Soil microbiota as game-changers in restoration of degraded lands

Standardized framework for assessing soil quality at antimony smelting site by considering microbial-induced resilience and heavy metal contamination

Antimony smelting activities damage the soil and vegetation surroundings while generating economic value. However, no standardized methods are available to diagnose the extent of soil degradation at antimony smelting sites. This study developed a standardized framework for assessing soil quality by considering microbial-induced resilience and heavy metal contamination at Xikuangshan antimony smelting site. The soil resilience index (SRI) and soil contamination index (SCI) were calculated by Minimum Data Set and geo-accumulation model, respectively. After standardized by a multi-criteria quantitative procedure of modified Nemerow's pollution index (NPI), the integrated assessment of soil quality index (SQI), which is the minimum of SRINPI and SCINPI, was achieved. The results showed that Sb and As were the prominent metal(loid) pollutants, and significant correlations between SQI and SRI indicated that the poor soil quality was mainly caused by the low level of soil resilience. The primary limiting factors of SRI were Fungi in high and middle contaminated areas, and Skermanella in low contaminated area, suggesting that the weak soil resilience was caused by low specific microbial abundances. Microbial regulation and phytoremediation are greatly required to improve the soil quality at antimony smelting sites from the perspectives of pollution control and resilience improvement. This study improves our understanding of ecological effects of antimony smelting sites and provides a theoretical basis for ecological restoration and sustainable development of mining areas.

Metal nanoparticles and pesticides under global climate change: Assessing the combined effects of multiple abiotic stressors on soil microbial ecosystems

The soil is a vital resource that hosts many microorganisms crucial in biogeochemical cycles and ecosystem health. However, human activities such as the use of metal nanoparticles (MNPs), pesticides and the impacts of global climate change (GCCh) can significantly affect soil microbial communities (SMC). For many years, pesticides and, more recently, nanoparticles have contributed to sustainable agriculture to ensure continuous food production to sustain the significant growth of the world population and, therefore, the demand for food. Pesticides have a recognized pest control capacity. On the other hand, nanoparticles have demonstrated a high ability to improve water and nutrient retention, promote plant growth, and control pests. However, it has been reported that their accumulation in agricultural soils can also adversely affect the environment and soil microbial health. In addition, climate change, with its variations in temperature and extreme water conditions, can lead to drought and increased soil salinity, modifying both soil conditions and the composition and function of microbial communities. Abiotic stressors can interact and synergistically or additively affect soil microorganisms, significantly impacting soil functioning and the capacity to provide ecosystem services. Therefore, this work reviewed the current scientific literature to understand how multiple stressors interact and affect the SMC. In addition, the importance of molecular tools such as metagenomics, metatranscriptomics, proteomics, or metabolomics in the study of the responses of SMC to exposure to multiple abiotic stressors was examined. Future research directions were also proposed, focusing on exploring the complex interactions between stressors and their long-term effects and developing strategies for sustainable soil management. These efforts will contribute to the preservation of soil health and the promotion of sustainable agricultural practices.

Differential responses of soil bacteria, fungi and protists to root exudates and temperature

The impact of climate warming on soil microbes has been well documented, with studies revealing its effects on diversity, community structure and network dynamics. However, the consistency of soil microbial community assembly, particularly in response to diverse plant root exudates under varying temperature conditions, remains an unresolved issue. To address this issue, we employed a growth chamber to integrate temperature and root exudates in a controlled experiment to examine the response of soil bacteria, fungi, and protists. Our findings revealed that temperature independently regulated microbial diversity, with distinct patterns observed among bacteria, fungi, and protists. Both root exudates and temperature significantly influenced microbial community composition, yet interpretations of these factors varied among prokaryotes and eukaryotes. In addition to phototrophic bacteria and protists, as well as protistan consumers, root exudates determined to varying degrees the enrichment of other microbial functional guilds at specific temperatures. The effects of temperature and root exudates on microbial co-occurrence patterns were interdependent; root exudates primarily simplified the network at low and high temperatures, while responses to temperature varied between single and mixed exudate treatments. Moreover, temperature altered the composition of keystone species within the microbial network, while root exudates led to a decrease in their number. These results emphasize the substantial impact of plant root exudates on soil microbial community responses to temperature, underscoring the necessity for future climate change research to incorporate additional environmental variables.

Response of bacterial ecological and functional properties to anthropogenic interventions during maturation of mine sand soil

Soil formation is a complex process that starts from the biological development. The ecological principles and biological function in soil are of great importance, whereas their response to anthropogenic intervention has been poorly understood. In this study, a 150-day microcosmic experiment was conducted with the addition of sludge and/or fermented wood chips (FWC) to promote the soil maturation. The results showed that, compared to the control (natural development without anthropogenic intervention), sludge, FWC, and their combination increased the availability of carbon, nitrogen, and potassium, and promoted the soil aggregation. They also enhanced the cellulase activity, microbial biomass carbon (MBC) and bacterial diversity, indicating that anthropogenic interventions promoted the maturation of sand soil. Molecular ecology network and functional analyses indicated that soil maturation was accomplished with the enhancement of ecosystem functionality and stability. Specifically, sludge promoted a transition in bacterial community function from denitrification to nitrification, facilitated the degradation of easily degradable organic matter, and enhanced the autotrophic nutritional mode. FWC facilitated the transition of bacterial function from denitrification to ammonification, promoted the degradation of recalcitrant organic matter, and simultaneously enhanced both autotrophic and heterotrophic nutritional modes. Although both sludge and FWC promoted the soil functionality, they showed distinct mechanistic actions, with sludge enhancing the physical structure, and FWC altering chemical composition. It is also worth emphasizing that sludge and FWC exhibited a synergistic effect in promoting biological development and ecosystem stability, thereby providing an effective avenue for soil maturation.

Biochar immobilized hydrolase degrades PET microplastics and alleviates the disturbance of soil microbial function via modulating nitrogen and phosphorus cycles

Microplastics (MPs) pose an emerging threat to soil ecological function, yet effective solutions remain limited. This study introduces a novel approach using magnetic biochar immobilized PET hydrolase (MB-LCC-FDS) to degrade soil polyethylene terephthalate microplastics (PET-MPs). MB-LCC-FDS exhibited a 1.68-fold increase in relative activity in aquatic solutions and maintained 58.5 % residual activity after five consecutive cycles. Soil microcosm experiment amended with MB-LCC-FDS observed a 29.6 % weight loss of PET-MPs, converting PET into mono(2-hydroxyethyl) terephthalate (MHET). The generated MHET can subsequently be metabolized by soil microbiota to release terephthalic acid. The introduction of MB-LCC-FDS shifted the functional composition of soil microbiota, increasing the relative abundances of Microbacteriaceae and Skermanella while reducing Arthobacter and Vicinamibacteraceae. Metagenomic analysis revealed that MB-LCC-FDS enhanced nitrogen fixation, P-uptake and transport, and organic-P mineralization in PET-MPs contaminated soil, while weakening the denitrification and nitrification. Structural equation model indicated that changes in soil total carbon and Simpson index, induced by MB-LCC-FDS, were the driving factors for soil carbon and nitrogen transformation. Overall, this study highlights the synergistic role of magnetic biochar-immobilized PET hydrolase and soil microbiota in degrading soil PET-MPs, and enhances our understanding of the microbiome and functional gene responses to PET-MPs and MB-LCC-FDS in soil systems.

Superiority of native soil core microbiomes in supporting plant growth

Native core microbiomes represent a unique opportunity to support food provision and plant-based industries. Yet, these microbiomes are often neglected when developing synthetic communities (SynComs) to support plant health and growth. Here, we study the contribution of native core, native non-core and non-native microorganisms to support plant production. We construct four alternative SynComs based on the excellent growth promoting ability of individual stain and paired non-antagonistic action. One of microbiome based SynCom (SC2) shows a high niche breadth and low average variation degree in-vitro interaction. The promoting-growth effect of SC2 can be transferred to non-sterile environment, attributing to the colonization of native core microorganisms and the improvement of rhizosphere promoting-growth function including nitrogen fixation, IAA production, and dissolved phosphorus. Further, microbial fertilizer based on SC2 and composite carrier (rapeseed cake fertilizer + rice husk carbon) increase the net biomass of plant by 129%. Our results highlight the fundamental importance of native core microorganisms to boost plant production.

Isolation of bacteria with plant growth-promoting properties from microalgae-bacterial flocs produced in high-rate oxidation ponds

Exploring plant growth-promoting (PGP) bacterial activity of microbial components aggregated by wastewater treatment can reduce dependence on fossil fuel-derived fertilisers. This study describes the isolation and identification of bacteria from microalgae-bacteria flocs (MaB-flocs) generated in high-rate algal oxidation ponds (HRAOP) of an integrated algal pond system (IAPS) remediating municipal wastewater. Amplified 16S rRNA gene sequence analysis determined the molecular identity of the individual strains. Genetic relatedness to known PGP rhizobacteria in the NCBI GenBank database was by metagenomics. Isolated strains were screened for the production of indoles (measured as indole-3-acetic acid; IAA) and an ability to mineralise NH 4 + , PO 4 3 - , and K + . Of the twelve bacterial strains isolated from HRAOP MaB-flocs, four produced indoles, nine mineralised NH 4 + , seven solubilised P, and one K. Potential of isolated strains for PGP activity according to one-way ANOVA on ranks was: ECCN 7b > ECCN 4b > ECCN 6b > ECCN 3b = ECCN 10b > ECCN 1b = ECCN 5b > ECCN 8b > ECCN 2b > ECCN 12b > ECCN 9b = ECCN 11b. Further study revealed that cell-free filtrate from indole-producing cultures of Aeromonas strain ECCN 4b, Enterobacter strain ECCN 7b, and Arthrobacter strain ECCN 6b promoted mung bean adventitious root formation suggestive of the presence of auxin-like biological activity.

Practical applications of soil microbiota to improve ecosystem restoration: current knowledge and future directions

Soil microbiota are important components of healthy ecosystems. Greater consideration of soil microbiota in the restoration of biodiverse, functional, and resilient ecosystems is required to address the twin global crises of biodiversity decline and climate change. In this review, we discuss available and emerging practical applications of soil microbiota into (i) restoration planning, (ii) direct interventions for shaping soil biodiversity, and (iii) strategies for monitoring and predicting restoration trajectories. We show how better planning of restoration activities to account for soil microbiota can help improve progress towards restoration targets. We show how planning to embed soil microbiota experiments into restoration projects will permit a more rigorous assessment of the effectiveness of different restoration methods, especially when complemented by statistical modelling approaches that capitalise on existing data sets to improve causal understandings and prioritise research strategies where appropriate. In addition to recovering belowground microbiota, restoration strategies that include soil microbiota can improve the resilience of whole ecosystems. Fundamentally, restoration planning should identify appropriate reference target ecosystem attributes and - from the perspective of soil microbiota - comprehensibly consider potential physical, chemical and biological influences on recovery. We identify that inoculating ecologically appropriate soil microbiota into degraded environments can support a range of restoration interventions (e.g. targeted, broad-spectrum and cultured inoculations) with promising results. Such inoculations however are currently underutilised and knowledge gaps persist surrounding successful establishment in light of community dynamics, including priority effects and community coalescence. We show how the ecological trajectories of restoration sites can be assessed by characterising microbial diversity, composition, and functions in the soil. Ultimately, we highlight practical ways to apply the soil microbiota toolbox across the planning, intervention, and monitoring stages of ecosystem restoration and address persistent open questions at each stage. With continued collaborations between researchers and practitioners to address knowledge gaps, these approaches can improve current restoration practices and ecological outcomes.

Research on the optimal ratio of improved electrolytic manganese residue substrate about Pennisetum sinese Roxb growth effects

Electrolytic manganese slag (EMR) is a solid waste generated in the manganese hydrometallurgy process. It not only takes up significant land space but also contains Mn2+, which can lead to environmental contamination. There is a need for research on the treatment and utilization of EMR. Improved EMR substrate for Pennisetum sinese Roxb growth was determined in pot planting experiments. The study tested the effects of leaching solution, microorganisms, leaf cell structures, and growth data. Results indicated a substrate of 45% EMR, 40% phosphogypsum, 5% Hericium erinaceus fungi residue, 5% quicklime, and 5% dolomite sand significantly increased the available phosphorus content (135.54 ± 2.88 μg·g-1) by 17.95 times, compared to pure soil, and enhanced the relative abundance of dominant bacteria. After 240 days, the plant height (147.00 ± 0.52 cm), number of tillers (6), and aerial dry weight (144.00 ± 15.99g) of Pennisetum sinese Roxb increased by 5.81%, 200%, and 32.58%, respectively. Analyses of leaves and leaching solution revealed that the highest leaf Mn content (46.84 ± 2.91 μg·g-1) being 3.38 times higher than in pure soil, and the leaching solution Mn content (0.66 ± 0.13 μg·g-1) was lowest. Our study suggested P. sinese Roxb grown in an improved EMR substrate could be a feasible option for solidification treatment and resource utilization of EMR.

Harnessing co-evolutionary interactions between plants and Streptomyces to combat drought stress

Streptomyces is a drought-tolerant bacterial genus in soils, which forms close associations with plants to provide host resilience to drought stress. Here we synthesize the emerging research that illuminates the multifaceted interactions of Streptomyces spp. in both plant and soil environments. It also explores the potential co-evolutionary relationship between plants and Streptomyces spp. to forge mutualistic relationships, providing drought tolerance to plants. We propose that further advancement in fundamental knowledge of eco-evolutionary interactions between plants and Streptomyces spp. is crucial and holds substantial promise for developing effective strategies to combat drought stress, ensuring sustainable agriculture and environmental sustainability in the face of climate change.

Anthropogenic restoration exhibits more complex and stable microbial co-occurrence patterns than natural restoration in rubber plantations

Forest restoration is an effective method for restoring degraded soil ecosystems (e.g., converting primary tropical forests into rubber monoculture plantations; RM). The effects of forest restoration on microbial community diversity and composition have been extensively studied. However, how rubber plantation-based forest restoration reshapes soil microbial communities, networks, and inner assembly mechanisms remains unclear. Here, we explored the effects of jungle rubber mixed (JRM; secondary succession and natural restoration of RM) plantation and introduction of rainforest species (AR; anthropogenic restoration established by mimicking the understory and overstory tree species of native rainforests) to RM stands on soil physico-chemical properties and microbial communities. We found that converting tropical rainforest (RF) to RM decreased soil fertility and simplified microbial composition and co-occurrence patterns, whereas the conversion of RM to JRM and AR exhibited opposite results. These changes were significantly correlated with pH, soil moisture content (SMC), and soil nutrients, suggesting that vegetation restoration can provide a favorable soil microenvironment that promotes the development of soil microorganisms. The complexity and stability of the bacterial-fungal cross-kingdom, bacterial, and fungal networks increased with JRM and AR. Bacterial community assembly was primarily governed by stochastic (78.79 %) and deterministic (59.09 %) processes in JRM and AR, respectively, whereas stochastic processes (limited dispersion) predominantly shaped fungal assembly across all forest stands. AR has more significant benefits than JRM, such as a relatively slower and natural vegetation succession with more nutritive soil conditions, microbial diversity, and complex and stable microbial networks. These results highlight the importance of sustainable forest management to restore soil biodiversity and ecosystem functions after extensive soil degradation and suggest that anthropogenic restoration can more effectively improve soil quality and microbial communities than natural restoration in degraded rubber plantations.

Nutrient limitation mediates soil microbial community structure and stability in forest restoration

Soil microorganisms are often limited by nutrients, representing an important control of heterotrophic metabolic processes. However, how nutrient limitations relate to microbial community structure and stability remains unclear, which creates a knowledge gap to understanding microbial biogeography and community changes during forest restoration. Here, we combined an eco-enzymatic stoichiometry model and high-throughput DNA sequencing to assess the potential roles of nutrient limitation on microbial community structure, assembly, and stability along a forest restoration sequence in the Qinling Mountains, China. Results showed that nutrient limitations tended to decrease during the oak forest restoration. Carbon and phosphorus limitations enhanced community dissimilarity and significantly increased bacterial alpha diversity, but not fungal diversity. Stochastic assembly processes primarily structured both bacterial (average contribution of 74.73 % and 74.17 % in bulk and rhizosheath soils, respectively) and fungal (average contribution of 77.23 % and 72.04 % in bulk and rhizosheath soils, respectively) communities during forest restoration, with nutrient limitation also contributing to the importance of stochastic processes in the bacterial communities. The migration rate (m) for bacteria was 0.19 and 0.23, respectively in both bulk soil and rhizosheath soil, and was greater than that for the fungi (m was 1.19 and 1.41, respectively), indicating a stronger dispersal limitation for fungal communities. Finally, nutrient limitations significantly affected bacterial and fungal co-occurrence with more interconnections occurring among weakly nutrient-limited microbial taxa and nutrient limitations reducing community stability when nutrient availability changed during forest restoration. Our findings highlight the fundamental effects of nutrient limitations on microbial communities and their self-regulation under changing environmental resources.

Submerged macrophyte restoration enhanced microbial carbon utilization in shallow lakes

Submerged macrophytes are integral to the functioning of shallow lakes through their interaction with microorganisms. However, we have a limited understanding of how microbial communities in shallow lakes respond when macrophytes are restored after being historically extirpated. Here, we explored the interactions between prokaryotic communities and carbon utilization in two lakes where submerged macrophytes were restored. We found restoration reduced total carbon in sediment by 8.9 %-27.9 % and total organic carbon by 16.7 %-36.9 % relative to control treatment, but had no effects on carbon content in the overlying water. Sediment microbial communities were more sensitive to restoration than planktonic microbes and showed enhanced utilization of simple carbon substrates, such as Tween 40, after restoration. The increase in carbon utilization was attributed to declines in the relative abundance of some genera, such as Saccharicenans and Desertimonas, which were found weakly associated with the utilization of different carbon substrates. These genera likely competed with microbes with high carbon utilization in restored areas, such as Lubomirskia. Our findings highlight how restoring submerged macrophytes can enhance microbial carbon utilization and provide guidance to improve the carbon sequestration capacity of restored shallow lakes.

Prairie restoration promotes the abundance and diversity of mutualistic arbuscular mycorrhizal fungi

Predicting how biological communities assemble in restored ecosystems can assist in conservation efforts, but most research has focused on plants, with relatively little attention paid to soil microbial organisms that plants interact with. Arbuscular mycorrhizal (AM) fungi are an ecologically significant functional group of soil microbes that form mutualistic symbioses with plants and could therefore respond positively to plant community restoration. To evaluate the effects of plant community restoration on AM fungi, we compared AM fungal abundance, species richness, and community composition of five annually cultivated, conventionally managed agricultural fields with paired adjacent retired agricultural fields that had undergone prairie restoration 5-9 years prior to sampling. We hypothesized that restoration stimulates AM fungal abundance and species richness, particularly for disturbance-sensitive taxa, and that gains of new taxa would not displace AM fungal species present prior to restoration due to legacy effects. AM fungal abundance was quantified by measuring soil spore density and root colonization. AM fungal species richness and community composition were determined in soils and plant roots using DNA high-throughput sequencing. Soil spore density was 2.3 times higher in restored prairies compared to agricultural fields, but AM fungal root colonization did not differ between land use types. AM fungal species richness was 2.7 and 1.4 times higher in restored prairies versus agricultural fields for soil and roots, respectively. The abundance of Glomeraceae, a disturbance-tolerant family, decreased by 25% from agricultural to restored prairie soils but did not differ in plant roots. The abundance of Claroideoglomeraceae and Diversisporaceae, both disturbance-sensitive families, was 4.6 and 3.2 times higher in restored prairie versus agricultural soils, respectively. Species turnover was higher than expected relative to a null model, indicating that AM fungal species were gained by replacement. Our findings demonstrate that restoration can promote a relatively rapid increase in the abundance and diversity of soil microbial communities that had been degraded by decades of intensive land use, and community compositional change can be predicted by the disturbance tolerance of soil microbial taxonomic and functional groups.

Diversity and growth-promoting characteristics of rhizosphere bacteria of three naturally growing plants at the sand iron ore restoration area in Qinghe County

It is a great challenge to restore northern mines after mining and achieve optimal results due to the extremely harsh environment and climate, as in Qinghe County of Xinjiang Province, China. Qinghe County has a climate of drought, cold, strong winds, and high altitude. After sand and iron mining, the soil in this area contains a large amount of sand and gravel with extremely low organic matter, nitrogen deficiency, and a high pH of 9.26. Our preliminary studies disclosed that only three plants, including Caligonum junceum, Atraphaxis virgata, and Melilotus albus Medic, can grow naturally in this environment without any artificial management. For effective ecology restoration, this study explored the mechanism of plant-microbial interaction and stress resistance in this environment. It was found that although the soil condition in the sand iron ore landfill area is extreme, the bacterial diversity remained high, with Shannon and Simpson indices reaching 9.135 and 0.994, respectively. The planting of three types of remediation plants did not significantly improve, or even decreased, the soil bacterial diversity index, but greatly changed the composition of dominant bacterial genera. Significant differences in the composition of rhizosphere soil bacterial communities among these three remediation plants were observed. Potential new bacterial species accounted for 9.8 %, and the proportion of unique genera reached 30 % or 50 %, respectively. Among all the isolated strains, 74 % had nitrogen fixation and other growth-promoting properties. In summary, the soil microbial community structure in this extreme environment is unique and diverse. The types of remediation plants play a major role in the composition of the rhizosphere bacterial community structure, and the recruited growth-promoting bacteria are diverse and functional. This study may offer valuable information for further studies in vegetation restoration and aid in ecology restoration, especially under extreme conditions.

The role of the plant microbiome for forestry, agriculture and urban greenspace in times of environmental change

This Lilliput article provides a literature overview on ecological effects of the plant microbiome with a focus on practical application in forestry, agriculture and urban greenspace under the spectre of climate change. After an overview of the mostly bacterial microbiome of the model plant Arabidopsis thaliana, worldwide data from forests reveal ecological differentiation with respect to major guilds of predominantly fungal plant root symbionts. The plant-microbiome association forms a new holobiont, an integrated unit for ecological adaptation and evolutionary selection. Researchers explored the impact of the microbiome on the capacity of plants to adapt to changing climate conditions. They investigated the impact of the microbiome in reforestation programs, after wildfire, drought, salination and pollution events in forestry, grasslands and agriculture. With increasing temperatures plant populations migrate to higher latitudes and higher altitudes. Ecological studies compared the dispersal capacity of plant seeds with that of soil microbes and the response of soil and root microbes to experimental heating of soils. These studies described a succession of microbiome associations and the kinetics of a release of stored soil carbon into the atmosphere enhancing global warming. Scientists explored the impact of synthetic microbial communities (SynComs) on rice productivity or tea quality; of whole soil addition in grassland restoration; or single fungal inoculation in maize fields. Meta-analyses of fungal inoculation showed overall a positive effect, but also a wide variation in effect sizes. Climate change will be particularly prominent in urban areas ("urban heat islands") where more than half of the world population is living. Urban landscape architecture will thus have an important impact on human health and studies started to explore the contribution of the microbiome from urban greenspace to ecosystem services.

Nano zerovalent Fe did not reduce metal(loid) leaching and ecotoxicity further than conventional Fe grit in contrasting smelter impacted soils: A 1-year field study

The majority of the studies on nanoscale zero-valent iron (nZVI) are conducted at a laboratory-scale, while field-scale evidence is scarce. The objective of this study was to compare the metal(loid) immobilization efficiency of selected Fe-based materials under field conditions for a period of one year. Two contrasting metal(loid) (As, Cd, Pb, Zn) enriched soils from a smelter-contaminated area were amended with sulfidized nZVI (S-nZVI) solely or combined with thermally stabilized sewage sludge and compared to amendment with microscale iron grit. In the soil with higher pH (7.5) and organic matter content (TOC = 12.7 %), the application of amendments resulted in a moderate increase in pH and reduced As, Cd, Pb, and Zn leaching after 1-year, with S-nZVI and sludge combined being the most efficient, followed by iron grit and S-nZVI alone. However, the amendments had adverse impacts on microbial biomass quantity, S-nZVI being the least damaging. In the soil with a lower pH (6.0) and organic matter content (TOC = 2.3 %), the results were mixed; 0.01 M CaCl2 extraction data showed only S-nZVI with sludge as remaining effective in reducing extractable concentrations of metals; on the other hand, Cd and Zn concentrations were increased in the extracted soil pore water solutions, in contrast to the two conventional amendments. Despite that, S-nZVI with sludge enhanced the quantity of microbial biomass in this soil. Additional earthworm avoidance data indicated that they generally avoided soil treated with all Fe-based materials, but the presence of sludge impacted their preferences somewhat. In summary, no significant differences between S-nZVI and iron grit were observed for metal(loid) immobilization, though sludge significantly improved the performance of S-nZVI in terms of soil health indicators. Therefore, this study indicates that S-nZVI amendment of soils alone should be avoided, though further field evidence from a broader range of soils is now required.

Synthetic microbiology in sustainability applications

Microorganisms are a promising means to address many societal sustainability challenges owing to their ability to thrive in diverse environments and interface with the microscale chemical world via diverse metabolic capacities. Synthetic biology can engineer microorganisms by rewiring their regulatory networks or introducing new functionalities, enhancing their utility for target applications. In this Review, we provide a broad, high-level overview of various research efforts addressing sustainability challenges through synthetic biology, emphasizing foundational microbiological research questions that can accelerate the development of these efforts. We introduce an organizational framework that categorizes these efforts along three domains - factory, farm and field - that are defined by the extent to which the engineered microorganisms interface with the natural external environment. Different application areas within the same domain share many fundamental challenges, highlighting productive opportunities for cross-disciplinary collaborations between researchers working in historically disparate fields.

Arbuscular mycorrhizal fungal interactions bridge the support of root-associated microbiota for slope multifunctionality in an erosion-prone ecosystem

The role of diverse soil microbiota in restoring erosion-induced degraded lands is well recognized. Yet, the facilitative interactions among symbiotic arbuscular mycorrhizal (AM) fungi, rhizobia, and heterotrophic bacteria, which underpin multiple functions in eroded ecosystems, remain unclear. Here, we utilized quantitative microbiota profiling and ecological network analyses to explore the interplay between the diversity and biotic associations of root-associated microbiota and multifunctionality across an eroded slope of a Robinia pseudoacacia plantation on the Loess Plateau. We found explicit variations in slope multifunctionality across different slope positions, associated with shifts in limiting resources, including soil phosphorus (P) and moisture. To cope with P limitation, AM fungi were recruited by R. pseudoacacia, assuming pivotal roles as keystones and connectors within cross-kingdom networks. Furthermore, AM fungi facilitated the assembly and composition of bacterial and rhizobial communities, collectively driving slope multifunctionality. The symbiotic association among R. pseudoacacia, AM fungi, and rhizobia promoted slope multifunctionality through enhanced decomposition of recalcitrant compounds, improved P mineralization potential, and optimized microbial metabolism. Overall, our findings highlight the crucial role of AM fungal-centered microbiota associated with R. pseudoacacia in functional delivery within eroded landscapes, providing valuable insights for the sustainable restoration of degraded ecosystems in erosion-prone regions.

Mechanism on the promotion of host growth and enhancement of salt tolerance by Bacillaceae isolated from the rhizosphere of Reaumuria soongorica

Salt stress is a major abiotic stress that affects the growth of Reaumuria soongorica and many psammophytes in the desert areas of Northwest China. However, various Plant Growth-Promoting Rhizobacteria (PGPR) have been known to play an important role in promoting plant growth and alleviating the damaging effects of salt stress. In this study, three PGPR strains belonging to Bacillaceae were isolated from the rhizosphere of Reaumuria soongorica by morphological and molecular identification. All isolated strains exhibited capabilities of producing IAA, solubilizing phosphate, and fixing nitrogen, and were able to tolerate high levels of NaCl stress, up to 8-12%. The results of the pot-based experiment showed that salt (400 mM NaCl) stress inhibited Reaumuria soongorica seedlings' growth performance as well as biomass production, but after inoculation with strains P2, S37, and S40, the plant's height significantly increased by 26.87, 17.59, and 13.36%, respectively (p < 0.05), and both aboveground and root fresh weight significantly increased by more than 2 times compared to NaCl treatment. Additionally, inoculation with P2, S37, and S40 strains increased the content of photosynthetic pigments, proline, and soluble protein in Reaumuria soongorica seedlings under NaCl stress, while reducing the content of malondialdehyde and soluble sugars. Metabolomic analysis showed that strain S40 induces Reaumuria soongorica seedling leaves metabolome reprogramming to regulate cell metabolism, including plant hormone signal transduction and phenylalanine, tyrosine, and tryptophan biosynthesis pathways. Under NaCl stress, inoculation with strain S40 upregulated differential metabolites in plant hormone signal transduction pathways including plant hormones such as auxins (IAA), cytokinins, and jasmonic acid. The results indicate that inoculation with Bacillaceae can promote the growth of Reaumuria soongorica seedlings under NaCl stress and enhance salt tolerance by increasing the content of photosynthetic pigments, accumulating osmoregulatory substances, regulating plant hormone levels This study contributes to the enrichment of PGPR strains capable of promoting the growth of desert plants and has significant implications for the psammophytes growth and development in desert regions, as well as the effective utilization and transformation of saline-alkali lands.

Who inhabits the built environment? A microbiological point of view on the principal bacteria colonizing our urban areas

Modern lifestyle greatly influences human well-being. Indeed, nowadays people are centered in the cities and this trend is growing with the ever-increasing population. The main habitat for modern humans is defined as the built environment (BE). The modulation of life quality in the BE is primarily mediated by a biodiversity of microbes. They derive from different sources, such as soil, water, air, pets, and humans. Humans are the main source and vector of bacterial diversity in the BE leaving a characteristic microbial fingerprint on the surfaces and spaces. This review, focusing on articles published from the early 2000s, delves into bacterial populations present in indoor and outdoor urban environments, exploring the characteristics of primary bacterial niches in the BE and their native habitats. It elucidates bacterial interconnections within this context and among themselves, shedding light on pathways for adaptation and survival across diverse environmental conditions. Given the limitations of culture-based methods, emphasis is placed on culture-independent approaches, particularly high-throughput techniques to elucidate the genetic and -omic features of BE bacteria. By elucidating these microbiota profiles, the review aims to contribute to understanding the implications for human health and the assessment of urban environmental quality in modern cities.

Tea and Pleurotus ostreatus intercropping modulates structure of soil and root microbial communities

Intercropping with Pleurotus ostreatus has been demonstrated to increase the tea yield and alleviate soil acidification in tea gardens. However, the underlying mechanisms remain elusive. Here, high-throughput sequencing and Biolog Eco analysis were performed to identify changes in the community structure and abundance of soil microorganisms in the P. ostreatus intercropped tea garden at different seasons (April and September). The results showed that the soil microbial diversity of rhizosphere decreased in April, while rhizosphere and non-rhizosphere soil microbial diversity increased in September in the P. ostreatus intercropped tea garden. The diversity of tea tree root microorganisms increased in both periods. In addition, the number of fungi associated with organic matter decomposition and nutrient cycling, such as Penicillium, Trichoderma, and Trechispora, was significantly higher in the intercropped group than in the control group. Intercropping with P. ostreatus increased the levels of total nitrogen (TN), total phosphorus (TP), and available phosphorus (AP) in the soil. It also improved the content of secondary metabolites, such as tea catechins, and polysaccharides in tea buds. Microbial network analysis showed that Unclassified_o__Helotiales, and Devosia were positively correlated with soil TN and pH, while Lactobacillus, Acidothermus, and Monascus were positively correlated with flavone, AE, and catechins in tea trees. In conclusion, intercropping with P. ostreatus can improve the physical and chemical properties of soil and the composition and structure of microbial communities in tea gardens, which has significant potential for application in monoculture tea gardens with acidic soils.

Restoring soil biodiversity

Soil health is crucial for all terrestrial life, supporting, among other processes, food production, water purification and carbon sequestration. Soil biodiversity - the variety of life within soils - is key to these processes and thus key to soil restoration. Human activities that degrade ecosystems threaten soil biodiversity and associated ecosystem processes. Indeed, 75% of the world's soils are affected by degradation - a figure that could rise to 90% by 2050 if deforestation, overgrazing, urbanisation and other harmful practices persist. Restoring soil biodiversity is a prerequisite for planetary health, and it comes with many challenges and opportunities. Soil directly supports around 60% of all species on Earth, and land degradation poses a major problem for this biodiversity and the ecosystem services that sustain human populations. Indeed, 98% of human calories come from soil, and earthworms alone underpin 6.5% of the world's grain production. Moreover, the total carbon in terrestrial ecosystems is around 3,170 gigatons (1 gigaton (Gt) = 1 billion metric tons), of which approximately 80% (2,500 Gt) is found in soil. Therefore, restoring soil biodiversity is not just a human need but an ecological and Earth-system imperative. It is pivotal for maintaining ecosystem resilience, sustaining agricultural productivity and mitigating climate change impacts.

Sustainable strategies: Nature-based solutions to tackle antibiotic resistance gene proliferation and improve agricultural productivity and soil quality

The issue of antibiotic resistance is now recognized by the World Health Organisation (WHO) as one of the major problems in human health. Although its effects are evident in the healthcare settings, the root cause should be traced back to the One Health link, extending from animals to the environment. In fact, the use of organic fertilizers in agroecosystems represents one, if not the primary, cause of the introduction of antibiotics and antibiotic-resistant bacteria into the soil. Since the concentrations of antibiotics introduced into the soil are residual, the agroecosystem has become a perfect environment for the selection and proliferation of antibiotic resistance genes (ARGs). The continuous influx of these emerging contaminants (i.e., antibiotics) into the agroecosystem results in the selection and accumulation of ARGs in soil bacteria, occasionally giving rise to multi-resistant bacteria. These bacteria may harbour ARGs related to various antibiotics on their plasmids. In this context, these bacteria can potentially enter the human sphere when individuals consume food from contaminated agroecosystems, leading to the acquisition of multi-resistant bacteria. Once introduced into the nosocomial environment, these bacteria pose a significant threat to human health. In this review, we analyse how the use of digestate as an organic fertilizer can mitigate the spread of ARGs in agroecosystems. Furthermore, we highlight how, according to European guidelines, digestate can be considered a Nature-Based Solution (NBS). This NBS not only has the ability to mitigate the spread of ARGs in agroecosystems but also offers the opportunity to further improve Microbial-Based Solutions (MBS), with the aim of enhancing soil quality and productivity.

Deterministic assembly of grassland soil microbial communities driven by climate warming amplifies soil carbon loss

Perturbations in soil microbial communities caused by climate warming are expected to have a strong impact on biodiversity and future climate-carbon (C) feedback, especially in vulnerable habitats that are highly sensitive to environmental change. Here, we investigate the impact of four-year experimental warming on soil microbes and C cycling in the Loess Hilly Region of China. The results showed that warming led to soil C loss, mainly from labile C, and this C loss is associated with microbial response. Warming significantly decreased soil bacterial diversity and altered its community structure, especially increasing the abundance of heat-tolerant microorganisms, but had no effect on fungi. Warming also significantly increased the relative importance of homogeneous selection and decreased "drift" of bacterial and fungal communities. Moreover, warming decreased bacterial network stability but increased fungal network stability. Notably, the magnitude of soil C loss was significantly and positively correlated with differences in bacterial community characteristics under ambient and warming conditions, including diversity, composition, network stability, and community assembly. This result suggests that microbial responses to warming may amplify soil C loss. Combined, these results provide insights into soil microbial responses and C feedback in vulnerable ecosystems under climate warming scenarios.

Restoration age affects microbial-herbaceous plant interactions in an oak woodland

In degraded ecosystems, soil microbial communities (SMCs) may influence the outcomes of ecological restoration. Restoration practices can affect SMCs, though it is unclear how variation in the onset of restoration activities in woodlands affects SMCs, how those SMCs influence the performance of hard-to-establish woodland forbs, and how different woodland forbs shape SMCs. In this study, we quantified soil properties and species abundances in an oak woodland restoration chronosequence (young, intermediate, and old restorations). We measured the growth of three woodland forb species when inoculated with live whole-soil from young, intermediate, or old restorations. We used DNA metabarcoding to characterize SMCs of each inoculum treatment and the soil after conditioning by each plant species. Our goals were to (1) understand how time since the onset of restoration affected soil abiotic properties, plant communities, and SMCs in a restoration chronosequence, (2) test growth responses of three forb species to whole-soil inoculum from restoration sites, and (3) characterize changes in SMCs before and after conditioning by each forb species. Younger restored woodlands had greater fire-sensitive tree species and lower concentrations of soil phosphorous than intermediate or older restored woodlands. Bacterial and fungal soil communities varied significantly among sites. Forbs exhibited the greatest growth in soil from the young restoration. Each forb species developed a unique soil microbial community. Our results highlight how restoration practices affect SMCs, which can in turn affect the growth of hard-to-establish forb species. Our results also highlight that the choice of forb species can alter SMCs, which could have long-term potential consequences for restoration success.

Leaf carbon chemistry effectively manipulated soil microbial profiles and induced metabolic adjustments under different revegetation types in the loess Plateau, China

Microorganisms are essential components of underground life systems and drive elemental cycling between plants and soil. Yet, in the ecologically fragile Loess Plateau, scant attention has been paid to the response of microbial communities to organic carbon (C) chemistry of both leaves and soils under different revegetation conditions, as well as subsequent alternation in their C metabolic functions. Here, Fourier transform infrared (FTIR) spectrum, amplicon sequencing of 16S rRNA and ITS, and temporal incubation with Biolog-Eco 96 plates were combined to explore the vegetative heterogeneity of microbial community properties and metabolic functions, as well as their regulatory mechanisms in three typical revegetation types including Robinia pseudoacacia L. (RF), Caragana korshinskii KOM. (SL), and abandoned grassland (AG). We observed higher bacterial-to-fungal ratios (B: F = 270.18) and richer copiotrophic bacteria (Proteobacteria = 33.08%) in RF soil than those in AG soil, suggesting that microbes were dominated by r-strategists in soil under RF treatment, which is mainly related to long-term priming of highly bioavailable leaf C (higher proportion of aromatic and hydrophilic functional groups and lower hydrophobicity). Conversely, microbial taxa in AG soil, which was characterized by higher leaf organic C hydrophobicity (1.39), were dominated by relatively more abundant fungi (lower B: F ratio = 149.49) and oligotrophic bacteria (Actinobacteria = 29.30%). The co-occurrence network analysis showed that microbial interactive associations in RF and AG soil were more complex and connective than in SL soil. Furthermore, Biolog-Eco plate experiments revealed that microorganisms tended to utilize labile C compounds (carbohydrates and amino acids) in RF soil and resistant C compounds (polymers) in AG soil, which were consistent with the substrate adaptation strategies of predominant microbial trophic groups in different revegetation environments. Meanwhile, we observed greater microbial metabolic activity and diversity advantages in RF vegetation. Collectively, we suggest that besides the nutrient variables in the leaf-soil system, the long-term regulation of the microbial community by the C chemistry of the leaf sequentially alters the microbial metabolic profiles in a domino-like manner. RF afforestation is more conducive to restoring soil microbial fertility (including microbial abundance, diversity, interactive association, and metabolic capacity). Our study potentially paves the way for achieving well-managed soil health and accurate prediction of C pool dynamics in areas undergoing ecological restoration of the Loess Plateau.

Management of excessive soil H+ ion induced toxicities by application of organic seaweed amendment enhances photosynthesis and resource use efficiencies in rice (Oryza sativa)

Globally, soil acidification is a serious environmental issue that reduces commercial agricultural production. Rice is subjected to nutritional stress due to acidic soil, which is a major impediment to rice production. Since acid soil threatens rice plants with soil compaction, nutrient loss, and plant stress-induced oxidative cell damage that results in affecting the photosynthetic system, restricting the availability of water, and reducing overall plant growth and productivity. Since contemporary soil acidification management strategies provide mediocre results, the use of Sargassum wightii seaweed-based biostimulants (BS) and soil amendments is sought as an environmentally friendly alternative strategy, and therefore its potential isevaluated in this study. BS was able to mediate soil quality by improving soil pH and structure along with facilitating nitrogen phytoavailability. BS also increased the activity of the antioxidant enzyme system, superoxide dismutase ((48%), peroxidase (76.6%), and ascorbate peroxidase (63.5%), aggregating the monaldehyde-mediating accumulation of osmoprotective proline in roots, that was evident from rapid initiation of root hair growth in treated seedlings. BS was also able to physiologically modulate photosynthetic activities and chlorophyll production (24.31%) in leaves, maintaining the efficiency of plant water use by regulating the stomatal conductance (0.91 mol/m/s) and the transpiration rate (13.2 mM/m/s). The BS compounds were also successful in facilitating nitrogen uptake resulting in improved plant growth (59%), tiller-panicle number, and yield (52.57%), demonstrating a resourceful nitrogen use efficiency (71.96%) previously affected by stress induced by acid soil. Therefore, the study affirms the competent potential of S. wightii-based soil amendment to be applied not only to improve soil quality, but also to increase plant production and yield.

Terrihabitans rhizophilus sp. nov., isolated from the rhizosphere soil of plant in temperate semi-arid steppe

A bacterial strain PJ23T was isolated from the rhizosphere soil of Elymus dahuricus Turcz. sampled from a temperate semi-arid steppe in the northern of Inner Mongolia Autonomous Region, China. The strain is Gram-stain-negative, aerobic, light-pink, short rod-shaped, and non-spore-forming. Cell growth could be observed at 4-29℃ (optimal at 24℃), pH 6.0-8.6 (optimal at 8.0) and in the presence of 0-5.0% (w/v) NaCl (optimal at 2.5%). The major cellular fatty acids of strain PJ23T were Summed feature 8 (C18:1 ω6c and/or C18:1 ω7c) (39.42%) and C16:0 (9.60%). The polar lipids were phosphatidylcholine, two unidentified glycolipids, one unidentified aminophospholipid, and two other unidentified polar lipids. The major respiratory quinone was ubiquinone-10. Phylogeny analysis based on 16S rRNA gene sequences retrieved from the genomes showed that, the strain was closely related to the species Terrihabitans soli IZ6T and Flaviflagellibacter deserti SYSU D60017T, with the sequence similarities of 96.79% and 96.15%, respectively. The G + C content was 65.23 mol% calculated on draft genome sequencing. Between the strains PJ23T and Terrihabitans soli IZ6T, the average nucleotide identity (ANI), amino acid identity (AAI) and digital DNA-DNA hybridization (dDDH) was 73.39%,71.12% and 15.7%, these values were lower than the proposed and generally accepted species boundaries of ANI, AAI and dDDH, respectively. Based on phenotypic, chemotaxonomic, and phylogenetic characteristics, strain PJ23T represents a novel species of Terrihabitans, for which the name Terrihabitans rhizophilus sp. nov. is proposed. The type strain is PJ23T (= KCTC 92977 T = CGMCC 1.61577 T).

Changes in soil microbe-mediated carbon, nitrogen and phosphorus cycling during spontaneous succession in abandoned PbZn mining areas

The mechanism through which soil microorganisms mediate carbon and nutrient cycling during mine wasteland restoration remained unknown. Using soil metagenome sequencing, we investigated the dynamic changes in soil microbial potential metabolic functions during the transition from biological soil crusts (BSC) to mixed broad-conifer forest (MBF) in a typical PbZn mine. The results showed soil microorganisms favored carbon sequestration through anaerobic and microaerobic pathways, predominantly using efficient, low-energy pathways during succession. Genes governing carbon degradation and aerobic respiration increased by 19.56 % and 24.79 %, respectively, reflecting change toward more efficient and intensive soil carbon utilization in late succession. Nitrogen-cycling genes mediated by soil microorganisms met their maximum influence during early succession (sparse grassland, SGL), leading to a respective increase of 75.29 % and 76.81 % in the net potential nitrification rate and total nitrogen content. Mantel and correlation analyses indicated that TOC, TN, Zn and Cd contents were the main factors affecting the soil carbon and phosphorus cycles. Soil AP content emerged as the primary influencer of genes associated with the nitrogen cycle. These results shed light on the dynamic shifts in microbial metabolic activities during succession, providing a genetic insight into biogeochemical cycling mechanisms and underscoring crucial factors influencing soil biogeochemical processes in mining regions.

Biological Interactions Mediate Soil Functions by Altering Rare Microbial Communities

Soil microbes, the main driving force of terrestrial biogeochemical cycles, facilitate soil organic matter turnover. However, the influence of the soil fauna on microbial communities remains poorly understood. We investigated soil microbiota dynamics by introducing competition and predation among fauna into two soil ecosystems with different fertilization histories. The interactions significantly affected rare microbial communities including bacteria and fungi. Predation enhanced the abundance of C/N cycle-related genes. Rare microbial communities are important drivers of soil functional gene enrichment. Key rare microbial taxa, including SM1A02, Gammaproteobacteria, and HSB_OF53-F07, were identified. Metabolomics analysis suggested that increased functional gene abundance may be due to specific microbial metabolic activity mediated by soil fauna interactions. Predation had a stronger effect on rare microbes, functional genes, and microbial metabolism compared to competition. Long-term organic fertilizer application increased the soil resistance to animal interactions. These findings provide a comprehensive understanding of microbial community dynamics under soil biological interactions, emphasizing the roles of competition and predation among soil fauna in terrestrial ecosystems.

A comparative analysis of soil physicochemical properties and microbial community structure among four shelterbelt species in the northeast China plain

Conducting studies that focus on the alterations occurring in the soil microbiome within protection forests in the northeast plain is of utmost importance in evaluating the ecological rehabilitation of agricultural lands in the Mollisols region. Nevertheless, the presence of geographic factors contributes to substantial disparities in the microbiomes, and thus, addressing this aspect of influence becomes pivotal in ensuring the credibility of the collected data. Consequently, the objective is to compare the variations in soil physicochemical properties and microbial community structure within the understory of diverse shelterbelt species. In this study, we analyzed the understory soils of Juglans mandshurica (Jm), Fraxinus mandschurica (Fm), Acer mono (Am), and Betula platyphylla (Bp) from the same locality. We employed high-throughput sequencing technology and soil physicochemical data to investigate the impact of these different tree species on soil microbial communities, chemical properties, and enzyme activities in Mollisols areas. Significant variations in soil nutrients and enzyme activities were observed among tree species, with soil organic matter content ranging from 49.1 to 67.7 g/kg and cellulase content ranging from 5.3 to 524.0 μg/d/g. The impact of tree species on microbial diversities was found to be more pronounced in the bacterial community (Adnoism: R = 0.605) compared to the fungal community (Adnoism: R = 0.433). The linear discriminant analysis effect size (LEfSe) analysis revealed a total of 5 (Jm), 3 (Bp), and 6 (Am) bacterial biomarkers, as well as 2 (Jm), 6 (Fm), 4 (Bp), and 1 (Am) fungal biomarker at the genus level (LDA3). The presence of various tree species was observed to significantly alter the relative abundance of specific microbial community structures, specifically in Gammaproteobacteria, Ascomycota, and Basidiomycota. Furthermore, environmental factors, such as pH, total potassium, and available phosphorus were important factors influencing changes in bacterial communities. We propose that Fm be utilized as the primary tree species for establishing farmland protection forests in the northeastern region, owing to its superior impact on enhancing soil quality.

IMPORTANCE

The focal point of this study lies in the implementation of a controlled experiment conducted under field conditions. In this experiment, we deliberately selected four shelterbelts within the same field, characterized by identical planting density, and planting year. This deliberate selection effectively mitigated the potential impact of extraneous factors on the three microbiomes, thereby enhancing the reliability and validity of our findings.

Rhizosphere microbial markers (micro-markers): A new physical examination indicator for traditional Chinese medicines

Rhizosphere microorganisms, as one of the most important components of the soil microbiota and plant holobiont, play a key role in the medicinal plant-soil ecosystem, which are closely related to the growth, adaptability, nutrient absorption, stress tolerance and pathogen resistance of host plants. In recent years, with the wide application of molecular biology and omics technologies, the outcomes of rhizosphere microorganisms on the health, biomass production and secondary metabolite biosynthesis of medicinal plants have received extensive attention. However, whether or to what extent rhizosphere microorganisms can contribute to the construction of the quality evaluation system of Chinese medicinal materials is still elusive. Based on the significant role of rhizosphere microbes in the survival and quality formation of medicinal plants, this paper proposed a new concept of rhizosphere microbial markers (micro-markers), expounded the relevant research methods and ideas of applying the new concept, highlighted the importance of micro-markers in the quality evaluation and control system of traditional Chinese medicines (TCMs), and introduced the potential value in soil environmental assessment, plant pest control and quality assessment of TCMs. It provides reference for developing ecological planting of TCMs and ensuring the production of high quality TCMs by regulating rhizosphere microbial communities.

Biological interactions control bacterial but not fungal β diversity during vegetation degradation in saline-alkaline soil

The patterns and mechanisms by which soil bacterial and fungal community β-diversity respond to vegetation degradation in saline-alkaline soils are currently not clear, and in particular, the role of biotic interactions is relatively unknown. To investigate the assembly of bacterial and fungal communities in topsoil (0-10 cm) in saline-alkaline soils at different stages of vegetation degradation, the β-Mean Nearest Classification Unit Distance, the β-Nearest Taxon Index, and the Raup-Crick index were calculated. The relative importance of biotic and environmental factors in controlling β diversity under deterministic processes was also quantified by using relative importance analyses. The β diversity of soil bacterial and fungal communities responded differently in different stages of vegetation degradation in saline-alkaline soils, with bacterial β diversity increasing with increasing vegetation degradation but fungal β diversity showing few differences. Deterministic processes regulated soil bacterial community assembly, and biotic factors were important in driving changes in β diversity, whereas both deterministic and stochastic processes were essential in soil fungal community assembly, and environmental factors were important in affecting fungal β diversity. Furthermore, fungal β diversity is far more affected by interactions between fungus and bacteria than bacteria. Our study demonstrates the different effects of vegetation degradation on bacterial and fungal communities in saline soils to provide the overall implications for saline soils microorganisms in deteriorating ecosystems.

Interaction of microplastics with heavy metals in soil: Mechanisms, influencing factors and biological effects

Microplastics (MPs) and heavy metals (HMs) in soil contamination are considered an emerging global problem that poses environmental and health risks. However, their interaction and potential biological effects remain unclear. Here, we reviewed the interaction of MPs with HMs in soil, including its mechanisms, influencing factors and biological effects. Specifically, the interactions between HMs and MPs mainly involve sorption and desorption. The type, aging, concentration, size of MPs, and the physicochemical properties of HMs and soil have significant impacts on the interaction. In particular, MP aging affects specific surface areas and functional groups. Due to the small size and resistance to decomposition characteristics of MPs, they are easily transported through the food chain and exhibit combined biological effects with HMs on soil organisms, thus accumulating in the human body. To comprehensively understand the effect of MPs and HMs in soil, we propose combining traditional experiments with emerging technologies and encouraging more coordinated efforts.

Dryland rock detention structures increase herbaceous vegetation cover and stabilize shrub cover over 10 years but do not directly affect soil fertility

Rock detention structures (RDS) such as check dams, gabions, and one rock dams are commonly used to mitigate erosion impacts in dryland ephemeral stream channels. RDS increase local water infiltration and floodplain connectivity, reduce sediment transport, and enhance vegetation growth and establishment. In addition to increasing overall vegetation cover, RDS may also buffer against a cycle of vegetation growth and collapse during years of extremely variable precipitation, helping to maintain stable cover. Although widely employed by land managers, success as reported in scientific literature varies, especially with regard to RDS effects on vegetation and soil fertility. We present the results of a 10-year field experiment in southeastern Arizona, USA, designed in collaboration with local land practitioners to measure local in-channel effects of RDS. Over 10 years, cover of herbaceous vegetation (forbs and grasses) doubled from 11 % to 22 % in channels treated with RDS, but did not significantly increase in untreated control channels. Shrub cover in treated channels was significantly less variable than in control channels over time. We analyzed the complex relationships between RDS, vegetation cover, and soil fertility using structural equation modeling (SEM), which represented conditions of the tenth year alone. SEM revealed that RDS did not directly affect soil fertility, as measured by total soil nitrogen, total soil carbon, soil organic matter, microbial richness, and potential nutrient cycling capacity. Notably, SEM did not yield the same trends as temporal monitoring, possibly because our structural equation models could not capture change over time. This discrepancy highlights the need for long-term, frequent monitoring of aboveground and belowground conditions to evaluate treatment success on a management scale. Overall, installing rock detention structures in ephemeral channels in arid and semiarid regions is a low-cost, feasible way to increase channel sediment aggradation, forb, and grass cover; stabilize shrub cover; and combat dryland degradation.

Effects of grazing exclusion on soil microbial diversity and its functionality in grasslands: a meta-analysis

Grazing exclusion (GE) is considered an effective strategy for restoring the degradation of overgrazed grasslands on the global scale. Soil microbial diversity plays a crucial role in supporting multiple ecosystem functions (multifunctionality) in grassland ecosystems. However, the impact of grazing exclusion on soil microbial diversity remains uncertain. Here, we conducted a meta-analysis using a dataset comprising 246 paired observations from 46 peer-reviewed papers to estimate how GE affects microbial diversity and how these effects vary with climatic regions, grassland types, and GE duration ranging from 1 to 64 years. Meanwhile, we explored the relationship between microbial diversity and its functionality under grazing exclusion. Overall, grazing exclusion significantly increased microbial Shannon (1.9%) and microbial richness (4.9%) compared to grazing group. For microbial groups, GE significantly increased fungal richness (8.6%) and bacterial richness (5.3%), but decreased specific microbial richness (-11.9%). The responses of microbial Shannon to GE varied among climatic regions, grassland types, and GE duration. Specifically, GE increased microbial diversity in in arid, semi-arid, and dry sub-humid regions, but decreased it in humid regions. Moreover, GE significantly increased microbial Shannon in semidesert grasslands (5.9%) and alpine grasslands (3.0%), but not in temperate grasslands. Long-term (>20 year) GE had greater effects on microbial diversity (8.0% for Shannon and 6.7% for richness) compared to short-term (<10 year) GE (-0.8% and 2.4%). Furthermore, grazing exclusion significantly increased multifunctionality, and both microbial and plant Shannon positively correlated with multifunctionality. Overall, our findings emphasize the importance of considering climate, GE duration, and grassland type for biodiversity conservation and sustainable grassland ecosystem functions.

Soil, Plant, and Microorganism Interactions Drive Secondary Succession in Alpine Grassland Restoration

Plant secondary succession has been explored extensively in restoring degraded grasslands in semiarid or dry environments. However, the dynamics of soil microbial communities and their interactions with plant succession following restoration efforts remain understudied, particularly in alpine ecosystems. This study investigates the interplay between soil properties, plant communities, and microbial populations across a chronosequence of grassland restoration on the Qinghai-Tibet Plateau in China. We examined five succession stages representing artificial grasslands of varying recovery durations from 0 to 19. We characterized soil microbial compositions using high-throughput sequencing, enzymatic activity assessments, and biomass analyses. Our findings reveal distinct plant and microbial secondary succession patterns, marked by increased soil organic carbon, total phosphorus, and NH4+-N contents. Soil microbial biomass, enzymatic activities, and microbial community diversity increased as recovery time progressed, attributed to increased plant aboveground biomass, cover, and diversity. The observed patterns in biomass and diversity dynamics of plant, bacterial, and fungal communities suggest parallel plant and fungal succession occurrences. Indicators of bacterial and fungal communities, including biomass, enzymatic activities, and community composition, exhibited sensitivity to variations in plant biomass and diversity. Fungal succession, in particular, exhibited susceptibility to changes in the soil C: N ratio. Our results underscore the significant roles of plant biomass, cover, and diversity in shaping microbial community composition attributed to vegetation-induced alterations in soil nutrients and soil microclimates. This study contributes valuable insights into the intricate relationships driving secondary succession in alpine grassland restoration.

Substation of vermicompost mitigates Cd toxicity, improves rice yields and restores bacterial community in a Cd-contaminated soil in Southern China

Cadmium (Cd) contamination in agricultural soil is a global concern for soil health and food sustainability because it can cause Cd accumulation in cereal grains. An in-situ stabilizing technology (using organic amendments) has been widely used for Cd remediation in arable lands. Therefore, the current study examined the influence of vermicompost (VC) on soil biochemical traits, bacterial community diversity and composition, Cd uptake and accumulation in rice plants and grain yield in a Cd-contaminated soil during the late growing season in 2022. Different doses of VC (i.e., V1 = 0 t ha-1, V2 = 3 t ha-1 and V3 = 6 t ha-1) and two concentrations of Cd (i.e., Cd1 = 0 and Cd2 = 50 mg Cd Kg-1 were used. We performed high-throughput sequencing of 16S ribosomal RNA gene amplicons to characterize soil bacterial communities. The addition of VC considerably affected the diversity and composition of the soil bacterial community; and increased the relative abundance of phyla Chloroflexi, Proteobacteria, Acidobacteriota, Plantomycetota, Gemmatimonadota, Patescibacteria and Firmicute. In addition, VC application, particularly High VC treatment, exhibited the highest bacterial diversity and richness (i.e., Simpson, Shannon, ACE, and Chao 1 indexes) of all treatments. Similarly, the VC application increased the soil chemical traits, including soil pH, soil organic carbon (SOC), available nitrogen (AN), total nitrogen (TN), total potassium (TK), total phosphorous (TP) and enzyme activities (i.e., acid phosphatase, catalase, urease and invertase) compared to non-VC treated soil under Cd stress. The average increase in SOC, TN, AN, TK and TP were 5.75%, 41.15%, 18.51%, 12.31%, 25.45% and 29.67%, respectively, in the High VC treatment (Pos-Cd + VC3) compared with Cd stressed soil. Redundancy analysis revealed that the leading bacterial phyla were associated with SOC, AN, TN, TP and pH, although the relative abundance of Firmicutes, Proteobacteria, Bacteroidata, and Acidobacteria on a phylum basis and Actinobacteria, Gammaproteobacteria and Myxococcia on a class basis, were highly correlated with soil environmental factors. Moreover, the VC application counteracted the adverse effects of Cd on plants and significantly reduced the Cd uptake and accumulation in rice organs, such as roots, stem + leaves and grain under Cd stress conditions. Similarly, applying VC significantly increased the fragrant rice grain yield and yield traits under Cd toxicity. The correlation analysis showed that the increased soil quantities traits were crucial in obtaining high rice grain yield. Generally, the findings of this research demonstrate that the application of VC in paddy fields could be useful for growers in Southern China by sustainably enhancing soil functionality and crop production.

Host genotype-specific rhizosphere fungus enhances drought resistance in wheat

BACKGROUND

The severity and frequency of drought are expected to increase substantially in the coming century and dramatically reduce crop yields. Manipulation of rhizosphere microbiomes is an emerging strategy for mitigating drought stress in agroecosystems. However, little is known about the mechanisms underlying how drought-resistant plant recruitment of specific rhizosphere fungi enhances drought adaptation of drought-sensitive wheats. Here, we investigated microbial community assembly features and functional profiles of rhizosphere microbiomes related to drought-resistant and drought-sensitive wheats by amplicon and shotgun metagenome sequencing techniques. We then established evident linkages between root morphology traits and putative keystone taxa based on microbial inoculation experiments. Furthermore, root RNA sequencing and RT-qPCR were employed to explore the mechanisms how rhizosphere microbes modify plant response traits to drought stresses.

RESULTS

Our results indicated that host plant signature, plant niche compartment, and planting site jointly contribute to the variation of soil microbiome assembly and functional adaptation, with a relatively greater effect of host plant signature observed for the rhizosphere fungi community. Importantly, drought-resistant wheat (Yunhan 618) possessed more diverse bacterial and fungal taxa than that of the drought-sensitive wheat (Chinese Spring), particularly for specific fungal species. In terms of microbial interkingdom association networks, the drought-resistant variety possessed more complex microbial networks. Metagenomics analyses further suggested that the enriched rhizosphere microbiomes belonging to the drought-resistant cultivar had a higher investment in energy metabolism, particularly in carbon cycling, that shaped their distinctive drought tolerance via the mediation of drought-induced feedback functional pathways. Furthermore, we observed that host plant signature drives the differentiation in the ecological role of the cultivable fungal species Mortierella alpine (M. alpina) and Epicoccum nigrum (E. nigrum). The successful colonization of M. alpina on the root surface enhanced the resistance of wheats in response to drought stresses via activation of drought-responsive genes (e.g., CIPK9 and PP2C30). Notably, we found that lateral roots and root hairs were significantly suppressed by co-colonization of a drought-enriched fungus (M. alpina) and a drought-depleted fungus (E. nigrum).

CONCLUSIONS

Collectively, our findings revealed host genotypes profoundly influence rhizosphere microbiome assembly and functional adaptation, as well as it provides evidence that drought-resistant plant recruitment of specific rhizosphere fungi enhances drought tolerance of drought-sensitive wheats. These findings significantly underpin our understanding of the complex feedbacks between plants and microbes during drought, and lay a foundation for steering "beneficial keystone biome" to develop more resilient and productive crops under climate change. Video Abstract.

Grassland degradation amplifies the negative effect of nitrogen enrichment on soil microbial community stability

Although nitrogen (N) enrichment is known to threaten the temporal stability of aboveground net primary productivity, it remains unclear how it alters that of belowground microbial abundance and whether its impact can be regulated by grassland degradation. Using data from N enrichment experiments at temperate grasslands with no, moderate, severe, and extreme degradation degrees, we quantified the temporal stability of soil microbial abundance (hereafter 'microbial community stability') using the ratio of the mean quantitative PCR to its standard deviation over 4 years. Both bacterial and fungal community stability sharply decreased when N input exceeded 30 g N m-2  year-1 in non-degraded grasslands, whereas a reduction in this threshold occurred in degraded grasslands. Microbial species diversity, species asynchrony, and species associations jointly altered microbial community stability. Interestingly, the linkages between plant and microbial community stability were strengthened in degraded grasslands, suggesting that plants and soil microbes might depend on each other to keep stable communities in harsh environments. Our findings highlighted the importance of grassland degradation in regulating the responses of microbial community stability to N enrichment and provided experimental evidence for understanding the relationships between plant and microbial community stability.

Fungal community composition changes and reduced bacterial diversity drive improvements in the soil quality index during arable land restoration

Arable land is facing the growing challenge of land degradation due to intensive use and this is beginning to affect global food security. However, active and passive restoration can improve soil characteristics and reshape microbial communities. Despite the increasing focus on changes in microbial communities during restoration, the mechanisms underlying how microbes drive the soil quality index (SQI) in arable land restoration remain unclear. In this study, we selected conventional farmland (CF, heavily intensified) and two restoration strategies (AR, artificial restoration; NR, natural restoration), with the same context (including soil texture, climate, etc.), and measured the microbial indicators over 2 years to investigate the mechanisms driving SQI improvement on restored arable land. The AR and NR treatments resulted in a 50% and 58% increase in SQI, respectively, compared to CF as soil nutrient levels increased, resulting in higher microbial biomasses and enzyme activities. Microbial abundance on the AR land was approximately two times greater than on the NR land due to the introduction of legumes. Bacterial diversity declined, while fungi developed in a more diverse direction under the restoration strategies. The AR and NR areas were mainly enriched with rhizobium (Microvirga, Bradyrhizobium), which contribute to healthy plant growth. The pathogenic fungi (Gibberella, Fusarium, Volutella) were more abundant in the CF area and the plant pathogen guild was about five times higher in the restored areas. Following arable land restoration, microbial life history strategies shifted from r-to K-strategists due to the higher proportion of recalcitrant SOC (DOC/SOC decreased by 18%-30%). The altered microbial community in the restored areas created new levels of functionality, with a 2.6%-4.3% decrease in bacterial energy metabolism (oxidative phosphorylation, C fixation, and N metabolism decreased by 7%, 4%, and 6%, respectively). Structural equation modelling suggested that restoration strategy affected SQI either directly by increasing total soil nutrient levels or indirectly by altering the microbial community and that fungal community composition and bacterial diversity made the largest contributions to SQI. These results provided new insights into soil quality improvement from a microbial perspective and can help guide future arable land restoration.

Manipulating soil microbial community assembly by the cooperation of exogenous bacteria and biochar for establishing an efficient and healthy CH4 biofiltration system

Manipulating the methanotroph (MOB) composition and microbial diversity is a promising strategy to optimize the methane (CH4) biofiltration efficiency of an engineered landfill cover soil (LCS) system. Inoculating soil with exogenous MOB-rich bacteria and amending soil with biochar show strong manipulating potential, but how the two stimuli interactively shape the microbial community structure and diversity has not been clarified. Therefore, three types of soils with active CH4 activities, including paddy soil, river wetland soil, and LCS were selected for enriching MOB-dominated communities (abbreviated as B_PS, B_RWS, and B_LCS, respectively). They were then inoculated to LCS which was amended with two distinct biochar. Besides the aerobic CH4 oxidation efficiencies, the evolution of the three microbial communities during the MOB enrichment processes and their colonization in two-biochar amended LCS were obtained. During the MOB enriching, a lag phase in CH4 consumption was observed merely for B_LCS. Type II MOB Methylocystis was the primary MOB for both B_PS and B_LCS; while type I MOB dominated for B_RWS and the major species were altered by gas concentrations. Compared to biochar, a more critical role was demonstrated for the bacteria inoculation in determining the community diversity and function of LCS. Instead, biochar modified the community structures by mainly stimulating the dominant MOB but could induce stochastic processes in community assembly, possibly related to its inorganic nutrients. Particularly, combined with biochar advantages, the paddy soil-derived bacteria consortiums with diverse MOB species demonstrated the potent adaption to LCS niches, not only retaining the high CH4-oxidizing capacities but also shaping a community structure with more diverse soil function. The results provided new insights into the optimization of an engineered CH4-mitigation soil system by manipulating the soil microbiomes with the cooperation of exogenous bacteria and biochar.

Unraveling plant-microbe interactions: can integrated omics approaches offer concrete answers?

Advances in high throughput omics techniques provide avenues to decipher plant microbiomes. However, there is limited information on how integrated informatics can help provide deeper insights into plant-microbe interactions in a concerted way. Integrating multi-omics datasets can transform our understanding of the plant microbiome from unspecified genetic influences on interacting species to specific gene-by-gene interactions. Here, we highlight recent progress and emerging strategies in crop microbiome omics research and review key aspects of how the integration of host and microbial omics-based datasets can be used to provide a comprehensive outline of complex crop-microbe interactions. We describe how these technological advances have helped unravel crucial plant and microbial genes and pathways that control beneficial, pathogenic, and commensal plant-microbe interactions. We identify crucial knowledge gaps and synthesize current limitations in our understanding of crop microbiome omics approaches. We highlight recent studies in which multi-omics-based approaches have led to improved models of crop microbial community structure and function. Finally, we recommend holistic approaches in integrating host and microbial omics datasets to achieve precision and efficiency in data analysis, which is crucial for biotic and abiotic stress control and in understanding the contribution of the microbiota in shaping plant fitness.

Bioaerosols in the atmosphere: A comprehensive review on detection methods, concentration and influencing factors

In the past few decades, especially since the outbreak of the coronavirus disease (COVID-19), the effects of atmospheric bioaerosols on human health, the environment, and climate have received great attention. To evaluate the impacts of bioaerosols quantitatively, it is crucial to determine the types of bioaerosols in the atmosphere and their spatial-temporal distribution. We provide a concise summary of the online and offline observation strategies employed by the global research community to sample and analyze atmospheric bioaerosols. In addition, the quantitative distribution of bioaerosols is described by considering the atmospheric bioaerosols concentrations at various time scales (daily and seasonal changes, for example), under various weather, and different underlying surfaces. Finally, a comprehensive summary of the reasons for the spatiotemporal distribution of bioaerosols is discussed, including differences in emission sources, the impact process of meteorological factors and environmental factors. This review of information on the latest research progress contributes to the emergence of further observation strategies that determine the quantitative dynamics of public health and ecological effects of bioaerosols.

Biological roles of soil microbial consortium on promoting safe crop production in heavy metal(loid) contaminated soil: A systematic review

Heavy metal(loid) (HM) pollution of agricultural soils is a growing global environmental concern that affects planetary health. Numerous studies have shown that soil microbial consortia can inhibit the accumulation of HMs in crops. However, our current understanding of the effects and mechanisms of inhibition is fragmented. In this review, we summarise extant studies and knowledge to provide a comprehensive view of HM toxicity on crop growth and development at the biological, cellular and the molecular levels. In a meta-analysis, we find that microbial consortia can improve crop resistance and reduce HM uptake, which in turn promotes healthy crop growth, demonstrating that microbial consortia are more effective than single microorganisms. We then review three main mechanisms by which microbial consortia reduce the toxicity of HMs to crops and inhibit HMs accumulation in crops: 1) reducing the bioavailability of HMs in soil (e.g. biosorption, bioaccumulation and biotransformation); 2) improving crop resistance to HMs (e.g. facilitating the absorption of nutrients); and 3) synergistic effects between microorganisms. Finally, we discuss the prospects of microbial consortium applications in simultaneous crop safety production and soil remediation, indicating that they play a key role in sustainable agricultural development, and conclude by identifying research challenges and future directions for the microbial consortium to promote safe crop production.

Interactive Effects of Microbial Fertilizer and Soil Salinity on the Hydraulic Properties of Salt-Affected Soil

Significant research has been conducted on the effects of fertilizers or agents on the sustainable development of agriculture in salinization areas. By contrast, limited consideration has been given to the interactive effects of microbial fertilizer (MF) and salinity on hydraulic properties in secondary salinization soil (SS) and coastal saline soil (CS). An incubation experiment was conducted to investigate the effects of saline soil types, salinity levels (non-saline, low-salinity, and high-salinity soils), and MF amounts (32.89 g kg-1 and 0 g kg-1) on soil hydraulic properties. Applied MF improved soil water holding capacity in each saline soil compared with that in CK, and SS was higher than CS. Applied MF increased saturated moisture, field capacity, capillary fracture moisture, the wilting coefficient, and the hygroscopic coefficient by 0.02-18.91% in SS, while it was increased by 11.62-181.88% in CS. It increased soil water supply capacity in SS (except for high-salinity soil) and CS by 0.02-14.53% and 0.04-2.34%, respectively, compared with that in CK. Soil available, readily available, and unavailable water were positively correlated with MF, while soil gravity and readily available and unavailable water were positively correlated with salinity in SS. Therefore, a potential fertilization program with MF should be developed to increase hydraulic properties or mitigate the adverse effects of salinity on plants in similar SS or CS areas.

Programmed microalgae-gel promotes chronic wound healing in diabetes

Chronic diabetic wounds are at lifelong risk of developing diabetic foot ulcers owing to severe hypoxia, excessive reactive oxygen species (ROS), a complex inflammatory microenvironment, and the potential for bacterial infection. Here we develop a programmed treatment strategy employing live Haematococcus (HEA). By modulating light intensity, HEA can be programmed to perform a variety of functions, such as antibacterial activity, oxygen supply, ROS scavenging, and immune regulation, suggesting its potential for use in programmed therapy. Under high light intensity (658 nm, 0.5 W/cm2), green HEA (GHEA) with efficient photothermal conversion mediate wound surface disinfection. By decreasing the light intensity (658 nm, 0.1 W/cm2), the photosynthetic system of GHEA can continuously produce oxygen, effectively resolving the problems of hypoxia and promoting vascular regeneration. Continuous light irradiation induces astaxanthin (AST) accumulation in HEA cells, resulting in a gradual transformation from a green to red hue (RHEA). RHEA effectively scavenges excess ROS, enhances the expression of intracellular antioxidant enzymes, and directs polarization to M2 macrophages by secreting AST vesicles via exosomes. The living HEA hydrogel can sterilize and enhance cell proliferation and migration and promote neoangiogenesis, which could improve infected diabetic wound healing in female mice.

Synthetic microbial communities: Sandbox and blueprint for soil health enhancement

We summarize here the use of SynComs in improving various dimensions of soil health, including fertility, pollutant removal, soil-borne disease suppression, and soil resilience; as well as a set of useful guidelines to assess and understand the principles for designing SynComs to enhance soil health. Finally, we discuss the next stages of SynComs applications, including highly diverse and multikingdom SynComs targeting several functions simultaneously.

Broad environmental adaptation of abundant microbial taxa in Robinia pseudoacacia forests during long-term vegetation restoration

Vegetation restoration has significant impacts on ecosystems, and a comprehensive understanding of microbial environmental adaptability could facilitate coping with ecological challenges such as environmental change and biodiversity loss. Here, abundant and rare soil bacterial and fungal communities were characterized along a 15-45-year chronosequence of forest vegetation restoration in the Loess Plateau region. Phylogenetic-bin-based null model analysis (iCAMP), niche breadth index, and co-occurrence network analysis were used to assess microbial community assembly and environmental adaptation of a Robinia pseudoacacia plantation under long-term vegetation restoration. The drift process governed community assembly of abundant and rare soil fungi and bacteria. With increasing soil total phosphorus content, the relative importance of drift increased, while dispersal limitation and heterogeneous selection exhibited opposite trends for abundant and rare fungi. Rare soil fungal composition dissimilarities were dominated by species replacement processes. Abundant microbial taxa had higher ecological niche width and contribution to ecosystem multifunctionality than rare taxa. Node property values (e.g., degree and betweenness) of abundant microbial taxa were substantially higher than those of rare microbial taxa, indicating abundant species occupied a central position in the network. This study provides insights into the diversity and stability of microbial communities during vegetation restoration in Loess Plateau. The findings highlight that abundant soil fungi and bacteria have broad environmental adaptation and major implications for soil multifunctionality under long-term vegetation restoration.