The Effects of Tetracycline Residues on the Microbial Community Structure of Tobacco Soil in Pot Experiment

The responses of soil microbes to climatic and anthropological factors in the Tibetan grasslands

Effects of grassland afforestation on structure and function of soil bacterial and fungal communities

Effects of 7 years experimental warming on soil bacterial and fungal community structure in the Northern Tibet alpine meadow at three elevations

Soil microbial communities have been influenced by global changes, which might negatively regulate aboveground communities and affect nutrient resource cycling. However, the influence of warming and nitrogen (N) addition and their combined effects on soil microbial community composition and structure are still not well understood. To explore the effect of warming and N addition on the composition and structure of soil microbial communities, a five-year field experiment was conducted in a temperate meadow. We examined the responses of soil fungal and bacterial community compositions and structures to warming and N addition using ITS gene and 16S rRNA gene MiSeq sequencing methods, respectively. Warming and N addition not only increased the diversity of soil fungal species but also affected the soil fungal community structure. Warming and N addition caused significant declines in soil bacterial richness but had few impacts on bacterial community structure. The changes in plant species richness affected the soil fungal community structure, while the changes in plant cover also affected the bacterial community structure. The response of the soil bacterial community structure to warming and N addition was lower than that of the fungal community structure. Our results highlight that the influence of global changes on soil fungal and bacterial community structures might be different, and which also might be determined, to some extent, by plant community, soil physicochemical properties, and climate characteristics at the regional scale.

The selection of tree species used for the afforestation of urban forests is very important for maintaining the urban ecosystem, while soil microbe is one of the driving factors of material cycling in the urban forest ecosystem and for health of forests. In this study, the characteristics of surface soil bacterial and fungal community structure in four urban forests (primarily composed of Fraxinus mandshurica (Fm), Quercus mongolica (Qm), Pinus sylvestris var. mongolica (Ps), and Pinus tabulaeformis var. Mukdensis (Pt) as the main dominant tree species, respectively) were investigated by high-throughput sequencing. Our results showed that the alphadiversity of the soil microbial community in the Fm urban forest was the highest, while the lowest was in the Ps urban forest. In the bacterial community, Proteobacteria was the most predominant phylum in soils from Fm, Ps, and Pt urban forests. The most relatively abundant phylum of the Qm urban forest soil was Acidobacteria. The relative abundances of the bacterial communities at the genus level in the soil of four urban forests were significantly different. The soil bacterial communities in Ps and Pt urban forests were moresimilar, and Qm and Fm were also moresimilar. In the fungal community, Basidiomycota was the most predominant phylum in soils from Qm, Ps, and Pt urban forests. The phylum with the greatest relative abundance in the Fm urban forest soil was Ascomycota. There were differences in the fungal community between Qm, Fm, Ps, and Pt urban forests. Soil microbial community composition was affected by environmental factors: soil bacterial and fungal community compositions were significantly related to soil electrical conductivity (EC), alkali hydrolysable nitrogen (AHN), total nitrogen (TN), and total phosphorus (TP).In conclusion, the soil microbial community structure was related to both forest's tree species and soil properties.

Soil microbes are the primary drivers of the material cycling of the forest ecosystem, and understanding how microbial structure and composition change across succession assists in clarifying the mechanisms behind succession dynamics. However, the response of soil microbial communities and assembly processes to succession is poorly understood in subtropical forests. Thus, through the “space instead of time” and high throughput sequencing method, the dynamics of the soil bacterial and fungal communities and assembly process along the succession were studied, where five succession stages, including Abandoned lands (AL), Deciduous broad-leaved forests (DB), Coniferous forests (CF), Coniferous broad-leaved mixed forests (CB), and Evergreen broad-leaved forests (EB), were selected in a subtropical forest on the western slope of Wuyi Mountain, southern China. The results demonstrated that succession significantly decreased soil bacterial α-diversity but had little effect on fungal α-diversity. The composition of soil bacterial and fungal communities shifted along with the succession stages. LEfSe analysis showed the transition from initial succession microbial communities dominated by Firmicutes, Bacteroidota, Ascomycota, and Chytridiomycota to terminal succession communities dominated by Actinobacteriota and Basidiomycota. Distance-based redundancy analysis (db-RDA) revealed that soil total organic carbon (TOC) was the main factor explaining variability in the structure of soil bacterial communities, and multiple soil environmental factors such as the TOC, soil total nitrogen (TN), C:N ratio, and pH co-regulated the structure of fungi. The null models illustrated that deterministic processes were dominant in the soil bacterial communities, while the stochastic processes contributed significantly to the soil fungal communities during succession. Collectively, our results suggest that different patterns are displayed by the soil bacterial and fungal communities during the succession. These findings enhance our comprehension of the processes that drive the formation and maintenance of soil microbial diversity throughout forest succession.

Soil microorganisms are one of the primary driving factors of biogeochemical cycles in floodplain ecosystems. Vegetation type has an impact on the activities of soil microorganisms. However, it is currently unclear whether the composition and structure of soil bacterial and fungal communities in floodplain ecosystems have a consistent response pattern to vegetation communities. In this research, Illumina Mi-Seq sequencing technology was employed to study the soil fungal and bacterial communities covered by three typical vegetation communities in the Yellow River floodplain ecosystem. Our results showed that the underground biomass, total carbon (TC) and nitrogen (TN) were significantly different between the three vegetation communities. In the surface soil of summer, the Shannon index of fungi community was the highest in Tamarix chinensis (T. chinensis) and the lowest in Phragmites australis (P.australis). In autumn, the Shannon and Simpson indices of bacterial communities in surface soil were the highest in the P.australis and the lowest in the Sonchus arvensis (S.arvensis), but there was no significant difference in the β-diversity of bacterial community among the three vegetation communities. In autumn, the Chao1 index of fungal community in subsoil was the highest in P.australis and the lowest in S.arvensis, while there was no significant difference in the α-diversity of bacterial community among the three vegetation communities. In addition, there were considerable disparities in the fungal and bacteria community structure in various vegetation soils. Redundancy analysis (RDA analysis) showed that TN, TC, AP, pH, NO3 -, NH4 + and moisture content were key factors driving bacterial community structure, while TP, NH4 +, pH and moisture content were essential factors driving fungal community composition. These outcomes help to improve our understanding of the ecological model of soil fungal and bacterial community in floodplain ecosystems and give assistance in improving the role of an ecological barrier and floodplain service possibilities.

Secondary salinization is a serious environmental issue and a major threat to the sustainable use of grasslands. Information about the response of microbial communities and soil properties in already saline soils to increasing salinity is lacking. We investigated soil properties and the structures of soil bacterial and fungal communities across a gradient of salinization in the Horqin Grassland, China. Three sites with relatively lightly (average soluble salt content = 0.11%), relatively moderately (average soluble salt content = 0.44%), and heavily (average soluble salt content = 1.07%) degraded grassland, were selected as experimental sites. We examined variations in the composition and structure of the soil bacterial and fungal communities by using high-throughput sequencing of the 16S and 18S rRNA genes, respectively. We found degrading effects of salinization on soil properties, i.e., decreased soil moisture, organic matter, total N, NH4-N, and NO3-N and increased soil bulk density, pH, and electrical conductivity. The bacterial and fungal community structures changed with increasing salinity. However, dominant microbial taxa (including phylum, genus, and operational taxonomic unit levels) were similar among experimental sites, indicating that increasing salinization slightly affected the basic compositions of microbial communities in already saline grasslands. Furthermore, the relative abundances of most dominant taxa sensitively responded to the soil salt content. Acidobacteria, Actinobacteria, Chloroflexi, RB4, Rubrobacter, Blastocatella, H16, Glomeromycota, and Aspergillus linearly increased with increasing salinization, suggesting that they could be used as bioindicators for salt-tolerant communities. Overall, the changes in the structures of soil bacterial and fungal communities were determined by the relative quantities of dominant taxa rather than community composition. The structures of soil bacterial and fungal communities were linked to soil properties and vegetation. Increasing soil salt content, and thereby varied pH and organic matter, were likely the direct influencing factors of microbial communities in these saline grasslands.

Atmospheric nitrogen (N) deposition is known to alter soil microbial communities, but how canopy and understory N addition affects soil bacterial and fungal communities in different soil layers remains poorly understood. Conducting a 6-year canopy and understory N addition experiment in a temperate forest, we showed that soil bacterial and fungal communities in the organic layer exhibited different responses to N addition. The main effect of N addition decreased soil bacterial diversity and altered bacterial community composition in the organic layer, but not changed fungal diversity and community composition in all layers. Soil pH was the main factor that regulated the responses of soil bacterial diversity and community composition to N addition, whereas soil fungal diversity and community composition were mainly controlled by soil moisture and nutrient availability. In addition, compared with canopy N addition, the understory N addition had stronger effects on soil bacterial Shannon diversity and community composition but had a weaker effect on soil bacteria richness in the organic soil layer. Our study demonstrates that the bacterial communities in the organic soil layer were more sensitive than the fungal communities to canopy and understory N addition, and the conventional method of understory N addition might have skewed the effects of natural atmospheric N deposition on soil bacterial communities. This further emphasizes the importance of considering canopy processes in future N addition studies and simultaneously evaluating soil bacterial and fungal communities in response to global environmental changes.

Current Australian legislation permits the beneficial application of grease trap waste (GTW) to agricultural soil, viewing it as a beneficial source of organic matter and soil conditioner containing no/low amounts of metals or pathogenic organisms. However, little is known about the influence of GTW on soil bacterial community. A field experiment was established at Menangle in south western Sydney in Australia to quantitatively assess the impacts of different types (GTW CO and GTW CL) and amounts of GTW application on the soil bacterial community and diversity. Furthermore, a municipal solid waste (MSW) compost was simultaneously examined to compare against the other organic wastes. Knowledge about the shifts in microbial community structure and diversity following the applications of organic wastes could help to evaluate the ecological consequences on the soil and thus to develop sound regulatory guidelines for the beneficial reuse of organic wastes in agricultural lands. Soil samples were collected from recycled organics plots treated with different types and quantity of organic wastes. The field experimental treatments included control (CK, without application of any organic wastes), low amount of GTW CO (COL), GTW CL (CLL), and MSW (ML), and high amounts of GTW CO (COH), GTW CL (CLH), and MSW compost (MH). Microbial DNA was extracted from soil samples and the 16S rRNA genes were polymerase chain reaction (PCR)-amplified. The PCR products were analyzed by denaturing gradient gel electrophoresis (DGGE), cloning, and sequencing. The bacterial community structures and diversity were assessed using the DGGE profiles and clone libraries constructed from the excised DGGE bands. DGGE-based analyses showed that application of the GTW CO, regardless of the amount applied, had significant negative effects on soil bacterial genotypic diversity and community structure compared with the control, while the applications of other organic wastes including the GTW CL and MSW had no clear effects. The effects of the rate of organic waste application on soil bacterial community characteristics varied with the types of organic wastes applied. Sequence-based analyses of 126 clones indicated that Proteobacteria (53.2%) was the dominant taxa at the experimental site, followed by Actinobacteria (9.5%), Bacteroidetes (7.9%), Firmicutes (7.9%), Gemmatimonadetes (5.6%), Chloroflexi (2.4%), Acidobacteria (1.6%) and the unclassified group (11.9%). In the COH treatment, Acidobacteria, Bacteroidetes, and Gemmatimonadetes were not detected; the percentages of Firmicutes, Proteobacteria, and Actinobacteria in the COH treatment were significantly different from those in CK. There is a significant positive correlation (r = 0.71, p = 0.002) between the C/N ratio of organic wastes and the bacterial genotypic communities. Both the type and the amount of GTW applied affected soil bacterial genotypic diversity and community structure. The different effects of various types of organic wastes on soil bacterial characteristics may be predicted by the differences in specific properties of organic wastes such as C/N ratio, as evidenced by the strong and significant positive relationship between the bacterial community distance and the environmental distance of C/N ratio. This also indicates that the C/N ratio of GTW applied can be a major driver for the shift in the soil bacterial community. Our results revealed that the effects of organic wastes on soil bacterial communities varied with the types of organic wastes, and depending on the rate of application. Application of the GTW CO led to significant shifts in soil bacterial community diversity and structure. The effects of different types of organic wastes on the soil bacterial characteristics can be predicted by the differences of specific properties of organic wastes, such as the C/N ratio. Sequence-based analyses of 126 clones indicated that Proteobacteria was the dominant taxa at the experimental site. Our results have important implications for developing sound regulatory guidelines for the beneficial reuse of organic wastes, indicating that GTW CO and similar organic waste treatments may not be suitable for application in agricultural soils due to its significant negative effect on soil bacterial community.

Earthworms are soil macrofauna that control soil ecosystems by strongly influencing soil nematodes, microorganisms, and nutrient cycling, as well as soil environmental factors. We have discovered an earthworm cyclic peptide that disrupts nematode DNA, affecting its lifespan, reproduction, and feeding preferences. To investigate the effects of this peptide on soil, it was added to soil, and changes in soil nematode, bacterial and fungal communities, soil nutrient contents, and basal respiration were measured on days 5 and 21. The results showed that the peptide reduced soil basal respiration on day 5 and soil NO3-N on day 21, decreased soil fungivores nematodes on day 5 and soil nematode abundance on day 21, and increased soil fungal community richness and diversity. It also altered the soil bacterial community structure between day 5 and the soil fungal community structure on days 5 and 21. The peptide regulates the soil environment by influencing the structure of soil bacterial and fungal communities through the soil nematode community, as demonstrated by partial least squares path modelling (PLS-PM) analyses. Earthworm cyclic peptides mediates tri-trophic interactions between earthworms, nematodes, microbes, and environmental factors, providing new insights into soil biota interactions and feedback in dynamic soil food webs.

Soil microbes are a crucial component of karst ecosystems, and exploring their community changes during succession can help to elucidate the mechanisms driving succession dynamics. However, the variation of soil microbial communities during vegetation succession in karst ecosystems is still poorly understood. We studied the variations in community structure and potential functions of soil microbes within the four successional stages of grassland (GL), shrubland (SL), secondary forest (SF), and primary forest (PF) for the topsoil (0–10 cm) and subsoil (10–20 cm) in a karst area using high-throughput sequencing. The research findings showed that the bacterial and fungal community diversity and composition changed more obviously in the topsoil than in the subsoil across the succession. With vegetation succession, the structural and functional characteristics of soil bacterial and fungal communities show different trends, with soil fungal communities having a greater response to successional stage changes. Actinobacteria and Acidobacteria were dominant in secondary and primary forests, respectively, while Bacteroidetes was prevalent in grassland. However, the change in Proteobacteria was not significant at both soil depths. Ascomycota was the dominant phylum of soil fungi throughout the succession. The function of soil bacteria was mainly carbohydrate metabolism, which had the highest proportion in the shrubland at different soil depths. The dominant fungal functional groups were saprotroph, pathotroph, and pathotroph–saprotroph. The soil bacterial communities were observably affected by soil organic carbon, total nitrogen, total potassium, ammonia nitrogen, nitrate nitrogen, and leucine aminopeptidase, among which soil organic carbon, ammonia nitrogen, and leucine aminopeptidase mainly influenced the bacterial community in the topsoil, while nitrate nitrogen chiefly influenced the bacterial community in the subsoil. The soil fungal community was only significantly affected by soil organic carbon. Collectively, these results indicate that the effects of vegetation succession on soil microbial communities are largely driven by successional stage and soil properties, with soil fungi being more susceptible to the vegetation successional stage and soil bacteria being more sensitive to the soil properties. During this process, soil bacterial and fungal communities follow different succession patterns.

Soil microbes play crucial roles in grassland ecosystem functions, such as soil carbon (C) pool and nutrient cycle. Soil microbes in grasslands are susceptible to the degradation mediated by climate change and anthropogenic disturbance. However, research on how the degradation influences the diversity and community structure of different soil microbial taxa is relatively scarce. We conducted a large-scale field survey to describe the effects of four degradation levels (PD: potential degradation, LD: light degradation, MD: moderate degradation, and SD: severe degradation) on soil bacterial and fungal community in the semi-arid grasslands of northern China. We found that soil moisture, nutrients, and clay content decreased, but soil sand content increased along the increasing degradation gradient. However, the degradation had no effects on soil pH and the C:N ratio. Grassland degradation had non-significant effect on soil bacterial diversity, but it significantly affected soil bacterial community structure. The degradation decreased soil fungal diversity and had a relatively larger influence on the community structure of soil fungi than that of bacteria. The community composition and structure of soil fungi were mainly affected by soil nutrients and texture, while those of soil bacteria were mainly affected by soil pH. These results indicate that changes in soil properties induced by grassland degradation mainly drive the variation in the soil fungal community and have less effect on the soil bacterial community. This study reveals the sensitivity of soil fungal community to grassland degradation, highlighting the priority of soil fungal community for the management and restoration of degraded grasslands.

Long-term effects of gravel mulching and straw mulching on soil physicochemical properties and bacterial and fungal community composition in the Loess Plateau of China

Nitrogen (N) fertilization is a key factor that affects soil biogeochemical properties and microbial community structures across ecosystems. However, we know less about the responses of soil microbial community dynamics and biogeochemical properties to long-term N fertilization practices in a loess dryland soil in Northwest China. We sampled dryland soils at the 0–20-cm soil layer from a long-term field experiment (initiated in 2004) conducted in Northwest China, which has three treatments (i.e., N0 (control), N160 (160 kg N ha−1 year−1), and N320 (320 kg N ha−1 year−1). We determined soil biogeochemical properties and used 454 pyrosequencing of internal transcribed spacer (ITS) regions (for fungi) and V1–V3 regions of 16S rRNA (for bacteria) genes to explore soil microbial communities. Increased concentrations of soil organic carbon (SOC), total N (TN), nitrate N and microbial biomass N, and decreased soil pH were found in N-fertilized treatments and probably due to N fertilizer additions. However, N fertilization had no significant effect on soil microbial biomass C, available phosphorus, available potassium, and electrical conductivity. N fertilization did not affect the fungal species number, but it decreased the abundance of phylum Zygomycota and increased genus Fusarium. The predominant bacterial phyla in N0 were Bacteroidetes, Firmicutes, and Fusobacteria, but in N160 and N320 were Acidobacteria, Actinobacteria, and Proteobacteria. At the bacterial genus level, N fertilization decreased the relative abundances of Bacteroides, Fusobacterium, and Faecalibacterium and increased other genera (e.g., Bacillus, Lactococcus, Rhodoplanes, Steroidobacter). However, there was no difference in community structure between N160 and N320. The bacterial community structure had close correlation to soil properties SOC, TN, and pH, while no correlations were observed between fungal community structure and these soil properties, which indicated that soil bacterial community structure was easily changed by soil properties as affected by N fertilization. N fertilization changed soil biogeochemical properties and thereby altered soil fungal community compositions and bacterial community structure, but it did not impact the fungal diversity. These results demonstrated that a reasonable rate of N fertilizer applied to wheat field can improve soil fertility and microbial communities.