 14–76%. The effect of CD‐M on methane production and ruminal fermentation was further investigated in vivo using four Holstein steers in a cross‐over design. The steers were fed Sudangrass hay and concentrate mixture (1.5:1) with or without CD‐M (2% of feed dry matter) as a supplement. Ruminal proportion of acetate tended to decrease and that of propionate was increased (P < 0.05) 2 h after CD‐M dosing. Total viable counts, cellulolytic, sulfate reducing, acetogenic bacteria and protozoa were unaffected while methanogenic bacteria were decreased (P < 0.05) by CD‐M. The plasma concentration of glucose was increased, whereas that of urea‐N was decreased (P < 0.05). Methane was inhibited (P < 0.05) from 36.4 to 30.1 L/kg dry matter intake by the addition of CD‐M. Apparent digestibilities of dry matter and neutral detergent fiber were not affected while that of crude protein was increased (P < 0.05) in the medicated steers. These data suggested that dietary supplementation of CD‐M decreased methane production and improved nutrient use.     

Long-term fertilization effects on active ammonia oxidizers in an acidic upland soil in China

The effects of long-term fertilization of acidic soils on ammonia-oxidizing archaea (AOA) and bacteria (AOB) communities and its ecological implications remain poorly understood. We chose an acidic upland soil site under long-term (27-year) fertilization to investigate ammonia oxidizer communities under four different regimes: mineral N fertilizer (N), mineral NPK fertilizer (NPK), organic manure (OM) and an unfertilized control (CK). Soil net nitrification rates were significantly higher in OM soils than in CK, N or NPK soils. Quantitative analysis of the distribution of amoA genes by DNA-based stable isotope probing revealed that AOA dominate in CK, N and NPK soils, while AOB dominate in OM soils. Denaturing gradient gel electrophoresis and clone library analyses of amoA genes revealed that Group 1.1a-associated AOA (also referred to as Nitrosotalea) were the most dominant active AOA population (>92%), while Nitrosospira Cluster 3 and Cluster 9 were predominant among active AOB communities. The functional diversity of active ammonia oxidizers in acidic soils is affected by long-term fertilization practices, and the responses of active ammonia oxidizers to mineral fertilizer and organic manure are clearly different. Our results provide strong evidence that AOA are more highly adapted to growth at low pH and low substrate availability than AOB, and they suggest that the niche differentiation and metabolic diversity of ammonia oxidizers in acidic soils are more complex than previously thought.     

不同施肥方式对红壤蔬菜田氨氧化细菌和氨氧化古菌群落的影响

通过构建氨单加氧酶基因(amoA)克隆文库,研究在红壤蔬菜田上只施用磷钾化肥(PK)、只施氮磷钾化肥(NPK)、施用腐熟有机肥(DNPK)和施用新鲜有机肥(FNPK)等4种不同施肥处理的土壤氨氧化细菌(AOB)和氨氧化古菌(AOA)群落多样性及与土壤脲酶活性的相关性。结果表明:施加有机肥处理(DNPK和FNPK)的蔬菜田土壤的AOB文库和AOA文库OTU数量和Shannon指数高于只施用无机肥(NPK和PK)处理的蔬菜田土壤;DNPK和FNPK处理的土壤优势AOB菌群为多形亚硝化叶菌(Nitrosolobus multiformis),比例分别为88.5%和68.5%,NPK和PK处理的土壤优势AOB菌群为亚硝化单胞菌属(Nitrosospirasp.),比例分别为54.8%和65.5%;DNPK、FNPK、NPK和PK处理土壤优势AOA菌群均为阿伯丁土壤亚硝化细杆菌侯选种(CandidatusNitrosotalea devanaterra),比例分别为90.9%、84.4%、77.8%和45.2%;施加有机肥处理(DNPK和FNPK)的土壤脲酶活性和氨氧化微生物的多样性指数都高于只施用无机肥处理(NPK和PK);AOA群落多样性指数与土壤脲酶活性呈显著正相关,而AOB群落多样性与土壤脲酶活性相关性不显著。总体来看,有机肥比无机肥处理提高了AOA和AOB群落多样性,且AOA在红壤蔬菜田土壤氨氧化过程中起着更为重要的作用。     

人工养殖西伯利亚狍肠道微生物组成的雌雄差异

肠道微生物是一个复杂的生态系统,与宿主的健康、疾病以及其他因素有着密切的关系。目前,关于肠道菌群结构和功能的研究较多,但是对西伯利亚狍肠道菌群的研究还未见报道。西伯利亚狍(Capreolus pygargus)属于反刍动物,有独特的消化特性和微生物群来帮助它们适应高纤维的食物。本研究利用高通量测序技术在Illumina MiSeq平台上对14只狍肠道微生物进行16S rRNA基因分析。结果表明:个体样本中门类组成的差异,雌性个体JY3和雄性个体JY9除Firmicutes,Bacteroidetes,Proteobacteria这3类菌群外,其他门类菌群所占比例都很低。在科水平上,雌性个体中Ruminococcaceae在JY7和JY13肠道内含量相对较少,Bacteroidaceae在JY7,JY10和JY13中含量较高。雄性个体中Ruminococcaceae在JY11和JY14肠道内含量较少,Prevotellaceae在JY4中含量较少。在属水平上,雌性个体特有的菌属为Roseburia,Alloprevotella,Lachnospiraceae_incertae_sedis和Coprococcus;雄性个体特有的菌属为Fusobacterium,Succiniclasticum,Streptococcus和Clostridium sensu stricto。Alpha多样性分析表明,Ace指数范围2128.93—772.98,Chao1指数范围2128.89—785.27,Shannon指数范围5.44—3.78,Simpson指数范围0.07—0.01。在不同物种分类水平上,雌雄狍肠道内的优势菌群有些不同。PCoA(principal co-ordinates analysis)分析显示,狍样本几乎混在一起,没有明显差异。     

保护性耕作对土壤团聚体、微生物及线虫群落的影响研究进展

保护性耕作具有良好的生态效益,有利于农业生态系统的可持续发展。本文对比分析了国内外有关常规耕作和保护性耕作措施对土壤团聚体、土壤有机碳、土壤微生物及土壤线虫影响的研究进展。结果表明：保护性耕作减少土壤大团聚体的破坏,降低团聚体周转速率,提高土壤结构的稳定性;保护性耕作提高表层土壤总有机碳及活性有机碳含量;保护性耕作可以提高耕层微生物生物量,尤其对真菌生物量影响显著;保护性耕作不同程度地提高了团聚体中微生物量和微生物多样性,但并未改变微生物在团聚体中的分布模式;保护性耕作可提高土壤线虫多度,提高原状土壤和土壤各粒级团聚体中线虫群落的成熟度指数和结构指数,但并未改变线虫总数、营养类群、功能团及生态指数在团聚体中的分布模式。针对目前国内外研究现状,展望了保护性耕作今后的研究重点,以期为因地制宜选取保护性耕作措施提供理论支持,推进我国农业可持续发展。     

黄河下游滩地杨树人工林土壤微生物分析

对山东省济南市长清区黄河下游滩地杨树人工林林地土壤微生物数量及分布特征进行了分析,结果表明:滩地杨树人工林土壤微生物主要分布在0～20cm的土层,20～50cm土层的微生物较少;各林地土壤微生物数量明显高于新淤地微生物数量;细菌是滩地杨树人工林林地土壤微生物的主要组成成分,在上、下层土壤中所占比例分别为81.7%～99.1%和75.1%～98.8%;土壤微生物数量随林龄的增长呈现高—低—高的变化趋势,但至林木主伐前,固氮菌和纤维素分解菌数量有所降低;不同管理模式影响微生物的数量,集约经营管理的林分土壤微生物数量较多;滩地杨树人工林土壤微生物数量与土壤颗粒组成密切相关。     

博斯腾湖沉积物氨氧化细菌的筛选与鉴定

为了解干旱区淡水湖泊沉积物微生物在氨氧化中的功能,利用铵盐培养基对博斯腾湖不同深度沉积物进行驯化培养,结合水环境因子分析混合菌株产亚硝酸盐能力,从中分离纯化氨氧化细菌并对其氨转化能力进行试验。结果表明,6个采样位点12个样品中,11号位点深层沉积物(20～40 cm)混合菌株能有效利用铵盐产生亚硝酸盐,且连续6 d稳定维持其质量浓度高达20 mg/L以上。进而,从该混合菌液中分离得到30株单菌,其中有2株呈现出明显的氨氧化细菌特性。通过16S rRNA基因序列比对及形态学分析分别鉴定其为弯曲芽孢杆菌(Bacillus flexus)和赤红球菌(Rhodococcus ruber)。     

鹅肠道微生物研究进展

肠道微生物是当前研究的热点,鹅肠道微生物的组成与丰富程度不仅和鹅的生长性能密切相关,而且在鹅机体生理活动中具有一定的调节作用,同时与疾病的发生和发展具有密切的联系.通过研究鹅肠道微生物的调节,从而达到促生长或者治疗疾病的目的,是目前鹅研究探寻的新方向.文章主要综述了鹅肠道微生物的组成及其变化规律,以期为鹅产业生物饲料的...     

不同水肥条件对农田土壤细菌生理菌群的影响

采用田间试验研究了大豆苗期、花期和鼓粒期在干旱、自然和充足三种水分及无肥、无机肥和无机肥+有机肥三种施肥方式条件下,根际士壤中氨氧化细菌、自生周氮菌和反硝化细菌三种不同生理菌群的变化.结果表明:施用无机肥条件下自然降水使氨氧化细菌数量高于充足水和干旱处理,干旱使好气性自生固氮菌和反硝化细菌数量高于自然降水和充足水,在自然降水条件不同施肥使功能性细菌发生变化,施肥促进三种功能菌的生长,其中,有机肥配施化肥的效果最为显著反硝化细菌符处理数量相近,有机肥数量稍高.