Microbial Community Characteristics Research Articles

The Grain for Green Program Promotes Soil Organic Matter Accumulation and Improves Soil Fungal Diversity in the Southwestern Karst Region

Soil microorganisms play pivotal roles in terrestrial ecological processes. However, how soil microbial biomass and community characteristics respond to changes in land utilization in karst regions remains largely unknown. The present study investigated the impacts of land-use change on soil chemical properties, microbial community structure, and biomass in a karst region of southwest China across four land-use types: shrubland (natural vegetation restoration), plantation forest (managed vegetation restoration), orchards, and croplands. Vegetation restoration increased microbial biomass carbon and microbial biomass nitrogen. Shrubland had the highest bacterial and fungal abundance and fungal diversity; in addition, the soil microbial community structure differed significantly among land-use types. The dominant bacterial phyla were Actinobacteria, Proteobacteria, Acidobacteria, and Chloroflexi, whereas Ascomycota was the predominant fungal phylum, with its abundance declining significantly following vegetation restoration. Soil properties, including soil organic matter and available phosphorus, were strongly associated with microbial community composition and diversity in karst areas. The findings of this study are essential for gaining a deeper understanding of how changes in land-use affect soil properties and microbial dynamics, and provide valuable insights for ecological restoration and agricultural management in karst regions.

Effects of reduced flow gradient on benthic biofilm communities' ecological network and community assembly.

The intensification of human activities has led to flow reduction and cut-off in most global rivers, seriously affecting riverine organisms and the biogeochemical processes. As key indicators of river ecosystems' structure and function, benthic biofilms play a critical role in driving primary production and material cycling in rivers. This research aimed to investigate the characteristics of microbial communities' complexity and stability during river flow reduction. Benthic biofilms were grown in artificial channels and subjected to eight gradients of flow reduction (represented by flow velocity from 0.4 to 110cm/s). Biofilms' biodiversity, ecological networks and community assembly of bacteria, fungi and algae were investigated by high-throughput sequencing. Results showed significant differences in community composition and structure under different flow conditions. The eight flow gradients' microbial communities were divided into three groups: low, medium and high flows. The flow reduction led to significant decreases in bacterial and fungal communities' Chao1 index. Low flow conditions enriched the bacterial phyla Oxyphotobacteria, Alphaproteobacteria and Mollicutes, but significantly decreased the fungal phylum Chytridiomycota. Lowering flow reduced the fungal network's number of nodes and increased the algal network's number of edges. Cross-domain interactions network analysis showed a gradual increase in node and edge numbers with decreasing flow, while decreasing average path length. The neutral model predicted stochastic processes primarily drove biofilm community assembly, and that model's explanations decreased as the flow gradient decreased. The null model analysis revealed diffusion limitation as the most common stochastic ecological process for bacterial and algal communities, with reduced flow reducing heterogeneous selection and increasing diffusion-limited processes. This study provides an in-depth analysis of flow reduction's effects on biofilm communities' ecological networks and community assembly.

Distribution and environmental dissemination of antibiotic resistance genes in poultry farms and surrounding ecosystems.

Antibiotic resistance poses a significant threat to human and animal health worldwide, with farms serving as crucial reservoirs of Antibiotic Resistance Genes (ARGs) and Antibiotic-resistant bacteria. However, the distribution of ARGs in poultry farms and their transmission patterns in the environment remain poorly understood. This study collected samples of aerosol microorganisms, cloacal matter, soil, and vegetables from poultry farms and surrounding environments at three different distances. We used 16S rRNA gene sequencing and HT-qPCR to analyze the characteristics of aerosol microbial communities and the abundance of ARGs. At the phylum level, Proteobacteria, Firmicutes, and Bacteroidetes were dominant in cloacal samples, aerosol samples, and vegetable samples, while Proteobacteria Actinobacteriota and Acidobacteria dominated soil. Pseudomonas was dominant in cloacal samples at the genus level, whereas Fusobacterium was prevalent in soil. The diversity and richness of bacterial communities were more similar between cloacal samples than those observed between either sample type compared with soil. Our results showed that tetracycline and aminoglycoside ARG relative abundance was high across all sample types but significantly increased within feces/air compared to soils/vegetables. Association analysis revealed five potential host genera for ARG/MGE presence among various microbiota populations studied here. Our findings confirm that farms are important sources for the environmental dissemination of pathogens and ARGs.

Long-term and seasonal evaluation on environmental microbiology and water quality of Shanmei reservoir in southeast China.

As a crucial source of potable water, the quality of water in Shanmei reservoir strongly and directly impacts the safety and well-being of downstream residents. Microorganisms play a pivotal role in the reservoir's resource and energy cycle. However, ecological protection efforts for the Shanmei reservoir have encountered numerous challenges in recent years. This study conducted an extensive visual analysis of microbial communities in sediment from the Shanmei reservoir between 2022 and 2024 using amplicon sequencing technology targeting 16S rRNA gene. The results showed that the microbial diversity of sediment showed an obvious seasonal pattern. At the same time, microbial composition also changes with the long-term evolution of time, which may be closely related to the change in environmental conditions. In addition, we have also carried out long-term multi-dimensional monitoring of the water quality of the Shanmei reservoir, and the results show that the water quality has reached the national drinking water grade. In conclusion, this study not only unveiled the interseasonal dynamics and long-term evolutionary characteristics of sediment microbial communities but also elucidated the significant influence of environmental factors on their composition, structure and function. These findings offer a fresh perspective for understanding the freshwater ecosystem microbial dynamics and provide a scientific foundation for reservoir management and water quality protection.

Methane emission fluxes and associated microbial community characteristics in a temperate seagrass meadow.

Seagrass meadows are acknowledged as blue carbon ecosystems, yet they are also ideal habitats for methane (CH4) release, offsetting their ability to mitigate climate change. The global CH4 fluxes in seagrass meadows remain highly uncertain due to regional and species biases, and the microbial mechanisms driving methane release are poorly understood. Here, we investigated CH4 air-sea fluxes, sediment CH4 emission potential and microbes involved in CH4 release using geochemical techniques combined with qPCR and Illumina sequencing in a temperate Zostera japonica and Zostera marina mixed meadow. The CH4 air-sea fluxes fluctuated from -0.42 to 11.42μmol·m-2·d-1, showing a strong seasonal variation. CH4 emission potential was significantly higher in seagrass vegetated sediments (10.34±2.72nmol·g-1·d-1) than in the adjacent bare sediments (1.55±1.15nmol·g-1·d-1), primarily attributed to variations in sediment organic matter content. Diverse methanogens occurred in the seagrass meadow, with Methanolobus dominating in seagrass sediments, while Methanococcoides, Methanosarcina, and Methanoculleus being prevalent in bare sediments. Meanwhile, a variety of methylotrophic groups were detected, including aerobic Gammaproteobacteria, anaerobic Desulfobacterota and Methylomirabilota, as well as archaea Candidatus Methanoperedens. The co-occurrence of these functional groups implied the presence of complex CH4 production and oxidation pathways, which regulated the CH4 budget in the seagrass ecosystems. Taken together, our findings enhance the comprehension of the methane emission process and driving mechanism in seagrass ecosystems.

Microbial Characteristics and Functions in Coffee Fermentation: A Review

Based on coffee’s unique and fascinating flavor, coffee has become the most popular nonalcoholic drink in the world and is a significant agricultural economic crop in tropical- and subtropical-planted coffee countries and regions. It is also beneficial for human health because of its rich active compounds, such as caffeine, chlorogenic acids, trigonelline, tryptophan alkaloids, diterpenes, melanoidins, etc. These compounds often relate to the prevention of cardiovascular disease, Alzheimer’s disease, and antibacterial, anti-diabetic, neuroprotection, and anti-cancer activities. The formation of coffee’s flavor results from various influence factors, including genetics, shade, elevation, post-harvest processing, fermentation, roasted methods, etc. The first stage of coffee production is obtaining green coffee beans through the primary process. Fermentation is critical in the primary process of coffee, which is often related to yeasts, bacteria, and filamentous fungi. Therefore, microorganisms play a key role in coffee fermentation and coffee flavor. To provide an understanding of the role of microorganisms in coffee fermentation, the coffee fermentation overview and microbial characteristics in different coffee primary processing methods and different coffee fermentation regions were reviewed in this paper. Brazil and China are the main study countries in coffee fermentation, which contribute a large number of technologies and methods to improve coffee flavor by fermentation. Different primary processing methods (wet, dry, or semi-dry processing) and coffee producer countries had obvious microbial community characteristics. Moreover, the application of yeast and bacteria for improving coffee flavor by microbial fermentation was also introduced.

The Response Mechanism of the cbbM Carbon Sequestration Microbial Community in the Alpine Wetlands of Qinghai Lake to Changes in Precipitation.

The dramatic changes in precipitation patterns on the Tibetan Plateau affected the carbon-sequestering microbial communities within wetland ecosystems, which were closely related to the responses and adaptation mechanisms of alpine wetland ecosystems to climate change. This study focused on wetland soils subjected to different precipitation gradient treatments and employed high-throughput sequencing technology to analyze the soil cbbM carbon-sequestering microbial communities. The results indicated that Proteobacteria were the dominant microbial community responsible for carbon sequestration in the Wayan Mountain wetland. A 50% increase in precipitation significantly raised the soil moisture content, while a 50% reduction and a 25% increase in precipitation notably enhanced the total soil carbon content. The 25% reduction in precipitation increased the differences in microbial community composition, whereas both the 50% increase and the 50% reduction in precipitation decreased these differences. The soil pH and temperature had the most significant impact on the carbon-sequestering microbial communities. In conclusion, changes in precipitation affect the cbbM carbon sequestration characteristics of soil microbial communities, and a moderate reduction in water input benefited carbon sequestration in wetlands.

A salt-tolerant growth-promoting phyllosphere microbial combination from mangrove plants and its mechanism for promoting salt tolerance in rice

BackgroundMangrove plants growing in the high salt environment of coastal intertidal zones colonize a variety of microorganisms in the phyllosphere, which have potential salt-tolerant and growth-promoting effects. However, the characteristics of microbial communities in the phyllosphere of mangrove species with and without salt glands and the differences between them remain unknown, and the exploration and the agricultural utilization of functional microbial resources from the leaves of mangrove plants are insufficient.ResultsIn this study, we examined six typical mangrove species to unravel the differences in the diversity and structure of phyllosphere microbial communities between mangrove species with or without salt glands. Our results showed that a combination of salt-tolerant growth-promoting strains of Pantoea stewartii A and Bacillus marisflavi Y25 (A + Y25) was constructed from the phyllosphere of mangrove plants, which demonstrated an ability to modulate osmotic substances in rice and regulate the expression of salt-resistance-associated genes. Further metagenomic analysis revealed that exogenous inoculation with A + Y25 increased the rice rhizosphere’s specific microbial taxon Chloroflexi, thereby elevating microbial community quorum sensing and ultimately enhancing ionic balance and overall microbial community function to aid salt resistance in rice.ConclusionsThis study advances our understanding of the mutualistic and symbiotic relationships between mangrove species and their phyllosphere microbial communities. It offers a paradigm for exploring agricultural beneficial microbial resources from mangrove leaves and providing the potential for applying the salt-tolerant bacterial consortium to enhance crop adaptability in saline–alkaline land.-b8tYoWqwFfV9a2SY3Js-8Video Graphical abstractThe sources of the photos used in this figure are provided below:Avicennia marina: https://guru.sanook.com/6011/Acanthus ilicifolius: https://tracuuduoclieu.vn/acanthus-ilicifolius-l.htmlAegiceras corniculatum: https://apps.lucidcentral.org/plants_se_nsw/text/entities/aegiceras_corniculatum.htmlSonneratia apetala: http://www.fpcn.net/a/shuishengzhiwu/20131109/Sonneratia_apetala.htmlExcoecaria agallocha: https://efloraofindia.com/2011/03/01/excoecaria-agallocha/Kandelia candel: https://www.szhb.org/6539.htmlBackground photo: https://www.discovery.com/nature/the-world-is-waking-up-to-the-importance-of-mangroves

Vertical distribution characteristics of microplastics and bacterial communities in the sediment columns of Jianhu lake in China.

Microorganisms change the properties of microplastics, at the same time, microplastics can also affect the distribution of microorganisms. To investigate this issue, we chose to study Jianhu Lake, a plateau lake in southwestern China, by collecting data at three sampling locations. The microplastics and bacterial communities in the sediment columns of Jianhu Lake were sampled within a 0 to 60cm profile, and the basic characteristics of microplastic abundance, shape, color, size, and polymer type were determined accordingly, via their collection, separation, extraction, and identification. The bacterial community in the sediment samples were identified using 16S rRNA high-throughput sequencing, and we assessed whether those microplastic characteristics influenced the community composition and structure. We found the abundance of microplastics ranged from 624 to 3050 particles/kg (dw [dry weight]) in the three sediment columns. Line microplastics accounted for the largest proportion and these were found distributed in each layer. The polymer types present in the largest proportions were rayon (RY), polyester terephthalate (PET) and low-density styrene-butadiene-styrene (SBS). Among the bacterial communities in the sediment columns, the dominant phyla were Chloroflexi, Sva0485, Acidobacteriota, etc. The co-occurrence network analysis between the bacterial community and microplastic features in the sediment columns of Jianhu Lake revealed that there was a correlation between them, and the network were more complex at a depth of 20-40cm. Our results demonstrate that microplastics can affect the diversity and structural characteristics of microbial communities in a lake ecosystem.

Potential role of alginate in marine bacteria-yeast interactions.

The ability of microorganisms to decompose brown algae has attracted attention. This study aims to clarify the characteristics of marine microbial communities in which prokaryotic and eukaryotic microorganisms interact via the metabolism of brown algae carbohydrates. Amplicon-based microbiome analysis revealed the predominance of the genera Marinomonas and Vibrio in seawater and seaweed samples mixed with alginate and mannitol, which are the primary carbohydrates in brown algae. Three Vibrio species and Candida intermedia were isolated via alginate enrichment culture. Although C. intermedia did not utilize alginate as a nutrient source, the yeast grew in the spent alginate medium in which Vibrio algivorus had been cultured. Coculture with C. intermedia and the Vibrio isolates, especially V. algivorus, also enhanced the growth of the yeast on alginate. These results suggested that C. intermedia grew because of the supply of nutrients via alginate metabolism by Vibrio species. In the coculture medium, the amount of phosphatidylserine increased in the early phase but decreased with the growth of C. intermedia, indicating that phosphatidylserine secreted by Vibrio is involved in the putative mutualistic interaction. We examined whether such interaction is applicable to the production of useful substances and succeeded in lipid production by oleaginous marine yeast Yarrowia lipolytica through coculture with V. algivorus. Our study suggested the potential of mutualistic interaction via degradation of alginate by marine Vibrio for production of industrially useful substances in yeast cells.IMPORTANCEIn this study, we analyzed the microbiome of seawater and seaweed in the presence of brown algae carbohydrates and reconstructed the putative mutualistic relationship of marine Vibrio and Candida intermedia mediated by metabolism of brown algae in the ocean.

High density sampling reveals the spatiotemporal characteristics of microbial communities in a full-scale municipal wastewater treatment plant

Insights into the microbial communities in municipal wastewater treatment plants (WWTPs) are critical for the optimization of biological nutrient removal process. However, our understanding about the spatiotemporal characteristics of the microbial communities in WWTPs remains limited. In the present study, 264 samples were collected biweekly from four spatially independent corridors in a typical municipal WWTP. The annual compositional and metagenomic characteristics were investigated based on multiple ecological indicators using statistical tests. The results revealed that the microbial community compositions from the four corridors showed significantly high similarities, as revealed by the statistical analysis at the operational taxonomic unit (OTU) level. Consistent with the OTU level results, the functionality of the microbial communities in the four independent corridors also showed significant similarity. In comparison, the dynamics of the microbial community over the year showed two successional peaks of the microbial communities with the spatial similarity, and this resulted in three alternative stable states of the microbial communities in a calendar year. The microbial communities only drifted in July and November, suggesting an uneven community succession pattern driven by seasonal variation in environmental conditions. The functional characteristics were found to be relatively conservative compared to the microbial community succession, which revealed the decoupling between the composition and functionality of the microbial community in the municipal WWTP. The present study provides an in-depth overview of the microbial communities in a municipal WWTP and will be useful for the establishment of the connection between ecological characteristics and the operational stability of WWTPs.

Physicochemical property and microbial community characteristics of the casing soil for cultivating Oudemansiella raphanipes.

Casing soil is critical for the cultivation process of Oudemansiella raphanipes and promotes the formation of mushroom fruiting bodies. Therefore, reliable casing soil indicators are crucial for obtaining high yields of high-quality mushrooms. In this study, soil enzyme activity, physicochemical properties, and microorganisms at five cultivation stages [namely casing (A1), mycelial (A2), primordial (A3), fruiting (A4), and harvesting (A5)] of O. raphanipes cultivation were evaluated in casing soils. The results indicated that sucrase and catalase activities were significantly increased with increasing cultivation time (p < 0.01), and the activities peaked [16.67 and 0.25 g/(g·h), respectively] at A4. Urease activity peaked [1.56 g/(g·h)] at A1, and it decreased gradually (p < 0.01). Polyphenol oxidase activity was significantly higher at A2 [0.95 g/(g·h)] than at the other stages and was significantly lower at A1 [0.06 g/(g·h)]. Soil pH peaked at A1 (8.20) and decreased gradually (p = 0.003). Soil total organic carbon content increased significantly with increasing cultivation time (p < 0.001) and was the highest at A5 (8.40 g/kg). The available phosphorus at A1 (0.40 g/kg) was significantly higher than those at the other stages (p = 0.004), and the available nitrogen at A1 (0.28 g/kg) and A3 (0.26 g/kg) was significantly higher than those at the other stages (p < 0.001). The number and diversity of bacteria and fungi in soil increased gradually, and nine bacterial and four fungal genera were identified. This study offers soil characteristic and microbial community data for O. raphanipes casing soil at different cultivation stages, which could facilitate sustainable cultivation of O. raphanipes and reduction of live contaminants.

Grey and harbor seals in France (mainland and Saint-Pierre et Miquelon): microbial communities and identification of a microbial source tracking seal marker.

Seals, protected wild marine mammals, are widely found in waters around the world. However, rising concerns about their increasing numbers in some areas have led to potential worries regarding microbiological contamination of coastal areas by their feces, which could impact bathing and shellfish-harvesting activities. To the best of our knowledge, no study has been conducted on the bacterial and RNA viral communities present in the feces of both grey and harbor seals, which are the two main seal species observed in mainland France and overseas. Fecal bacterial (n = 132) and RNA viral (n = 40) communities of seals were analyzed using 16S rRNA gene amplicon high-throughput sequencing and viral RNA sequencing methods, respectively. In addition, to identify the specific characteristics of seal fecal microbial communities compared to other animal fecal microbial communities that may also contaminate coastal areas, the bacterial communities of seals were compared to those of wild waterbirds and breeding animals (i.e., cattle and pigs) which could be present in upstream catchments of coastal areas. Finally, ANCOM was used to identify unique and seal-associated Amplicon Sequence Variants (ASVs), aiming to develop a Microbial Source Tracking (MST) bacterial qPCR marker associated with seals. The bacterial communities of grey and harbor seals were not found to be significantly different and were characterized by a predominance of Firmicutes, including the genera Clostridium sensu stricto 1 and Peptoclostridium, followed by Fusobacteriota with the genus Fusobacterium, and Bacteroidota with the genus Bacteroides. However, variations in bacterial communities between sites and individuals were observed. Similar observations were made for the RNA viral communities being characterized by a predominance of Picobirnaviridae (44% of total reads) and Astroviridae (15%). This study successfully developed a sensitive (89.8%) and specific (97.1%) MST qPCR marker targeting grey seal-associated bacteria belonging to the Bifidobacteriaceae family. This marker can be used to identify potential fecal contamination of coastal areas by seals and complements the MST toolboxes of markers already developed for humans, wild birds and livestock.

Study on substrates purification effect and microbial community structure of vertical subsurface flow constructed wetland under siphon effect

To explore the pollutants removal effects of siphon composite vertical flow constructed wetlands (Sc-VSsFCW), alongside the characteristics of microbial communities and the varying trends of extracellular polymeric substances (EPS) content across substrate layers. Two kinds of distinct Sc-VSsFCW, with loess sphere and clay ceramic grain as substrate materials, respectively, were established. During the experiment, water quality of influent and effluent were detected to investigate system pollutant removal efficiency, routine index detection, microbial diversity analysis and EPS content determination, and substrates were analyzed by scanning electron microscopy (SEM) and X-ray diffraction (XRD). Results indicated that both substrate systems exhibited good pollutant removal effect, with the average removal rate of 90 % for ammonia nitrogen (NH4+-N), and chemical oxygen demand (COD) removal rate within the range of 60–70 %. The long-term re‑oxygenation process inherent in the system successfully augmented the dissolved oxygen (DO) content within the wastewater, and facilitate relative high abundance of Nakamurella, Bacillus, and Nitrospira in these two substrate systems, which enhanced organic matter degradation and nitrification processes. Moreover, the hydraulic conductivity and EPS content in both substrate systems displayed a declining trend, suggesting that the system's unique hydraulic conditions strategies effectively mitigated EPS accumulation and diminished the likelihood of biological clogging. Consequently, the system's distinctive re‑oxygenation and siphon drainage methods boast advantages over traditional vertical flow constructed wetlands in terms of enhancing dissolved oxygen levels and mitigating the risk of biological clogging. This study contributes theoretical underpinnings for the application of constructed wetlands in wastewater treatment and clogging mitigation.

Thermal Adaptation of Enzyme‐Mediated Processes Reduces Simulated Soil CO2 Fluxes Upon Soil Warming

AbstractUnderstanding factors influencing carbon effluxes from soils to the atmosphere is important in a world experiencing climatic change. Two important uncertainties related to soil organic carbon (SOC) stock responses to a changing climate are (a) whether soil microbial communities acclimate or adapt to changes in soil temperature and (b) how to represent this process in SOC models. To further explore these issues, we included thermal adaptation of enzyme‐mediated processes in a mechanistic SOC model (ReSOM) using the macromolecular rate theory. Thermal adaptation is defined here to encompass all potential responses of soil microbes and microbial communities following a change in temperature. To assess the effects of thermal adaptation of enzyme‐mediated processes on simulated SOC losses, ReSOM was applied to data collected from a 13‐year soil warming experiment. Results show that a model omitting thermal adaptation of enzyme‐mediated processes substantially overestimates observed CO2 effluxes during the initial years of soil warming. The bias against observed CO2 effluxes was lower for models including thermal adaptation of enzyme‐mediated processes. In addition, for a simulated linear 3°C soil warming over 100 years, models including thermal adaptation of enzyme‐mediated processes simulated SOC losses of a factor of three smaller than models omitting this process. As thermal adaptation of microbial community characteristics is generally not included in models simulating feedback between the soil, biosphere and atmosphere, we encourage future studies to assess the potential impact that microbial adaptation has on soil carbon – climate feedback representations in models.

Rational eucalypt logging site management patterns enhance soil phosphorus bioavailability and reshape phoD-harboring bacterial community structure

Continuous planting of eucalypt plantations negatively affects soil nutrient effectiveness, especially soil phosphorus (P) availability. Therefore, exploring the response characteristics of soil P-mineralising microbial communities and the distribution mechanism of soil P fractions under different transformation patterns on eucalypts logging sites holds great practical significance for improving soil nutrient effectiveness in plantations. This experiment investigated the effects and correlations between four different transformation patterns on soil phoD-harboring bacterial communities, alkaline phosphatase (ALP) activity, and P fractions. Management patterns mainly included non-forest area formed upon eucalypt stump germination suppression after two generations of Eucalyptus afforestation (TWE), the third generation of pure plantation planting (THE), mixing of Eucalyptus with Manglietia glauca (EM), and rotation of pure M. glauca plantation (MM), with previous mixed coniferous and broadleaf forest (CK) as the control. The results showed that, TWE and THE significantly reduced soil (0–10 cm and 10–20 cm) organic carbon (SOC), total nitrogen (TN), bioavailable P, and labile Po, and increased the occluded P and ALP activity compared to CK; however, SOC, TN, bioavailable P, and labile Po indices improved in plantations of EM or MM compared to TWE and THE. Meanwhile, the four management patterns on the logging site caused significant differences in phoD gene community structure and diversity. TWE and THE significantly increased the relative abundances (RAs) of Pseudomonadaceae and Comamonadaceae, which correlated negatively with soil bioavailable P and HCl-P and positively with ALP activity, suggesting a positive effect on Po mineralization and insoluble P mobilization. In contrast, Streptomycetaceae and Oxalobacteraceae were significantly enriched in EM or MM, implying that not all microorganisms carrying phoD genes play important roles in synthesizing ALP. The structure equation model showed that TN, resin-Pi, NaHCO3-Pi, and HCl-P had indirect effects on ALP through phoD-harbouring bacterial diversity and community composition. These findings provide a basis for understanding the soil P cycling mechanism after eucalypt plantations logging site transformation.

Changes in soil microbial community and carbon use efficiency in freeze-thaw period restored after growth season under warming and straw return

Microbial communities and metabolic activities play key roles in carbon (C) turnover in terrestrial ecosystems, which are directly and indirectly affected by freeze-thaw cycles. However, the immediate and legacy effects of freeze-thaw periods on soil microbial community structure and C metabolic activity in agricultural ecosystems were still not fully understood. In this study, we evaluated the changes in soil microbial community structure and C metabolic activity during the freeze-thaw period and the growth season under the condition of warming and straw return. The results showed that the microbial biomass and the ratio of fungi to bacteria (F/B) were sensitive to freeze-thaw cycles and straw return. Both gradually decreased during the freeze-thaw period. The ratio of gram-positive to gram-negative bacteria (GP/GN) gradually increased during the freeze-thaw period. Then all these changes recovered during the growth season. Microorganisms have a certain self-regulating ability to deal with freeze-thaw stress. In contrast, microbial C use efficiency (CUE) did not significantly change during the freeze-thaw period, but increased during the growth season. Microbial CUE had no significant correlations with microbial biomass, the F/B, and the GP/GN, while it was negatively related with the ratio of dissoluble organic C to dissoluble total nitrogen (N) and the imbalance ratio between resources and microorganisms (C:N imbalance). These findings suggested that soil stoichiometric ratio played important role in regulating microbial CUE, instead of microbial community characteristics.

Biotic Interaction Underpins the Assembly Processes of the Bacterial Community Across the Sediment-Water Interface in a Subalpine Lake.

The sediment-water interface is the most active region for biogeochemical processes and biological communities in aquatic ecosystems. As the main drivers of biogeochemical cycles, the assembly mechanisms and the distribution characteristics of microbial communities at this boundary remain unclear. This study investigated the microbial communities across the sediment-water interface in a natural subalpine lake in China. The results indicated that the diversity of bacterial communities in middle sediment was significantly higher than that in overlying water and other sediments (p < 0.001). Pearson's correlation analysis indicated that the diversity was significantly influenced by biotic factors (e.g., diversity of fungus, protozoan and alga) and physicochemical parameters (e.g., total carbon, total organic carbon, nitrate, ammonium and pH) (p < 0.01). Null model analysis revealed that the homogeneous selection dominated the assembly of the bacteria community in sediment, whereas the heterogeneous selection dominated that in overlying water. The least squares path analysis showed that interactions between protozoa and bacteria had a greater impact on bacterial community assembly (p < 0.001). Important taxa influence the assembly by regulating biotic interactions. These findings provided a basis for understanding the importance of biotic interactions in maintaining subalpine lakes' ecosystems across the sediment-water interface.

Bacterial wilt alters the microbial community characteristics of tobacco root and rhizosphere soil

The root-related microorganisms have good effects of stress resistance and disease resistance, and promote the healthy growth of plants. It is important to understand the characteristics of microbial communities in healthy and infected tobacco roots and rhizosphere soil for controlling tobacco bacterial wilt by using beneficial microorganisms in specific niches. In this study, the soil properties and microbial composition of the rhizosphere soil and roots of healthy and bacterial wilt-diseased tobacco plants were analyzed to evaluate their potential influence on plant health. Soil properties including total carbon and total nitrogen have show significant differences in bacterial wilt-infected tobacco. The microbial community diversity and composition are high related to the occurrence of bacterial wilt. Fungal, bacterial and actinobacterial community varied between two different health systems with the increase/decrease of beneficial microbiomes. Results of community functions of rhizosphere microbiomes have showed the differences in Metabolic pathways. This study clarified the impact of bacterial wilt caused by Ralstonia solanacearum on tobacco root and rhizosphere soil microbial communities, providing a theoretical basis for studying the relationship between rhizosphere-soil microorganisms-plant health, and offering a new perspective for utilizing beneficial microorganisms to defend against pathogen invasion in specific ecological niches.

Bio-augmentation driven sulfur autotrophic denitrification process: Focusing on denitrification performance, microbial community and gene characteristics

The long time and poor efficiency of transforming activated sludge directly into autotrophic denitrifiers pose considerable challenges to sulfur autotrophic denitrification (SAD) technology. To address these issues, bio-augmentation was used to rapidly enrich numerous sulfur autotrophic denitrifiers and maintain high nitrate removal efficiency. The results showed that bio-augmentation with 10 % mixed autotrophic denitrifiers reduced the construction time of the SAD system and significantly improved the total nitrogen (TN) removal efficiency. Even at influent NO3--N concentrations of 150 mg/L and 200 mg/L, the TN removal efficiency in the bio-augmented system improved to 97.1 % and 66.0 %, respectively, whereas it was, only 1.4 % and 1.5 % in a black system. The bio-augmented system operated stably, showing a greater TN removal efficiency (57.6 %) even at an influent composition of 222.3 mg/L NO2--N and 152.7 mg/L NO3--N. This study revealed that bio-augmentation accelerated the alteration of microbial community structures, enriched autotrophic denitrifier species, and increased the abundance of autotrophic denitrifiers. Additionally, network analysis between microorganisms revealed well-connected associations and cooperation among the microbes induced by bio-augmentation. Furthermore, according to predicted function profiles, bio-augmentation enhanced the activity of nitrate reduction enzymes, especially the napAB, nirK, norBC, and nosZ genes, thereby improving nitrogen removal efficiency. Genes involved in sulfur oxidation included fccAB, dsrAB, sorA, and SUOX, whereas sat, aprAB, cysJI and sir were involved in sulfate reduction. These results enable the rapid construction of SAD systems.