Jul 2020, Volume 2 Issue 2

Cover illustration

  • Global warming accelerates deglaciations in both high elevation and high latitude regions over the past 100 years. Glacier retreats expose large masses of previously-buried rock and sediment, which are known as the glacier foreland. Microorganisms are pioneering species in the forelands, whose colonization and succession drive elemental biogeochemical cycling and the accumulation of nutrients for plant establishment. While the processes of microbial colonization and successio [Detail] ...

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    Ajmal Khan, Weidong Kong, Mukan Ji, Linyan Yue, Yue Xie, Jinbo Liu, Baiqing Xu

    Global warming leads to deglaciations in high-elevation regions, which exposes deglaciated soils to microbial colonization. Disparity in year-to-year successional patterns of bacterial community and influencing factors in freshly deglaciated soils remain unclear. We explored the abundance of bacterial 16S rRNA gene and community succession in deglaciated soils along a 14-year chronosequence after deglaciation using qPCR and Illumina sequencing on the Tibetan Plateau. The results showed that the abundance of bacterial 16S rRNA gene gradually increased with increasing deglaciation age. Soil bacterial community succession was clustered into three deglaciation stages, which were the early (zero-year old), transitional (1–7 years old) and late (8–14 years old) stages. A significantly abrupt bacterial community succession occurred from the early to the transitional stage (P<0.01), while a mild succession (P = 0.078) occurred from the transitional to the late stage. The bacterial community at the early and transitional stages were dominated by Proteobacteria, while the late stage was dominated by Actinobacteria. Less abundant (<10%) Acidobacteria, Gemmatimonadetes, Verrucomicrobia, Chloroflexi, Planctomycetes, unclassified bacteria dominantly occurred in the transition and late stage and Cyanobacteria in the early stage. Total organic carbon (24.7%), post deglaciation age (21%), pH (16.5%) and moisture (10.1%) significantly contributed (P<0.05) to the variation of bacterial community succession. Our findings provided a new insight that short time-scale chronosequence is a good model to study yearly resolution of microbial community succession.

    Shan Xu, Weixin Geng, Emma J. Sayer, Guoyi Zhou, Ping Zhou, Chengshuai Liu

    The activity of soil microbes is strongly constrained by water availability. However, it is unclear how microbial activity responds to spatial and temporal changes in precipitation, particularly to long-term precipitation changes. To identify the spatiotemporal patterns of microbial responses to precipitation changes of differing durations, we conducted a meta-analysis of data from 95 field studies with drought treatments and 109 field studies with elevated precipitation treatments. Our results indicated that microbial biomass carbon (MBC) decreased by 17% under drought and increased by 18% under elevated precipitation. Across all studies, the phospholipid fatty acid (PLFA) biomarkers for fungi and bacteria decreased significantly under drought but increased under elevated precipitation. In addition, the negative effect of drought on MBC tended to be greater at sites with a high aridity index, but the effect of elevated precipitation on MBC did not differ among sites. More importantly, the responses of MBC, fungal and bacterial PLFA abundance did not vary with treatment duration under drought, but under elevated precipitation, they increased in the first five years of treatment and declined thereafter. These results are important for our prediction of microbial responses to long-term precipitation change, because they imply that microbes acclimate to long-term elevated precipitation.

    Haiyang Liu, Xing Huang, Wenfeng Tan, Hongjie Di, Jianming Xu, Yong Li

    Long-term application of chemical fertilizers causes soil degradation and nitrogen (N) loss, but these effects could be alleviated by organic fertilizers. In addition, crop rotation is a feasible practice to increase soil fertility, soil quality and crop yields comparing with monocultural cropping patterns. However, questions remain concerning how the soil microbiome responds to different manure application rates under crop rotations. Here, we collected soil samples from a rice-rape system to investigate the response of the soil microbiome to nine years of pig manure application at different rates (CK: 0 kg ha-1, M1: 1930 kg ha-1, M2: 3860 kg ha-1 and M3: 5790 kg ha-1). Our results revealed that the bacterial α-diversity (Chao1 and Shannon index) in the rape season increased first and then decreased with increasing manure application rates, and a high manure load tended to decrease the bacterial α-diversity in the rice season. Long-term manure application enriched some copiotrophic bacteria, such as Proteobacteria and Actinobacteria, while it decreased the relative abundance of Nitrospirae. Redundancy analysis (RDA) and the Mantel test indicated that soil pH, TC, TN, AP, C/P and N/P ratios were the main factors influencing bacterial communities. Moreover, network analysis showed that a low manure application rate shaped a complexly connected and stable bacterial community, while higher manure application rate decreased the stability of the bacterial network. These findings improve our understanding of bacterial responses to long-term manure application under crop rotations and their relationships with soil factors, especially in the context of increasing fertilizer inputs.

    Eva Högfors-Rönnholm, Stephan Christel, Tom Lillhonga, Sten Engblom, Peter Österholm, Mark Dopson

    To efficiently mitigate bacterial mediated acid and metal discharge from acid sulfate soils, iron and sulfur-oxidizing microorganisms that catalyze the iron sulfide dissolution should be inactivated. An organic carbon source could further be introduced into the soil to promote the growth of iron and sulfur reducing bacteria. In this study, acid sulfate soil was amended with a mobile form of ultrafine calcium carbonate alone or in combination with fractions of peat, sodium acetate, or sodium lactate. The introduction of ultrafine calcium carbonate resulted in a raised pH that appeared to inactivate the acidophiles, but did not reactivate iron or sulfur reducing bacteria. The addition of organic matter resulted in higher microbial diversities and retention of metals, although acid-tolerant and acidophilic microbes still dominated. A low abundance of an iron reducing bacteria was identified in the all treatments with both peat fractions and pure organic carbon compounds. These results indicated that biodegraded peat could be used as an energy source for at least iron reducing bacteria in the acid sulfate soil at the same time as it retains metals in the soil. These findings are of value for further developing mitigation methods for the sustainable use of acid sulfate soils.

    Xinqiang Liang, Fayong Li, Sheng Wang, Guifen Hua, Miaomiao He, Guangming Tian, Sangar Khan, Ravin Poudel, Karen A. Garrett

    It is well documented that rice paddy fields act as agricultural wetlands that remove or retain nutrients; however, their associated effects on soil microbial communities are rarely reported. The present study evaluates the impact of rice variety on nutrient removal via plant uptake, nutrient retention in the soil, and bacterial associations in rice paddy fields, using a network analysis that compares the soil bacterial communities of two rice varieties. We found that the high-straw rice variety (YD-1) allows uptake of a high amount of nitrogen (N) and phosphorus (P) from paddy rice fields via harvesting, but causes less residual total N and P to remain in the soil. However, both rice varieties (YD-1 and XS-134(Xiushui-134)) had non-significant effects on the dominant bacterial taxa. The short-term response of bacterial community diversity to rice variety is found to be mainly due to less frequently recovered species. A network analysis that incorporates soil nutrients as nodes, as well as bacterial taxa, found that only one node that denotes the total P related to the non-dominant species had an indirect association with the rice straw biomass. The observed short-term impact of the two rice varieties (XS-134 and YD-1) on soil bacterial diversity and nutrient surplus in these agricultural wetlands is limited under a high level of fertilization.

    Dong Liu, Baorong Wang, Parag Bhople, Fayzmamad Davlatbekov, Fuqiang Yu

    Rehabilitation of farmland improves the local eco-environmental conditions. But to what extent this transformation influences soil microbial properties is less known. In our study we compared variations in soil microbial attributes following changes in land-use types to understand the influence of altered soil properties on microbial biomass and their community structure using chloroform fumigation extraction method and phospholipid fatty acid (PLFA) analysis. For this purpose, 3 agricultural (AL) (farmland, apple orchard and 2 years abandoned land) and 4 rehabilitated lands (RL) of various vegetations grassland, shrubland, mixed forest (Amorpha fruticosa and Pinus tabuliformis Carr.) and forest (Robinia pseudoacacia) were selected. Our results showed higher soil organic carbon (SOC) contents in RL soils (forest>mixed forest>grassland>shrub land) than that in AL soils. In RL soils, soil microbial biomass and abundance of group specific PLFA were significantly higher than those in AL soils. Under different land-use types, microbial community was bacteria dominated over fungi. The microbial physiological indices (G+/G, cyc/prec and S/M) indicated decreased environmental stress in RL soils in comparison with AL soils. In loess soils, SOC and total N correlated positively (p<0.05) with microbial biomass C, N and P and also with fungal and bacterial PLFA, indicating a positive microbial mediation in improving soil fertility. Taking together, our findings suggest that land rehabilitation, especially Robinia pseudoacacia planation, improves overall edaphic conditions and accelerates soil microbial biomass accumulation in local regions.

    Zhijian Mou, Luhui Kuang, Biyue Yan, Xinyu Zhang, Yunqiang Wang, Zhanfeng Liu

    Soil amino sugars have been widely used to evaluate the potential roles of microbes in mediating soil carbon (C) cycling and various pretreatment methods were used for its extraction. However, few studies assessed their potential influences on the soil amino sugar extraction. In this study, we investigated the effects of sample storage method and grinding on amino sugar extraction across different climatic zone and land uses. Results showed that the concentrations of soil amino sugars varied greatly among sample pretreatments and their impacts were highly dependent on climatic condition and land use. Specifically, higher concentrations of amino sugars were extracted from field-moist samples than dried samples in subtropical grassland, temperate forest and arable land with no significant differences among storage methods for the samples from subtropical forest, arable land, and temperate grassland. Moreover, grinding improved the extraction efficiency of amino sugars for the dried soils. Due to the reduced extraction concentration in dried soils, field-moist samples were recommended in priority. For the dried soils used for the long-term storage, grinding can be an option to improve the extraction efficiency. Such information will be valuable for reducing the uncertainty and improving the accuracy during the determination of soil amino sugars.