Abiotic drivers and plant traits explain landscape‐scale patterns in soil microbial communities

The controls on aboveground community composition and diversity have been extensively studied, but our understanding of the drivers of belowground microbial communities is relatively lacking, despite their importance for ecosystem functioning. In this study, we fitted statistical models to explain landscape‐scale variation in soil microbial community composition using data from 180 sites covering a broad range of grassland types, soil and climatic conditions in England. We found that variation in soil microbial communities was explained by abiotic factors like climate, pH and soil properties. Biotic factors, namely community‐weighted means (CWM) of plant functional traits, also explained variation in soil microbial communities. In particular, more bacterial‐dominated microbial communities were associated with exploitative plant traits versus fungal‐dominated communities with resource‐conservative traits, showing that plant functional traits and soil microbial communities are closely related at the landscape scale.     

茶园根际土壤细菌群落结构及多样性

【背景】茶园根际土壤的细菌群落结构与茶园生境土壤营养循环密切相关,其组成及多样性可以作为健康茶园的一个生物指标。【方法】采用PCR．变性梯度凝胶电泳（PCR—DGGE）分子指纹图谱技术,检测安溪铁观音种植区不同海拔茶园根际土壤样本的细菌群落结构,利用Shannon．Wiener多样性指数分析其多样性,采用非加权组平均法进行聚类分析得到其分布特征,利用蒙特卡罗检验和冗余分析分别揭示影响细菌群落分布的环境因子及细菌群落分布和环境变量之间的关系。【结果】茶园根际土壤细菌的DGGE结果显示,检测到的14种主要细菌中有11种细菌是不可培养的,3种细菌是可培养的,分别属于根瘤菌属、中华根瘤菌属和苍白杆菌属。聚类分析得到,同一海拔梯度茶园根际土壤细菌群落结构相似。Shan-non—Wiener多样性指数分析表明,400m海拔处茶园根际土壤细菌群落多样性最高。蒙特卡罗检验分析得到环境因子协同作用对茶园根际土壤细菌群落结构贡献率为59．6％。冗余分析显示,茶园根际土壤细菌群落结构与海拔密切相关。【结论与意义】茶园根际土壤细菌群落结构分布与海拔梯度密切相关,考虑不同海拔高度土壤细菌群落对茶园营养循环的影响,在铁观音的健康栽培和管理过程中具有重要意义。     

低分子有机酸对土壤中菲降解及细菌群落结构的影响

多环芳烃是一类普遍存在于环境中的持久性有机污染物,其通过食物链进入生态系统,直接危害人类健康和整个生态系统的安全。为探讨低分子有机酸对土壤中菲降解及细菌群落结构的影响,通过室内培养的方式研究了在添加不同种类有机酸处理下第0—180天土壤中菲含量的变化状况,并采用高通量Illumina Miseq技术分析了土壤细菌群落种类和数量的变化特征。结果表明,低分子有机酸对于土壤中菲的降解有明显的促进作用,由一级动力学方程得出乙酸对菲降解的促进作用最明显。从细菌群落结构来看,土壤细菌的数量及其多样性或许不是导致土壤菲降解的主要因素,反而特定的菲降解菌的丰度对菲降解有重要影响。添加低分子有机酸减少了细菌OTU数及细菌菌群多样性,但增加了PAHs降解菌的丰度。随着时间推移细菌总OTU数呈现下降趋势,独有种类数均呈现出先增长后下降的趋势。检测到了6种典型的菲降解菌,分别为:Bacillus、鞘氨醇单胞菌属、Massilia、Azospirillum、Burkholderia-paraburkholderia、红球菌。研究结果可为多环芳烃污染土壤的植物修复提供基础数据和科学参考。     

Links between soil microbial communities and plant traits in a species‐rich grassland under long‐term climate change

Climate change can influence soil microorganisms directly by altering their growth and activity but also indirectly via effects on the vegetation, which modifies the availability of resources. Direct impacts of climate change on soil microorganisms can occur rapidly, whereas indirect effects mediated by shifts in plant community composition are not immediately apparent and likely to increase over time. We used molecular fingerprinting of bacterial and fungal communities in the soil to investigate the effects of 17 years of temperature and rainfall manipulations in a species‐rich grassland near Buxton, UK. We compared shifts in microbial community structure to changes in plant species composition and key plant traits across 78 microsites within plots subjected to winter heating, rainfall supplementation, or summer drought. We observed marked shifts in soil fungal and bacterial community structure in response to chronic summer drought. Importantly, although dominant microbial taxa were largely unaffected by drought, there were substantial changes in the abundances of subordinate fungal and bacterial taxa. In contrast to short‐term studies that report high resistance of soil fungi to drought, we observed substantial losses of fungal taxa in the summer drought treatments. There was moderate concordance between soil microbial communities and plant species composition within microsites. Vector fitting of community‐weighted mean plant traits to ordinations of soil bacterial and fungal communities showed that shifts in soil microbial community structure were related to plant traits representing the quality of resources available to soil microorganisms: the construction cost of leaf material, foliar carbon‐to‐nitrogen ratios, and leaf dry matter content. Thus, our study provides evidence that climate change could affect soil microbial communities indirectly via changes in plant inputs and highlights the importance of considering long‐term climate change effects, especially in nutrient‐poor systems with slow‐growing vegetation.     

Significant and persistent impact of timber harvesting on soil microbial communities in Northern coniferous forests

Forest ecosystems have integral roles in climate stability, biodiversity and economic development. Soil stewardship is essential for sustainable forest management. Organic matter (OM) removal and soil compaction are key disturbances associated with forest harvesting, but their impacts on forest ecosystems are not well understood. Because microbiological processes regulate soil ecology and biogeochemistry, microbial community structure might serve as indicator of forest ecosystem status, revealing changes in nutrient and energy flow patterns before they have irreversible effects on long-term soil productivity. We applied massively parallel pyrosequencing of over 4.6 million ribosomal marker sequences to assess the impact of OM removal and soil compaction on bacterial and fungal communities in a field experiment replicated at six forest sites in British Columbia, Canada. More than a decade after harvesting, diversity and structure of soil bacterial and fungal communities remained significantly altered by harvesting disturbances, with individual taxonomic groups responding differentially to varied levels of the disturbances. Plant symbionts, like ectomycorrhizal fungi, and saprobic taxa, such as ascomycetes and actinomycetes, were among the most sensitive to harvesting disturbances. Given their significant ecological roles in forest development, the fate of these taxa might be critical for sustainability of forest ecosystems. Although abundant bacterial populations were ubiquitous, abundant fungal populations often revealed a patchy distribution, consistent with their higher sensitivity to the examined soil disturbances. These results establish a comprehensive inventory of bacterial and fungal community composition in northern coniferous forests and demonstrate the long-term response of their structure to key disturbances associated with forest harvesting.     

林龄对刺槐人工林土壤团聚体、有机碳和细菌群落的影响

探究刺槐人工林土壤团聚体、有机碳及细菌群落的变化特征,可为提升土壤质量与功能提供理论依据。以黄土高原沟壑区不同林龄刺槐人工林(8年生、18年生和30年生)和刚撂荒的农耕地(CK)为研究对象,利用最适湿度筛分法获得不同粒径团聚体,测定其有机碳含量和细菌群落结构特征。结果表明:(1)各林龄土壤团聚体均以>0.25 mm粒径为主,含量为92.74%-95.78%。土壤团聚体稳定性随着林龄的增加显著提高,以30年生林地最高,团聚体平均重量直径(MWD)、几何平均直径(GMD)分别较CK显著增加48.19%和91.38%(P<0.05)。(2)各林龄均以<0.25 mm粒径有机碳含量最高。土壤有机碳含量和>2 mm粒径团聚体有机碳含量均随着林龄的增长而显著增加。(3)团聚体细菌群落主要由变形菌门(Proteobacteria)、放线菌门(Actinobacteria)和酸杆菌门(Acidobacteria)组成。随着林龄的增加,各粒径团聚体中放线菌门相对丰度先降低后增加,18年生林地最低。酸杆菌门变化趋势与放线菌门相反。变形菌门无明显变化。土壤有机碳、pH、全氮和全磷是影响团聚体细菌群落的主要因素。(4)>2 mm和2-0.25 mm粒径团聚体中,己科河菌门(Rokubacteria)对团聚体稳定性影响最大,既对团聚体稳定性产生直接正效应,又通过增加有机碳的含量间接提高团聚体稳定性。在<0.25 mm粒径团聚体中,有机碳含量对其稳定性的影响最大,有机碳含量越高,团聚体稳定性越强。综上,营造刺槐人工林有利于提高土壤团聚体稳定性,促进土壤有机碳的积累,可作为该区域生态恢复的有效措施。在生长发育过程中,人工林可通过改变土壤团聚体细菌群落和有机碳含量从而影响团聚体的稳定性。     

Comparison of DNA‐ and RNA‐based bacterial community structures in soil exposed to 2,4‐dichlorophenol

Aims: To examine the effect of the pollutant 2,4‐dichlorophenol on DNA‐ and RNA‐based bacterial communities in soil. Methods and Results: Soil was exposed to 100 mg kg^?1 of 2,4‐dichlorophenol (2,4‐DCP), and degradation was monitored over 35 days. DNA and RNA were coextracted, and terminal restriction fragment length polymorphism (T‐RFLP) was used to report changes in bacterial communities in response to the presence of the chlorophenol. The phylogenetic composition of the soil during degradation was determined by creating a clone library of amplified 16S rRNA sequences from both DNA and reverse‐transcribed RNA from exposed soil. Resulting clones were sequenced, and putative identities were assigned. Conclusions: A significant difference between active (RNA‐based) and total (DNA‐based) bacterial community structure was observed for both T‐RFLP and phylogenetic analyses in response to 2,4‐DCP, with more pronounced changes seen in RNA‐based communities. Phylogenetic analysis indicated the dominance of Proteobacteria in both profiles. Significance and Impact of the Study: This study describes the response of soil bacterial communities to the addition of the xenobiotic compound 2,4‐DCP, and highlights the importance of including RNA‐based 16S rRNA analysis to complement any molecular study in a perturbed soil.     

Interactive effects of acclimation temperature and short‐term stress exposure on resistance traits in the butterfly Bicyclus anynana

The ability to buffer detrimental effects of environmental stress on fitness is of great ecological importance because, in nature, pronounced environmental variation may regularly induce stress. Furthermore, several stressors may interact in a synergistic manner. In the present study, plastic responses in cold, heat and starvation resistance are investigated in the tropical butterfly Bicyclus anynana Butler, 1879, using a full factorial design with two acclimation temperatures (20 and 27 °C) and four short‐term stress treatments (control, cold, heat, starvation). Warm‐acclimated butterflies are more heat‐ but less cold‐tolerant as expected. Short‐term cold and starvation exposure reduce cold and heat resistance, and short‐term heat exposure decreases cold but increases heat resistance. Starvation resistance is not affected by any of the short‐term treatments. Thus, the effects of short‐term stress exposure are either neutral or negative, except for a positive effect of heat exposure on heat resistance, indicating the negative effects of pre‐exposure to stress. Interestingly, significant interactions between acclimation temperature and short‐term stress exposure for heat and cold resistance are found, demonstrating that larger temperature differences incur more damage. Therefore, animals may not generally be able to benefit from pre‐exposure to stress (through ‘hardening’), depending on their previously experienced conditions. The complex interactions between environmental variation, stress and resistance are highlighted, warranting further investigations.     

The active microbial diversity drives ecosystem multifunctionality and is physiologically related to carbon availability in Mediterranean semi‐arid soils

Biogeochemical processes and ecosystemic functions are mostly driven by soil microbial communities. However, most methods focus on evaluating the total microbial community and fail to discriminate its active fraction which is linked to soil functionality. Precisely, the activity of the microbial community is strongly limited by the availability of organic carbon (C) in soils under arid and semi‐arid climate. Here, we provide a complementary genomic and metaproteomic approach to investigate the relationships between the diversity of the total community, the active diversity and ecosystem functionality across a dissolved organic carbon (DOC) gradient in southeast Spain. DOC correlated with the ecosystem multifunctionality index composed by soil respiration, enzyme activities (urease, alkaline phosphatase and β‐glucosidase) and microbial biomass (phospholipid fatty acids, PLFA). This study highlights that the active diversity (determined by metaprotoemics) but not the diversity of the whole microbial community (evaluated by amplicon gene sequencing) is related to the availability of organic C and it is also connected to the ecosystem multifunctionality index. We reveal that DOC shapes the activities of bacterial and fungal populations in Mediterranean semi‐arid soils and determines the compartmentalization of functional niches. For instance, Rhizobales thrived at high‐DOC sites probably fuelled by metabolism of one‐C compounds. Moreover, the analysis of proteins involved in the transport and metabolism of carbohydrates revealed that Ascomycota and Basidiomycota occupied different nutritional niches. The functional mechanisms for niche specialization were not constant across the DOC gradient.     

Differences in the soil microbial community and carbon‐use efficiency following development of Vochysia guatemalensis tree plantations in unproductive pastures in Costa Rica

This study shows that Vochysia guatemalensis tree plantations were associated with enhanced soil biotic and abiotic characteristics in previously cleared forests in the northern zone of Costa Rica, suggesting the possible use of this practice as a restoration strategy for local land owners. Soil samples from a primary forest, secondary forest, and a 13‐year‐old plantation of V. guatemalensis had greater relative abundances of DNA sequences of microbial genera critical for carbon‐use (C‐use) efficiency (i.e. the saprobe, complex C and wood rot/lignin decomposer fungi, and bacterial lignin and other complex C degraders), and greater levels of total organic carbon, C‐biomass, and microbial quotients as indicators of enhanced C‐use efficiency, than found in soils of adjacent 5‐year‐old V. guatemalensis plantations and abandoned non‐productive pasture/grasslands (GRs). The major research conclusions were that (1) conversion of forested land into abandoned pasture/GRs decreased the C‐use efficiency in the soils and the microbial groups associated with C‐use efficiency; (2) soils in plantations of V. guatemalensis were associated with increased abundances of the DNA of these same microbial groups and enhanced C‐use efficiency; (3) DNA‐based taxonomic analysis of microbes and analysis of the microbial quotient values can be used to monitor soil ecosystems for assessment of the efficacy of restoration activities. Thus, planting V. guatemalensis on damaged lands in the Maquenque National Wildlife Refuge should be encouraged to provide a sustainable forestry crop that can be harvested rotationally, while improving soil ecosystem health and reducing the pressure to harvest other forest sites.     

Seed germination responses to seasonal temperature and drought stress are species‐specific but not related to seed size in a desert steppe: Implications for effect of climate change on community structure

Investigating how seed germination of multiple species in an ecosystem responds to environmental conditions is crucial for understanding the mechanisms for community structure and biodiversity maintenance. However, knowledge of seed germination response of species to environmental conditions is still scarce at the community level. We hypothesized that responses of seed germination to environmental conditions differ among species at the community level, and that germination response is not correlated with seed size. To test this hypothesis, we determined the response of seed germination of 20 common species in the Siziwang Desert Steppe, China, to seasonal temperature regimes (representing April, May, June, and July) and drought stress (0, ?0.003, ?0.027, ?0.155, and ?0.87 MPa). Seed germination percentage increased with increasing temperature regime, but Allium ramosum, Allium tenuissimum, Artemisia annua, Artemisia mongolica, Artemisia scoparia, Artemisia sieversiana, Bassia dasyphylla, Kochia prastrata, and Neopallasia pectinata germinated to >60% in the lowest temperature regime (April). Germination decreased with increasing water stress, but Allium ramosum, Artemisia annua, Artemisia scoparia, Bassia dasyphylla, Heteropappus altaicus, Kochia prastrata, Neopallasia pectinata, and Potentilla tanacetifolia germinated to near 60% at ?0.87 MPa. Among these eight species, germination of six was tolerant to both temperature and water stress. Mean germination percentage in the four temperature regimes and the five water potentials was not significantly correlated with seed mass or seed area, which were highly correlated. Our results suggest that the species‐specific germination responses to environmental conditions are important in structuring the desert steppe community and have implications for predicting community structure under climate change. Thus, the predicted warmer and dryer climate will favor germination of drought‐tolerant species, resulting in altered proportions of germinants of different species and subsequently change in community composition of the desert steppe.