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

Dependence of soil microbial community structure and function on land use types and management regimes

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

Nitrogen deposition and climate warming can alter soil bacterial communities. However, the response of soil bacteria in an alpine steppe to these changes is largely unknown. In this study, a field experiment was performed on the northeastern Qinghai-Tibetan Plateau to determine the changes in soil bacterial communities of alpine steppes in response to nitrogen application and warming. The experiment consisted of four treatments, namely no-N application with no-warming (CK), N application (8 kg N ha−1 year−1) with no-warming (N), warming with no-N application (W), and N application (8 kg N ha−1 year−1) with warming (W&N). This study aimed to investigate (1) the changes in soil bacterial diversity and community structure under simulated nitrogen deposition and warming conditions, and (2) the key environmental factors responsible for these changes. Based on the results, soil bacterial diversity and community composition did not change significantly in the short term. Warming had a significant effect on overall bacterial composition, rare species composition, and individual bacterial taxa. Besides, the interaction between nitrogen application and warming had a significant effect on community β-diversity. Above-ground plant variables were highly correlated with bacterial community characteristics. Nitrogen application and warming did not significantly alter the distribution range of the bacterial community. Overall, this study suggests that soil bacterial communities can remain relatively stable at the level of simulated nitrogen application and warming and that short-term climatic changes may have no significant impacts on soil bacterial communities.

Soil microbial communities are directly and indirectly influenced by a complex system of cross-interactions between different biotic and abiotic factors influencing each other, such as plant species and their respective traits, soil nutrient content, and pH. Microorganisms shape their environment, as important drivers of the C and N cycle. Within the present thesis, several studies were conducted under controlled field and laboratory conditions as well as under natural conditions to unravel the contribution of different influencing factors. The soil prokaryotic community composition of the different soil samples was analyzed DNA-based and RNA-based using 16S rRNA genes and 16S rRNA as phylogenetic marker. The amplicon-based data were processed and diversity and richness estimates were calculated. Betadiversity analyses were conducted to assess overall differences between the different treatments. The obtained DGGE profiles were used for cluster analyses to reveal similarities or differences in the bacterial community structure. The present thesis provided insight into the impact of tree species, tree species diversity, leaf litter and sampling time on the composition and diversity of soil bacterial communities. The obtained data revealed that the leaf litter layer was the major driver of the bacterial community composition in the rhizosphere of young beech and ash trees. It was indicated that different tree species and tree species diversity levels as well as seasonal differences have a minor effect on bacterial community composition. The results revealed that the microbial community composition was not affected significantly by beech and ash saplings, possibly due to the early developmental stage of the tree saplings. Nevertheless, the obtained data revealed that beech saplings inhibited bacterial growth and promoted fungal growth by a root exudation induced soil pH shift. Tree species, differing in their morphology differentially impact soil microbial communities. The analysis of the soil bacterial and fungal communities in natural forest soils under adult beech and spruce trees revealed a significant impact of the analyzed tree species on soil bacterial and fungal community composition. It was indicated that the bacterial and fungal diversity in the analyzed spruce forest soil was driven by soil pH. The impact of high NO3- depositions on CH4 and N2O gas fluxes, and the soil-inhabiting active bacterial and archaeal communities was studied in mesocosms containing soil from a temperate broad-leaved forest. Strong impacts of NO3- fertilization on CH4 uptake rates and N2O emissions in fertilized soil columns were recorded. N fertilization inhibited the CH4 uptake, while the N2O emission increased. The soil bacterial community shifted over the course of the survey towards a denitrifying community, which was dominated by the genus Rhodanobacter. Furthermore, the bacterial diversity and CO2 emissions were reduced within the N-fertilized soil columns. Moreover, CO2 emission rates dropped in both treatments throughout the experiment. This indicated a reduced activity of soil microorganisms, which might be due to C limitation in the used forest soil. Although a shift in the relative abundance of the nitrifying archaeal genus Nitrosotalea occurred, a significant shift in the archaeal community composition was not observed. The results indicate a considerable contribution of methylotrophic, methanotrophic and nitrifying bacterial species, occurring in low abundance, to the observed CH4 uptake. The impact of ants and their activity on the activity and diversity of soil microbial communities were studied. Ant activity channeled honeydew into soils and thereby reduced the microbial biomass in the litter layer. The δ15N signature, the basal respiration and microbial biomass increased in the soil. In contrast, the cluster analysis of the derived DGGE profiles revealed no distinct differences of the microbial community structure in response to the different treatments. Ant activity affected the structure of bacterial communities in grasslands, due to nest building activity and the input of organic substances. Cluster analysis of the obtained DGGE profiles revealed differences in bacterial community composition in response to the sampling site and ant activity. In addition, bacterial community structures in ant nests differed from the surrounding soil. A secondary project of this thesis was the assessment and comparison of microbial communities present in biological soil crusts, sampled at two sites in extrazonal mountain dry steppes in northern Mongolia. The study revealed clear differences in microbial community structure of the two sampling sites differing in their disturbance history.

Controlling factors for soil bacterial and fungal diversity and composition vary with vegetation types in alpine 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.

Disentangling the effects of driving forces on soil bacterial and fungal communities under shrub encroachment on the Guizhou Plateau of China

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.

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.

Soil microorganisms play key roles in terrestrial biogeochemical cycles and ecosystem functions. However, few studies address how long-term nitrogen (N) addition gradients impact soil bacterial and fungal diversity and community composition simultaneously. Here, we investigated soil bacterial and fungal diversity and community composition based on a long-term (17years) N addition gradient experiment (six levels: 0, 2, 4, 8, 16, 32 gN m-2year-1) in temperate grassland, using the high-throughput Illumina MiSeq sequencing. Results showed that both soil bacterial and fungal alpha diversity responded nonlinearly to the N input gradient and reduced drastically when the N addition rate reached 32gNm-2year-1. The relative abundance of soil bacterial phyla Proteobacteria increased and Acidobacteria decreased significantly with increasing N level. In addition, the relative abundance of bacterial functional groups associated with aerobic ammonia oxidation, aerobic nitrite oxidation, nitrification, respiration of sulfate and sulfur compounds, and chitinolysis significantly decreased under the highest N addition treatment. For soil fungi, the relative abundance of Ascomycota increased linearly along the N enrichment gradient. These results suggest that changes in soil microbial community composition under elevated N do not always support the copiotrophic-oligotrophic hypothesis, and some certain functional bacteria would not simply be controlled by soil nutrients. Further analysis illustrated that reduced soil pH under N addition was the main factor driving variations in soil microbial diversity and community structure in this grassland. Our findings highlight the consistently nonlinear responses of soil bacterial and fungal diversity to increasing N input and the significant effects of soil acidification on soil microbial communities, which can be helpful for the prediction of underground ecosystem processes in light of future rising N deposition.

Soil microbial communities are critical in regulating grassland biogeochemical cycles and ecosystem functions, but the mechanisms of how environmental factors affect changes in the structural composition and diversity of soil microbial communities in different grassland soil types is not fully understood in northwest Liaoning, China. We investigated the characteristics and drivers of bacterial and fungal communities in 4 grassland soil types with 11 sites across this region using high-throughput Illumina sequencing. Actinobacteria and Ascomycota were the dominant phyla of bacterial and fungal communities, respectively, but their relative abundances were not significantly different among different grassland soil types. The abundance, number of OTUs, number of species and diversity of both bacterial and fungal communities in warm and temperate ecotone soil were the highest, while the warm-temperate shrub soil had the lowest microbial diversity. Besides, environmental factors were not significantly correlated with soil bacterial Alpha diversity index. However, there was a highly significant negative correlation between soil pH and Shannon index of fungal communities, and a highly significant positive correlation between plant cover and Chao1 index as well as Observed species of fungal communities. Analysis of similarities showed that the structural composition of microbial communities differed significantly among different grassland soil types. Meanwhile, the microbial community structure of temperate steppe-sandy soil was significantly different from that of other grassland soil types. Redundancy analysis revealed that soil total nitrogen content, pH and conductivity were important influencing factors causing changes in soil bacterial communities, while soil organic carbon, total nitrogen content and conductivity mainly drove the differentiation of soil fungal communities. In addition, the degree of connection in the soil bacterial network of grassland was much higher than that in the fungal network and soil bacterial and fungal communities were inconsistently limited by environmental factors. Our results showed that the microbial community structure, composition and diversity of different grassland soil types in northwest Liaoning differed significantly and were significantly influenced by environmental factors. Microbial community structure and the observation of soil total nitrogen and organic carbon content can predict the health changes of grassland ecosystems to a certain extent.

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 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.

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.

五大连池火山土壤细菌多样性及其群落结构