High-elevation-induced decrease in soil pH weakens ecosystem multifunctionality by influencing soil microbiomes.

Plant environmental stress response has become a global research hotspot, yet there is a lack of clear understanding regarding the mechanisms that maintain microbial diversity and their ecosystem services under environmental stress. In our research, we examined the effects of moderate elevation on the rhizosphere soil characteristics, microbial community composition, and ecosystem multifunctionality (EMF) within agricultural systems. Our findings revealed a notable negative correlation between EMF and elevation, indicating a decline in multifunctionality at higher elevations. Additionally, our analysis across bacterial and protistan communities showed a general decrease in microbial richness with increasing elevation. Using random forest models, pH was identified as the key environmental stressor influencing microbial communities. Furthermore, we found that microbial community diversity is negatively correlated with stability by mediating complexity. Interestingly, while pH was found to affect the complexity within bacterial networks, it did not significantly impact the ecosystem stability along the elevation gradients. Using a Binary-State Speciation and Extinction (BiSSE) model to explore the evolutionary dynamics, we found that Generalists had higher speciation rates and lower extinction rates compared to specialists, resulting in a skewed distribution towards higher net diversification for generalists under increasing environmental stress. Moreover, structural equation modeling (SEM) analysis highlighted a negative correlation between environmental stress and community diversity, but showed a positive correlation between environmental stress and degree of cooperation & competition. These interactions under environmental stress indirectly increased community stability and decreased multifunctionality. Our comprehensive study offers valuable insights into the intricate relationship among environmental factors, microbial communities, and ecosystem functions, especially in the context of varying elevation gradients. These findings contribute significantly to our understanding of how environmental stressors affect microbial diversity and ecosystem services, providing a foundation for future ecological research and management strategies in similar contexts.

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.

Low Carbon Loss from Long-Term Manure-Applied Soil during Abrupt Warming Is Realized through Soil and Microbiome Interplay.

Manure application is a global approach for enhancing soil organic carbon (SOC) sequestration. However, the response of SOC decomposition in manure-applied soil to abrupt warming, often occurring during diurnal temperature fluctuations, remains poorly understood. We examined the effects of long-term (23 years) continuous application of manure on SOC chemical composition, soil respiration, and microbial communities under temperature shifts (15 vs 25 °C) in the presence of plant residues. Compared to soil without fertilizer, manure application reduced SOC recalcitrance indexes (i.e., aliphaticity and aromaticity) by 17.45 and 21.77%, and also reduced temperature sensitivity (Q10) of native SOC decomposition, plant residue decomposition, and priming effect by 12.98, 15.98, and 52.83%, respectively. The relative abundances of warm-stimulated chemoheterotrophic bacteria and fungi were lower in the manure-applied soil, whereas those of chemoautotrophic Thaumarchaeota were higher. In addition, the microbial network of the manure-applied soil was more interconnected, with more negative connections with the warm-stimulated taxa than soils without fertilizer or with chemical fertilizer applied. In conclusion, our study demonstrated that the reduced loss of SOC to abrupt warming by manure application arises from C chemistry modification, less warm-stimulated microorganisms, a more complex microbial community, and the higher CO2 intercepting capability by Thaumarchaeota.

Microeukaryotic plankton community dynamics under ecological water replenishment: Insights from eDNA metabarcoding.

Ecological water replenishment (EWR) is an important strategy for river restoration globally, but timely evaluation of its ecological effects at a large spatiotemporal scale to further adjust the EWR schemes is of great challenge. Here, we examine the impact of EWR on microeukaryotic plankton communities in three distinct river ecosystems through environmental DNA (eDNA) metabarcoding. The three ecosystems include a long-term cut-off river, a short-term connected river after EWR, and long-term connected rivers. We analyzed community stability by investigating species composition, stochastic and deterministic dynamics interplay, and ecological network robustness. We found that EWR markedly reduced the diversity and complexity of microeukaryotic plankton, altered their community dynamics, and lessened the variation within the community. Moreover, EWR disrupted the deterministic patterns of community organization, favoring dispersal constraints, and aligning with trends observed in naturally connected rivers. The shift from an isolated to a temporarily connected river appeared to transition community structuring mechanisms from deterministic to stochastic dominance, whereas, in permanently connected rivers, both forces concurrently influenced community assembly. The ecological network in temporarily connected rivers post-EWR demonstrated significantly greater stability and intricacy compared to other river systems. This shift markedly bolstered the resilience of the ecological network. The eDNA metabarcoding insights offer a novel understanding of ecosystem resilience under EWR interventions, which could be critical in assessing the effects of river restoration projects throughout their life cycle.

Dynamics of benthic microeukaryotic communities in a mangrove wetland invaded by Spartina alterniflora: Effects of vegetation, seasonality, and sediment depth.

Benthic microeukaryotes are crucial mediators of biogeochemical cycles in coastal wetland ecosystems, yet their spatial and temporal variability remains poorly understood. This study delineates the diversity patterns of benthic microeukaryotes in a Spartina alterniflora-invaded mangrove ecosystem in Fujian, China. Using high-throughput sequencing of 18S rRNA gene transcripts, we identified the influences of vegetation, seasonality, and sediment depth on microeukaryotic communities. We discovered that vegetation cover significantly affects community composition, primarily driven by nutrient concentrations and pH. The community structure of microeukaryotes varied seasonally and vertically, correlating with changes in sediment temperature, pH, salinity, and fucoxanthin concentration. Notably, invasive Spartina alterniflora habitats showed enhanced heterotrophic interactions, suggesting that invasive species can reshape benthic microeukaryotic co-occurrence patterns. Seasonal co-occurrence patterns revealed dominant Bacillariophyta assemblages exhibited distinct network modules enriched in the cold (spring) and warm (summer and fall) seasons, respectively, which indicated potential ecological niche differentiation. Our findings reveal the complex relationships between environmental factors and benthic microeukaryotic diversity, offering insights into microbial responses to natural and invasive vegetation influences.

Soil microbiota plays a key regulatory role in the outbreak of tobacco root rot.

Introduction: Root rot caused by the fungal pathogen Fusarium sp. poses significant challenges to tobacco cultivation in China, leading to major economic setbacks. The interplay between this pathogen and the wider soil microbial community remains poorly understood. Methods: High-throughput sequencing technology was utilized to evaluate soil prokaryotic, fungal, and protistan communities. We compared microbial communities in infected soils to those in healthy soils from the same field. Additionally, the influence of pH on the microbial communities was assessed. Results: Infected soils displayed elevated levels of soil nutrients but diminished observed richness across prokaryotic, fungal, and protistan groups. The pathogenic fungi Fusarium solani f sp. eumartii's abundance was notably increased in infected soils. Infection with F. solani significantly altered the soil's microbial community structure and interactions, manifested as a decrease in network scale and the number of keystone species. An evaluation of prokaryotes' role in F. solani's invasion revealed an increased number of connecting nodes in infected soils. Additionally, relationships between predatory protists and fungi were augmented, whereas predation on F. solani declined. Discussion: The study underscores the significance of comprehending the interactions among soil microorganisms and brings to light the susceptibility of soil microbial communities to pathogen invasion. It offers insights into the multifaceted relationships and potential vulnerabilities within the soil ecosystem in the context of Fusarium sp. invasion.

Temperature-mediated microbial carbon utilization in China's lakes.

Microbes play an important role in aquatic carbon cycling but we have a limited understanding of their functional responses to changes in temperature across large geographic areas. Here, we explored how microbial communities utilized different carbon substrates and the underlying ecological mechanisms along a space-for-time substitution temperature gradient of future climate change. The gradient included 47 lakes from five major lake regions in China spanning a difference of nearly 15°C in mean annual temperatures (MAT). Our results indicated that lakes from warmer regions generally had lower values of variables related to carbon concentrations and greater carbon utilization than those from colder regions. The greater utilization of carbon substrates under higher temperatures could be attributed to changes in bacterial community composition, with a greater abundance of Cyanobacteria and Actinobacteriota and less Proteobacteria in warmer lake regions. We also found that the core species in microbial networks changed with increasing temperature, from Hydrogenophaga and Rhodobacteraceae, which inhibited the utilization of amino acids and carbohydrates, to the CL500-29-marine-group, which promoted the utilization of all almost carbon substrates. Overall, our findings suggest that temperature can mediate aquatic carbon utilization by changing the interactions between bacteria and individual carbon substrates, and the discovery of core species that affect carbon utilization provides insight into potential carbon sequestration within inland water bodies under future climate warming.

Grass-Legume Mixture with Rhizobium Inoculation Enhanced the Restoration Effects of Organic Fertilizer.

The establishment of artificial grassland is crucial in restoring degraded grassland and resolving the forage-livestock conflict, and the application of organic fertilizer and complementary seeding of grass-legume mixture are effective methods to enhance grass growth in practice. However, its mechanism behind the underground is largely unclear. Here, by utilizing organic fertilizer in the alpine region of the Qinghai-Tibet Plateau, this study assessed the potential of grass-legume mixtures with and without the inoculation of Rhizobium for the restoration of degraded grassland. The results demonstrated that the application of organic fertilizer can increase the forage yield and soil nutrient contents of degraded grassland, and they were 0.59 times and 0.28 times higher than that of the control check (CK), respectively. The community composition and structure of soil bacteria and fungi were also changed by applying organic fertilizer. Based on this, the grass-legume mixture inoculated with Rhizobium can further increase the contribution of organic fertilizer to soil nutrients and thus enhance the restoration effects for degraded artificial grassland. Moreover, the application of organic fertilizer significantly increased the colonization of gramineous plant by native mycorrhizal fungi, which was ~1.5-2.0 times higher than CK. This study offers a basis for the application of organic fertilizer and grass-legume mixture in the ecological restoration of degraded grassland.

Grass-microbial inter-domain ecological networks associated with alpine grassland productivity.

Associations between grasses and soil microorganisms can strongly influence plant community structures. However, the associations between grass productivity and diversity and soil microbes, as well as the patterns of co-occurrence between grass and microbes remain unclear. Here, we surveyed grass productivity and diversity, determined soil physicochemical, and sequenced soil archaea, bacteria and fungi by metabarcoding technology at 16 alpine grasslands. Using the Distance-decay relationship, Inter-Domain Ecological Network (IDEN), and Mantel tests, we investigated the relationship between grass productivity, diversity and microbial diversity, and the patterns of co-occurrence between grass and microbial inter-domain network in alpine grassland. We found the archaea richness, bacteria richness and Shannon, and fungi α-diversity were significantly negatively correlation with grass diversity, but archaea and bacteria diversity were positively correlation with grass productivity. Moreover, an increase in microbial ß-diversity was observed along with increased discrepancy in grass diversity and productivity and soil variables. Variance partitioning analysis suggested that the contribution of grass productivity on microbial community was higher than that of soil variables and grass diversity, which implies that microbial community was more related to grass productivity. Inter-Domain Ecological Network showed that the grass species formed complex and stable ecological networks with some bacterial, archaeal, and fungal species, and the grass-fungal ecological networks showed the highest robustness, which indicated that soil fungi could better co-coexist with aboveground grass in alpine grasslands. Besides, the connectivity degrees of the grass-microbial network were significantly positively correlated with grass productivity, suggesting that the coexistence pattern of grasses and microbes had a positive feedback effect on the grass productivity. The results are important for establishing the regulatory mechanisms between plants and microorganisms in alpine grassland ecosystems.

Spatial distribution patterns across multiple microbial taxonomic groups.

Even in the vertical dimension, soil bacterial communities are spatially distributed in a distance-decay relationship (DDR). However, whether this pattern is universal among all soil microbial taxonomic groups, and how body size influences this distribution, remains elusive. Our study consisted of obtaining 140 soil samples from two adjacent ecosystems in the Yellow River Delta (YRD), both nontidal and tidal, and measuring the DDR between topsoil and subsoil for bacteria, archaea, fungi and protists (rhizaria). Our results showed that the entire community generally fitted the DDR patterns (P < 0.001), this was also true at the kingdom level (P < 0.001, with the exception of the fungal community), and for most individual phyla (47/75) in both ecosystems and with soil depth. Meanwhile, these results presented a general trend that the community turnover rate of nontidal soils was higher than tidal soils (P < 0.05), and that the rate of topsoil was also higher than that of subsoil (P < 0.05). Additionally, microbial spatial turnover rates displayed a negative relationship with body sizes in nontidal topsoil (R2 = 0.29, P = 0.009), suggesting that the smaller the body size of microorganisms, the stronger the spatial limitation was in this environment. However, in tidal soils, the body size effect was negligible, probably owing to the water's fluidity. Moreover, community assembly was judged to be deterministic, and heterogeneous selection played a dominant role in the different environments. Specifically, the spatial distance was much more influential, while the soil salinity in these ecosystems was the major environmental factor in selecting the distributions of microbial communities. Overall, this study revealed that microbial community compositions at different taxonomic levels followed relatively consistent distribution patterns and mechanisms in this coastal area.