Effect of intermediate disturbance on soil microbial functional diversity depends on the amount of effective resources

Nitrogen deposition mediates more stochastic processes in structuring plant community than soil microbial community in the Eurasian steppe

Anthropogenic environmental changes may affect community assembly through mediating both deterministic (e.g., competitive exclusion and environmental filtering) and stochastic processes (e.g., birth/death and dispersal/colonization). It is traditionally thought that environmental changes have a larger mediation effect on stochastic processes in structuring soil microbial community than aboveground plant community; however, this hypothesis remains largely untested. Here we report an unexpected pattern that nitrogen (N) deposition has a larger mediation effect on stochastic processes in structuring plant community than soil microbial community (those <2 mm in diameter, including archaea, bacteria, fungi, and protists) in the Eurasian steppe. We performed a ten-year nitrogen deposition experiment in a semiarid grassland ecosystem in Inner Mongolia, manipulating nine rates (0-50 g N m-2 per year) at two frequencies (nitrogen added twice or 12 times per year) under two grassland management strategies (fencing or mowing). We separated the compositional variation of plant and soil microbial communities caused by each treatment into the deterministic and stochastic components with a recently-developed method. As nitrogen addition rate increased, the relative importance of stochastic component of plant community first increased and then decreased, while that of soil microbial community first decreased and then increased. On the whole, the relative importance of stochastic component was significantly larger in plant community (0.552±0.035; mean±standard error) than in microbial community (0.427±0.035). Consistently, the proportion of compositional variation explained by the deterministic soil and community indices was smaller for plant community (0.172-0.186) than microbial community (0.240-0.767). Meanwhile, as nitrogen addition rate increased, the linkage between plant and microbial community composition first became weaker and then became stronger. The larger stochasticity in plant community relative to microbial community assembly suggested that more stochastic strategies (e.g., seeds addition) should be adopted to maintain above- than below-ground biodiversity under the pressure of nitrogen deposition.

Long-term fencing can't benefit plant and microbial network stability of alpine meadow and alpine steppe in Three-River-Source National Park

A great number of fencing facilities has been established in Three-River-Source National Park. However, with the transformation of wild animals into the main consumers of grassland ecosystem and the increasing years of fence (>15 years), whether the fence still has a positive effect on grassland ecosystem has become controversial. Therefore, taking the alpine steppe and alpine meadow in Three-River-Source National Park as the case study, this study focused on the effects of long-term enclosure on different ecological components by investigating plant communities, soil physical and chemical characteristics and soil microbial characteristics (16S, ITS). Furthermore, we evaluated the ecological benefits of long-term fencing based on the stability of plant communities and microbial networks. We found that fencing did not significantly promote the stability of plant community in different grassland types. The analysis of bacteria-fungal symbiotic network indicated that fencing significantly reduced the stability of soil microbial network in alpine meadows. The results of structural equation showed that the microbial community was indirectly affected by the changes of soil moisture content (SMC) and soil total nutrient content in the alpine steppe, and the stability of microbial network was significantly correlated with the diversity of fungal community. In alpine meadows, fencing indirectly affected soil microbial community by changing SMC and pH. High SMC was not conducive to microbial network stability, while high plant community stability was beneficial to microbial network stability. Network stability was remarkably related to bacterial community composition and diversity, as well as fungal community diversity. Therefore, in Three-River-Source National Park, the positive effects of long-term fencing on various components in different grassland types are weak, especially the negative effects on the stability of soil microbial community in alpine meadows may also weaken the stability of the ecosystem, which is not conducive to the ecological protection of grassland ecosystem.

Effects of a long-term operation wetland for wastewater treatment on the spatial pattern and function of microbial communities in groundwater

Constructed wetlands have been used globally for wastewater treatment owing to low energy inputs and operating costs. However, the impact of their long-term operation on groundwater microbial communities is still unclear. This study aims to investigate the effects and further reveal the linkage between a large-scale surface flow constructed wetland (in operation for 14 years) and groundwater. Changes in the characteristics of groundwater microbial communities and their potential influencing factors were studied based on hydrochemical analysis, Illumina MiSeq sequencing, and multivariate statistical analysis methods. Results show that the long-term operation wetland significantly elevated groundwater nutrient levels and increased the risk of ammonia nitrogen pollution compared to background values. An apparent heterogeneity of microbial communities exhibited in the vertical direction and a similarity in the horizontal direction. Wetland operations substantially altered the structure of microbial communities at 3, 5, and 12 m depths, particularly a reduced abundance of denitrifying and chemoheterotrophic functional genera. The formation and evolution of groundwater microbial community structure mainly subjected to the contributions of dissolved oxygen (33.70%), total nitrogen (21.40%), dissolved organic carbon (11.09%), and pH (10.60%) variations resulted from the wetland operation and largely differed in depths. A combined effect of these factors on the groundwater should be concerned for such a long-term running wetland system. This study provides a new insight into the responses of groundwater microbial community structure driving by wetland operation and a better understanding of corresponding variation of microbial-based geochemical processes.

Response of soil fungal community to chromium contamination in agricultural soils with different physicochemical properties

Chromium (Cr) contamination has been of great concern in agricultural soil health due to its persistence, toxicity and bioaccumulation. Fungi, as an essential regulator of soil remediation and biochemical processes, had an unclear response to Cr contamination. In this study, the composition, diversity and interaction mechanisms of fungal communities in agricultural soils from ten different provinces of China were investigated in order to elucidate the fungal community response to varying soil properties and Cr concentrations. The results showed that high concentrations of Cr led to substantial alterations in the fungal community composition. The complex soil properties had a far greater impact on the fungal community structure than the single factor of Cr concentration, with soil available phosphorus (AP) and pH being most influential. Function predictions based on FUNGuild indicated that high concentrations of Cr have a significant impact on certain functional groups of fungi, including mycorrhizal fungi and plant saprotroph. The fungal community tended to resist Cr stress by enhancing interactions and clustering among network modules, while generating new keystone taxa. This study allowed insights into the response of soil fungal community to Cr contamination in different agricultural soils from different provinces and provided a theoretical basis for soil Cr ecological risk assessment and the development of bioremediation techniques for Cr-contaminated soils.

Dynamics of soil bio-physicochemical properties under different disturbance regimes in sal forests in western Himalaya, India

Disturbance is a key factor in controlling vegetation diversity, nutrient influx rate, and biochemical cycling in terrestrial forest ecosystems. Limited studies are available on changes in tree diversity, soil nutrients and enzyme activities in response to different intensities of land disturbances in the Himalayan forests. Present study investigated the impact of varying intensities of disturbances on tree diversity and their relationship with soil physical and bio-chemical properties in sal forests, Western Himalayas. Sites were categorized into four different classes of disturbances, namely, No disturbance (ND), Low disturbance (LD), Moderate disturbance (MD), and High disturbance (HD). Composite samples were collected at two depths (0-15 and 15-30 cm) in each plot to investigate soil physical and biochemical properties. Multivariate analyses were conducted to find relationship between tree vegetation and soil physical and biochemical properties. Soil organic carbon (C_org), total nitrogen (N_ttl), available phosphorous (P_avl), microbial biomass carbon (C_mic), nitrogen (N_mic), phosphorous (P_mic), and enzymes (dehydrogenase (DHA), Urease, acid and alkaline phosphatase) followed the order: MD > ND > LD > HD. Across disturbances, soil physical and biochemical characteristics significantly (p < 0.05) decreased with increasing soil depths. Across the sites, positive correlation was observed among soil microbial biomass, enzymes, C_org, clay, and moisture. Redundancy analysis (RDA) results revealed that species distribution is essential regulator in the variation of prominent soil variables, viz., nutrients (N_ttl and P_avl), C_mic, and DHA across disturbance categories and soil depths. Moreover, variance partitioning analysis (VPA) showed that changes in vegetation composition across disturbance levels explain 13.12 % of the variation in soil biochemical subset higher than soil physicochemical subset. The result illustrated that moderate disturbance increases species composition, soil nutrient properties and microbial activity. These findings would help understand microbial activity and its relationship with disturbances, suggesting site-specific measurements for soil nutrient availability and above-below ground interactions.

From the Mountain to the Valley: Drivers of Groundwater Prokaryotic Communities along an Alpine River Corridor

Rivers are the “tip of the iceberg”, with the underlying groundwater being the unseen freshwater majority. Microbial community composition and the dynamics of shallow groundwater ecosystems are thus crucial, due to their potential impact on ecosystem processes and functioning. In early summer and late autumn, samples of river water from 14 stations and groundwater from 45 wells were analyzed along a 300 km transect of the Mur River valley, from the Austrian alps to the flats at the Slovenian border. The active and total prokaryotic communities were characterized using high-throughput gene amplicon sequencing. Key physico-chemical parameters and stress indicators were recorded. The dataset was used to challenge ecological concepts and assembly processes in shallow aquifers. The groundwater microbiome is analyzed regarding its composition, change with land use, and difference to the river. Community composition and species turnover differed significantly. At high altitudes, dispersal limitation was the main driver of groundwater community assembly, whereas in the lowland, homogeneous selection explained the larger share. Land use was a key determinant of the groundwater microbiome composition. The alpine region was more diverse and richer in prokaryotic taxa, with some early diverging archaeal lineages being highly abundant. This dataset shows a longitudinal change in prokaryotic communities that is dependent on regional differences affected by geomorphology and land use.

Which soil microbiome? Bacteria, fungi, and protozoa communities show different relationships with urban green space type and use-intensity

Exposure to diverse microbial communities early in life can help support healthy human immune function. Soil microbiomes in public and private urban green spaces are potentially important sources of contact with diverse microbiomes for much of the global population. However, we lack understanding of how soil microbial communities vary across and within urban green spaces, and whether these patterns vary across microbial kingdoms; closing this knowledge gap may help us optimise green spaces' capacities to provide this ecosystem service. Here we explore the diversity and community compositions of soil microbiomes across urban green space types in Tasmania, Australia. Specifically, we analysed soil bacterial, fungal, and protozoan diversity and composition across private backyards and public parks. Within parks, we conducted separate sampling for areas of high and low intensity use. We found that: (i) bacteria, fungi, and protozoa showed different patterns of variation, (ii) bacterial alpha-diversity was lowest in low-intensity use areas of parks, (iii) there was relatively little variation in the community composition across backyards, and high and low intensity-use park areas and (iv) neither human-associated bacteria, nor potential microbial community function of bacteria and fungi differed significantly across green space types. To our knowledge, this is the first urban soil microbiome analysis which analyses these three soil microbial kingdoms simultaneously across public and private green space types and within public spaces according to intensity of use. These findings demonstrate how green space type and use intensity may impact on soil microbial diversity and composition, and thus may influence our opportunity to gain healthy exposure to diverse environmental microbiomes.

Effects of Forest Gaps on the Structure and Diversity of Soil Bacterial Communities in Weeping Cypress Forest Plantations

The decline in forest ecological function caused by pure forest plantations planted in the Yangtze River basin is becoming increasingly serious. To investigate this problem, we selected the local low-efficiency weeping cypress plantations for forest gap transformation. Three forest gap sizes, specifically large, medium, and small gaps, were established, and the effects of gap sizes on soil bacterial community structure and diversity in winter and summer were studied compared to no gaps (CK; control). Compared to CK, forest gaps had a significant effect on soil organic carbon (SOC) and soil total nitrogen (TN), and the highest values of SOC and soil TN under two seasons occurred in large forest gaps. The interactions of forest gap sizes and seasons had significant effects on pH, SOC, TN, and alpha diversity indices, including Simpson, Chao1, and ACE indices. Compared to winter, forest gaps significantly increased the soil bacterial community diversity indices in summer. Forest gap sizes significantly affected the composition of the bacterial community, but the composition of the dominant bacteria at the phyla and genera levels was similar. Linear discriminant effect size (LEfSe) analysis showed that there were 32 indicator bacterial species in two seasons. Co-occurrence network analysis revealed that the relationship of the soil bacterial community at the phyla level was complex, and there was a significant positive correlation among bacterial species. Soil bulk density (BD) and soil moisture (SM) significantly affected the soil bacterial alpha diversity indices. The composition of the dominant bacteria at the phyla level was significantly affected by soil microbial carbon (MBC), whereas the composition of dominant bacteria at the genera level was affected by soil hydrolysable nitrogen (AN) and the carbon/nitrogen (C/N) ratio. In this study, compared to the other forest gaps, large forest gaps were more conducive to the accumulation of soil nutrients, thus improving the structure of the soil bacterial community. Importantly, changes in the soil bacterial community structure due to gap formation may have profound effects on soil biogeochemical processes in weeping cypress forest plantations.

Disturbance-mediated invasions are dependent on community resource abundance

Disturbances can facilitate biological invasions, with the associated increase in resource availability being a proposed cause. Here, we experimentally tested the interactive effects of disturbance regime (different frequencies of biomass removal at equal intensities) and resource abundance on invasion success using a factorial design containing five disturbance frequencies and three resource levels. We invaded populations of the bacterium Pseudomonas fluorescens with two ecologically different invader morphotypes: a fast‐growing “colonizer” type and a slower growing “competitor” type. As resident populations were altered by the treatments, we additionally tested their effect on invader success. Disturbance frequency and resource abundance interacted to affect the success of both invaders, but this interaction differed between the invader types. The success of the colonizer type was positively affected by disturbance under high resources but negatively under low. However, disturbance negatively affected the success of the competitor type under high resource abundance but not under low or medium. Resident population changes did not alter invader success beyond direct treatment effects. We therefore demonstrate that the same disturbance regime can either be beneficial or detrimental for an invader depending on both community resource abundance and its life history. These results may help to explain some of the inconsistencies found in the disturbance‐invasion literature.

Adaptation of Soil Fungal Community Structure and Assembly to Long- Versus Short-Term Nitrogen Addition in a Tropical Forest

Soil fungi play critical roles in ecosystem processes and are sensitive to global changes. Elevated atmospheric nitrogen (N) deposition has been well documented to impact on fungal diversity and community composition, but how the fungal community assembly responds to the duration effects of experimental N addition remains poorly understood. Here, we aimed to investigate the soil fungal community variations and assembly processes under short- (2 years) versus long-term (13 years) exogenous N addition (∼100 kg N ha^–1 yr^–1) in a N-rich tropical forest of China. We observed that short-term N addition significantly increased fungal taxonomic and phylogenetic α-diversity and shifted fungal community composition with significant increases in the relative abundance of Ascomycota and decreases in that of Basidiomycota. Short-term N addition also significantly increased the relative abundance of saprotrophic fungi and decreased that of ectomycorrhizal fungi. However, unremarkable effects on these indices were found under long-term N addition. The variations of fungal α-diversity, community composition, and the relative abundance of major phyla, genera, and functional guilds were mainly correlated with soil pH and NO₃^––N concentration, and these correlations were much stronger under short-term than long-term N addition. The results of null, neutral community models and the normalized stochasticity ratio (NST) index consistently revealed that stochastic processes played predominant roles in the assembly of soil fungal community in the tropical forest, and the relative contribution of stochastic processes was significantly increased by short-term N addition. These findings highlighted that the responses of fungal community to N addition were duration-dependent, i.e., fungal community structure and assembly would be sensitive to short-term N addition but become adaptive to long-term N enrichment.

Shift of bacterial communities in heavy metal-contaminated agricultural land during a remediation process

Anthropogenic activities accompanied by heavy metal waste threaten the environment. Heavy metal pollution alters the soil microbial community composition, and the microorganisms that adapt to this stress increase in abundance. The remediation process of contaminated soil not only reduces the concentration of heavy metals but also alters the bacterial communities. High-throughput 16S rDNA sequencing techniques were applied to understand the changes in soil microbial communities. Using the remediation approach of the soil mixing, the concentrations of heavy metals in the contaminated areas were diluted and the soil environment was changed. The change of soil environment as a disturbance contributed to the alteration of microbial diversity of the remediated areas. The pH and heavy metals (Cr, Cu, Ni, and Zn) were the most influential factors driving the changes in community structure. The bacterial community structure was significantly different among sample areas. The decrease of heavy metals in soil may be the important factors that changed the microbial composition. This study provides the better understanding of the changes in composition of microbial communities affected by the remediation process in heavy metal-contaminated soil.

Land use in urban areas impacts the composition of soil bacterial communities involved in nitrogen cycling. A case study from Lefkosia (Nicosia) Cyprus

The different types of land-use and soil lithology in urban and peri-urban areas of modern cities compose a complex mosaic of soil ecosystems. It is largely unknown how these differences result in changes in bacterial community composition and structure as well as in functional guilds involved in N cycling. To investigate the bacterial composition and the proportion of denitrifiers in agricultural, forested, schoolyard and industrial areas, 24 samples were collected from urban and peri-urban sites of Lefkosia. Bacterial diversity and the proportion of denitrifiers were assessed by NGS and qPCR, respectively. Proteobacteria, Actinobacteria, Bacteriodetes, Chloroflexi, Acidobacteria and Planctomycetes were identified as the most dominant phyla across all sites, while agricultural sites exhibited the highest bacterial diversity. Heavy metals such as Co, Pb, V and Al were identified as key factors shaping bacterial composition in industrial and schoolyard sites, while the bacterial assemblages in agricultural and forested sites were associated with Ca. Variance partitioning analysis showed that 10.2% of the bacterial community variation was explained by land use management, 5.1% by chemical elements due to soil lithology, and 1.4% by sampling location. The proportion of denitrifiers varied with land use management. In industrial and schoolyard sites, the abundance of the nosZII bacterial community increased while nirK abundance declined. Our data showed that land use and lithology have a moderate impact on the bacterial assemblages in urban and peri-urban areas of Lefkosia. As the nosZII bacterial community is important to the N₂O sink capacity of soils, it would be interesting to elucidate the factors contributing to the proliferation of the nosZII clade in these soils.

Disturbance-level-dependent post-disturbance succession in a Eurasian steppe

Anthropogenic disturbances may decrease as we take measures to control them. However, the patterns and mechanisms of post-disturbance ecosystem succession have rarely been studied. Here we reported that disturbance level determined the importance of stochastic relative to deterministic changes in ecosystem components (plant community composition, soil microbial community composition, and soil physicochemical indices), and thus predefined the pattern of post-disturbance ecosystem succession. We proposed a theoretical framework with five disturbance levels corresponding to distinct succession patterns. We conducted a nitrogen addition experiment in a temperate steppe, monitored these ecosystem components during "disturbance" treatment (2010-2014) and post-treatment "succession" (2014-2018). The disturbance level experienced by each component in each treatment was inferred by fitting the observed succession patterns into the theoretical framework. The mean disturbance level of these components was found to increase quadratically with nitrogen addition rate. This was because increasing nitrogen addition reduced the importance of stochastic relative to deterministic changes in these components, and these changes had a quadratic relationship with disturbance level. Overall, our results suggested that by monitoring the importance of stochastic relative to deterministic changes in an ecosystem, we can estimate disturbance levels and predict succession patterns, as well as propose disturbance-level-dependent strategies for post-disturbance restoration.