Factors Affecting Soil Microbial Communities Research Articles

How Organic Mulching Influences the Soil Bacterial Community Structure and Function in Urban Forests.

Urban forest soil is often disturbed by frequent human activity. Organic mulching is effective for improving soil quality; however, the effects of organic mulching on soil bacterial communities in urban forests are still largely unexplored. This study evaluated how organic mulching changed the urban forest soil bacterial community through an incubation experiment. Four treatments were applied: (1) no organic mulch (CK); (2) wood chips alone (5 g, Mw); (3) wood compost alone (5 g, Mc); and (4) wood chips + wood compost (This mulch was divided into two layers, i.e., the upper layer of wood chips (2.5 g) and the lower layer wood compost (2.5 g, Mw+c).) We found significant differences in the soil physicochemical properties under organic mulching after incubation. Overall, organic mulching can alter soil bacterial community structure. Soil alkali-hydrolyzable nitrogen, soil organic carbon, soil total nitrogen, and carbon-nitrogen ratio were the main factors affecting soil microbial community structures. Soil bacterial groups under organic mulching treatments mainly acted on the C and N cycling of functional pathways in soil. This study suggests that organic mulching could maintain the development of soil bacteria, which establishes a theoretical foundation for enhancing the microbiological environment of urban forest soils.

The competition between Bidens pilosa and Setaria viridis alters soil microbial composition and soil ecological function

Bidens pilosa is recognized as one of the major invasive plants in China. Its invasion has been associated with significant losses in agriculture, forestry, husbandry, and biodiversity. Soil ecosystems play an important role in alien plant invasion. Microorganisms within the soil act as intermediaries between plants and soil ecological functions, playing a role in regulating soil enzyme activities and nutrient dynamics. Understanding the interactions between invasive plants, soil microorganisms, and soil ecological processes is vital for managing and mitigating the impacts of invasive species on the environment. In this study, we conducted a systematic analysis focusing on B. pilosa and Setaria viridis, a common native companion plant in the invaded area. To simulate the invasion process of B. pilosa, we constructed homogeneous plots consisting of B. pilosa and S. viridis grown separately as monocultures, as well as in mixtures. The rhizosphere and bulk soils were collected from the alien plant B. pilosa and the native plant S. viridis. In order to focus on the soil ecological functional mechanisms that contribute to the successful invasion of B. pilosa, we analyzed the effects of B. pilosa on the composition of soil microbial communities and soil ecological functions. The results showed that the biomass of B. pilosa increased by 27.51% and that of S. viridis was significantly reduced by 66.56%. The organic matter contents in the bulk and rhizosphere soils of B. pilosa were approximately 1.30 times those in the native plant soils. The TN and NO3– contents in the rhizosphere soil of B. pilosa were 1.30 to 2.71 times those in the native plant soils. The activities of acid phosphatase, alkaline phosphatase, and urease in the rhizosphere soil of B. pilosa were 1.98–2.25 times higher than in the native plant soils. Using high-throughput sequencing of the 16S rRNA gene, we found that B. pilosa altered the composition of the soil microbial community. Specifically, many genera in Actinobacteria and Proteobacteria were enriched in B. pilosa soils. Further correlation analyses verified that these genera had significantly positive relationships with soil nutrients and enzyme activities. Plant biomass, soil pH, and the contents of organic matter, TN, NO3–, TP, AP, TK, and AK were the main factors affecting soil microbial communities. This study showed that the invasion of B. pilosa led to significant alterations in the composition of the soil microbial communities. These changes were closely linked to modifications in plant traits as well as soil physical and chemical properties. Some microbial species related to C, N and P cycling were enriched in the soil invaded by B. pilosa. These findings provide additional support for the hypothesis of soil-microbe feedback in the successful invasion of alien plants. They also offer insights into the ecological mechanism by which soil microbes contribute to the successful invasion of B. pilosa. Overall, our research contributes to a better understanding of the complex interactions between invasive plants, soil microbial communities, and ecosystem dynamics.

Explore the soil factors driving soil microbial community and structure in Songnen alkaline salt degraded grassland.

Saline-alkali degradation in grassland significantly affects plant community composition and soil physical and chemical properties. However, it remains unclear whether different degradation gradients affect soil microbial community and the main soil driving factors. Therefore, it is important to elucidate the effects of saline-alkali degradation on soil microbial community and the soil factors affecting soil microbial community in order to develop effective solutions to restore the degraded grassland ecosystem. In this study, Illumina high-throughput sequencing technology was used to study the effects of different saline-alkali degradation gradients on soil microbial diversity and composition. Three different gradients were qualitatively selected, which were the light degradation gradient (LD), the moderate degradation gradient (MD) and the severe degradation gradient (SD). The results showed that salt and alkali degradation decreased the diversity of soil bacterial and fungal communities, and changed the composition of bacterial and fungal communities. Different degradation gradients had different adaptability and tolerance species. With the deterioration of salinity in grassland, the relative abundance of Actinobacteriota and Chytridiomycota showed a decreasing trend. EC, pH and AP were the main drivers of soil bacterial community composition, while EC, pH and SOC were the main drivers of soil fungal community composition. Different microorganisms are affected by different soil properties. The changes of plant community and soil environment are the main factors limiting the diversity and composition of soil microbial community. The results show that saline-alkali degradation of grassland has a negative effect on microbial biodiversity, so it is important to develop effective solutions to restore degraded grassland to maintain biodiversity and ecosystem function.

Revealing the Effect of Saline Water Drip Irrigation on Soil Microorganisms in Cotton Fields Based on Metagenomics

Saline water irrigation has become an important means to alleviate the shortage of freshwater in arid areas. However, long-term saline water irrigation can cause soil salinity accumulation, affect soil microbial community structure, and then affect soil nutrient transformation. In this study, we used metagenomics to investigate the effects of long-term saline water drip irrigation on soil microbial community structure in a cotton field. In the experiment, the salinity of irrigation water (ECw) was set to two treatments:0.35 dS·m-1 and 8.04 dS·m-1 (denoted as FW and SW, respectively), and the nitrogen application rates were 0 kg·hm-2and 360 kg·hm-2 (denoted as N0 and N360, respectively). The results showed that saline water irrigation increased soil water content, salinity, organic carbon, and total nitrogen content and decreased soil pH and available potassium content. Nitrogen fertilizer application increased soil organic carbon, salinity, and total nitrogen content and decreased soil water content, pH, and available potassium content. The dominant bacterial phyla in each treatment were:Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi, and Gemmatimonadetes. Saline water irrigation significantly increased the relative abundances of Actinobacteria, Chloroflexi, Gemmatimonadetes, and Firmicutes but significantly decreased the relative abundances of Proteobacteria, Acidobacteria, Cyanobacteria, and Nitrospira. Nitrogen fertilizer application significantly increased the relative abundances of Chloroflexi and Nitrospira but significantly decreased the relative abundances of Acidobacteria, Gemmatimonadetes, Planctomycetes, Cyanobacteria, and Verrucomicrobia. LEfSe analysis showed that saline water irrigation had no significant effect on the number of potential biomarkers, and nitrogen fertilizer application decreased the number of potential biomarkers in soil microbial communities. The correlation network diagram showed that the 20 genera had different degrees of correlation, including 44 positive correlations and 48 negative correlations. The core species in the network diagram were Nocardioides, Streptomyces, Pyrinomonas, Candidatus_Solibacter, and Bradyrhizobium spp. Saline water irrigation increased the relative abundances of the denitrification genes nirK, nirS, nasB, and norC and decreased the relative abundances of the nitrification genes amoB, amoC, and nxrA, whereas nitrogen fertilizer application increased the relative abundances of the nitrification genes amoA, amoB, amoC, hao, and nxrA and decreased the relative abundances of the denitrifying genes narB, napA, nasA, and nosZ. Saline water irrigation could adversely affect soil physicochemical properties; SWC, EC1:5, and BD were the main driving factors affecting soil microbial community structure and function genes; and soil microorganisms adapted to soil salt stress by regulating species composition.

Agronomic performances of biodegradable and non-biodegradable plastic film mulching on a maize cropping system in the semi-arid Loess Plateau, China

Biodegradable plastic film mulch (PFM) is considered an alternative to non-biodegradable PFM to mitigate the negative impacts of residual film. However, the agronomic performance of biodegradable PFM in comparison to non-biodegradable PFM still needs to be tested. In this study, we evaluated the effects of biodegradable and non-biodegradable PFM on soil physicochemical properties, microbial community, and enzyme activities, as well as maize growth performance. Biodegradable and non-biodegradable PFM both increased soil temperature, water content, N content, and microbial biomass and maize yield by up to 30%, but decreased soil enzyme activities as compared to no mulching (control, CK). Most soil physicochemical properties, microbial community, and enzyme activities were similar under non-biodegradable and biodegradable PFM at the early stages of maize growth. However, at the late stages, soil temperature, water content, mineral N, NO3--N, ammonia monooxygenase (AMO) activity, and total phospholipid fatty acids (PLFAs) decreased under biodegradable PFM owing to film fragmentation. White PFM increased soil temperature, water content, and total PLFAs at the early stages of maize growth but decreased soil mineral N and total PLFAs at the late stages, as compared to black PFM. As soil temperature and N availability were the major factors affecting soil microbial community, microbial activity decreased after the fragmentation of biodegradable PFM, owing to the decreased soil temperature, water content, and mineral N. Notably, biodegradable PFM could decrease NO3--N accumulation in topsoil by decreasing N transformation due to the lower microbial and N-related enzyme (e.g., AMO) activities, compared with non-biodegradable PFM, which may avoid negative environmental impacts, such as NO3--N leaching or gas emission after harvest. Maize yield, height, aboveground biomass, and N uptake under biodegradable PFM were similar to those under non-biodegradable PFM during maize growth, implying that biodegradable PFM has no negative impact on crop growth and yield. In general, biodegradable PFM was equivalent to non-biodegradable PFM in terms of maize yield increase and N uptake, but was environmentally friendly. Therefore, biodegradable PFM can be used as an alternative to non-biodegradable PFM in semi-arid areas for sustainable agricultural practices.

Soil properties under different ecological restoration modes for the quarry in Yanshan mountains of Hebei province, China.

The ecological environment of quarry mining area is fragile, and the vegetation restoration cycle is long and difficult, so scientific and appropriate artificial vegetation is of great significance to ecological restoration. The purpose of this study was to evaluate the herbaceous and woody vegetation restoration, including Medicago sativa (Me), artificial miscellaneous grass (Mg), Rhus typhina (Rh), fruit orchard (Or) and Pinus tabulaeformis (Pi), to investigate the soil physicochemical properties and the structure of the microbial communities, and to reveal the correlation between them. The results addressed that Medicago sativa and artificial miscellaneous grass had significant effect on soil remediation, which were conducive to scientific and efficient ecological restoration, and could promote ecological restoration in the damaged ecosystems. While, the modes of Rh and Pi were not suitable for ecological restoration in this study area because they had strong allelopathy. Another arborous restoration mode of Or showed a better improvement effect (including soil nutrients, soil microbial diversity, etc.) than that of Rh and Pi. The findings also indicated that the herbaceous vegetation restoration modes of Me and Mg significantly increased the relative abundance of Proteobacteria, Acidobacteria, Actinobacteria bacteria, Ascomycota and Mortierllomycota fungi, and reduced the relative abundance of Firmicutes bacteria and Basidiomycota fungi. This study also revealed that the trend of bacterial localization in the fruit orchard, artificial miscellaneous grass and Medicago sativa was more obvious. Among many soil abiotic factors, the contents of organic matter, available nitrogen and pH were the most important factors affecting soil microbial community.

Phytoremediation of Secondary Salinity in Greenhouse Soil with Astragalus sinicus, Spinacea oleracea and Lolium perenne

Phytoremediation is an effective and ecological method used to control soil secondary salinization in greenhouses. However, the plant–soil interactions for phytoremediation have not been studied sufficiently. In this study, three crop species (Astragalus sinicus (CM), Spinacea oleracea (SP) and Lolium perenne (RY)) were compared in a greenhouse experiment. The results showed that all three crops increased the soil microbial biomass, the abundance of beneficial microorganisms, available phosphorus and soil pH, and reduced the soil salt content. The crop nutrient accumulation was positively correlated with the relative abundance of bacterial 16S rRNA sequences in the soil. CM and RY respectively increased the relative abundances of norank_f_Gemmatimonadaceae and norank_f_Anaerolineaceae within the soil bacterial community, while SP increased the relative abundances of Gibellulopsis within the fungal community. Correlation analysis revealed that pH and total dissolved salts were the vital factors affecting soil microbial communities in the secondary salinized soil. Our results suggest that phytoremediation could effectively alleviate secondary salinization by regulating the balance of soil microbial community composition and promoting crop nutrient accumulation.

人参种植对林地土壤细菌群落结构和代谢功能的影响

PDF HTML阅读 XML下载 导出引用 引用提醒 人参种植对林地土壤细菌群落结构和代谢功能的影响 DOI: 10.5846/stxb201909201963 作者: 作者单位: 作者简介: 通讯作者: 中图分类号: 基金项目: 国家自然科学基金项目（31670614） Effects of Ginseng cultivation on soil microbial community structure and metabolic functions in forest land Author: Affiliation: Fund Project: 摘要 | 图/表 | 访问统计 | 参考文献 | 相似文献 | 引证文献 | 资源附件 | 文章评论 摘要:揭示人参种植对土壤微生物群落结构和代谢功能的影响，对防治人参连作障碍具有重要的理论意义。利用高通量测序技术研究了林地和由林地开垦耕种人参3a和4a后土壤微生物群落结构和代谢功能的变化。结果表明，变形菌门（Proteobacteria）、放线菌门（Actinobacteria）、酸杆菌门（Acidobacteria）、疣微菌门（Verrucomicrobia）、绿弯菌门（Chloroflexi）是林地和人参种植土壤微生物的主要优势类群。林地开垦种植人参后，土壤放线菌门和疣微菌门的相对丰度显著增加，土壤酸杆菌门的相对丰度显著降低；而土壤微生物多样性指数明显降低。除趋势对应分析（DCA）显示不同种植a限人参的土壤微生物群落结构存在明显差异。Tax4Fun功能预测表明，人参种植后土壤微生物的萜类化合物和聚酮类化合物代谢与信号转导功能的相对丰度显著降低，而膜转运功能的相对丰度增加。典范对应分析（CCA）和Partial Mantel Test分析表明，土壤速效钾、全钾含量和土壤pH值是影响土壤微生物群落结构的重要因子。因此，林地开垦种植人参对土壤微生物群落结构、多样性以及代谢功能产生了显著影响，土壤速效钾、全钾含量和pH值是影响土壤微生物群落结构的重要因素。 Abstract:The aim of this research is to reveal changes in soil microbial community structure and metabolic function in forested land after planting Panax ginseng. This study used high-throughput sequencing technology to analyze the soil microbial community structure and metabolic function of forested land and forested land cultivated with ginseng for 3 and 4 years. The results showed that Proteobacteria, Actinobacteria, Acidobacteria, Verrucomicrobia, and Chloroflexi were the dominant phyla. After ginseng was planted, the relative abundance of Actinomycetes and Verrucomicrobia significantly increased while the relative abundance of Acidobacteria significantly decreased. Overall soil bacteria diversity also significantly decreased. Detrended correspondence analysis (DCA) showed significant differences in soil bacteria community structure of ginseng across different cultivation years. The relative abundance of metabolism of terpenoids and polyketides and signal transduction significantly decreased, while the relative abundance of membrane transport significantly increased. Canonical correspondence analysis (CCA) and the Partial Mantel Test showed that potassium availability, total potassium content and soil pH were key factors affecting soil microbial community structure. The results show that soil microbial community structure, diversity and metabolic function changed significantly after planting ginseng in forested land. This work has important theoretical significance for the prevention and treatment of ginseng continuous cropping obstacles. 参考文献 相似文献 引证文献

Response of Soil Microbial Communities to Warming and Clipping in Alpine Meadows in Northern Tibet

In order to explore responses of soil microbial communities among different alpine meadows under warming and clipping, soil microorganisms of three alpine meadow sites (low altitude: 4313 m, alpine steppe meadow, 30°30′ N, 91°04′ E; mid-altitude: 4513 m, alpine steppe meadow, 30°31′ N, 91°04′ E; and high altitude: 4693, alpine Kobresia meadow, 30°32′ N, 91°03′ E) were measured using the phospholipid fatty acid (PLFA) method. Both warming and clipping significantly reduced PLFA content and changed the community composition of soil microbial taxa, which belong to bacterial and fungal communities in the alpine Kobresia meadow. Warming significantly reduced the soil total PLFA content by 36.1% and the content of soil fungi by 37.0%; the clipping significantly reduced the soil total PLFA content by 57.4%, the content of soil fungi by 49.9%, and the content of soil bacteria by 60.5% in the alpine Kobresia meadow. Only clipping changed the total fungal community composition at a low altitude. Neither clipping nor warming changed the microbial community composition at a moderate altitude. Soil temperature, soil moisture, and pH were the main factors affecting soil microbial communities. Therefore, the effects of warming and clipping on soil microbial communities in alpine meadows were related to grassland types and soil environmental conditions.

Variations of soil microbial communities accompanied by different vegetation restoration in an open-cut iron mining area

Overexploitation of iron mining in China has caused serious environmental pollution. Therefore, establishing a stable ecological restoration with vegetation in mining areas has gradually aroused people's awareness and obtained extensive concerns. This study aimed to evaluate vegetation restoration with Robinia pseudoacacia (RP), Acer mono (AM) and Pinus koraiensis (PK) in iron mining compared with unrestored area, to investigate the soil environment factors and microbial communities, and to better understand the correlations between soil environment factors and soil microbial communities. Vegetation restoration could reduce soil pH and alleviate soil alkaline, and remarkably increase soil nutrients, especially in RP site. Analysis of 16S rRNA and ITS rRNA gene sequences provided a total of 645,004 and 906, 276 valid sequences clustered into 7091 OTUs and 1689 OTUs at a 0.03 genetic distance for bacteria and fungi, respectively. The predominant bacterial and fungal phyla were Actinobacteria and Ascomycota in studied sites, respectively. Additionally, revegetation significantly increased the relative abundances of Proteobacteria, Gemmatimonadetes, Bacteroidetes and Patescibacteria, and decreased the relative abundance of Actinobacteria. Robinia pseudoacacia harbored the highest soil fungal community diversity, and bacterial Simpson index and Shannon index. Vegetation restoration with RP could clearly shifted soil communities compared to AM and PK. Along with the restoration of vegetation, the remarkable abiotic changes were the accumulation of total C, total N, total P, available P, available N and available K and the decreasing of soil pH, which were the most important factors affecting soil microbial communities. Our results addressed that Robinia pseudoacacia was the best preferable species than AM and PK in improving soil nutrients, soil community diversity and structure in Fe mining, providing a helpful guideline for selection of tree species.

Temporal dynamics and influencing factors of soil microbes in Larix gmelinii forest soil during spring freezing-thawing period

Soil microbial community dynamics during the spring freezing-thawing period could affect carbon and nutrient cycling in the subsequent growing season. During spring soil freezing-thawing period, we monitored temporal dynamics of soil microbial community in different soil substrates for Larix gmelinii forest using phospholipid fatty acids (PLFAs) as biomarkers every 3-7 days. The results were as followed: 1) the total PLFAs content, the PLFAs content and relative abundance of each soil microbial group, the ratio of Gram-positive bacteria to Gram-negative bacteria (G+/G-), the ratio of saturated PLFAs to unsaturated PLFAs (S/NS) and the ratio of bacteria to total fungi (fungi + arbuscular mycorrhizal fungi) (B/F) all varied among sampling times; 2) soil total organic carbon (TOC) and nitrogen (TN) were the main factors affecting soil microbial community in the early stage of soil freezing-thawing period; soil moisture, TOC and TN were the main driving factors in the middle stage of soil freezing-thawing period; soil microbes were affected by soil tempera-ture, moisture, TOC, TN and C/N in the late stage of soil freezing-thawing period; 3) the total PLFAs content, the PLFAs content and relative abundance of each soil microbial group (except the relative abundance of bacteria), B/F, G+/G- and S/NS all showed significant difference between soil substrates, and soil TOC, TN and C/N were the key determination factors. Soil temperature, moisture, and nutrient availability were the main factors affecting soil microbial community during the spring soil freezing-thawing period, but the degree of influence varied with the freezing-thawing stages and microbial groups.

Effects of long-term fertilization on soil microbial abundance in farmland of the Loess Plateau, China

Based on a long-term experiment in the Changwu Agro-ecological Experimental Station, the real-time PCR analysis was used to examine the soil microbial abundance and to reveal the effects on soil microbial community under different long-term fertilization systems. The results showed that compared to the CK (barren field), the population of bacteria increased by 21% and archaea by 32% in treatment with inorganic fertilizer application. The abundance of bacteria in the treatment of chemical fertilizer combined with organic fertilizer increased by 37% and archaea by 36%. The treatment with chemical fertilizer mixed with organic fertilizer significantly increased the abundance of bacteria and archaea. The soil AOB increased by 7.13 times while the soil AOA only by 0.2 folds after 30-year application of chemical nitrogen fertilizer. AOB was highly responsive to fertilizer application, especially to nitrogen fertilizer. Compared with the single nitrogen application and the application of nitrogen fertilizer mixed with organic fertilizer, phosphorus fertilizer significantly increased the abundance of nifH and pmoA. The content of nifH, nirS cd and pmoA in the abandoned land was significantly higher than that in the cultivated soil. Results from the correlation analysis on soil basic physical and chemical properties indicated that soil pH, total nitrogen and organic carbon were key factors affecting soil microbial community abundance. In conclusion, long-term fertilization significantly changed soil microbial abundance, and fertilization patterns and cultivating methods had significant effect on microbial community abundance.

Microbial biodiversity in rhizospheric soil of Torreya grandis 'Merrillii' relative to cultivation history

To examine the effects of different cultivation history (5 a,10 a, and 15 a) on soil microbial communities, we used Illumina sequencing to investigate the diversity and structure of soil bacterial and fungal communities from Torreya grandis 'Merrillii' fields. The results showed that bacterial Shannon index, the richness estimators Chao1 and ACE were lower in soil in 15 year-old stand than those in other cultivation histories, while Simpson index showed no significant variation. Results from bacterial community NMDS showed that cultivation history played a vital role in driving the changes of soil bacteria communitiy structure. The bacterial communities in 5 and 10 year-old stand had the similar composition. The variations of bacterial richness and diversity as well as community structure (comprised basically of Proteobacteria, Actinobacteria, Acidobacteria, and Chloroflexi) were significantly correlated with soil organic matters, soil C/N, and total nitrogen. The fungi richness estimators of Chao1 and ACE were significantly decreased with increasing cultivation history. Shannon and Simpson indices were significantly higher in soil with 10 year-old stand than soils with other cultivation history. Fungal NMDS could be clustered in the same era. Fungal communities were comprosed of Ascomycota, Basidiomycota and Zygomycota. Changes in fungal richness/diversity and community structure were mainly controlled by the variation of soil organic matter. In conclusion, the predominant factors affecting soil microbial communities were the cultivation history, soil C/N, total nitrogen and organic matter, respectively.

Microbial community diversity and the interaction of soil under maize growth in different cultivation techniques

Soil microbial functional diversity under maize grown in different agricultural management practices was determined using the Biolog EcoPlates and other microbial and biochemical methods. Comparisons of substrate utilization and the diversity indices showed differences in community composition of microorganisms related to different cultivation techniques and seasons. The soil samples collected in spring were characterized by statistically significant lower indices of biological activity in comparison to the soil collected from the flowering stage of maize. The soils collected in spring from the plots with full tillage had a similarly high biological activity as the soils obtained from maize flowering season. The principal component of PC analysis, showed the strong correlation between the parameters of soil quality and biodiversity indicators. Selected indicators of soil microbial diversity explained 71.51% of biological variability in soils. Based on the PC analysis, two major groups of soils have been indicated. Management practices and seasons were two important factors affecting soil microbial communities.

The microbial gene diversity along an elevation gradient of the Tibetan grassland

Tibet is one of the most threatened regions by climate warming, thus understanding how its microbial communities function may be of high importance for predicting microbial responses to climate changes. Here, we report a study to profile soil microbial structural genes, which infers functional roles of microbial communities, along four sites/elevations of a Tibetan mountainous grassland, aiming to explore the potential microbial responses to climate changes via a strategy of space-for-time substitution. Using a microarray-based metagenomics tool named GeoChip 4.0, we showed that microbial communities were distinct for most but not all of the sites. Substantial variations were apparent in stress, N and C-cycling genes, but they were in line with the functional roles of these genes. Cold shock genes were more abundant at higher elevations. Also, gdh converting ammonium into urea was more abundant at higher elevations, whereas ureC converting urea into ammonium was less abundant, which was consistent with soil ammonium contents. Significant correlations were observed between N-cycling genes (ureC, gdh and amoA) and nitrous oxide flux, suggesting that they contributed to community metabolism. Lastly, we found by Canonical correspondence analysis, Mantel tests and the similarity tests that soil pH, temperature, NH4(+)-N and vegetation diversity accounted for the majority (81.4%) of microbial community variations, suggesting that these four attributes were major factors affecting soil microbial communities. On the basis of these observations, we predict that climate changes in the Tibetan grasslands are very likely to change soil microbial community functional structure, with particular impacts on microbial N-cycling genes and consequently microbe-mediated soil N dynamics.

Impact of No-Tillage and Conventional Tillage Systems on Soil Microbial Communities

Soil management practices influence soil physical and chemical characteristics and bring about changes in the soil microbial community structure and function. In this study, the effects of long-term conventional and no-tillage practices on microbial community structure, enzyme activities, and selected physicochemical properties were determined in a continuous corn system on a Decatur silt loam soil. The long-term no-tillage treatment resulted in higher soil carbon and nitrogen contents, viable microbial biomass, and phosphatase activities at the 0–5 cm depth than the conventional tillage treatment. Soil microbial community structure assessed using phospholipid fatty acid (PLFA) analysis and automated ribosomal intergenic spacer analysis (ARISA) varied by tillage practice and soil depth. The abundance of PLFAs indicative of fungi, bacteria, arbuscular mycorrhizal fungi, and actinobacteria was consistently higher in the no-till surface soil. Results of principal components analysis based on soil physicochemical and enzyme variables were in agreement with those based on PLFA and ARISA profiles. Soil organic carbon was positively correlated with most of the PLFA biomarkers. These results indicate that tillage practice and soil depth were two important factors affecting soil microbial community structure and activity, and conservation tillage practices improve both physicochemical and microbiological properties of soil.

Quantitative Analyses of Ammonia-oxidizing Archaea (AOA) and Ammonia-oxidizing Bacteria (AOB) in Fields with Different Soil Types

Soil type is one of the key factors affecting soil microbial communities. With regard to ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), however, it has not been determined how soil type affects their community size and soil nitrification activity. Here we quantitatively analyzed the ammonia monooxygenase genes (amoA) of these ammonia oxidizers in fields with three different soil types (Low-humic Andosol [LHA], Gray Lowland Soil [GLS], and Yellow Soil [YS]) under common cropping conditions, and assessed the relationships between soil nitrification activity and the abundance of each amoA. Nitrification activity of LHA was highest, followed by that of GLS and YS; this order was consistent with that for the abundance of AOB amoA. Abundance of AOB amoA showed temporal variation, which was similar to that observed in nitrification activity, and a strong relationship (adjusted R(2)=0.742) was observed between the abundance of AOB amoA and nitrification activity. Abundance of AOA amoA also exhibited a significant relationship (adjusted R(2)=0.228) with nitrification activity, although this relationship was much weaker. Our results indicate that soil type affects the community size of AOA and AOB and the resulting nitrification activity, and that AOB are major contributors to nitrification in soils, while AOA are partially responsible.

Factors affecting soil microbial community structure in tomato cropping systems

Soil and rhizosphere microbial communities in agroecosystems may be affected by soil, climate, plant species, and management. The management and environmental factors controlling microbial biomass and community structure were identified in a three-year field experiment. The experiment consisted of a tomato production agroecosystem with the following nine treatments: bare soil, black polyethylene mulch, white polyethylene mulch, vetch cover crop, vetch roots only, vetch shoots only, rye cover crop, rye roots only, and rye shoots only. The following hypotheses were tested: (1) Temperature and moisture differences between polyethylene-covered and cover-cropped treatments are partly responsible for treatment effects on soil microbial community composition, and (2) Different species of cover crops have unique root and shoot effects on soil microbial community composition. Microbial biomass and community composition were measured by phospholipid fatty acid analysis. Microbial biomass was increased by all cover crop treatments, including root only and shoot only. Cover cropping increased the absolute amount of all microbial groups, but Gram-positive bacteria decreased in proportion under cover crops. We attribute this decrease to increased readily available carbon under cover-cropped treatments, which favored other groups over Gram-positive bacteria. Higher soil temperatures under certain treatments also increased the proportion of Gram-positive bacteria. Vetch shoots increased the amount and proportion of Gram-negative bacteria, fungi, and arbuscular mycorrhizal fungi in the rhizosphere of tomato plants. The imposed treatments were much more significant than soil temperature, moisture, pH, and texture in controlling microbial biomass and community structure.