喀斯特土壤固氮微生物群落与植被、土壤的关系

固氮微生物作为土壤中重要的功能微生物群之一,其与地上植物群落、土壤环境之间的关系尚不清楚。在桂西北的环江县、都安县和大化县选取喀斯特典型植被类型(草丛、灌丛、次生林)建立样方,通过植被调查、测定土壤理化性质和构建克隆文库的方法,研究了土壤固氮微生物群落的结构与组成,分析了固氮微生物群落与植物群落、土壤理化性质之间的关系。结果表明:研究区典型植被类型土壤中的优势固氮微生物为慢生根瘤菌。Mantel相关性分析表明植物群落与固氮微生物群落显著相关(r=0.6116,P=0.011);结合PCo A分析和Venn图可看出,植物群落组成与结构越相似,土壤固氮微生物群落结构与组成也越相似。CCA分析前两轴的解释率之和仅为22.72%,其中总氮、有效态钾、有效态钙对固氮微生物群落的影响显著,这表明本研究涵盖的土壤理化性质指标并不能完全解释固氮微生物群落的变异,需要补充更多的土壤数据进行更深入的研究。由此可见,在喀斯特生态恢复过程中,不仅要关注地上植被群落的恢复与重建,同时也应重视地下功能微生物群落的恢复与重建。     

Flooding forested groundwater recharge areas modifies microbial communities from top soil to groundwater table

Subsurface microorganisms are crucial for contaminant degradation and maintenance of groundwater quality. This study investigates the microbial biomass and community composition [by phospholipid fatty acids (PLFAs)], as well as physical and chemical soil characteristics at woodland flooding sites of an artificial groundwater recharge system used for drinking water production. Vertical soil profiles to c . 4 m at two watered and one nonwatered site were analyzed. The microbial biomass was equal in watered and nonwatered sites, and considerable fractions (25–42%) were located in 40–340 cm depth. The microbial community structure differed significantly between watered and nonwatered sites, predominantly below 100 cm depth. Proportions of the bacterial PLFAs 16:1ω5, 16:1ω7, cy17:0 and 18:1ω9t, and the long-chained PLFAs 22:1ω9 and 24:1ω9 were more prominent at the watered sites, whereas branched, saturated PLFAs (iso/anteiso) dominated at the nonwatered site. PLFA community indices indicated stress response ( trans / cis ratio), higher nutrient availability (unsaturation index) and changes in membrane fluidity (iso/anteiso ratio) due to flooding. In conclusion, water recharge processes led to nutrient input and altered environmental conditions, which resulted in a highly active and adapted microbial community residing in the vadose zone that effectively degraded organic compounds.     

Comparison of acid mine drainage microbial communities in physically and geochemically distinct ecosystems

This study presents population analyses of microbial communities inhabiting a site of extreme acid mine drainage (AMD) production. The site is the inactive underground Richmond mine at Iron Mountain, Calif., where the weathering of a massive sulfide ore body (mostly pyrite) produces solutions with pHs of approximately 0.5 to approximately 1.0. Here we used a suite of oligonucleotide probes, designed from molecular data recently acquired from the site, to analyze a number of microbial environments by fluorescent in situ hybridization. Microbial-community analyses were correlated with geochemical and mineralogical data from those environments. The environments investigated were within the ore body and thus at the site of pyrite dissolution, as opposed to environments that occur downstream of the dissolution. Few organism types, as defined by the specificities of the oligonucleotide probes, dominated the microbial communities. The majority of the dominant organisms detected were newly discovered or organisms only recently associated with acid-leaching environments. "Ferroplasma" spp. were detected in many of the communities and were particularly dominant in environments of lowest pH and highest ionic strength. Leptospirillum spp. were also detected in many slime and pyrite-dominated environments. In samples of an unusual subaerial slime, a new uncultured Leptospirillum sp. dominated. Sulfobacillus spp. were detected as a prominent inhabitant in warmer ( approximately 43 degrees C) environments. The information gathered here is critical for determining organisms important to AMD production at Iron Mountain and for directing future studies of this process. The findings presented here also have relevance to the microbiology of industrial bioleaching and to the understanding of geochemical iron and sulfur cycles.     

岩溶区植被和季节对土壤微生物遗传多样性的影响

基于土壤微生物遗传多样性随植被和季节的变化而变化的假设,运用变性梯度凝胶电泳技术(DGGE)检测岩溶区草丛(T)、灌丛(S)、次生林(SF)和原生林(PF)群落演替过程中土壤细菌和真菌群落的遗传多样性及其季节变化.随着地上植被的演替土壤细菌群落具有连续性但优势种群不明显,真菌群落没有连续性但优势种群明显.植被和季节对于细菌和真菌群落的Shannon多样性具有不同程度的显著影响,同时存在显著的植被和季节交互作用.草丛土壤中细菌和真菌群落的Shannon多样性有显著的季节变化(p<0.01);灌丛土壤中仅细菌群落多样性有显著季节变化(p<0.05);而森林土壤中细菌和真菌群落多样性没有显著的季节变化.土壤真菌和细菌多样性具有显著正相关关系.随着地上植被的正向演替,土壤微生物遗传结构逐渐稳定;植被恢复早期阶段,土壤中存在着丰富的微生物遗传多样性,但并不稳定.     

广西喀斯特地区毛唇芋兰根内与根际土壤真菌群落组成分析

为探索兰科(Orchidaceae)植物毛唇芋兰(Nervilia fordii)根内和根际土壤真菌群落多样性，该研究采用Illumina MiSeq高通量测序技术，分析了大新(DX)和龙州(LZ)两个样地(简称两地)毛唇芋兰根内和根际土壤的真菌组成。结果表明：(1)两地的毛唇芋兰根内和根际土壤真菌多样性很丰富，根际土壤真菌多样性均高于根内，主根的真菌多样性高于走茎。(2)通过测序共获得有效序列118 040条，207个可操作分类单元(OTUs)涉及8门19纲42目86科123属。(3)担子菌门(Basidiomycota)真菌是两地毛唇芋兰根内真菌的共同优势菌群，涉及胶膜菌科(Tulasnellaceae)、Trimorphomycetaceae、角担菌科(Ceratobasidiaceae)、马拉色菌科(Malasseziaceae)和小皮伞科(Marasmiaceae)等，其中优势科和优势属分别是胶膜菌科(75%)和瘤菌根菌属(Epulorhiza)(56%),而土壤中的优势菌属则是镰刀菌属(Fusarium)。综上认为，毛唇芋兰根内与根际土壤中的优势菌群既差异显著也存在一些共同...     

Sediment microbial communities in Great Boiling Spring are controlled by temperature and distinct from water communities

Great Boiling Spring is a large, circumneutral, geothermal spring in the US Great Basin. Twelve samples were collected from water and four different sediment sites on four different dates. Microbial community composition and diversity were assessed by PCR amplification of a portion of the small subunit rRNA gene using a universal primer set followed by pyrosequencing of the V8 region. Analysis of 164 178 quality-filtered pyrotags clearly distinguished sediment and water microbial communities. Water communities were extremely uneven and dominated by the bacterium Thermocrinis. Sediment microbial communities grouped according to temperature and sampling location, with a strong, negative, linear relationship between temperature and richness at all taxonomic levels. Two sediment locations, Site A (87–80 °C) and Site B (79 °C), were predominantly composed of single phylotypes of the bacterial lineage GAL35 ($\widehat{p}$=36.1%), Aeropyrum ($\widehat{p}$=16.6%), the archaeal lineage pSL4 ($\widehat{p}$=15.9%), the archaeal lineage NAG1 ($\widehat{p}$=10.6%) and Thermocrinis ($\widehat{p}$=7.6%). The ammonia-oxidizing archaeon ‘Candidatus Nitrosocaldus'' was relatively abundant in all sediment samples <82 °C ($\widehat{p}$=9.51%), delineating the upper temperature limit for chemolithotrophic ammonia oxidation in this spring. This study underscores the distinctness of water and sediment communities in GBS and the importance of temperature in driving microbial diversity, composition and, ultimately, the functioning of biogeochemical cycles.     

Comparison of soil microbial communities inhabiting vineyards and native sclerophyllous forests in central Chile

Natural ecosystems provide services to agriculture such as pest control, soil nutrients, and key microbial components. These services and others in turn provide essential elements that fuel biomass productivity. Responsible agricultural management and conservation of natural habitats can enhance these ecosystem services. Vineyards are currently driving land‐use changes in many Mediterranean ecosystems. These land‐use changes could have important effects on the supporting ecosystems services related to the soil properties and the microbial communities associated with forests and vineyard soils. Here, we explore soil bacterial and fungal communities present in sclerophyllous forests and organic vineyards from three different wine growing areas in central Chile. We employed terminal restriction fragment length polymorphisms (T‐RFLP) to describe the soil microbial communities inhabiting native forests and vineyards in central Chile. We found that the bacterial community changed between the sampled growing areas; however, the fungal community did not differ. At the local scale, our findings show that fungal communities differed between habitats because fungi species might be more sensitive to land‐use change compared to bacterial species, as bacterial communities did not change between forests and vineyards. We discuss these findings based on the sensitivity of microbial communities to soil properties and land‐use change. Finally, we focus our conclusions on the importance of naturally derived ecosystem services to vineyards.     

若尔盖沙化土地治理土壤微生物群落与功能基因比较研究

【目的】在高寒沙地中建立以赖草和沙生苔草等先锋植物为主的人工草方格,探究其土壤微生物群落动态变化以及养分循环过程。【方法】采用宏基因组测序和qPCR方法进行土壤微生物群落结构组成分析、功能基因注释和绝对丰度测定,并结合土壤理化因子数据进行冗余分析。【结果】人工建立草方格后,沙地土壤中全氮、速效磷以及有机碳含量分别提高了20%-68%、10%-247%、19%-56%;细菌和真菌的群落数量分别提高了17%-81%和2%-95%,与植物促生长相关的鞘氨醇单胞菌属(Sphingomonas)、慢生根瘤菌属(Bradyrhizobium)、硝化螺旋菌属(Nitrospira)、Solirubrobacter属和类诺卡氏菌属(Nocardioides)等细菌种类的相对丰度呈上升趋势;氮循环中与氨氧化和亚硝酸盐氧化相关的amoCAB基因簇和nxrAB基因簇显著富集,发现了完全氨氧化的基因标志。【结论】人工建立草方格有效提升了高寒沙地土壤养分和微生物群落数量,促进了养分循环。适度放牧可以增加沙地生态系统的氮汇扩散性,有助于本土先锋植物定植,为今后在同等高海拔地区采取沙地生态修复措施提供理论参考。     

Sulfur disproportionating microbial communities in a dynamic,microoxic-sulfidic karst system

Biogeochemical sulfur cycling in sulfidic karst systems is largely driven by abiotic and biological sulfide oxidation, but the fate of elemental sulfur (S⁰) that accumulates in these systems is not well understood. The Frasassi Cave system (Italy) is intersected by a sulfidic aquifer that mixes with small quantities of oxygen-rich meteoric water, creating Proterozoic-like conditions and supporting a prolific ecosystem driven by sulfur-based chemolithoautotrophy. To better understand the cycling of S⁰ in this environment, we examined the geochemistry and microbiology of sediments underlying widespread sulfide-oxidizing mats dominated by Beggiatoa. Sediment populations were dominated by uncultivated relatives of sulfur cycling chemolithoautotrophs related to Sulfurovum, Halothiobacillus, Thiofaba, Thiovirga, Thiobacillus, and Desulfocapsa, as well as diverse uncultivated anaerobic heterotrophs affiliated with Bacteroidota, Anaerolineaceae, Lentimicrobiaceae, and Prolixibacteraceae. Desulfocapsa and Sulfurovum populations accounted for 12%–26% of sediment 16S rRNA amplicon sequences and were closely related to isolates which carry out autotrophic S⁰ disproportionation in pure culture. Gibbs energy (∆G_r) calculations revealed that S⁰ disproportionation under in situ conditions is energy yielding. Microsensor profiles through the mat-sediment interface showed that Beggiatoa mats consume dissolved sulfide and oxygen, but a net increase in acidity was only observed in the sediments below. Together, these findings suggest that disproportionation is an important sink for S⁰ generated by microbial sulfide oxidation in this oxygen-limited system and may contribute to the weathering of carbonate rocks and sediments in sulfur-rich environments.     

Biodiversity of soil microbial communities in agricultural systems

The productivity and health of agricultural systems depend greatly upon the functional processes carried out by soil microorganisms and soil microbial communities. The biodiversity of the soil microbial communities and the effect of diversity on the stability of the agricultural system, is unknown. Taxonomic approaches to estimating biodiversity of soil microbial communities are limited by difficulties in defining suitable taxonomic units and the apparent non-culturability of the majority of the microbial species present in the soil. Analysis of functional diversity may be a more meaningful approach but is also limited by the need to culture organisms. Approaches which do not rely on culturing organisms such as fatty acid analysis and 16S/18S rRNA analysis have provided an insight into the extent of genetic diversity within communities and may be useful in the analysis of community structure. Scale effects, including successional processes associated with organic matter decomposition, local effects associated with abiotic soil factors, and regional effects including the effect of agricultural management practices, on the diversity of microbial communities are considered. Their impact is important in relation to the minimum biodiversity required to maintain system function.     

Evaluation of the state of soil microbial communities in two types of Siberian forest ecosystems

Microbial respiration and biomass were evaluated in soils of the Ermak Tree Nursery and Pogorel’skii Forest under different coniferous species. The degree of disturbance of each biocenosis was determined from the metabolic coefficient (qCO₂). The microbial investigation demonstrated a lower resistance to ecological factors of the tree nursery biocenosis as compared to those of the Pogorel’skii Forest.     

Structure and function of microbial communities in soil from the southern Taiga

General regularities in the structure of the microbial communities of southern taiga soil ecosystems and taxonomic differences between the microbial communities of soils with different hydrothermal characteristics are discussed with reference to the main types of soils of the Central State Forest Biosphere Reserve.     

Oral cavity contains distinct niches with dynamic microbial communities

Microbes colonize human oral surfaces within hours after delivery. During postnatal development, physiological changes, such as the eruption of primary teeth and replacement of the primary dentition with permanent dentition, greatly alter the microbial habitats, which, in return, may lead to community composition shifts at different phases in people's lives. By profiling saliva, supragingival and mucosal plaque samples from healthy volunteers at different ages and dentition stages, we observed that the oral cavity is a highly heterogeneous ecological system containing distinct niches with significantly different microbial communities. More importantly, the phylogenetic microbial structure varies with ageing. In addition, only a few taxa were present across the whole populations, indicating a core oral microbiome should be defined based on age and oral niches.     

凋落物分解过程中土壤微生物群落的变化

凋落物分解是生态系统碳循环和营养物质循环的关键过程, 受多种因素共同影响。土壤微生物是影响凋落物分解的重要因素, 其群落组成在一定程度上依赖于所处植物群落的特征。因此, 研究分解过程中微生物群落组成的变化及其对植物多样性的响应, 有利于对凋落物分解机制的理解。本文采用分解袋野外原位分解的方法, 对凋落物分解过程中微生物群落的变化及其对所处森林环境中树木的种类和遗传多样性的响应进行了研究。结果表明: (1)凋落物分解183天后, 土壤中微生物群落的多样性降低, 并且森林群落的物种多样性与微生物群落多样性呈负相关关系; (2)凋落物分解前后, 土壤中真菌和细菌群落的磷脂脂肪酸(PLFA)量均有所增加, 说明凋落物分解为微生物生存和繁殖提供了养分; (3)地形因素是影响微生物群落变化最显著的因素, 可解释微生物群落变化的29.55%; 其次是凋落物的基质质量, 可以解释15.39%; 最后是森林群落的多样性, 可以解释8.45%; 这3种因素共同解释率为2.97%。综上所述, 与森林群落的植物多样性相比, 样地的地形因素与凋落物的基质质量对微生物群落的影响更显著。     

On maintenance and metabolisms in soil microbial communities

Plant and Soil - Biochemistry is an essential yet undervalued aspect of soil ecology, especially when analyzing soil C cycling. We assume, based on tradition, intuition or hope, that the complexity...     

Functional gene diversity of soil microbial communities from five oil-contaminated fields in China

To compare microbial functional diversity in different oil-contaminated fields and to know the effects of oil contaminant and environmental factors, soil samples were taken from typical oil-contaminated fields located in five geographic regions of China. GeoChip, a high-throughput functional gene array, was used to evaluate the microbial functional genes involved in contaminant degradation and in other major biogeochemical/metabolic processes. Our results indicated that the overall microbial community structures were distinct in each oil-contaminated field, and samples were clustered by geographic locations. The organic contaminant degradation genes were most abundant in all samples and presented a similar pattern under oil contaminant stress among the five fields. In addition, alkane and aromatic hydrocarbon degradation genes such as monooxygenase and dioxygenase were detected in high abundance in the oil-contaminated fields. Canonical correspondence analysis indicated that the microbial functional patterns were highly correlated to the local environmental variables, such as oil contaminant concentration, nitrogen and phosphorus contents, salt and pH. Finally, a total of 59% of microbial community variation from GeoChip data can be explained by oil contamination, geographic location and soil geochemical parameters. This study provided insights into the in situ microbial functional structures in oil-contaminated fields and discerned the linkages between microbial communities and environmental variables, which is important to the application of bioremediation in oil-contaminated sites.     

Responses of soil microbial communities to prescribed burning in two paired vegetation sites in southern China

Prescribed burning is a common site preparation practice for forest plantation in southern China. However, the effects of prescribed burning on soil microbial communities are poorly understood. This study examined changes in microbial community structure, measured by phospholipid fatty acids (PLFAs), after a single prescribed burning in two paired vegetation sites in southern China. The results showed that the total amount of PLFA (totPLFA) was similar under two vegetation types in the wet season but differed among vegetation type in the dry season, and was affected significantly by burning treatment only in the wet season. Bacterial PLFA (bactPLFA) and fungal PLFA (fungPLFA) in burned plots all decreased compared to the unburned plots in both seasons (P = 0.059). Fungi appeared more sensitive to prescribed burning than bacteria. Both G⁺ bacterial PLFA and G⁻ bacterial PLFA were decreased by the burning treatment in both dry and wet seasons. Principal component analysis of PLFAs showed that the burning treatment induced a shift in soil microbial community structure. The variation in soil microbial community structure was correlated significantly to soil organic carbon, total nitrogen, available phosphorus and exchangeable potassium. Our results suggest that prescribed burning results in short-term changes in soil microbial communities but the long-term effects of prescribed burning on soil microbial community remain unknown and merit further investigation.