Temperature adaptation of soil bacterial communities along an Antarctic climate gradient: predicting responses to climate warming

Soil microorganisms, the central drivers of terrestrial Antarctic ecosystems, are being confronted with increasing temperatures as parts of the continent experience considerable warming. Here we determined short‐term temperature dependencies of Antarctic soil bacterial community growth rates, using the leucine incorporation technique, in order to predict future changes in temperature sensitivity of resident soil bacterial communities. Soil samples were collected along a climate gradient consisting of locations on the Antarctic Peninsula (Anchorage Island, 67 °34′S, 68 °08′W), Signy Island (60 °43′S, 45 °38′W) and the Falkland Islands (51 °76′S 59 °03′W). At each location, experimental plots were subjected to warming by open top chambers (OTCs) and paired with control plots on vegetated and fell‐field habitats. The bacterial communities were adapted to the mean annual temperature of their environment, as shown by a significant correlation between the mean annual soil temperature and the minimum temperature for bacterial growth (T_min). Every 1 °C rise in soil temperature was estimated to increase T_min by 0.24–0.38 °C. The optimum temperature for bacterial growth varied less and did not have as clear a relationship with soil temperature. Temperature sensitivity, indicated by Q₁₀ values, increased with mean annual soil temperature, suggesting that bacterial communities from colder regions were less temperature sensitive than those from the warmer regions. The OTC warming (generally <1 °C temperature increases) over 3 years had no effects on temperature relationship of the soil bacterial community. We estimate that the predicted temperature increase of 2.6 °C for the Antarctic Peninsula would increase T_min by 0.6–1 °C and Q₁₀ (0–10 °C) by 0.5 units.     

Effect of drying and rewetting on bacterial growth rates in soil

The effect of soil moisture on bacterial growth was investigated, and the effects of rewetting were compared with glucose addition because both treatments increase substrate availability. Bacterial growth was estimated as thymidine and leucine incorporation, and was compared with respiration. Low growth rates were found in air-dried soil, increasing rapidly to high stable values in moist soils. Respiration and bacterial growth at different soil moisture contents were correlated. Rewetting air-dried soil resulted in a linear increase in bacterial growth with time, reaching the levels in moist soil (10 times higher) after about 7 h. Respiration rates increased within 1 h to a level >10 times higher than that in moist soil. After the initial flush, there was a gradual decrease in respiration rate, while bacterial growth increased to levels twice that of moist soil 24 h after rewetting, and decreased to levels similar to those in moist soil after 2 days. Adding glucose resulted in no positive effect on bacterial growth during the first 9 h, despite resulting in more than five times higher respiration. This indicated that the initial increase in bacterial growth after rewetting was not due to increased substrate availability.     

Temperature and moisture sensitivities of CO2 efflux from lowland and alpine meadow soils

Aims This study was conducted to (i) determine if soil CO₂ efflux is more sensitive to temperature changes in alpine areas than in lowland grasslands, (ii) examine the effects of temperature and moisture on soil respiration, and (iii) evaluate the potential for change in soil carbon storage in response to global warming in different grasslands in East Asia.Methods We collected soil samples from two different temperate grasslands, an alpine meadow on the Qinghai-Tibetan plateau, China, and a lowland grassland in Tsukuba, Japan. The CO₂ emission rate was then measured for these soil samples after they were incubated at 25°C and 60% of the water holding capacity for 7 days.Important findings (i)?The soil respiration rate was more sensitive to temperature change in the alpine soil than in the lowland soil. The average Q 10 was 7.6 for the alpine meadow soil but only 5.9 for the lowland soil. The increased sensitivity appears to be due, at least in part, to the soil organic carbon content and/or soil carbon to nitrogen ratio, especially in the surface layer. (ii) The relationship between the CO₂ emission rate and the soil moisture content revealed that the alpine meadow had a more clear response than the lowland soil. (iii) This study suggests that changes in soil moisture and soil temperature may have larger impacts on soil CO₂ efflux in the alpine meadow than in the lowland grassland evaluated here.     

Adaptation of soil microbial communities to temperature: comparison of fungi and bacteria in a laboratory experiment

Temperature not only has direct effects on microbial activity, but can also affect activity indirectly by changing the temperature dependency of the community. This would result in communities performing better over time in response to increased temperatures. We have for the first time studied the effect of soil temperature (5–50 °C) on the community adaptation of both bacterial (leucine incorporation) and fungal growth (acetate-in-ergosterol incorporation). Growth at different temperatures was estimated after about a month using a short-term assay to avoid confounding the effects of temperature on substrate availability. Before the experiment started, fungal and bacterial growth was optimal around 30 °C. Increasing soil temperature above this resulted in an increase in the optimum for bacterial growth, correlated to soil temperature, with parallel shifts in the total response curve. Below the optimum, soil temperature had only minor effects, although lower temperatures selected for communities growing better at the lowest temperature. Fungi were affected in the same way as bacteria, with large shifts in temperature tolerance at soil temperatures above that of optimum for growth. A simplified technique, only comparing growth at two contrasting temperatures, gave similar results as using a complete temperature curve, allowing for large scale measurements also in field situations with small differences in temperature.     

Seedling growth declines in warmed tropical forest soils

The response of plants to a warming climate could have a large feedback on further climatic change. This feedback is especially important for tropical forests, where the global peak in plant productivity and biodiversity occurs. Here we test the response of tropical forest tree seedling growth, photosynthesis and herbivory to 3 years of in situ full-soil profile warming. We studied six species, three of which are known nitrogen-fixers and we hypothesized that the warming response of growth will be mediated by nutrient availability to plants. Across species, growth was significantly lower in warmed soil compared to soil at ambient temperature, and the same pattern was observed for light-saturated photosynthesis, pointing toward a growth decline associated with decreased C fixation. Within species, the relative growth decline was significant for two species, Inga laurina and Tachigali versicolor, both of which are N-fixers. Together our results suggest a growth decline may have resulted from a negative effect of warming on N-fixation, rather than via changes in nutrient mineralization from soil organic matter, which was unchanged for N and increased for P during the dry-to-wet season transition. Overall, our study demonstrates that belowground warming causes species-specific declines in the growth and photosynthesis of seedlings, with a suggestion—requiring further investigation—that this growth decline is larger in N-fixing species.     

Fungal and bacterial growth in soil with plant materials of different C/N ratios

Fungal (acetate-in-ergosterol incorporation) and bacterial (leucine/thymidine incorporation) growth resulting from alfalfa (C/N=15) and barley straw (C/N=75) addition was studied in soil microcosms for 64 days. Nitrogen amendments were used to compensate for the C/N difference between the substrates. Fungal growth increased to a maximum after 3–7 days, at five to eight times the controls, following the addition of straw, and three to four times the controls following the addition of alfalfa. After 20–30 days, the fungal growth rate converged with the controls, resulting in a cumulative fungal growth two to three times the controls following straw addition and about 20% higher than the controls following alfalfa addition. The bacterial growth rate reached rates five times the controls following alfalfa addition and twice that of the controls following straw addition after 3–7 days. It remained elevated after 64 days. The cumulative bacterial growth was two and four times the controls following straw and alfalfa addition, respectively. A negative correlation was found between N addition and bacterial growth, while N stimulated fungal growth. Thus, the C/N ratio of the additions (substrate and extra N) could not entirely explain the different results regarding fungal and bacterial growths. Respiration was not always related to the combined growth of the microorganisms, emphasizing the requirement for a better understanding of growth efficiencies of fungi and bacteria.     

Seasonality and resource availability control bacterial and archaeal communities in soils of a temperate beech forest

It was hypothesized that seasonality and resource availability altered through tree girdling were major determinants of the phylogenetic composition of the archaeal and bacterial community in a temperate beech forest soil. During a 2-year field experiment, involving girdling of beech trees to intercept the transfer of easily available carbon (C) from the canopy to roots, members of the dominant phylogenetic microbial phyla residing in top soils under girdled versus untreated control trees were monitored at bimonthly intervals through 16S rRNA gene-based terminal restriction fragment length polymorphism profiling and quantitative PCR analysis. Effects on nitrifying and denitrifying groups were assessed by measuring the abundances of nirS and nosZ genes as well as bacterial and archaeal amoA genes. Seasonal dynamics displayed by key phylogenetic and nitrogen (N) cycling functional groups were found to be tightly coupled with seasonal alterations in labile C and N pools as well as with variation in soil temperature and soil moisture. In particular, archaea and acidobacteria were highly responsive to soil nutritional and soil climatic changes associated with seasonality, indicating their high metabolic versatility and capability to adapt to environmental changes. For these phyla, significant interrelations with soil chemical and microbial process data were found suggesting their potential, but poorly described contribution to nitrification or denitrification in temperate forest soils. In conclusion, our extensive approach allowed us to get novel insights into effects of seasonality and resource availability on the microbial community, in particular on hitherto poorly studied bacterial phyla and functional groups.     

Relationships between temperature responses and bacterial community structure along seasonal and altitudinal gradients

In this study, soil bacterial communities and the temperature responses (Q10) of substrate-induced respiration were compared between an alpine dry meadow and a subalpine forest in the Colorado Rocky Mountains. Bacterial communities in three seasons from each environment were described with 16S rRNA gene clone libraries. The main goal of this comparison was to relate phylogenetic differences among bacterial communities with variation in soil respiratory temperature sensitivities along seasonal and altitudinal gradients. The warmer, lower elevation, subalpine forest soil exhibited large seasonal variations in Q10. Subalpine Q10 values were highest in summer, and were higher than alpine values in all seasons except winter. Q10 in alpine soils were consistently low throughout the year. Alpine and subalpine bacterial communities both varied seasonally, and were markedly distinct from each other. Based on Fst analysis, subalpine communities from colder times of year were more similar to the alpine communities than were subalpine summer communities. Principle component analysis of the pairwise genetic distances (Fst) between communities produced two factors that accounted for 69% and 22% of the total variance in the data set. These factors demonstrated a significant relationship between bacterial community structure and temperature response when regressed on log-transformed Q10 data.     

Adaptation of soil bacterial communities to prevailing pH in different soils

Abstract: The bacterial community response to pH was studied for 16 soils with pH(H₂O) ranging between 4 and 8 by measuring thymidine incorporation into bacteria extracted from the soil into a solution using homogenization-centrifugation. The pH of the bacterial solution was altered to six different values with dilute sulfuric acid or different buffers before measuring incorporation. The resulting pH response curve for thymidine incorporation was used to compare bacterial communities from the different soils. There was a correlation between optimum pH for thymidine incorporation and the soil pH(H₂O). Even bacterial communities from acid soils had optima corresponding to the soil pH, indicating that they were adapted to these conditions. Thymidine incorporation was also compared with leucine incorporation for some soils. The leucine to thymidine incorporation ratio was constant over the tested pH interval when incorporation values were adjusted for isotope dilution. A good correlation was found between the scores along the first component (explaining 80% of the variation) and soil pH ( r ² = 0.85), if principal component analysis of the pH response curves for thymidine incorporation was used. The pH response curves differed most for the extreme pH values used, and a linear relationship was found between the logarithm of the ratio of thymidine incorporation at pH 4.3 to incorporation at pH 8.2 and the soil pH ( r ² = 0.86). Thus, a simplified technique using only two pH values, when measuring the thymidine incorporation, could be used to compare the response to pH of bacterial communities.     

Temperature adaptation in a geographically widespread zooplankter,Daphnia magna

Evidence for temperature adaptation in Daphnia magna was inferred from variation in the shape of temperature reaction norms for somatic growth rate, a fitness‐related trait. Ex‐ephippial clones from eight populations across Europe were grown under standardized conditions after preacclimation at five temperatures (17–29 °C). Significant variation for grand mean growth rates occurred both within populations (among clones) and between populations. Genetic variation for reaction norm shape was found within populations, with temperature‐dependent trade‐offs in clone relative fitness. However, the population average responses to temperature were similar, following approximately parallel reaction norms. The among‐population variation is not evidence for temperature adaptation. Lack of temperature adaptation at the population level may be a feature of intermittent populations where environmentally terminated diapause can entrain the planktonic stage of the life‐history within a similar range of temperatures.     

Spatial patterns in temperature sensitivity of soil respiration in China: Estimation with inverse modeling

Temperature sensitivity of soil respiration (Q₁₀) is an important parameter in modeling the effects of global warming on ecosystem carbon release. Experimental studies of soil respiration have ubiquitously indicated that Q₁₀ has high spatial heterogeneity. However, most biogeochemical models still use a constant Q₁₀ in projecting future climate change and no spatial pattern of Q₁₀ values at large scales has been derived. In this study, we conducted an inverse modeling analysis to retrieve the spatial pattern of Q₁₀ in China at 8 km spatial resolution by assimilating data of soil organic carbon into a process-based terrestrial carbon model (CASA model). The results indicate that the optimized Q₁₀ values are spatially heterogeneous and consistent to the values derived from soil respiration observations. The mean Q10 values of different soil types range from 1.09 to 2.38, with the highest value in volcanic soil, and the lowest value in cold brown calcic soil. The spatial pattern of Q₁₀ is related to environmental factors, especially precipitation and top soil organic carbon content. This study demonstrates that inverse modeling is a useful tool in deriving the spatial pattern of Q₁₀ at large scales, with which being incorporated into biogeochemical models, uncertainty in the projection of future carbon dynamics could be potentially reduced.     

Effects of prior exposure to antibiotics on bacterial adaptation to phages

Understanding adaptation to complex environments requires information about how exposure to one selection pressure affects adaptation to others. For bacteria, antibiotics and viral parasites (phages) are two of the most common selection pressures and are both relevant for treatment of bacterial infections: increasing antibiotic resistance is generating significant interest in using phages in addition or as an alternative to antibiotics. However, we lack knowledge of how exposure to antibiotics affects bacterial responses to phages. Specifically, it is unclear how the negative effects of antibiotics on bacterial population growth combine with any possible mutagenic effects or physiological responses to influence adaptation to other stressors such as phages, and how this net effect varies with antibiotic concentration. Here, we experimentally addressed the effect of pre‐exposure to a wide range of antibiotic concentrations on bacterial responses to phages. Across 10 antibiotics, we found a strong association between their effects on bacterial population size and subsequent population growth in the presence of phages (which in these conditions indicates phage‐resistance evolution). We detected some evidence of mutagenesis among populations treated with fluoroquinolones and β‐lactams at sublethal doses, but these effects were small and not consistent across phage treatments. These results show that, although stressors such as antibiotics can boost adaptation to other stressors at low concentrations, these effects are weak compared to the effect of reduced population growth at inhibitory concentrations, which in our experiments strongly reduced the likelihood of subsequent phage‐resistance evolution.     

Mechanism of bacterial adaptation to low temperature

Survival of bacteria at low temperatures provokes scientific interest because of several reasons. Investigations in this area promise insight into one of the mysteries of life science —namely, how the machinery of life operates at extreme environments. Knowledge obtained from these studies is likely to be useful in controlling pathogenic bacteria, which survive and thrive in cold-stored food materials. The outcome of these studies may also help us to explore the possibilities of existence of life in distant frozen planets and their satellites.     

Response of soil surface CO2 flux in a boreal forest to ecosystem warming

Soil surface carbon dioxide (CO₂) flux (R_S) was measured for 2 years at the Boreal Soil and Air Warming Experiment site near Thompson, MB, Canada. The experimental design was a complete random block design that consisted of four replicate blocks, with each block containing a 15 m × 15 m control and heated plot. Black spruce [Picea mariana (Mill.) BSP] was the overstory species and Epilobium angustifolium was the dominant understory. Soil temperature was maintained (～5 °C) above the control soil temperature using electric cables inside water filled polyethylene tubing for each heated plot. Air inside a 7.3‐m‐diameter chamber, centered in the soil warming plot, contained approximately nine black spruce trees was heated ～5 °C above control ambient air temperature allowing for the testing of soil‐only warming and soil+air warming. Soil surface CO₂ flux (R_S) was positively correlated (P < 0.0001) to soil temperature at 10 cm depth. Soil surface CO₂ flux (R_S) was 24% greater in the soil‐only warming than the control in 2004, but was only 11% greater in 2005, while R_S in the soil+air warming treatments was 31% less than the control in 2004 and 23% less in 2005. Live fine root mass (< 2 mm diameter) was less in the heated than control treatments in 2004 and statistically less (P < 0.01) in 2005. Similar root mass between the two heated treatments suggests that different heating methods (soil‐only vs. soil+air warming) can affect the rate of decomposition.     

The effects of temperature on bacterial production in a dimictic eutrophic lake

Abstract The incorporation of [³H](methyl)thymidine into DNA by the planktonic heterotropic bacteria of Little Crooked Lake (Noble Country, IN) was determined at different incubation temperatures. The highest rates of thymidine incorporation generally occurred at temperatures exceeding the in situ temperature of the sample. The optimal temperature for thymidine incorporation ranged from 1.0–3.4 times the in situ temperature. As the summer of 1983 progressed, the optimal temperatures for thymidine incorporation by epilimnetic samples and the in situ temperatures converged. This trend was reversed as fall overturn was approached.     

水热条件变化对黑土细菌群落结构的影响及其演替特征

全球气候变化导致的水热条件变化,对土壤微生物群落结构及功能产生重要影响。深入理解这些变化如何影响微生物群落的结构及其随时间的演替,对于有效预测和适应未来的气候变化至关重要。【目的】在气候变化背景下,本研究旨在探索黑土细菌群落的多样性、组成和结构,以及群落演替特征的变化情况。【方法】利用中国科学院海伦、封丘、鹰潭农田生态系统国家野外科学观测研究站长期土壤置换实验平台,选择寒温带地区(中国海伦)的黑土作为研究对象,并将其移置于暖温带地区(封丘)和中亚热带地区(鹰潭)以模拟水热条件增加。通过采集2005年至2011年的63个黑土样本(包括原位、移置封丘县和移置鹰潭市),利用16S rRNA基因高通量测序技术,研究了水热条件变化对黑土细菌群落多样性、组成和结构的影响;同时结合土壤理化性质,分析环境因素与微生物群落特征间的关系,并计算物种周转率(w)。【结果】经过6年的移置,将寒温带黑土移至暖温带和中亚热带后,土壤的理化性质发生了显著改变。土壤有机质和全氮含量显著降低,地上部生物量显著减少。土壤细菌群落的多样性下降,群落组成和结构发生了显著变化。主要细菌类群包括疣微菌门(Verrucomicrobia)、变形菌门(Proteobacteria)、酸杆菌门(Acidobacteria)和放线菌门(Actinobacteria)等,其中疣微菌门在移置鹰潭地区后的相对丰度显著增加。此外,气候因子与微生物群落特征高度相关。非度量多维尺度分析显示,群落结构随水热条件和时间的变化而演替,这与微生物时间周转率的增加相关。在不同水热条件下,细菌群落的时间周转率差异显著,依次为0.030 (海伦)<0.033 (封丘)<0.045 (鹰潭)。【结论】6年的水热条件增加显著降低了细菌群落的多样性,显著改变了其组成和结构,并加快了细菌群落时间周转率的响应。     

土壤细菌呼吸对西双版纳热带森林恢复的响应

揭示不同恢复阶段热带森林土壤细菌呼吸季节变化及其主控因素,对于探明土壤细菌呼吸对热带森林恢复的响应机制具有重要的科学意义。以西双版纳不同恢复阶段热带森林(白背桐群落、崖豆藤群落和高檐蒲桃群落)为研究对象,运用真菌呼吸抑制法及高通量宏基因组测序技术分别测定土壤细菌呼吸速率和细菌多样性,并采用回归分析及结构方程模型揭示热带森林恢复过程中土壤细菌多样性、pH、土壤碳氮组分变化对土壤细菌呼吸速率的影响特征。结果表明：1)不同恢复阶段热带森林土壤细菌呼吸速率表现为：高檐蒲桃群落((1.51±0.62)CO₂ mg g^-1 h^-1)显著高于崖豆藤群落((1.16±0.56)CO₂ mg g^-1 h^-1)和白背桐群落((0.82±0.60)CO₂ mg g^-1 h^-1)(P<0.05)。2)不同恢复阶段土壤细菌呼吸速率呈显著的单峰型季节变化(P<0.05),最大值均出现在9月：高檐蒲桃群落((...     

基于高通量测序的鄱阳湖典型湿地土壤细菌群落特征分析

采用高通量测序技术分析了鄱阳湖典型湿地土壤细菌群落特征。测序结果表明,不同植被土壤细菌群落丰度与多样性的排序相同:苔草带苔草-虉草带芦苇带泥滩带藜蒿带。沿湖面至坡地,空间位置相近的土壤细菌群落结构具有更大的相似性,苔草-虉草带、苔草带和芦苇带的细菌群落结构相近,泥滩带和藜蒿带的细菌群落结构差异较大。变形菌门(30.0%)是湿地土壤平均相对丰度最高的门,其次为酸杆菌门(16.7%)和绿弯菌门(16.5%);多数门分类细菌相对丰度沿湖面至坡地存在一定变化趋势。硝化螺菌属是第一大属分类水平细菌群落。在土壤化学指标中,与鄱阳湖湿地细菌群落相关性较大的是总磷、铵态氮和有机质含量。以上研究结果表明,鄱阳湖湿地不同植被土壤细菌群落具有结构性差异,但沿湖面至坡地存在规律性变化。     

Termination of belowground C allocation by trees alters soil fungal and bacterial communities in a boreal forest

The introduction of photosynthates through plant roots is a major source of carbon (C) for soil microbial biota and shapes the composition of fungal and bacterial communities in the rhizosphere. Although the importance of this process, especially to ectomycorrhizal fungi, has been known for some time, the extent to which plant belowground C allocation controls the composition of the wider soil community is not understood. A tree-girdling experiment enabled studies of the relationship between plant C allocation and microbial community composition. Girdling involves cutting the phloem of trees to prevent photosynthates from entering the soil. Four years after girdling, fungal and bacterial communities were characterized using DNA-based profiles and cloning and sequencing. Data showed that girdling significantly altered fungal and bacterial communities compared with the control. The ratio of ectomycorrhizal to saprobic fungal sequences significantly decreased in girdled treatments, and this decline was found to correlate with the fungal phospholipid fatty acid biomarker 18:2ω6,9. Bacterial communities also varied in the abundance of the two dominant phyla Acidobacteria and Alphaproteobacteria . Concomitant changes in fungal and bacterial communities suggest linkages between these two groups and point toward plant belowground C allocation as a key determinant of microbial community composition.