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

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

Soil pH and nutrients shape the vertical distribution of microbial communities in an alpine wetland

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.

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 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.

Qinghai–Tibet Plateau is considered a region vulnerable to the effects of climate change. Studying the effects of climate change on the structure and function of soil microbial communities will provide insight into the carbon cycle under climate change. However, to date, changes in the successional dynamics and stability of microbial communities under the combined effects of climate change (warming or cooling) remain unknown, which limits our ability to predict the consequences of future climate change. In this study, in situ soil columns of an Abies georgei var. smithii forest at 4,300 and 3,500 m elevation in the Sygera Mountains were incubated in pairs for 1 year using the PVC tube method to simulate climate warming and cooling, corresponding to a temperature change of ±4.7°C. Illumina HiSeq sequencing was applied to study alterations in soil bacterial and fungal communities of different soil layers. Results showed that warming did not significantly affect the fungal and bacterial diversity of the 0–10 cm soil layer, but the fungal and bacterial diversity of the 20–30 cm soil layer increased significantly after warming. Warming changed the structure of fungal and bacterial communities in all soil layers (0–10 cm, 10–20 cm, and 20–30 cm), and the effect increased with the increase of soil layers. Cooling had almost no significant effect on fungal and bacterial diversity in all soil layers. Cooling changed the structure of fungal communities in all soil layers, but it showed no significant effect on the structure of bacterial communities in all soil layers because fungi are more adapted than bacteria to environments with high soil water content (SWC) and low temperatures. Redundancy analysis (RDA) and hierarchical analysis showed that changes in soil bacterial community structure were primarily related to soil physical and chemical properties, whereas changes in soil fungal community structure primarily affected SWC and soil temperature (Soil Temp). The specialization ratio of fungi and bacteria increased with soil depth, and fungi were significantly higher than bacteria, indicating that climate change has a greater impact on microorganisms in deeper soil layers, and fungi are more sensitive to climate change. Furthermore, a warmer climate could create more ecological niches for microbial species to coexist and increase the strength of microbial interactions, whereas a cooler climate could have the opposite effect. However, we found differences in the intensity of microbial interactions in response to climate change in different soil layers. This study provides new insights to understand and predict future effects of climate change on soil microbes in alpine forest ecosystems.

Effect of chlorantraniliprole on soil bacterial and fungal diversity and community structure

Environmental selection and dispersal limitation are two basic processes underlying community assembly. The relative importance of those two processes differs across scales, community identities, and community types. The processes responsible for structuring microbial communities in soil of temperate subalpine forest are poorly understood. Here, we investigated the relationship between soil bacterial community structure and environmental factors, and quantified the relative role of edaphic factors, vegetation, and spatial variables in shaping the structure of six soil bacterial communities (LpMC1, LpMC2, PwMC, PmMC, PtMC, and BMC) in five forest types including Larix principis-rupprechtii, Picea wilsonii, Picea meyeri, Pinus tabulaeformis, and Betula platyphylla in Pangquangou Nature Reserve by using PCR-DGGE technology. Our results showed that the structure and biodiversity of bacterial communities were significantly different among six communities. The biodiversity of bacterial community were higher in LpMC2 and PtMC, lowest in PmMC, and highest in LpMC1. Soil environmental factors, such as pH, soil water content, total carbon, total nitrogen, soil organic matter, available phosphorous, and soil enzymes, were significantly correlated with biodiversity and structure of soil bacterial community. The beta diversity of bacterial communities were significantly correlated with geographic distance, indicating the influence of dispersal limitation on the structure of bacterial community. The order of driving force on the structure of bacterial community was edaphic factors (0.27), spatial factor (0.19) and vegetation (0.15) in six samples. Using regional soil microbes from 10 samples around reserve as source community, results from the microcosm experiments showed that the edaphic factors were the predominant driving factors (0.35) on structure of artificial dispersal bacterial community, while the high diversity of source microbial community affected the structure of microcosm soil. In summary, at local scale, environmental selection predominantly determined the structural and biodiversity of soil bacterial communities in temperate subalpine forest, while dispersal limitation played a significant role. Such a result indicated that deterministic processes and stochastic processes played important roles in shaping the structure of soil bacterial community at local scale, with the former having the leading role. The composition of dispersal soil bacteria community was source-dependent but also modulated by local environmental selection.

Investigating the response of soil microbial communities to nitrogen (N) deposition is critical to understanding biogeochemical processes and the sustainable development of forests. However, whether and to what extent different forms of N deposition affect soil microbial communities in temperate forests is not fully clear. In this work, a field experiment with three years of simulated nitrogen deposition was conducted in temperate forests. The glycine and urea were chosen as organic nitrogen (ON) source, while NH4NO3 was chosen as inorganic nitrogen (IN) source. Different ratios of ON to IN (CK = 0:0, Mix-1 = 10:0, Mix-2 = 7:3, Mix-3 = 5:5, Mix-4 = 3:7, Mix-5 = 0:10) were mixed and then used with equal total amounts of 10 kg·N·ha−1·a−1. We determined soil microbial diversity and community composition for bacteria and fungi (16S rRNA and ITS), and soil parameters. Different forms of N addition significantly changed the soil bacterial and fungal communities. Mixed N sources had a positive effect on soil bacterial diversity and a negative effect on fungal diversity. Bacterial and fungal community structures were significantly separated under different forms of N addition. Soil pH was the main factor affecting the change in fungal community structure, while bacterial community structure was mainly controlled by STN. We also found that Proteobacteria, Acidobacteriota, Basidiomycota and Ascomycota were the most abundant phyla, regardless of the form of N addition. RDA showed that C/P and NH4+ were the main factors driving the change in bacterial community composition, and C/P, pH and C/N were the main factors driving the change in fungal community composition. Our results indicate that different components of N deposition need to be considered when studying the effects of N deposition on soil microorganisms in terrestrial ecosystems.

Composition of soil viral and bacterial communities after long-term tillage, fertilization, and cover cropping management

The influence of soil properties on the structure of bacterial and fungal communities across land-use types

Soil bacterial communities are a critical component for stability and function of terrestrial ecosystems. Viruses are ubiquitous in soils and have significant impacts on the structure and functions of bacterial host communities. However, little is known about the variation of bacterial and viral communities and their connection under various land use management practices. In this study, we evaluated bacterial and viral diversity using 16s rRNA sequencing and RAPD-PCR, respectively, and estimated viral and bacterial abundances by enumeration method, and used structural equation model to reveal relationship between viruses, bacteria, and soil properties, in soils from a long-term conservation management experimental site in western Tennessee USA. Inorganic N fertilization, cover cropping, and tillage treatments showed no significant differences in bacterial alpha-diversity but significantly influenced the structure, as suggested by differences in beta-diversity of bacterial communities. Higher soil pH and water content were favorable to bacterial abundances. Cover cropping, soil water content, and bacterial abundances may explain the variation of viral abundances and community structure in soil. Structural equation modeling showed that bacterial abundances positively influenced viral abundances, and in turn virus abundances and bacterial alpha diversity affected the level of extractable dissolved organic C, which exerted a feedback effect on the structure of bacterial communities. This feedback loop suggests that viral lysates might significantly contribute to reshaping bacterial community structure and indirect influence bacterial alpha diversity. This supports the theory of the “viral shunt” in soil ecosystems. This study indicated that long-term conservation management can reshape soil bacterial and viral communities and influence their interactions in biogeochemical processes.

Methyl-mercury affects microbial activity and biomass, bacterial community structure but rarely the fungal community structure

Fire severity shapes plant colonization effects on bacterial community structure, microbial biomass, and soil enzyme activity in secondary succession of a burned forest

五大连池火山土壤细菌多样性及其群落结构