Dispersal alters soil microbial community response to drought

Microbial communities will experience novel climates in the future. Dispersal is now recognized as a driver of microbial diversity and function, but our understanding of how dispersal influences responses to novel climates is limited. We experimentally tested how the exclusion of aerially dispersed fungi and bacteria altered the compositional and functional response of soil microbial communities to drought. We manipulated dispersal and drought by collecting aerially deposited microbes after precipitation events and subjecting soil mesocosms to either filter-sterilized rain (no dispersal) or unfiltered rain (dispersal) and to either drought (25% ambient) or ambient rainfall for 6 months. We characterized community composition by sequencing 16S and ITS rRNA regions and function using community-level physiological profiles. Treatments without dispersal had lower soil microbial biomass and metabolic diversity but higher bacterial and fungal species richness. Dispersal also altered soil community response to drought; drought had a stronger effect on bacterial (but not fungal) community composition, and induced greater functional loss, when dispersal was present. Surprisingly, neither immigrants nor drought-tolerant taxa had higher abundance in dispersal treatments. We show experimentally that natural aerial dispersal rate alters soil microbial responses to disturbance. Changes in dispersal rates should be considered when predicting microbial responses to climate change.     

罕山土壤微生物群落组成对植被类型的响应

选取分布在中国东北部地区的阔叶林-针叶林-亚高山草甸这一明显的植被垂直带谱来研究植被类型对土壤微生物群落组成的影响。选取5种植被类型-山杨(Populus davidiana)(1250—1300 m),山杨(P.davidiana)与白桦(Betula platyphylla)的混交林(1370—1550 m),白桦(B.platyphylla)(1550—1720 m),落叶松(Larix principis-rupprechtii)(1840—1890 m),亚高山草甸(1900—1951 m),采用磷脂脂肪酸(Phopholipid Fatty Acids,PLFAs)分析方法测定不同植被类型下的土壤微生物群落组成。分别采用主成分分析(Principal Components Analysis,PCA)以及冗余分析(Redundancy Analysis,RDA)来解释单种特征PLFAs的分异以及土壤理化指标与微生物PLFAs指标间的相关性。结果表明不同植被类型下土壤有机碳(SOC)对土壤微生物PLFAs总量,各类群(真菌(f)、细菌(b)、革兰氏阳性菌(G+)、革兰氏阴性菌(G-))生物量以及群落结构影响显著;土壤微生物PLFAs总量及各类群的生物量随土层加深总体上表现降低趋势,G+/G-和f/b分别随土层加深总体上表现升高趋势。不同植被类型下,阔叶混交林土壤PLFAs总量及各类群生物量总体上最高;针叶林比阔叶林下的f/b和G+/G-高;亚高山草甸下低的p H值对有机碳的可利用性有一定的抑制作用,导致f/b和G+/G-的值相对较高。总之,不同植被类型下SOC对土壤微生物群落组成的影响最为显著,而较低的p H对有机碳的可利用性有一定的抑制作用;真菌对植被类型的变化比细菌更敏感,而细菌更易受可利用性养分和p H变异的影响,这对预测不同林型下的土壤微生物群落组成有重要的启示作用。     

Functional response of the soil microbial community to biochar applications

Biochar has the potential to mitigate the impacts of climate change and soil degradation by simultaneously sequestering C in soil and improving soil quality. However, the mechanism of biochar's effect on soil microbial communities remains unclear. Therefore, we conducted a global meta‐analysis, where we collected 2,110 paired observations from 107 published papers and used structural equation modeling (SEM) to analyze the effects of biochar on microbial community structure and function. Our result indicated that arbuscular mycorrhizal fungal abundance, microbial biomass C, and functional richness increased with biochar addition regardless of loads, time since application, and experiment types. Results from mixed linear model analysis suggested that soil respiration and actinomycetes (ACT) abundance decreased with biochar application. With the increase of soil pH, the effect of biochar on fungal abundance and C metabolic ability was lessened. Higher biochar pH associated with higher pyrolysis temperatures reduced the abundance of bacteria, fungi, ACT, and soil microbes feeding on miscellaneous C from Biolog Eco‐plate experiments. SEM that examined the effect of biochar properties, load, and soil properties on microbial community indicated that fungal abundance was the dominant factor affecting the response of the bacterial abundance to biochar. The response of bacterial abundance to biochar addition was soil dependent, whereas fungi abundance was mostly related to biochar load and pyrolysis temperature. Based on soil conditions, controlling biochar load and production conditions would be a direct way to regulate the effect of biochar application on soil microbial function and increase the capacity to sequester C.     

Increases in soil respiration following labile carbon additions linked to rapid shifts in soil microbial community composition

Organic matter decomposition and soil CO₂ efflux are both mediated by soil microorganisms, but the potential effects of temporal variations in microbial community composition are not considered in most analytical models of these two important processes. However, inconsistent relationships between rates of heterotrophic soil respiration and abiotic factors, including temperature and moisture, suggest that microbial community composition may be an important regulator of soil organic matter (SOM) decomposition and CO₂ efflux. We performed a short-term (12-h) laboratory incubation experiment using tropical rain forest soil amended with either water (as a control) or dissolved organic matter (DOM) leached from native plant litter, and analyzed the effects of the treatments on soil respiration and microbial community composition. The latter was determined by constructing clone libraries of small-subunit ribosomal RNA genes (SSU rRNA) extracted from the soil at the end of the incubation experiment. In contrast to the subtle effects of adding water alone, additions of DOM caused a rapid and large increase in soil CO₂ flux. DOM-stimulated CO₂ fluxes also coincided with profound shifts in the abundance of certain members of the soil microbial community. Our results suggest that natural DOM inputs may drive high rates of soil respiration by stimulating an opportunistic subset of the soil bacterial community, particularly members of the Gammaproteobacteria and Firmicutes groups. Our experiment indicates that variations in microbial community composition may influence SOM decomposition and soil respiration rates, and emphasizes the need for in situ studies of how natural variations in microbial community composition regulate soil biogeochemical processes.     

三种种植方式对土壤微生物群落组成的影响

土壤微生物是表征土壤质量变化的敏感指标之一。借助长期定位试验, 采用磷脂脂肪酸分析方法研究了3种种植方式(玉米(Zea mays)连作、玉米非连作和撂荒)对土壤微生物群落组成的影响。结果表明, 在不同的种植方式下, 土壤微生物群落组成有明显的差异。玉米连作的土壤中总磷脂脂肪酸和细菌磷脂脂肪酸含量最低, 分别为33.12 nmol·g^-1和18.09 nmol·g^-1。非连作的土壤真菌磷脂脂肪酸和真菌/细菌分别为0.61 nmol·g^-1和3.06%, 显著低于撂荒和连作(p < 0.05), 非连作方式下, 革兰氏阳性细菌/革兰氏阴性细菌增大。撂荒土壤的总磷脂脂肪酸和细菌磷脂脂肪酸分别为42.98和24.68 nmol·g^-1, 高于耕作处理。 同时, 在撂荒方式下, 革兰氏阳性细菌和革兰氏阴性细菌的含量增加, 革兰氏阳性细菌/革兰氏阴性细菌降低。主成分分析结果表明: 耕作处理(玉米连作和非连作)分布第一主成分负方向上, 第一主成分得分系数分别为-2.48和-1.84; 撂荒分布第一主成分正方向上, 第一主成分得分系数为2.31, 与连作和非连作差异显著(p < 0.05)。冗余分析(RDA)表明: 土壤pH、总氮、有效磷和土壤>0.25 mm水稳性团聚体含量与磷脂脂肪酸呈正相关, 并且土壤pH和土壤>0.25 mm水稳性团聚体含量对土壤微生物群落的影响最大。     

Shifts in bacterial community composition associated with increased carbon cycling in a mosaic of phytoplankton blooms

Marine microbes have a pivotal role in the marine biogeochemical cycle of carbon, because they regulate the turnover of dissolved organic matter (DOM), one of the largest carbon reservoirs on Earth. Microbial communities and DOM are both highly diverse components of the ocean system, yet the role of microbial diversity for carbon processing remains thus far poorly understood. We report here results from an exploration of a mosaic of phytoplankton blooms induced by large-scale natural iron fertilization in the Southern Ocean. We show that in this unique ecosystem where concentrations of DOM are lowest in the global ocean, a patchwork of blooms is associated with diverse and distinct bacterial communities. By using on-board continuous cultures, we identify preferences in the degradation of DOM of different reactivity for taxa associated with contrasting blooms. We used the spatial and temporal variability provided by this natural laboratory to demonstrate that the magnitude of bacterial production is linked to the extent of compositional changes. Our results suggest that partitioning of the DOM resource could be a mechanism that structures bacterial communities with a positive feedback on carbon cycling. Our study, focused on bacterial carbon processing, highlights the potential role of diversity as a driving force for the cycling of biogeochemical elements.     

Rhizosphere microbial community and its response to plant species and soil history

The plant rhizosphere is a dynamic environment in which many parameters may influence the population structure, diversity and activity of the microbial community. Two important factors determining the structure of microbial community present in the vicinity of plant roots are plant species and soil type. In the present study we assessed the structure of microbial communities in response to four plant species (i.e. maize (Zea mays L.), oat (Avena sativa L.), barley (Hordeum vulgare L.) and commercial grass mix) planted in soil with different land use history (i.e. arable land under crop rotation, maize monoculture and permanent grassland). Both factors, plant species and land use history, showed clear effects on microbial community and diversity as determined by PCR-DGGE fingerprinting with universal and group-specific bacterial primers. Moreover, we explored the rhizosphere effect of these plant species on the abundance of bacterial antagonists of the potato pathogen Rhizoctonia solani AG3. The data showed that the abundance and taxonomic composition of antagonists differed clearly between the different plants. The highest percentages of antagonists were found in maize and grass rhizosphere. When antagonistic Pseudomonas populations were compared, the highest, abundance and diversity of antagonists were detected in barley and oat rhizospheres, as compared to maize and grass rhizosphere. The results obtained in our study demonstrate clearly that plant species and soil type are two important factors affecting the structure of total bacterial, Pseudomonas and Bacillus community.     

磷脂脂肪酸法在土壤微生物群落分析中的应用

土壤微生物群落的组成一直是土壤学、微生物学和生态学研究的热点问题。我国在这方面的研究处于国际前列,越来越多的研究成果在国际重要刊物上发表。而磷脂脂肪酸(PLFA)法在土壤微生物群落分析中占有举足轻重的地位,国内外学者都热衷于使用该方法。但是PLFA法的使用仍存在一些不足的地方,需要研究学者们慎重使用。本文综述了国际上相关研究,概述了PLFA方法使用的发展历史,应用及挑战。总结了使用和数据解读时需要注意的问题,整理了PLFA法相关的生物标记以及与新方法结合的设想,方便以后研究的开展。     

Influence of soil pollution on the composition of a microbial community

The abundance dynamics and composition of indigenous soil microbial communities were studied in soils polluted with naphthalene, dioctyl phthalate, diesel fuel, and crude oil. DGGE analysis of the 16S rRNA genes amplified from the total soil DNA revealed that the bacterial community of uncontaminated soil was more diverse and included no dominant species. In the soil samples polluted with the crude oil, diesel fuel, or dioctyl phthalate, Pseudomonas became the dominant bacteria since the third day of the experiment. In the soil polluted with naphthalene, two genera of bacteria (Pseudomonas and Paenibacillus) were dominant in population on the third day of the experiment, while on the 21th day of the experiment Arthrobacter became dominant. During the experiment, the average number of indigenous bacterial degraders increased approximately by two orders of magnitude. While the key genes of naphthalene catabolism, nahAc and nahH, were not detected in the pristine soil, they were found in a significant amount on the third day after naphthalene addition. Three degrader strains harboring the plasmids of naphthalene biodegradation (IncP-9 group) were isolated on the third day from the soil polluted with naphthalene. Two of these plasmids, although isolated from various degraders, were shown to be identical.     

Silicon-rich soil amendments impact microbial community composition and the composition of arsM bearing microbes

Plant and Soil - Arsenic (As) cycling in flooded rice paddies is driven by soil microbes which among other transformations can cause conversion between inorganic and organic As species. Silicon...     

Altering the mineral composition of soil causes a shift in microbial community structure

This study tests the hypothesis that altering the mineral composition of soil influences microbial community structure in a nutrient-deficient soil. Microcosms were established by adding mica (M), basalt (B) and rock phosphate (P) to soil separately, and in combination (MBP), and by planting with Lolium rigidum, Trifolium subterraneum or by leaving unplanted. The effects of mineral and plant treatments on microbial community structure were assessed using automated ribosomal intergenic spacer analysis. Bacterial community structure was significantly affected by both mineral (global R=0.73 and P<0.001) and plant (global R=0.71 and P<0.001) treatments, as was the fungal community structure: mineral (global R=0.65 and P<0.001) and plant (global R=0.65 and P<0.001) treatments. All pairwise comparisons of bacterial and fungal communities between different mineral treatments and between different plant treatments were significantly different (P<0.05). This study has shown that mineral addition to soil microcosms resulted in substantial changes in both bacterial and fungal community structure, dependent on the type of mineral added and the plant species present. These results suggest that the mineral composition of soil may be an important factor influencing the microbial community structure in soil.     

Changes in soil microbial community composition induced by cometabolism of toluene and trichloroethylene

The effects of trichloroethylene (TCE) on microbial community composition were analyzed by reverse sample genome probing. Soil enrichments were incubated in dessicators containing an organic phase of either 1 or 10% (w/w) toluene in vacuum pump oil, delivering constant equilibrium aqueous concentrations of 16 and 143mg/l, respectively. Increasing the equilibrium aqueous concentration of TCE from 0 to 10mg/l led to shifts in community composition at 16, but not at 143mg/l of toluene. In closed system co-degradation studies, TCE at an aqueous concentration of 1mg/1 was effectively degraded by toluene-degrading soil enrichments once the aqueous toluene concentration dropped below 25mg/l. Little TCE degradation was observed at higher toluene concentrations (50–250mg/l). The results indicate that TCE changes microbial community composition under conditions where it is being actively metabolized.     

Labile soil carbon inputs mediate the soil microbial community composition and plant residue decomposition rates

Root carbon (C) inputs may regulate decomposition rates in soil, and in this study we ask: how do labile C inputs regulate decomposition of plant residues, and soil microbial communities? In a 14 d laboratory incubation, we added C compounds often found in root exudates in seven different concentrations (0, 0.7, 1.4, 3.6, 7.2, 14.4 and 21.7 mg C g(-1) soil) to soils amended with and without (13) C-labeled plant residue. We measured CO(2) respiration and shifts in relative fungal and bacterial rRNA gene copy numbers using quantitative polymerase chain reaction (qPCR). Increased labile C input enhanced total C respiration, but only addition of C at low concentrations (0.7 mg C g(-1)) stimulated plant residue decomposition (+2%). Intermediate concentrations (1.4, 3.6 mg C g(-1)) had no impact on plant residue decomposition, while greater concentrations of C (>7.2 mg C g(-1)) reduced decomposition (-50%). Concurrently, high exudate concentrations (>3.6 mg C g(-1)) increased fungal and bacterial gene copy numbers, whereas low exudate concentrations (<3.6 mg C g(-1)) increased metabolic activity rather than gene copy numbers. These results underscore that labile soil C inputs can regulate decomposition of more recalcitrant soil C by controlling the activity and relative abundance of fungi and bacteria.     

林下植物剔除对毛竹林土壤微生物群落结构的影响

本研究以中亚热带地区广泛分布的毛竹林为对象,采用随机区组实验设计,分析了林下植物剔除对毛竹林土壤微生物群落结构和土壤理化特性的影响,探讨林下植物对毛竹林土壤微生物群落结构的调控机制.结果 表明:林下植物剔除对土壤理化特性产生显著影响,主要表现为土壤全氮、硝态氮和有效磷含量增加,而土壤铵态氮、全磷含量及土壤pH值降低.此...     

Functional and structural response of the methanogenic microbial community in rice field soil to temperature change

The microbial community in anoxic rice field soil produces CH₄ over a wide temperature range up to 55°C. However, at temperatures higher than about 40°C, the methanogenic path changes from CH₄ production by hydrogenotrophic plus acetoclastic methanogenesis to exclusively hydrogenotrophic methanogenesis and simultaneously, the methanogenic community consisting of Methanosarcinaceae, Methanoseataceae, Methanomicrobiales, Methanobacteriales and Rice Cluster I (RC‐1) changes to almost complete dominance of RC‐1. We studied changes in structure and function of the methanogenic community with temperature to see whether microbial members of the community were lost or their function impaired by exposure to high temperature. We characterized the function of the community by the path of CH₄ production measuring δ¹³C in CH₄ and CO₂ and calculating the apparent fractionation factor (α_app) and the structure of the community by analysis of the terminal restriction fragment length polymorphism (T‐RFLP) of the microbial 16S rRNA genes. Shift of the temperature from 45°C to 35°C resulted in a corresponding shift of function and structure, especially when some 35°C soil was added to the 45°C soil. The bacterial community (T‐RFLP patterns), which was much more diverse than the archaeal community, changed in a similar manner upon temperature shift. Incubation of a mixture of 35°C and 50°C pre‐incubated methanogenic rice field soil at different temperatures resulted in functionally and structurally well‐defined communities. Although function changed from a mixture of acetoclastic and hydrogenotrophic methanogenesis to exclusively hydrogenotrophic methanogenesis over a rather narrow temperature range of 42–46°C, each of these temperatures also resulted in only one characteristic function and structure. Our study showed that temperature conditions defined structure and function of the methanogenic microbial community.     

The phylogenetic composition and structure of soil microbial communities shifts in response to elevated carbon dioxide

One of the major factors associated with global change is the ever-increasing concentration of atmospheric CO₂. Although the stimulating effects of elevated CO₂ (eCO₂) on plant growth and primary productivity have been established, its impacts on the diversity and function of soil microbial communities are poorly understood. In this study, phylogenetic microarrays (PhyloChip) were used to comprehensively survey the richness, composition and structure of soil microbial communities in a grassland experiment subjected to two CO₂ conditions (ambient, 368 p.p.m., versus elevated, 560 p.p.m.) for 10 years. The richness based on the detected number of operational taxonomic units (OTUs) significantly decreased under eCO₂. PhyloChip detected 2269 OTUs derived from 45 phyla (including two from Archaea), 55 classes, 99 orders, 164 families and 190 subfamilies. Also, the signal intensity of five phyla (Crenarchaeota, Chloroflexi, OP10, OP9/JS1, Verrucomicrobia) significantly decreased at eCO₂, and such significant effects of eCO₂ on microbial composition were also observed at the class or lower taxonomic levels for most abundant phyla, such as Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes and Acidobacteria, suggesting a shift in microbial community composition at eCO₂. Additionally, statistical analyses showed that the overall taxonomic structure of soil microbial communities was altered at eCO₂. Mantel tests indicated that such changes in species richness, composition and structure of soil microbial communities were closely correlated with soil and plant properties. This study provides insights into our understanding of shifts in the richness, composition and structure of soil microbial communities under eCO₂ and environmental factors shaping the microbial community structure.     

Orchard floor management practices that maintain vegetative or biomass groundcover stimulate soil microbial activity and alter soil microbial community composition

Groundcover management systems (GMS) are important in managing fruit-tree orchards because of their effects on soil conditions, nutrient availability, tree growth and yields. We employed a polyphasic approach, incorporating measures of soil microbial abundance, activity and community composition, to study the long-term effects of different GMS on biotic and abiotic factors in an orchard soil. Four GMS treatments – Pre-emergence residual herbicides (Pre-H), post-emergence herbicide (Post-H), mowed-sod (Grass), and hardwood bark mulch (Mulch) – were established in 2-m-wide strips within tree rows in an apple orchard in 1992, and have been maintained and monitored annually until the present. We have measured soil water and nutrient availability, tree growth, and yields annually from 1993 to 2003. Soil nematode numbers and trophic groups were evaluated in July and Oct. 2001, and Sept. 2003. Numbers of culturable bacteria and fungi, soil respiratory activity, eubacterial and fungal community composition were determined in May and Sept. 2003. The Pre-H treatment soil had the fewest culturable bacteria, while the Grass treatment had the largest population of culturable fungi. Soil nematode population size and diversity were also affected by GMS treatments; the Pre-H treatment had the lowest ratio of (bacteriovores + fungivores) to plant parasitic nematodes. Soil respiration rates were higher in the Mulch than in other treatments during a 40-day incubation period. Hierarchical cluster dendrograms of denaturing gradient gel electrophoresis (DGGE) fingerprints for eubacterial community 16S rRNA genes indicated that Post-H and Grass treatments clustered together and separately from the Pre-H and Mulch treatments, which were also grouped together. The influence of GMSs on the fungal community, as assessed by PCR-DGGE of the internal transcribed spacer (ITS) region, was not as pronounced as that observed for bacteria. Soil fungal community composition under the Mulch differed from that under other treatments. The effects of GMS on soil microbial community abundance, activity, and composition were associated with observed differences in soil organic matter inputs and turnover, nutrient availability, and apple tree growth and yields under the different GMS treatments.