Grazing-induced microbiome alterations drive soil organic carbon turnover and productivity in meadow steppe

Grazing intensity alters network complexity and predator-prey relationships in the soil microbiome

Grasslands are recognized as important reservoirs of soil biodiversity. Livestock grazing is implemented as a grassland management strategy to improve soil quality and enhance plant diversity. Soil microbial communities play a pivotal role in grassland ecosystems, so it is important to examine whether grazing practices affect the soil microbiome. Previous studies on grazing have primarily focused on bacteria and fungi, overlooking an important group-protists. Protists are vital in soil microbiomes as they drive nutrient availability and trophic interactions. Determining the impact of grazing on protists and their relationships with bacterial and fungal communities is important for understanding soil microbiome dynamics in grazed ecosystems. In this study, we investigated soil bacterial, fungal, and protist communities under four grazing levels: no grazing, moderate-use grazing, full-use grazing, and heavy-use grazing. Our results showed that heavy grazing led to a greater diversity of protists with specific groups, such as Discoba and Conosa, increasing in abundance. We also found strong associations between protist and bacterial/fungal members, indicating their intricate relationships within the soil microbiome. For example, the abundance of predatory protists increased under grazing while arbuscular mycorrhizal fungi decreased. Notably, arbuscular mycorrhizae were negatively associated with predatory groups. Furthermore, we observed that microbial network complexity increased with grazing intensity, with fungal members playing an important role in the network. Overall, our study reports the impact of temporal grazing intensity on soil microbial dynamics and highlights the importance of considering protist ecology when evaluating the effects of grazing on belowground communities in grassland ecosystems.

IMPORTANCE

The significance of this study lies in its exploration of the effects of temporal grazing intensity on the dynamics of the soil microbiome, specifically focusing on the often-neglected role of protists. Our findings provide insights into the complex relationships between protists, bacteria, and fungi, emphasizing their impact on trophic interactions in the soil. Gaining a better understanding of these dynamics is essential for developing effective strategies for grassland management and conservation, underscoring the importance of incorporating protist ecology into microbiome studies in grasslands.

The effects of livestock grazing on physicochemical properties and bacterial communities of perlite-rich soil

Livestock grazing has been proposed as a cost-effective way to reclaim post-mining lands. It can enhance soil fertility and biodiversity, but its impacts on soil quality and microbial communities vary across soil types. Moreover, waste from grazing raises concerns about pathogens that could pose risks to animal and human health. This study investigated the effects of grazing on post-mining perlite-rich soil in central Thailand. A comparative analysis of soil physicochemical properties and bacterial diversity was conducted between grazed and ungrazed sites. Bacterial diversity was assessed using 16S amplicon sequencing. The perlite-rich soil was found to be sandy, acidic, and to have low nutritional content. Grazing significantly improved the soil texture and nutrient content, suggesting its potential as a cost-effective reclamation strategy. The 16S metagenomic sequencing analysis revealed that microbial communities were impacted by livestock grazing. Specifically, shifts in the dominant bacterial phyla were identified, with increases in Firmicutes and Chloroflexi and a decrease in Actinobacteria. Concerns about increased levels of pathogenic Enterobacteriaceae due to grazing were not substantiated in perlite-rich soil. These bacteria were consistently found at low levels in all soil samples, regardless of livestock grazing. This study also identified a diverse population of Streptomycetaceae, including previously uncharacterized strains/species. This finding could be valuable given that this bacterial family is known for producing antibiotics and other secondary metabolites. However, grazing adversely impacted the abundance and diversity of Streptomycetaceae in this specific soil type. In line with previous research, this study demonstrated that the response of soil microbial communities to grazing varies significantly depending on the soil type, with unique responses appearing to be associated with perlite-rich soil. This emphasizes the importance of soil-specific research in understanding how grazing affects microbial communities. Future research should focus on optimizing grazing practices for perlite-rich soil and characterizing the Streptomycetaceae community for potential antibiotic and secondary metabolite discovery. The obtained findings should ultimately contribute to sustainable post-mining reclamation through livestock grazing and the preservation of valuable microbial resources.

Bacteria-Like Gaiella Accelerate Soil Carbon Loss by Decomposing Organic Matter of Grazing Soils in Alpine Meadows on the Qinghai-Tibet Plateau

The alpine meadows of the Qinghai-Tibet Plateau have significant potential for storing soil carbon, which is important to global carbon sequestration. Grazing is a major threat to its potential for carbon sequestration. However, grazing poses a major threat to this potential by speeding up the breakdown of organic matter in the soil and releasing carbon, which may further lead to positive carbon-climate change feedback and threaten ecological security. Therefore, in order to accurately explore the driving mechanism and regulatory factors of soil organic matter decomposition in grazing alpine meadows on the Qinghai-Tibet Plateau, we took the grazing sample plots of typical alpine meadows as the research object and set up grazing intensities of different life cycles, aiming to explore the relationship and main regulatory factors of grazing on soil organic matter decomposition and soil microorganisms. The results show the following: (1) soil microorganisms, especially Acidobacteria and Acidobacteria, drove the decomposition of organic matter in the soil, thereby accelerating the release of soil carbon, which was not conducive to soil carbon sequestration in grassland; (2) the grazing triggering effect formed a positive feedback with soil microbial carbon release, accelerating the decomposition of organic matter and soil carbon loss; and (3) the grazing ban and light grazing were more conducive to slowing down soil organic matter decomposition and increasing soil carbon sequestration.

Grazing exclusion-induced changes in soil fungal communities in a highly desertified Brazilian dryland

Soil desertification poses a critical ecological challenge in arid and semiarid climates worldwide, leading to decreased soil productivity due to the disruption of essential microbial community processes. Fungi, as one of the most important soil microbial communities, play a crucial role in enhancing nutrient and water uptake by plants through mycorrhizal associations. However, the impact of overgrazing-induced desertification on fungal community structure, particularly in the Caatinga biome of semiarid regions, remains unclear. In this study, we assessed the changes in both the total fungal community and the arbuscular mycorrhizal fungal community (AMF) across 1. Natural vegetation (native), 2. Grazing exclusion (20 years) (restored), and 3. affected by overgrazing-induced degradation (degraded) scenarios. Our assessment, conducted during both the dry and rainy seasons in Irauçuba, Ceará, utilized Internal Transcribed Spacer (ITS) gene sequencing via Illumina® platform. Our findings highlighted the significant roles of the AMF families Glomeraceae (∼71% of the total sequences) and Acaulosporaceae (∼14% of the total sequences) as potential key taxa in mitigating climate change within dryland areas. Moreover, we identified the orders Pleosporales (∼35% of the total sequences) and Capnodiales (∼21% of the total sequences) as the most abundant soil fungal communities in the Caatinga biome. The structure of the total fungal community differed when comparing native and restored areas to degraded areas. Total fungal communities from native and restored areas clustered together, suggesting that grazing exclusion has the potential to improve soil properties and recover fungal community structure amid global climate change challenges.

Understanding the Ecological Robustness and Adaptability of the Gut Microbiome in Plastic-Degrading Superworms (Zophobas atratus) in Response to Microplastics and Antibiotics

Recent discoveries indicate that several insect larvae are capable of ingesting and biodegrading plastics rapidly and symbiotically, but the ecological adaptability of the larval gut microbiome to microplastics (MPs) remains unclear. Here, we described the gut microbiome assemblage and MP biodegradation of superworms (Zophobas atratus larvae) fed MPs of five major petroleum-based polymers (polyethylene, polypropylene, polystyrene, polyvinyl chloride, and polyethylene terephthalate) and antibiotics. The shift of molecular weight distribution, characteristic peaks of C═O, and metabolic intermediates of residual polymers in egested frass proved depolymerization and biodegradation of all MPs tested in the larval intestines, even under antibiotic suppression. Superworms showed a wide adaptation to the digestion of the five polymer MPs. Antibiotic suppression negatively influenced the survival rate and plastic depolymerization patterns. The larval gut microbiomes differed from those fed MPs and antibiotics, indicating that antibiotic supplementation substantially shaped the gut microbiome composition. The larval gut microbiomes fed MPs had higher network complexity and stability than those fed MPs and antibiotics, suggesting that the ecological robustness of the gut microbiomes ensured the functional adaptability of larvae to different MPs. In addition, Mantel's test indicated that the gut microbiome assemblage was obviously related to the polymer type, the plastic degradability, antibiotic stress, and larval survival rate. This finding provided novel insights into the self-adaptation of the gut microbiome of superworms in response to different MPs.

Exclusion of livestock decouples the relationship between plant production and diversity, species richness on complex topography in typical steppe in the Loess Plateau, China

Grazing is widely used in more than one-forth of global terrestrial ecosystems, with three quarters are distributed on complex topography. Grazing and topography have both resulted in degradation of approximately 49 % of natural grasslands. However, research on the interaction between topography and livestock exclusion on grassland characteristics is scarce. This study was carried out on a typical steppe to explore the effect of topography and enclosure year on vegetation characteristics. Aboveground biomass, and species richness were examined for three different enclosure years (0, 3, and 6 years), on four slopes (0°, 15°, 30°, and 45° slope), and three aspects (flat, shady and sunny). The results indicated that: The aboveground biomass on the 0° slope had a greater value after 6 years of the enclosure. Aboveground biomass increased with the increasing enclosure year, while it decreased with increasing slope except enclosure for 0 year on shady slope. Aboveground biomass on the shady slopes was greater than on the sunny slopes. Species richness of community and perennial plants increased with increasing slope and enclosure year. The annual plants richness inversely correlated with slope and enclosure year. All plant diversity indexes increased with increasing enclosure year. Margalef and Shannon-wiener indexes decreased with increasing slope, while Simpson and Pielou indexes increased. This paper demonstrates that aspect, slope and enclosure affect aboveground biomass by affecting other vegetation characteristics. In conclusion, grassland production can be improved with moderate livestock exclusion under different topography.

Response of microbial communities to the changes in grazing intensity and season in a typical steppe

Livestock grazing is an influencing factor playing a key role in shaping the plant community, microbial community, and soil properties in grassland ecosystems. Northern China's Loess Plateau has been used for livestock grazing for centuries and is a vulnerable ecosystem. In this study, the fates of bacterial and fungal communities of the typical steppe of the Loess Plateau were investigated under increasing grazing intensities practiced in summer and winter seasons. The results revealed changes in soil physiochemical properties, plant community properties, and microbial diversity in response to alterations in the grazing intensity. The alpha diversity of microbial communities (including bacteria and fungi) exhibited an uneven trend during summer grazing due to an increase in grazing intensity, but it decreased during winter grazing; however, the observed changes were not significant. The beta diversity of the bacterial community was highly influenced by grazing intensity, the summer community clustered near nongrazing, and the winter community presented significantly different results. The beta diversity of the fungal community was not influenced by grazing intensity or season. Grazing induced the growth of fast-growing bacteria (such as Actinobacteria and Firmicutes) and saprophytic fungi and a reduction in overall pathogenic traits. Co-occurrence network analysis and a structural equation model revealed changes in soil and plant properties (such as soil nitrogen level, soil organic carbon level, aboveground biomass, and litter biomass), with an increase in grazing intensity contributing to alterations in bacterial and fungal diversities. This finding demonstrates that grazing intensity can directly affect soil microbes and play an indirect role by modifying soil nutrients and reducing plant biomass, which eventually contributes to changes in microbial communities. Overall, implementing low grazing intensity is suggested for maintaining the microbial community structure the same as that of the native microbiome (ungrazed) in the steppe ecosystems.

Rewilding by large ungulates contributes to organic carbon storage in soils

The concept of rewilding, which focuses on managing ecosystem functions through self-regulation by restoring trophic interactions through introduced animal species with little human intervention, has gained increasing attention as a proactive and efficient approach to restoring ecosystems quickly and on a large scale. However, the science of rewilding has been criticized for being largely theory-based rather than evidence-based, with available data being geographically biased towards the Netherlands and Scandinavian countries, and a lack of objective data on rewilding effects on soil processes and C sequestration. In response to a call for data-driven experimental rewilding projects focused on national contexts, we collected unique data on the effects of large herbivore rewilding on soil properties from eight sites in the Czech Republic. These include sites with a wide range of edaphic characteristics that were grazed by Exmoor ponies, European bison, and back-bred Bos primigenius cattle (singly or in combination) for 2-6 years on areas ranging from ≈30 to ≈250 ha. Despite the relatively short duration of rewilding actions and considerable variability in the response rate of soil properties to grazing, our results indicate improved nutrient availability (evidenced by higher nitrification rate or higher soluble nitrogen concentration) and accelerated ecosystem metabolism (higher soil microbial biomass and dissolved carbon content). On longer-grazed pastures, rewilding contributed to soil carbon sequestration associated with increased water holding capacity and improved soil structure. However, other soil properties (reduced dissolved P concentration or total P content) showed signs of low P availability in the soils of the rewilding sites. Therefore, carcass retention should be considered where possible. Our data, although limited in number and geographic coverage, allow us to conclude that large ungulate rewilding has the potential to enhance soil carbon sequestration and related ecosystem services in rewilding areas. At the same time, we urge similar monitoring as an essential part of other rewilding projects, which will ultimately allow much more robust conclusions about the effects of this management on soils.

Cattle grazing management affects soil microbial diversity and community network complexity in the Northern Great Plains

Soil microbial communities play a vital role in the biogeochemical cycling and ecological functioning of grassland, but may be affected by common land uses such as cattle grazing. Changes in microbial diversity and network complexity can affect key ecosystem functions such as nutrient cycling. However, it is not well known how microbial diversity and network complexity respond to grazing in the Northern Great Plains. Consequently, it is important to understand whether variation in grazing management alters the diversity and complexity of grassland microbial communities. We compared the effect of intensive adaptive multi-paddock (AMP) grazing and conventional grazing practices on soil microbial communities using 16S/ITS amplicon sequencing. Samples were collected from grasslands in 13 AMP ranches and 13 neighboring, conventional ranches located across the Canadian prairies. We found that AMP grazing increased fungal diversity and evenness, and led to more complex microbial associations. Acidobacteria, Actinobacteria, Gemmatimonadetes, and Bacteroidetes were keystone taxa associated with AMP grazing, while Actinobacteria, Acidobacteria, Proteobacteria, and Armatimonadetes were keystone taxa under conventional grazing. Besides overall grazing treatment effects, specific grazing metrics like cattle stocking rate and rest-to-grazing ratio affected microbial richness and diversity. Bacterial and fungal richness increased with elevated stocking rate, and fungal richness and diversity increased directly with the rest-to-grazing ratio. These results suggest that AMP grazing may improve ecosystem by enhancing fungal diversity and increasing microbial network complexity and connectivity.

Planting grass enhances relations between soil microbes and enzyme activities and restores soil functions in a degraded grassland

Introduction

Forage culture is a common way to restore degraded grasslands and soil functions, in which the reconstruction of the soil microbial community and its relationship with extracellular enzyme activity (EEAs) can characterize the recovery effects of degraded grasslands. However, the impacts of forage culture on the interaction between soil microbes and EEAs and whether the recovery effect of soil functions depends on the varying degradation statuses remain unclear.

Methods

We conducted a plantation of a dominant grass, Leymus chinensis, in the soil collected from severe, moderate, light, and non-degradation statuses in the Songnen grassland in northeastern China. We measured soil microbial diversity and soil EEAs, and predicted microbial functional groups using FUNGuild.

Results

The results showed that L. chinensis culture promoted soil bacterial alpha diversity and soil EEAs only in the moderate degradation status, indicating a dramatic dependence of the recovery effects of the grass culture on degradation status of the grassland. After planting L. chinensis for 10 weeks, a decreasing trend in the chemoheterotrophy and nitrate-reduction microbial functional groups was found. In contrast, the abundance of the nitrogen (N)-fixing microbial functional group tended to increase. The positive correlation between soil EEAs and the nitrate-reduction and N-fixing microbial functional groups was enhanced by planting L. chinensis, indicating that grass culture could promote soil N cycle functions.

Conclusion

We illuminate that grass culture may promote the restoration of soil functions, especially soil N cycling in degraded grasslands, and the recovery effect may depend on the grassland degradation status. We emphasized that selection of the plant species for restoration of grasslands needs to consider the restoration effects of microbial functional groups and soil functions.

Spatial Variation in Responses of Plant Spring Phenology to Climate Warming in Grasslands of Inner Mongolia: Drivers and Application

Plant spring phenology in grasslands distributed in the Northern Hemisphere is highly responsive to climate warming. The growth of plants is intricately influenced by not only air temperature but also precipitation and soil factors, both of which exhibit spatial variation. Given the critical impact of the plant growth season on the livelihood of husbandry communities in grasslands, it becomes imperative to comprehend regional-scale spatial variation in the response of plant spring phenology to climate warming and the effects of precipitation and soil factors on such variation. This understanding is beneficial for region-specific phenology predictions in husbandry communities. In this study, we analyzed the spatial pattern of the correlation coefficient between the start date of the plant growth season (SOS) and the average winter-spring air temperature (WST) of Inner Mongolia grassland from 2003 to 2019. Subsequently, we analyzed the importance of 13 precipitation and soil factors for the correlation between SOS and average WST using a random forest model and analyzed the interactive effect of the important factors on the SOS using linear mixing models (LMMs). Based on these, we established SOS models using data from pastoral areas within different types of grassland. The percentage of areas with a negative correlation between SOS and average WST in meadow and typical grasslands was higher than that in desert grasslands. Results from the random forest model highlighted the significance of snow cover days (SCD), soil organic carbon (SOC), and soil nitrogen content (SNC) as influential factors affecting the correlation between SOS and average WST. Meadow grasslands exhibited significantly higher levels of SCD, SOC, and SNC compared to typical and desert grasslands. The LMMs indicated that the interaction of grassland type and the average WST and SCD can effectively explain the variation in SOS. The multiple linear models that incorporated both average WST and SCD proved to be better than models utilizing WST or SCD alone in predicting SOS. These findings indicate that the spatial patterns of precipitation and soil factors are closely associated with the spatial variation in the response of SOS to climate warming in Inner Mongolia grassland. Moreover, the average WST and SCD, when considered jointly, can be used to predict plant spring phenology in husbandry communities.

The role of large mammalian herbivores in shaping and maintaining soil microbial communities of natural mineral licks: A case study on sika deer at the firebreak adjacent to the Sino-Russian border

Mineral licks are indispensable habitats to the life history of large mammal herbivores (LMH). Geophagy at licks may provide the necessary minerals for LMH, while LMH may be ecosystem engineers of licks by altering vegetation cover and soil physicochemical properties (SPCP). However, the precise relationship between the LMH and licks remains unclear. To clarify the geophagy function of licks for LMH and their influence on soil at licks, we recorded visitation patterns of sika deer around licks and compared SPCP and microbial communities with the surrounding matrix in a firebreak adjacent to the Sino-Russian border. Our study indirectly supports the "sodium supplementation" hypothesis. Proofs included (1) a significantly higher sodium, iron, and aluminum contents than the matrix, while lower carbon, nitrogen, and moisture contents; (2) significantly higher deer visitation during sodium-demand season (growing season), along with an avoidance of licks with high iron contents, which is toxic when overdose. The microbes at the licks differed from those at the matrix, mainly driven by low soil carbon and nitrogen and altered biogeochemical cycles. The microbial communities of licks are vulnerable because of their unstable state and susceptibility to SPCP changes. Structural equation modeling (SEM) clearly showed a much stronger indirect effect of deer on microbes at licks than at the matrix, especially for bacteria. Multiple deer behaviors at licks, such as grazing, trampling, and excretion, can indirectly shape and stabilize microbes by altering carbon and nitrogen input. Our study is the first to characterize soil microbial communities at mineral licks and demonstrate the processes by which LMH shapes those communities. More studies are required to establish a general relationship between the LMH and licks to promote the conservation of natural licks for wildlife.

The intrinsic and extrinsic mechanisms regulated by functional carbon nanodots for the phytoremediation of multi-metal pollution in soils

Functional carbon nanodots (FCNs) were currently demonstrated to regulate plant behavior in the agricultural and environmental areas. However, their regulation mechanisms on the interactions of plant-soil system during phytoremediation remain unrevealed. Here, Solanum nigrum L. was employed to explore the intrinsic and extrinsic mechanisms regulated by FCNs in the phytoremediation of Cd-Pb co-contaminated soils. The mediation of FCNs on metal removal and plant growth showed a hormesis manner, wherein the maximum induction effect was contributed by 15 mg kg-1 FCNs. Cd/Pb removal were enhanced by 8.5% and 31.6%, respectively. Moreover, FCNs reallocate metal distribution in plant by immobilized metals in roots and suppressed metal translocation to leaves. Improving plant growth (by 82.8% for root), stimulating plant hormesis, and activating plant detoxification pathways are the intrinsic mechanism for the phytoremediation smartly regulated by FCNs. Notably, FCNs induced soil enzyme activities that associated with soil nutrients recycling, up-regulated the microbial diversity and the soil immune system, and regulated S. nigrum L. to recruit beneficial microbials in the rhizosphere. The above-mentioned comprehensive improvement of soil micro-environment is the extrinsic mechanism regulated by FCNs. This study provides new insights to evaluate the interactions of nanomaterials with plant-soil system under soil contamination.

Overgrazing on unmanaged grassland interfered with the restoration of adjacent grazing-banned grassland by affecting soil properties and microbial community

A "grazing ban" policy has been implemented in some pastoral areas in China to fence degraded grasslands for restoration. However, fencing increased grazing pressures in unmanaged grasslands. Based on the mechanism of negative edge effect, we investigated whether overgrazing on unmanaged grassland interfered with the restoration of adjacent grazing-banned grassland by affecting soil properties and microbial community using a sample in Hulun Buir of Inner Mongolia, in order to optimize the "grazing ban" policy. Plant and soil were sampled in areas 30 m away from the fence in unmanaged grassland (UM) and in areas 30 m (adjacent to UM) and 30-60 m (not adjacent to UM) away from the fence in the grazing-banned grassland (F-30 m and F-60 m). The species richness and diversity of plant communities and the ASV number of fungal communities significantly decreased in F-30 m and UM, and the Simpson index of the bacterial community significantly decreased in F-30 m compared with F-60 m. The abundance of fungi involved in soil organic matter decomposition significantly decreased and the abundance of stress-resistant bacteria significantly increased, while the abundance of bacteria involved in litter decomposition significantly decreased in UM and F-30 m compared with F-60 m. The simplification of plant communities decreased in soil water and total organic carbon contents can explain the variations of soil microbial communities in both UM and F-30 m compared with F-60 m. The results of PLS-PM show that changes in plant community and soil microbial function guilds in UM may affect those in F-30 m by changing soil water and total organic carbon contents. These results indicate that overgrazing on unmanaged grassland interfered with the restoration of adjacent grazing-banned grassland by affecting soil properties and microbial community. The grazing-banned grasslands should be adjusted periodically in order to avoid negative edge effects.

Alteration of microbial carbon and nitrogen metabolism within the soil metagenome with grazing intensity at semiarid steppe

Grazing causes changes in microbiome metabolic pathways affecting plant growth and soil physicochemical properties. However, how grazing intensity affects microbial processes is poorly understood. In semiarid steppe grassland in northern China, shotgun metagenome sequencing was used to investigate variations in soil carbon (C) and nitrogen (N) cycling-related genes after six years of the following grazing intensities: G0, control, no grazing; G1, 170 sheep days ha-1 year-1; G2, 340 sheep days ha-1 year-1; and G3, 510 sheep days ha-1 year-1. Taxa and functions of the soil microbiome associated with the C cycle decreased with increasing grazing intensity. Abundances of genes involved in C fixation and organic matter decomposition were altered in grazed sites, which could effects on vegetation decomposition and soil dissolved organic carbon (DOC) content. Compared with the control, the abundances of nitrification genes were higher in G1, but the abundances of N reduction and denitrification genes were lower, suggesting that light grazing promoted nitrification, inhibited denitrification, and increased soil NO3- content. Q-PCR further revealed that the copies of genes responsible for carbon fixation (cbbL) and denitrification (norB) decreased with increasing grazing intensity. The highest copy numbers of the nitrification genes AOA and AOB were in G1, whereas copy numbers of the denitrification gene nirK were the lowest. A multivariate regression tree indicated that changes in C fixation genes were linked to changes in soil DOC content, whereas soil NO3- content was linked with nitrification and denitrification under grazing. Thus, genes associated with C fixation and the N cycle affected how C fixation and N storage influenced soil physicochemical properties under grazing. The findings indicate that grazing intensity affected C and N metabolism. Proper grassland management regimes (e.g., G1) are beneficial to the balances between ecological protection of grasslands and plant production in the semiarid steppe.

Grazing practices affect phyllosphere and rhizosphere bacterial communities of Kobresia humilis by altering their network stability

The primary utilization strategy for meadow grasslands on the Qinghai-Tibet Plateau (QTP) is livestock grazing. This practice is considered as one of the major drivers of plant-associated bacterial community construction and changes in soil properties. The species of Kobresia humilis is considered as the most dominant one in grasslands. However, how different grazing practices affect the phyllosphere and rhizosphere bacterial communities of K. humilis is unknown. To address this issue, the effects of the grazing enclosure (GE), single-species grazing (YG and SG, representing yak only and sheep only, respectively), and different ratios of grazing (ratio of yak to sheep is 1:2, 1:4, and 1:6, represented by MG1:2, MG1:4, and MG1:6, respectively) on the dominant plant of K. humilis, it's phyllosphere and rhizosphere bacteria, and soil properties were investigated using artificially controlled grazing and grazing enclosure. Our data showed that grazing enclosure enhanced vegetation coverage, and rhizosphere bacterial richness and diversity, while reduced plant number and bacterial network stability of K. humilis. The NO3--N, K+, and Cl- concentrations were lower under grazing compared to GE. SG reduced the concentration of NH4+-N, TN, K+, and Na+ compared to YG. Moderate grazing intensity had a lower relative abundance of the r-strategists (Bacteroidota and Gammaproteobacteria) with higher bacterial network stability. Yak and sheep grazing showed reversed impacts on the bacterial network stability between the phyllosphere and rhizosphere of K. humilis. Proteobacteria and Actinobacteriota were identified in the molecular ecological network analysis as keystone taxa in the phyllosphere and rhizosphere networks, respectively, under all treatments. This study explained why sheep grazing has more adverse effects on grazing-tolerant grass species, K. humilis, than yak grazing, and will contribute to a better understanding of the impacts of different grazing practices and grazing enclosure on alpine grassland ecosystems on the QTP.

Contrasting Effects of Grazing in Shaping the Seasonal Trajectory of Foliar Fungal Endophyte Communities on Two Semiarid Grassland Species

Fungal endophytes are harboured in the leaves of every individual plant host and contribute to plant health, leaf senescence, and early decomposition. In grasslands, fungal endophytes and their hosts often coexist with large herbivores. However, the influence of grazing by large herbivores on foliar fungal endophyte communities remains largely unexplored. We conducted a long-term (18 yr) grazing experiment to explore the effects of grazing on the community composition and diversity of the foliar fungal endophytes of two perennial grassland species (i.e., Artemisia capillaris and Stipa bungeana) across one growing season. Grazing significantly increased the mean fungal alpha diversity of A. capillaris in the early season. In contrast, grazing significantly reduced the mean fungal alpha diversity of endophytic fungi of S. bungeana in the late season. Grazing, growing season, and their interactions concurrently structured the community composition of the foliar fungal endophytes of both plant species. However, growing season consistently outperformed grazing and environmental factors in shaping the community composition and diversity of both plant species. Overall, our findings demonstrate that the foliar endophytic fungal community diversity and composition differed in response to grazing between A. capillaris and S. bungeana during one growing season. The focus on this difference will enhance our understanding of grazing's impact on ecological systems and improve land management practices in grazing regions. This variation in the effects of leaf nutrients and plant community characteristics on foliar endophytic fungal community diversity and composition may have a pronounced impact on plant health and plant-fungal interactions.

Effects of herbivore on seagrass, epiphyte and sediment carbon sequestration in tropical seagrass bed

Herbivores strongly affect the ecological structure and functioning in seagrass bed ecosystems, but may exhibit density-dependent effects on primary producers and carbon sequestration. This study examined the effects of herbivorous snail (Cerithidea rhizophorarum) density on snail intraspecific competition and diet, dominant seagrass (Thalassia hemprichii) and epiphyte growth metrics, and sediment organic carbon (SOC). The growth rates of the herbivorous snail under low density (421 ind m-2) and mid density (842 ind m-2) were almost two times of those at extremely high density (1684 ind m-2), indicating strong intraspecific competition at high density. Herbivorous snails markedly reduced the epiphyte biomass on seagrass leaves. Additionally, the seagrass contribution to herbivorous snail as food source under high density was about 1.5 times of that under low density, while the epiphyte contribution under low density was 3 times of that under high density. A moderate density of herbivorous snails enhanced leaf length, carbon, nitrogen, total phenol and flavonoid contents of seagrasses, as well as surface SOC content and activities of polyphenol oxidase and β-glucosidase. However, high density of herbivorous snails decreased leaf glucose, fructose, detritus carbon, and total phenols contents of seagrasses, as well as surface SOC content and activities of polyphenol oxidase and β-glucosidase. Therefore, the effects of herbivorous snail on seagrass, epiphyte and SOC were density-dependent, and moderate density of herbivorous snail could be beneficial for seagrasses to increase productivity. This provided theoretical guidance for enhancing carbon sink in seagrass bed and its better conservation.

Tapping the rhizosphere metabolites for the prebiotic control of soil-borne bacterial wilt disease

Prebiotics are compounds that selectively stimulate the growth and activity of beneficial microorganisms. The use of prebiotics is a well-established strategy for managing human gut health. This concept can also be extended to plants where plant rhizosphere microbiomes can improve the nutrient acquisition and disease resistance. However, we lack effective strategies for choosing metabolites to elicit the desired impacts on plant health. In this study, we target the rhizosphere of tomato (Solanum lycopersicum) suffering from wilt disease (caused by Ralstonia solanacearum) as source for potential prebiotic metabolites. We identify metabolites (ribose, lactic acid, xylose, mannose, maltose, gluconolactone, and ribitol) exclusively used by soil commensal bacteria (not positively correlated with R. solanacearum) but not efficiently used by the pathogen in vitro. Metabolites application in the soil with 1 µmol g^-1 soil effectively protects tomato and other Solanaceae crops, pepper (Capsicum annuum) and eggplant (Solanum melongena), from pathogen invasion. After adding prebiotics, the rhizosphere soil microbiome exhibits enrichment of pathways related to carbon metabolism and autotoxin degradation, which were driven by commensal microbes. Collectively, we propose a novel pathway for mining metabolites from the rhizosphere soil and their use as prebiotics to help control soil-borne bacterial wilt diseases.

Effects of livestock grazing on the relationships between soil microbial community and soil carbon in grassland ecosystems

Livestock grazing of grassland ecosystems may induce shifts in microbe community traits and soil carbon (C) cycling; however, impacts of grassland management (grazing) on soil C- microbe community trait (microbial biomass, diversity, community structure, and enzyme activity) relationships are unclear. To address this, we conducted a global meta-analysis of 95 articles of livestock grazing studies that vary in grazing intensities (light, moderate, and high) and durations (<5 years, 5-10 years, and > 10 years). We found that gazing decreased soil organic carbon content (SOC; 10.1 %), and activities of the enzymes of saccharase (SA; 31.1 %), urease (UA; 7.0 %), and acid phosphatase (11.9 %) in topsoil. Meanwhile, the SOC, soil microbial biomass and enzyme activities consistently decreased as grazing intensity and duration prolonged. Furthermore, we observed strong linear relationships of microbe community traits with SOC (p < 0.05), but weak relationships with soil N or P (p > 0.05) in grasslands, which also depends on the grazing intensity and duration. In conclusion, our results indicate that traits of soil carbon content, soil microbe community, and in particular their relationships in global grasslands are overall significantly affected by livestock grazing, but the effects strongly depend on the grazing intensity and duration.

Plant domestication shapes rhizosphere microbiome assembly and metabolic functions

BACKGROUND

The rhizosphere microbiome, which is shaped by host genotypes, root exudates, and plant domestication, is crucial for sustaining agricultural plant growth. Despite its importance, how plant domestication builds up specific rhizosphere microbiomes and metabolic functions, as well as the importance of these affected rhizobiomes and relevant root exudates in maintaining plant growth, is not well understood. Here, we firstly investigated the rhizosphere bacterial and fungal communities of domestication and wild accessions of tetraploid wheat using amplicon sequencing (16S and ITS) after 9 years of domestication process at the main production sites in China. We then explored the ecological roles of root exudation in shaping rhizosphere microbiome functions by integrating metagenomics and metabolic genomics approaches. Furthermore, we established evident linkages between root morphology traits and keystone taxa based on microbial culture and plant inoculation experiments.

RESULTS

Our results suggested that plant rhizosphere microbiomes were co-shaped by both host genotypes and domestication status. The wheat genomes contributed more variation in the microbial diversity and composition of rhizosphere bacterial communities than fungal communities, whereas plant domestication status exerted much stronger influences on the fungal communities. In terms of microbial interkingdom association networks, domestication destabilized microbial network and depleted the abundance of keystone fungal taxa. Moreover, we found that domestication shifted the rhizosphere microbiome from slow growing and fungi dominated to fast growing and bacteria dominated, thereby resulting in a shift from fungi-dominated membership with enrichment of carbon fixation genes to bacteria-dominated membership with enrichment of carbon degradation genes. Metagenomics analyses further indicated that wild cultivars of wheat possess higher microbial function diversity than domesticated cultivars. Notably, we found that wild cultivar is able to harness rhizosphere microorganism carrying N transformation (i.e., nitrification, denitrification) and P mineralization pathway, whereas rhizobiomes carrying inorganic N fixation, organic N ammonification, and inorganic P solubilization genes are recruited by the releasing of root exudates from domesticated wheat. More importantly, our metabolite-wide association study indicated that the contrasting functional roles of root exudates and the harnessed keystone microbial taxa with different nutrient acquisition strategies jointly determined the aboveground plant phenotypes. Furthermore, we observed that although domesticated and wild wheats recruited distinct microbial taxa and relevant functions, domestication-induced recruitment of keystone taxa led to a consistent growth regulation of root regardless of wheat domestication status.

CONCLUSIONS

Our results indicate that plant domestication profoundly influences rhizosphere microbiome assembly and metabolic functions and provide evidence that host plants are able to harness a differentiated ecological role of root-associated keystone microbiomes through the release of root exudates to sustain belowground multi-nutrient cycles and plant growth. These findings provide valuable insights into the mechanisms underlying plant-microbiome interactions and how to harness the rhizosphere microbiome for crop improvement in sustainable agriculture. Video Abstract.

Grazing lowers soil multifunctionality but boosts soil microbial network complexity and stability in a subtropical grassland of China

Introduction

Long-term grazing profoundly affects grassland ecosystems, whereas how the soil microbiome and multiple soil ecosystem functions alter in response to two-decades of grazing, especially how soil microbiome (diversity, composition, network complexity, and stability) forms soil multifunctionality is rarely addressed.

Methods

We used a long-term buffalo grazing grassland to measure the responses of soil physicochemical attributes, stoichiometry, enzyme activities, soil microbial niche width, structure, functions, and networks to grazing in a subtropical grassland of Guizhou Plateau, China.

Results

The evidence from this work suggested that grazing elevated the soil hardness, available calcium content, and available magnesium content by 6.5, 1.9, and 1.9 times (p = 0.00015-0.0160) and acid phosphatase activity, bulk density, pH by 59, 8, and 0.5 unit (p = 0.0014-0.0370), but decreased the soil water content, available phosphorus content, and multifunctionality by 47, 73, and 9-21% (p = 0.0250-0.0460), respectively. Grazing intensified the soil microbial carbon limitation (+78%, p = 0.0260) as indicated by the increased investment in the soil β-glucosidase activity (+90%, p = 0.0120). Grazing enhanced the complexity and stability of the bacterial and fungal networks but reduced the bacterial Simpson diversity (p < 0.05). The bacterial diversity, network complexity, and stability had positive effects, while bacterial and fungal compositions had negative effects on multifunctionality.

Discussions

This work is an original attempt to show that grazing lowered multifunctionality via the reduced bacterial diversity and shifted soil bacterial and fungal compositions rather than the enhanced bacterial and fungal network complexities and stability by grazing. Protecting the bacterial diversity from decreasing, optimizing the composition of bacteria and fungi, and enhancing the complexity and stability of bacterial network may be conducive to improving the soil multifunction of grazing grassland, on a subtropical grassland.

Land use intensification in a dry-hot valley reduced the constraints of water content on soil microbial diversity and multifunctionality but increased CO2 production

Conversion of abandoned land (mainly savanna) into cropland generally occurs in fragile ecosystems such as dry-hot valleys (DHVs) in southwest China, with the intent of increasing land productivity and conducting ecological restoration. However, the effects of conversion on soil microbial communities and carbon turnover of savanna ecosystems remain unclear, since savannas could be a vital but overlooked carbon sink. To illustrate the ecological consequences of land-use change (LUC) for savanna ecosystems, a 1-year field experiment was conducted in DHVs of southwest China. The soil properties, microbial respiration, and metagenomics from two different land-use types (grassland and mango plantation) were examined to reveal the effects of regional LUC on soil C turnover and microbial traits. Conversion from degraded grassland into cropland increased the contribution of soil microclimate to the microbial community composition, reduced the constraints of soil water content (SWC), and further decreased nutrient availability. LUC reshaped the composition and structure of soil bacterial communities. Specifically, soil dominant microbes that belonged to Actinobacteria and Proteobacteria were significantly enriched by conversion, while rare microbes that belonged to a wider range of phyla were generally depleted, leading to an overall decrease in community diversity. In addition, LUC-induced changes in soil characteristics and microbial communities further decreased soil multifunctionality as well as the carbon use efficiency of microbes. Intensified microbial respiration and a significant increase in the soil CO₂ efflux were observed following LUC, which could drive changes in soil microbial community composition and functions (such as growth and regeneration). In summary, through simultaneously reducing constraints on SWC and decreasing nutrient availability, conversion from degraded grassland to cropland in a DHV decreased soil microbial diversity and multifunctionality, and increased microbial respiration and soil CO₂ efflux. Our study provides new insights for understanding the role and mechanisms of LUC in soil carbon turnover in ecologically fragile areas such as DHVs.

Biodegradable microplastics impact the uptake of Cd in rice: The roles of niche breadth and assembly process

Biodegradable microplastics (MPs) can impact the accumulation of cadmium (Cd) by plants, however, its mechanisms have not been fully understood. In this study, two biodegradable MPs, polypropylene carbonate (PPC) and polylactic acid (PLA), were used to examine their influences on the uptake of Cd in rice plants. Results showed that PPC significantly reduced the accumulation of Cd in rice root and aerial part, whereas PLA increased the Cd concentrations in rice root. The random forest analysis revealed that the bacterial biomarkers enriched by two MPs were different at genus level. Niche breadths were significantly reduced under Cd stress, and PPC alleviated this environmental pressure for entire bacterial community, whereas PLA reduced the niche breadth for whole community and abundant taxa, which was further verified by co-occurrence network and normalized stochasticity ratio model. The abundant taxa of group PPC were primarily governed by deterministic process while rare taxa were more driven by stochastic process. Structural equation model and Mantel analysis identified that the niche breadth imposed a strong selection on Cd accumulation after co-exposure. This study reveals the underlying mechanism of assembly process and niche breadth of rice rhizosphere microbiome on Cd accumulation by rice plants.

Multiple anthropogenic pressures eliminate the effects of soil microbial diversity on ecosystem functions in experimental microcosms

Biodiversity is crucial for the provision of ecosystem functions. However, ecosystems are now exposed to a rapidly growing number of anthropogenic pressures, and it remains unknown whether biodiversity can still promote ecosystem functions under multifaceted pressures. Here we investigated the effects of soil microbial diversity on soil functions and properties when faced with an increasing number of simultaneous global change factors in experimental microcosms. Higher soil microbial diversity had a positive effect on soil functions and properties when no or few (i.e., 1–4) global change factors were applied, but this positive effect was eliminated by the co-occurrence of numerous global change factors. This was attributable to the reduction of soil fungal abundance and the relative abundance of an ecological cluster of coexisting soil bacterial and fungal taxa. Our study indicates that reducing the number of anthropogenic pressures should be a goal in ecosystem management, in addition to biodiversity conservation.

It is unclear whether the positive effects of biodiversity on ecosystem functioning are maintained under multifaceted anthropogenic disturbance. In this experiment, the authors show that multiple simultaneous stressors can negate the positive effect of microbial diversity on soil functions.

Effects of seasonal grazing on plant and soil microbial diversity of typical temperate grassland

Biodiversity is the decisive factor of grassland ecological function and process. As the most important human use of grassland, grazing inevitably affects the grassland biodiversity. However, comprehensive studies of seasonal grazing on plant and soil bacterial, archaeal and fungal diversity of typical temperate grassland are still lacking. We examined the impact of seasonal grazing, including no-grazing (NG), continuous grazing (CG), grazing in May and July (G57), grazing in June and August (G68), and grazing in July and September (G79) on grassland plant and soil microbial diversity based on a long-term field grazing experiment. The results showed that the aboveground plant biomass (AGB) of the seasonal grazing plots was significantly higher than that of the CG plots. Compared with NG, CG increased significantly the Margalef richness index of plant community, while did not significantly change the Shannon, Simpson and Pielou evenness of plant community. Grazing changed the composition and biomass of dominant vegetation. Long-term grazing decreased the proportion of Leymus chinensis (Trin.) Tzvel. and increased the proportion of Cleistogenes squarrosa (Trin.) Keng. There was no significant change in the Shannoneven, Shannon and Coverage indices of soil bacteria, archaea and fungi between NG and the grazing plots. But the Chao index of soil fungi in G57, G68 and G79 and archaea in G57, G79 was significantly higher than that in CG. The results of correlation analysis showed that the plant diversity in the CG plots was significantly negatively correlated with the soil bacterial diversity. The plant richness in the G57 and G68 plots was significantly positively correlated with the soil archaea richness. Our study showed that seasonal grazing was a sustainable grazing management strategy for maintaining typical grassland plant and soil microbial diversity in northern of China.

Grazing greatly reduces the temporal stability of soil cellulolytic fungal community in a steppe on the Tibetan Plateau

Excessive livestock grazing degrades grasslands ecosystem stability and sustainability by reducing soil organic matter and plant productivity. However, the effects of grazing on soil cellulolytic fungi, an important indicator of the degradation process for soil organic matter, remain less well understood. Using T-RFLP and sequencing methods, we investigated the effects of grazing on the temporal changes of cellulolytic fungal abundance and community structure in dry steppe soils during the growing months from May to September, on the Tibetan Plateau using T-RFLP and sequencing methods. The results demonstrated that the abundance of soil cellulolytic fungi under grazing treatment changed significantly from month to month, and was positively correlated with dissolved organic carbon (DOC) and soil temperature, but negatively correlated with soil pH. Contrastingly, cellulolytic fungal abundance did not change within the fencing treatment (ungrazed conditions). Cellulolytic fungal community structure changed significantly in the growing months in grazed soils, but did not change in fenced soils. Grazing played a key role in determining the community structure of soil cellulolytic fungi by explaining 8.1% of the variation, while pH and DOC explained 4.1% and 4.0%, respectively. Phylogenetically, the cellulolytic fungi were primarily affiliated with Ascomycota (69.65% in relative abundance) and Basidiomycota (30.35%). Therefore, grazing substantially reduced the stability of soil cellulolytic fungal abundance and community structure, as compared with the fencing treatment. Our finding provides a new insight into the responses of organic matter-decomposing microbes for grassland managements.

Soil aggregate microbiomes steer plant community overyielding in ungrazed and intensively grazed grassland soils

Plant and soil microbial community composition play a central role in maintaining ecosystem functioning. Most studies have focused on soil microbes in the bulk soil, the rhizosphere and inside plant roots, however, less is known about the soil community that exists within soil aggregates, and how these soil communities influence plant biomass production. Here, using field-conditioned soil collected from experimental ungrazed and grazed grasslands in Inner Mongolia, China, we examined the composition of microbiomes inside soil aggregates of various size classes, and determined their roles in plant-soil feedbacks (PSFs), diversity-productivity relationships, and diversity-dependent overyielding. We found that grazing induced significantly positive PSF effects, which appeared to be mediated by mycorrhizal fungi, particularly under plant monocultures. Despite this, non-additive effects of microbiomes within different soil aggregates enhanced the strength of PSF under ungrazed grassland, but decreased PSF strength under intensively grazed grassland. Plant mixture-related increases in PSF effects markedly enhanced diversity-dependent overyielding, primarily due to complementary effects. Selection effects played far less of a role. Our work suggests that PSF contributes to diversity-dependent overyielding in grasslands via non-additive effects of microbiomes within different soil aggregates. The implication of our work is that assessing the effectiveness of sustainable grassland restoration and management on soil properties requires inspection of soil aggregate size-specific microbiomes, as these are relevant determinants of the feedback interactions between soil and plant performance.

Altering microbial community for improving soil properties and agricultural sustainability during a 10-year maize-green manure intercropping in Northwest China

Maize is a crop that is cultivated worldwide. The Hexi Oasis is one of the most important areas for high-yield maize seed production in China. Green manure, a plant fertilizer, has great potential for increasing crop yield and agricultural sustainability. However, the role of microorganisms in soil health and the microbiological mechanism of green manure in improving soil fertility and crop production in the Hexi Oasis area remain unknown. The effects of maize-green manure intercropping on the soil microbial community structure and diversity and the mechanism of soil improvement were investigated in a 10-year field experiment. The study revealed that microbial phylotypes were grouped into four major ecological clusters. Module #2 is a soil core ecological cluster enriched with many plant growth-promoting rhizobacteria and arbuscular mycorrhizal fungi. The application of green manure led to significantly increased soil pH, nutrient contents, and enzyme activities, and significantly reduced the relative abundance of potential plant pathogens compared with monocropping, which should ensure high and stable maize yield under long-term continuous cropping. It also increased the economic benefits by 56.39% compared with monocropping, owing to the additional products produced by the green manure. These improvements were associated with changes in the microbial community structure and activity, consistent with the structural equation model results. Therefore, soil microorganisms are the key drivers of the potential benefits of maize-green manure on agricultural sustainability.

The effects of grazer exclosure duration on soil microbial communities on the Qinghai-Tibetan Plateau

While determining the response of soil microbes to grazer exclosure duration is critical to understanding ecosystem restoration processes, few studies have focused on this issue. With seasonal grazing as a control, microbes of alpine grassland soils under 5, 13, 22, and 39 years of grazer exclosure situated in the eastern part of the Qinghai-Tibetan Plateau, were examined. Microbial diversity was determined through Illumina high-throughput sequencing of the 16S rRNA gene and an internal transcription spacer (ITS). We found that soil bacterial α-diversity showed insignificant differences between seasonal grazing and grazer exclosure and among the grazer exclosures of different durations, while fungal α-diversity under the 5-year grazer exclosure was significantly different from those under the other treatments. Soil microbial community profiles under the 13-, 22-, and 39-year grazer exclosures were significantly different compared to those under the seasonal grazing or 5-year grazer exclosure. Briefly, longer exclosure durations led to a higher relative abundance of multiple copiotrophic microbial lineages (e.g., β-Proteobacteria, Rhizobiales, and Frankiales), whereas several oligotrophic microbial lineages (e.g., Chloroflexi, Leotiomycetes, and Xylariales) gradually and significantly decreased. Functional predictions suggest that as grazer exclosure duration was extended, the relative abundance of nitrogen fixers increased, while the proportions of plant pathogenic fungi decreased. This indicates that long-term grazer exclosure duration may contribute to enhanced soil nitrogen fixation and grassland health by maintaining plant growth and decreasing the risk of plant disease. However, this may have a resource cost as plant productivity and soil organic carbon both decreased with the extension of grazer exclosure duration. Therefore, the agroecology effect of grazer exclosure duration on the diversity and abundance of soil nitrogen fixing bacteria and plant pathogen fungi, should be given more attention in the cold and humid portion of the Qinghai-Tibetan Plateau.

Consequences of Grazing Cessation for Soil Environment and Vegetation in a Subalpine Grassland Ecosystem

Areas covered by seminatural grasslands have been in constant decline for decades in Europe. This trend is particularly strong for mountain territories, where such traditional agricultural practices as cattle grazing are no longer economically feasible. This study was conducted in the subalpine pasture of Cinte Tesino (TN, Italy), where local farmers have applied the following different management strategies: shorter and longer grazing durations during the season and a complete abandonment for the last 15 years. We aimed to study how these different management strategies impact the functioning and diversity of vegetation and the chemical and biological characteristics of the soil. Species richness was higher in plots subjected to longer grazing with a prevalence of D. caespitosa in terms of biomass share. A decline in species richness in abandoned plots was accompanied by an increase in the share of other graminoids in collected biomass. A concomitant increase in leaf N concentration and light availability in grazed plots resulted in higher photosynthetic efficiency in some species, as revealed by the δ¹³C of plant tissues. Soils under grazing were characterised by a higher concentration of total and extractable N, almost doubled microbial biomass C and increased extracellular enzymes activity, evidencing nutrient cycling mobilization. While the microbial pool was characterised by lower mineralization rates, C was lost from the soil with 15 years of abandonment. The longer grazing season demonstrated to be the most beneficial, promoting species richness, C accumulation and better soil microbial functioning. A change in soil pH from strongly acidic to moderately acidic with longer grazing is likely one of the important factors adding to the success in the functioning of primary producers and decomposers in this site.

Bait input altered microbial community structure and increased greenhouse gases production in coastal wetland sediment

Coastal wetland reclamation contributed to development of aquaculture industry, and the residual bait accumulation in aquaculture processes could influence biogeochemical elements cycling, which threaten ecological functions and services in aquaculture and adjacent ecosystems. However, systematic studies for changes in sediment microbial community structure and greenhouse gasses (GHGs) production, as well as environmental parameters following bait input at time scale are still rare. A 90-day incubation experiment was conducted using sediment collected from coastal wetland in Qi'ao Island in southern China, followed by the observations of temporal variations of physicochemical properties, sediment microbial community, and GHGs production in response to different amounts of bait input (0, 20, and 40 mg bait g^-1 wet sediment). The results showed that dissolved oxygen of overlying water was profoundly decreased owing to bait input, while dissolved organic carbon of overlying water and several sediment properties (e.g., organic matter, sulfide, and ammonium) varied in reverse patterns. Meanwhile, bait input led to significant loss of microbial community richness and diversity, and strongly altered microbial compositions from aerobic, slow-growing, and oligotrophic (Actinobacteriota, Chloroflexi, and Acidobacteriota) to anaerobic, fast-growing, and copiotrophic (Firmicutes and Bacteroidota). Moreover, both GHGs production and global warming potential were significantly enhanced by bait input, implying that aquaculture ecosystem is an important hotspot for global GHGs emission. Overall, bait input triggered quick responses of physicochemical properties, sediment microbial community, and GHGs production, followed by long-term resilience of the ecosystem. This study could provide new insight into temporal interactive effects of bait input on physicochemical properties, microbial community, and GHGs production, which can enhance the understanding of the temporal dynamics and ecological impacts of coastal aquaculture activities and emphasize the necessity of sustainable assessment and management in aquaculture ecosystems.

Soil Microbial Community Varied with Vegetation Types on a Small Regional Scale of the Qilian Mountains

Clarifying the response of soil microbial communities to the change of different vegetation types on a small regional scale is of great significance for understanding the sustainability of grassland development. However, the distribution patterns and driving factors of the microbial community are not well understood in the Qilian Mountains. Therefore, we characterized and compared the soil microbial communities underlying the four vegetation types in a national natural reserve (reseeded grassland, swamp meadow, steppe meadow, and cultivated grassland) using high-throughput sequencing of the 16S rRNA and ITS. Meanwhile, the plant community and soil physicochemical characteristics were also determined. The results showed that bacterial and fungal communities in all vegetation types had the same dominant species, but the relative abundance differed substantially, which caused significant spatial heterogeneities on the small regional scale. Specifically, bacteria showed higher variability among different vegetation types than fungi, among which the bacterial and fungal communities were more sensitive to the changes in soil than to plant characteristics. Furthermore, soil organic carbon affected the widest portion of the microbial community, nitrate-nitrogen was the main factor affecting bacteria, and aboveground plant biomass was the main factor affecting fungi. Collectively, these results demonstrate the value of considering multiple small regional spatial scales when studying the relationship between the soil microbial community and environmental characteristics. Our study may have important implications for grassland management following natural disturbances or human alterations.

Habitat Protection Approaches Facilitate Conservation of Overlooked Fungal Diversity - A Case Study From the Norwegian Coastal Heathland System

European coastal heathlands are distinct ecosystems shaped by land use tradition and they have experienced an 80% area reduction from their historical maximum. These mosaics of mires and wind exposed patches have ericaceous shrub dominated vegetation, and soils within coastal heathlands are characterized by low pH and high levels of recalcitrant debris. Using a culture-based approach with molecular identification of isolates, we characterized root-associated fungal communities of six ericaceous species in eight heathland localities along Norway's western coast. Site-level alpha diversity ranged from 21-38 OTUs, while the total estimated gamma diversity for culturable heathland root fungi was 190-231 OTUs. Most species recovered are previously reported at low abundance in Norway, suggesting the biodiversity in this community is underreported, rather than novel for science. The fungi recovered were primarily Ascomycota, specifically endophytic Phialocephala, and Pezicula, and no host specificity was observed in the communities. The fungal communities exhibited high turnover and low nestedness, both between ericaceous hosts and across heathland sites. We observed no spatial patterns in fungal betadiversity, and this heterogeneity may be a product of the unique historic land use practices at each locality creating a distinct mycofloral "fingerprint". Robust diversity estimates will be key for managing fungal biodiversity in coastal heathlands. Our results indicate that sampling schemes that maximize the number of host plants sampled per site, rather than the number of cultures per plant yield improved alpha diversity estimates. Similarly, gamma diversity estimates are improved by maximizing the total number of localities sampled, rather than increasing the number of plants sampled per locality. We argue that while the current protected status of coastal heathland habitats and restoration efforts have knock-on effects for the conservation of fungal biodiversity, fungi have a vital functional role in the ecosystem and holistic conservation plans that consider fungal biodiversity would be beneficial.

Grazing Changed Plant Community Composition and Reduced Stochasticity of Soil Microbial Community Assembly of Alpine Grasslands on the Qinghai-Tibetan Plateau

Grazing is a substantial threat to the sustainability of grassland ecosystems, while it is uncertain about the variety of plant and soil microbial community and the linkages between them limit the comprehensive understanding of grazing ecology. We conducted an experiment on the effects of the grazing regimes rotational grazing (RG), continuous grazing (CG), and grazing exclusion (GE) on an alpine meadow in Qinghai-Tibetan Plateau. The differences of plant community composition, soil microbial community assembly mechanism, and taxonomic and functional composition between grazing regimes were examined, and the relationship between plant species and the soil microbes was assessed by constructing a co-occurrence network. The results showed that the plant community composition varied with the grazing regimes, while the soil microbial community composition did not vary with the grazing regimes. The soil bacterial functional composition was similar under RG and CG, while the soil fungal functional composition was similar under GE and RG. The soil microbial community under all grazing regimes was assembled mainly according to stochastic rather than deterministic mechanisms, and RG and CG reduced the relative importance of the stochastic ratio. At the microbial phylum level, CG and GE increased the relative abundance of Acidobacteria and Armatimonadetes and CG and RG increased the relative abundance of Elusimicrobia. In the network of plant species and soil microbial classes, plants and bacteria themselves were mainly positively linked (symbiosis and promotion), while plants and soil microbes were mainly negatively linked (competition). There were five microbial generalists in the network, which connected with many microbes, and four showed no difference in their abundance among the grazing regimes. Overall, the stable key microbes in the network and the fact that many of the plants are unconnected with microbes weakened the impact of grazing-induced changes in the plant community on soil microbes, probably resulting in the stable soil microbial community composition. Moreover, there was still a dominant and tolerant plant species, Kobresia pygmaea, that connected the plant and microbial communities, implying that the dominant plant species not only played a crucial role in the plant community but also acted as a bridge between the plants and soil microbes; thus, its tolerance and dominance might stabilize the soil microbial community.

Maize root-associated niches determine the response variation in bacterial community assembly and function to phthalate pollution

Plant root-associated microbiome can be influenced by environmental stress like pollution. However, how organic pollution influences microbial communities in different root-associated niches and plant-microbe interaction remains unclear. We analyzed maize root-associated bacterial communities under stress of di-(2-ethylhexyl) phthalate (DEHP). The results demonstrate that structures and functions of bacterial communities are significantly different among four root-associated niches, and bacterial diversities gradually decline along bulk soil - rhizosphere - rhizoplane - endosphere. DEHP stress significantly reduces bacterial community diversities in both rhizosphere and rhizoplane, and changes their composition, enrichment and depleting process. DEHP stress led to the enrichment of some specific bacterial taxa like phthalate-degrading bacteria (e.g., Rhizobium and Agromyces) and functional genes involving in phthalate degradation (e.g., pht3 and pcaG). Notably, rhizoplane bacterial community is more sensitive to DEHP stress by enriching stress-resistant bacteria and more complex microbial network on rhizoplane than in rhizosphere. DEHP stress also disturbs the colonization and biofilm forming of root-associated bacteria on rhizoplane. Rhizoplane bacterial community is significantly correlated with maize growth while negatively influenced by DEHP stress. DEHP stress negatively influences plant-microbe interaction and inhibits maize growth. This study provides deep and comprehensive understanding for root-associated bacterial community in response to organic pollution.

Vegetation, water infiltration, and soil carbon response to Adaptive Multi-Paddock and Conventional grazing in Southeastern USA ranches

We examine Adaptive Multi-Paddock (AMP) grazed with short grazing events and planned recovery periods and paired ranches using Conventional Continuous Grazing (CG) at low stock density on vegetation, water infiltration, and soil carbon across SE USA. Increased vegetation standing biomass and plant species dominance-diversity were measured in AMP grazed ranches. Invasive perennial plant species richness and abundance increased with AMP grazing in the south, while in the north they increased on CG grazed ranches. Percent bare ground was significantly greater in CG at the Alabama and Mississippi sites, no different at the Kentucky and mid-Alabama sites, and greater on AMP at the Tennessee pair. On average, surface water infiltration was higher on AMP than paired CG ranches. Averaged over all locations, soil organic carbon stocks to a depth of 1 m were over 13% greater on AMP than CG ranches, and standing crop biomass was >300% higher on AMP ranches. AMP grazing supported substantially higher livestock stocking levels while providing significant improvements in vegetation, soil carbon, and water infiltration functions. AMP grazing also significantly increased available forage nutrition for key constituents, and increased soil carbon to provide significant resource and economic benefits for improving ecological health, resilience, and durability of the family ranch.

Simulation of Soil Organic Carbon Content Based on Laboratory Spectrum in the Three-Rivers Source Region of China

Soil organic carbon (SOC) changes affect the land carbon cycle and are also closely related to climate change. Visible-near infrared spectroscopy (Vis-NIRS) has proven to be an effective tool in predicting soil properties. Spectral transformations are necessary to reduce noise and ensemble learning methods can improve the estimation accuracy of SOC. Yet, it is still unclear which is the optimal ensemble learning method exploiting the results of spectral transformations to accurately simulate SOC content changes in the Three-Rivers Source Region of China. In this study, 272 soil samples were collected and used to build the Vis-NIRS simulation models for SOC content. The ensemble learning was conducted by the building of stack models. Sixteen combinations were produced by eight spectral transformations (S-G, LR, MSC, CR, FD, LRFD, MSCFD and CRFD) and two machine learning models of RF and XGBoost. Then, the prediction results of these 16 combinations were used to build the first-step stack models (Stack1, Stack2, Stack3). The next-step stack models (Stack4, Stack5, Stack6) were then made after the input variables were optimized based on the threshold of the feature importance of the first-step stack models (importance > 0.05). The results in this study showed that the stack models method obtained higher accuracy than the single model and transformations method. Among the six stack models, Stack 6 (5 selected combinations + XGBoost) showed the best simulation performance (RMSE = 7.3511, R2 = 0.8963, and RPD = 3.0139, RPIQ = 3.339), and obtained higher accuracy than Stack3 (16 combinations + XGBoost). Overall, our results suggested that the ensemble learning of spectral transformations and simulation models can improve the estimation accuracy of the SOC content. This study can provide useful suggestions for the high-precision estimation of SOC in the alpine ecosystem.

Experimental Warming Has Not Affected the Changes in Soil Organic Carbon During the Growing Season in an Alpine Meadow Ecosystem on the Qinghai-Tibet Plateau

The effects of climate warming and season on soil organic carbon (SOC) have received widespread attention, but how climate warming affects the seasonal changes of SOC remains unclear. Here, we established a gradient warming experiment to investigate plant attributes and soil physicochemical and microbial properties that were potentially associated with changes in SOC at the beginning (May) and end (August) of the growing season in an alpine meadow ecosystem on the Qinghai-Tibet Plateau. The SOC of August was lower than that of May, and the storage of SOC in August decreased by an average of 18.53 million grams of carbon per hectare. Warming not only failed to alter the content of SOC regardless of the season but also did not affect the change in SOC during the growing season. Among all the variables measured, microbial biomass carbon was highly coupled to the change in SOC. These findings indicate that alpine meadow soil is a source of carbon during the growing season, but climate warming has no significant impact on it. This study highlights that in the regulation of carbon source or pool in alpine meadow ecosystem, more attention should be paid to changes in SOC during the growing season, rather than climate warming.

Small-scale agricultural grassland management can affect soil fungal community structure as much as continental scale geographic patterns

A European transect was established, ranging from Sweden to the Azores, to determine the relative influence of geographic factors and agricultural small-scale management on the grassland soil microbiome. Within each of five countries (factor ‘Country’), which maximized a range of geographic factors, two differing growth condition regions (factor ‘GCR’) were selected: a favorable region with conditions allowing for high plant biomass production and a contrasting less favorable region with a markedly lower potential. Within each region, grasslands of contrasting management intensities (factor ‘MI’) were defined: intensive and extensive, from which soil samples were collected. Across the transect, ‘MI’ was a strong differentiator of fungal community structure, having a comparable effect to continental scale geographic factors (‘Country’). ‘MI’ was also a highly significant driver of bacterial community structure, but ‘Country’ was clearly the stronger driver. For both, ‘GCR’ was the weakest driver. Also at the regional level, strong effects of MI occurred on various measures of the soil microbiome (i.e. OTU richness, management-associated indicator OTUs), though the effects were largely regional-specific. Our results illustrate the decisive influence of grassland MI on soil microbial community structure, over both regional and continental scales, and, thus, highlight the importance of preserving rare extensive grasslands.

The soil microbiomics of intact, degraded and partially-restored semi-arid succulent thicket (Albany Subtropical Thicket)

This study examines the soil bacterial diversity in the Portulacaria afra-dominated succulent thicket vegetation of the Albany Subtropical Thicket biome; this biome is endemic to South Africa. The aim of the study was to compare the soil microbiomes between intact and degraded zones in the succulent thicket and identify environmental factors which could explain the community compositions. Bacterial diversity, using 16S amplicon sequencing, and soil physicochemistry were compared across three zones: intact (undisturbed and vegetated), degraded (near complete removal of vegetation due to browsing) and restored (a previously degraded area which was replanted approximately 11 years before sampling). Amplicon Sequence Variant (ASV) richness was similar across the three zones, however, the bacterial community composition and soil physicochemistry differed across the intact and degraded zones. We identified, via correlation, the potential drivers of microbial community composition as soil density, pH and the ratio of Ca to Mg. The restored zone was intermediate between the intact and degraded zones. The differences in the microbial communities appeared to be driven by the presence of plants, with plant-associated taxa more common in the intact zone. The dominant taxa in the degraded zone were cosmopolitan organisms, that have been reported globally in a wide variety of habitats. This study provides baseline information on the changes of the soil bacterial community of a spatially restricted and threatened biome. It also provides a starting point for further studies on community composition and function concerning the restoration of degraded succulent thicket ecosystems.

Carbon turnover times shape topsoil carbon difference between Tibetan Plateau and Arctic tundra

The Tibetan Plateau (TP) and Arctic permafrost constitute two large reservoirs of organic carbon, but processes which control carbon accumulation within the surface soil layer of these areas would differ due to the interplay of climate, soil and vegetation type. Here, we synthesized currently available soil carbon data to show that mean organic carbon density in the topsoil (0-10 cm) in TP grassland (3.12 ± 0.52 kg C m^-2) is less than half of that in Arctic tundra (6.70 ± 1.94 kg C m^-2). Such difference is primarily attributed to their difference in radiocarbon-inferred soil carbon turnover times (547 years for TP grassland versus 1609 years for Arctic tundra) rather than to their marginal difference in topsoil carbon inputs. Our findings highlight the importance of improving regional-specific soil carbon turnover and its controlling mechanisms across permafrost affected zones in ecosystem models to fully represent carbon-climate feedback.

Periphytic microbial response to environmental phosphate bioavailability - relevance to P management in paddy fields

Periphyton occurs widely in shallow-water ecosystems such as paddy fields and plays critical parts in regulating local phosphorus cycling. As such, understanding the mechanisms of the biofilm's response to environmental P variability may lead to better perceptions of P utilization and retention in rice farms. Present study aims at exploring the biological and biochemical processes underlying periphyton's P buffering capability through examining changes in community structure, phosphorus uptake and storage, and molecular makeup of exometabolome at different levels of P availability. Under stressed (both excessive and scarce) phosphorus conditions, we found increased populations of the bacterial genus capable of transforming orthophosphate to polyphosphate, as well as mixotrophic algae who can survive through phagotrophy. These results were corroborated by observed polyphosphate buildup under low and high P treatment. Exometabolomic analyses further revealed that periphytic organisms may substitute S-containing lipids for phospholipids, use siderophores to dissolve iron (hydr)oxides to scavenge adsorbed P, and synthesize auxins to resist phosphorus starvation. These findings not only shed light on the mechanistic insights responsible for driving the periphytic P buffer but attest to the ecological roles of periphyton in aiding plants such as rice to overcome P limitations in natural environment. Importance The ability of periphyton to buffer environmental P in shallow aquatic ecosystems may be a natural lesson on P utilization and retention in paddy fields. This work revealed the routes and tools through which periphytic organisms adapt to and regulate ambient P fluctuation. The mechanistic understanding further implicates that the biofilm may serve rice plants to alleviate P stress. Additional results from extracellular metabolite analyses suggest the dissolved periphytic exometabolome can be a valuable nutrient source for soil microbes and plants to reduce biosynthetic costs. These discoveries have the potential to improve our understanding of biogeochemical cycling of phosphorus in general and to refine P management strategies for rice farm in particular.

Coupling Between the Responses of Plants, Soil, and Microorganisms Following Grazing Exclusion in an Overgrazed Grassland

Grazing exclusion is an effective management practice to restore grassland ecosystem functioning. However, little is known about the role of soil microbial communities in regulating grassland ecosystem functioning during long-term ecosystem restorations. We evaluated the recovery of a degraded semiarid grassland ecosystem in northern China by investigating plant and soil characteristics and the role of soil microbial communities in ecosystem functioning after 22 years of grazing exclusion. Grazing exclusion significantly increased the alpha diversity and changed the community structure of bacteria, but did not significantly affect the alpha diversity or community structure of fungi. The higher abundance of copiotrophic Proteobacteria and Bacteroidetes with grazing exclusion was due to the higher carbon and nutrient concentrations in the soil, whereas the high abundance of Acidobacteria in overgrazed soils was likely an adaptation to the poor environmental conditions. Bacteria of the Sphingomonadaceae family were associated with C cycling under grazing exclusion. Bacteria of the Nitrospiraceae family, and especially of the Nitrospira genus, played an important role in changes to the N cycle under long-term exclusion of grazing. Quantitative PCR further revealed that grazing exclusion significantly increased the abundance of nitrogen fixing bacteria (nifH), ammonia oxidizers (AOA and AOB), and denitrifying bacteria (nirK and nosZ1). Denitrifying enzyme activity (DEA) was positively correlated with abundance of denitrifying bacteria. The increase in DEA under grazing exclusion suggests that the dependence of DEA on the availability of NO₃ ^- produced is due to the combined activity of ammonia oxidizers and denitrifiers. Our findings indicate that decades-long grazing exclusion can trigger changes in the soil bacterial diversity and composition, thus modulating the restoration of grassland ecosystem functions, carbon sequestration and soil fertility.

Linking soil bacterial diversity to satellite-derived vegetation productivity: a case study in arid and semi-arid desert areas

Increasing studies have begun to focus on biodiversity-productivity relationships for soil microorganisms through molecular ecology methods. However, most of these studies involve controlled experiments, and whether the relationship remains at large spatial scales is still largely unknown. To unravel this issue, archived desert soils from long-term experiments were analysed using high-throughput sequencing, and satellite-derived vegetation datasets were acquired to quantify productivity. Most of the abundant genera were significantly different between low- and high-productivity conditions, and soil bacterial communities were strongly impacted by productivity. Soil bacterial biodiversity, including observed operational taxonomic units and the Chao1, Shannon, and Faith's PD indexes, increased rapidly with productivity at low levels and then reached a relatively stable state, and similar phenomena were observed at multiple taxonomic ranks and for most of the dominant groups. Furthermore, we discovered that the mechanisms resulting in the observed relationship might be ecosystem resource availability in large-scale regions and species competition in local regions. Collectively, these results enhance our understanding of the linkage between belowground microorganisms and aboveground vegetation in arid and semi-arid areas and confirm the potential value of satellite-derived datasets in research on soil microbial diversity at large spatial scales.

Habitat heterogeneity induces regional differences in sediment nitrogen fixation in eutrophic freshwater lake

Biological nitrogen fixation (BNF) in sediments is an important source of bioavailable nitrogen in aquatic systems. However, the effect of habitat change caused by eutrophication on nitrogen fixation within sediments is still unclear. In this study, nitrogen fixation rates and diazotroph diversities in sediments with heterogeneous ecological status in one eutrophic lake were investigated by using an isotope tracer method and sequencing of nitrogen-fixing (nif) genes. The results showed that both nitrogenase activity (NA) and nifH abundance in sediments of blooms area were higher than those in vegetation-dominated habitats. Correlation analysis showed that NA was correlated closely to nifH abundance, dissolved sulfide, and iron. The diazotrophic assemblage contained mainly Proteobacterial sequences belonging to Cluster I and III, and the variations of diazotrophic community could be explained by total nitrogen content, total phosphorus content, organic matters, sulfides, ammonium and iron content. Moreover, the co-occurrence network analysis showed the Alphaproteobacteria shaped the major interactions in diazotrophic community, and sediment properties had stronger effect on diazotrophic community in cyanobacteria-dominated habitat. This study revealed that habitat heterogeneity in eutrophic lakes shaped different succession of BNF in sediments and cyanobacterial blooms significantly improved the nitrogen-fixing activity in sediments, which broadened our understanding of nitrogen cycle and nutrient management in eutrophic freshwater lakes.

Soil microbial community variation with time and soil depth in Eurasian Steppe (Inner Mongolia, China)

Purpose

Soil microorganisms play an indispensable role in the material and energy cycle of grassland ecosystems. The abundance of these organisms vary according to environmental factors, such as time of year and soil depth. There have been few studies on the transformation of soil microbial communities in degraded typical steppe according to these temporal and spatial changes. In this study, we analyze the community structure and diversity of soil bacteria and fungi, and the impact of these changing temporal and spatial factors upon the community structure.

Methods

From May to September 2018, we collected 90 soil samples from different depths (10, 20, and 30 cm) from the typical degraded steppe area of Xilingol. We carried out studies on soil physical and chemical properties and soil microbial diversity using high-throughput sequencing technology.

Results

We found that depth significantly affected abundance and diversity of bacteria and fungi. Bacteria and fungi diversity at 10 cm was higher than that at 20 cm and 30 cm. The abundance of Acidobacteria, Proteobacteria, Actinomycetes, Ascomycetes, and Basidiomycetes varies significantly with depth. In addition, soil pH increased significantly with increasing depth, while soil organic matter (SOM), available nitrogen (AN), volume water content of soil (VWC), and soil temperature (ST) decreased significantly with increasing depth. Finally, the depth, total organic carbon (TOC), and AN had a significant impact on the bacterial and fungal communities’ abundance (p < 0.05).

Conclusions

Spatial heterogeneity (in soil depth) is more significant than the time of year (month) in predicting changes in microbial community composition and soil properties. SOM, VWC, and the abundance of Proteobacteria and Actinomycetes positively correlate with soil depth, while pH and the abundance of Acidobacteria, Ascomycetes, and Basidiomycetes negatively correlate with soil depth. We speculate that SOM and VWC account for the variations in the abundance of Acidobacteria and Proteobacteria, while pH causes variations in the abundance of Actinomycetes, Ascomycetes and Basidiomycota.