Microbial Community Composition Research Articles

[Effects of Water Level Fluctuations and Vegetation Restoration on Soil Prokaryotic Microbial Community Structure in the Riparian Zone of the Three Gorges Reservoir].

Riparian zones are typical fragile and sensitive ecological areas. Fluctuations in water level are the main factor affecting the soil environment in these zones, and vegetation restoration is considered an important means of soil conservation there. However, the interactive effects of water level fluctuations and vegetation restoration on the soil microbial community structure in the reservoir riparian zone remain unclear. Therefore, we selected abandoned grassland and artificial forestland at different water level elevations as research objects in the riparian zone of the Three Gorges Reservoir. We used 16S rRNA high-throughput sequencing technology to explore the composition and diversity of soil prokaryotic microbial communities and investigated the main environmental factors driving the soil microbial community structure. The results showed that the α diversity of soil prokaryotes was the highest at the low water level of the riparian zone. The Pielou_e index, Shannon index, and Simpson index at the 163 m elevation were significantly higher than those at the 168 m elevation, and the Chao1 index and Shannon index were significantly higher than those at the 173 m elevation. However, no significant difference was found in the soil microbial community α diversity between abandoned grassland and artificial forestland. At the same time, water level fluctuations and vegetation restoration had significant effects on the community composition of soil prokaryotic microorganisms, and there were significant differences in biomarker categories in different study sites. Notably, the effects of vegetation restoration types on the soil prokaryotic microbial community structure were stronger than that of water level fluctuations. In addition, the results of hierarchical segmentation showed that soil pH was the main driving factor for the change in soil prokaryotic microbial community structure in the Three Gorges Reservoir. These results deepen our understanding of the variations in microbial community structure in the reservoir riparian zone and provide scientific reference for the restoration and reconstruction of the riparian zone ecosystem.

[Intensive Citrus Cultivation Suppresses Soil Phosphorus Cycling Microbial Activity].

Soil microbes are key drivers in regulating the phosphorus cycle. Elucidating the microbial mineralization process of soil phosphorus-solubilizing bacteria is of great significance for improving nutrient uptake and yield of crops. This study investigated the mechanism by which citrus cultivation affects the soil microbial acquisition strategy for phosphorus by measuring the abundance of the phoD gene, microbial community diversity and structure, and soil phosphorus fractions in the soils of citrus orchards and adjacent natural forests. The results showed that citrus cultivation could lead to a decrease in soil pH and an accumulation of available phosphorus in the soil, with a content as high as 112 mg·kg-1, which was significantly higher than that of natural forests (3.7 mg·kg-1). Citrus cultivation also affected the soil phosphorus fractions, with citrus soil having higher levels of soluble phosphorus (CaCl2-P), citrate-extractable phosphorus (Citrate-P), and mineral-bound phosphorus (HCl-P). The phosphorus fractions of natural forest soils were significantly lower than those of citrus soils, whereas the phoD gene abundance and alkaline phosphatase activity were significantly higher in natural forest soils than in citrus soils. High-throughput sequencing results showed that the Shannon diversity index of phosphate-solubilizing bacteria in citrus soils was 4.61, which was significantly lower than that of natural forests (5.35). The microbial community structure in natural forests was also different from that of citrus soils. In addition, the microbial community composition of phosphate-solubilizing bacteria in citrus soils was also different from that of natural forests, with the relative abundance of Proteobacteria being lower in natural forest soils than in citrus soils. Therefore, citrus cultivation led to a shift of soil microbial acquisition strategy for phosphorus, with external phosphorus addition being the main strategy in citrus soils, whereas microbial mineralization of organic phosphorus was the main strategy in natural forest soils to meet their growth requirements.

Synthesis of recovery patterns in microbial communities across environments

BackgroundDisturbances alter the diversity and composition of microbial communities. Yet a generalized empirical assessment of microbiome responses to disturbance across different environments is needed to understand the factors driving microbiome recovery, and the role of the environment in driving these patterns.ResultsTo this end, we combined null models with Bayesian generalized linear models to examine 86 time series of disturbed mammalian, aquatic, and soil microbiomes up to 50 days following disturbance. Overall, disturbances had the strongest effect on mammalian microbiomes, which lost taxa and later recovered their richness, but not their composition. In contrast, following disturbance, aquatic microbiomes tended away from their pre-disturbance composition over time. Surprisingly, across all environments, we found no evidence of increased compositional dispersion (i.e., variance) following disturbance, in contrast to the expectations of the Anna Karenina Principle.ConclusionsThis is the first study to systematically compare secondary successional dynamics across disturbed microbiomes, using a consistent temporal scale and modeling approach. Our findings show that the recovery of microbiomes is environment-specific, and helps to reconcile existing, environment-specific research into a unified perspective.FPVwQXB65-N4idcpgwJZ6_Video

Water physicochemical quality as driver of spatial and temporal patterns of microbial community composition in lake ecosystems

This study aimed at monitoring and management of the surface water and potentially pathogenic microbes of Lake Tonga (Algeria) with respect to. It characterized the main bacterial diversity patterns of Lake Tonga and predicted from water physicochemical parameters and water quality index (WQI) the distribution of bacterial species and the main indicator groups of faecal water contamination. Water samples were taken monthly at three sampling sites of different water depths. Several physicochemical parameters were measured; of which some were included in computing WQI to characterize the water quality of the lake. Counting, isolation and bacterial identification methods were used to characterize the existing aerobic heterotrophic bacteria. The composition of the microbial community of the waterbody of Lake Tonga included an abundant culturable bacterial flora belonging to several bacterial families and whose specific richness varied between water depths of the sites sampled. Species richness of the bacteria identified phenotypically varied between 7 and 11 per sample. The site with shallow water was the richest in bacterial species, compared to moderate and deep waters. The redundancy analysis showed the main physicochemical drivers of the microbial community composition. Our findings showed that high WQI scores indicated the water quality deterioration which triggered the increase in total load of faecal indicator bacterial groups. This study identified in Lake Tonga an important culturable aerobic bacterial flora whose specific richness and distribution varied spatially following the effects of water physicochemical parameters. Lake Tonga needs an integrated management plan to mitigate human disturbances declining water quality.

Effects of the fermentation quality and microbial community of waxy maize mixed with fodder soybean silage

Waxy maize (Zea mays L. sinensis Kulesh) is highly regarded for its high nutritional content and unique taste. Although the stalks and leaves contain high carbohydrate levels after ear harvesting, inadequate crude protein (CP) limits the utilization and promotion of waxy maize silage in animal husbandry. In this study, waxy maize and fodder soybeans were mixed for sowing in different proportions [1:0 (CK), 1:1 (A1), 1:2 (A2), 1:3 (A3), and 1:4 (A4)] to investigate the effects of different mixing ratios on the growth of the waxy maize, the chemical indices, fermentation quality, and the microbial community of the mixed silage after ear harvesting. The mixed planting of waxy maize and fodder soybeans in different proportions had no effect on the yield and quality of the waxy maize ears and increased the aboveground biomass after ear harvesting. After ear harvesting, the neutral detergent fiber (NDF) and acid detergent fiber (ADF) contents significantly decreased, and the CP content and relative feeding value (RFV) gradually increased in the mixed silage. The pH of the treatments was lower than 4.2 except for A4, and the lowest ammonia nitrogen (AN) concentration was observed in A3. With increasing proportions of fodder soybeans, the abundance of beneficial bacteria increased and that of harmful bacteria decreased; Firmicutes and Lactobacillus were the dominant phylum and genus, respectively, and both increased gradually. Redundancy analysis (RDA) revealed that the fermentation indices affecting the microbial community composition in the silage were inconsistent among the different mixed sowing combinations. The Mantel test showed that the composition of the microbial communities in the treatments was significantly correlated with the ADF, water-soluble carbohydrate (WSC), and propionic acid (PA) contents. Comprehensive analysis revealed that the optimal mixed sowing ratio of waxy maize to fodder soybeans was 1:3, and waxy maize and fodder soybeans silage can increase the utilization of aboveground biomass and improve the fermentation quality and feeding quality of silage by changing the microbial community. These findings lay a certain theoretical foundation for improving the utilization of waxy maize.

Gut microbiota and inflammatory factor characteristics in major depressive disorder patients with anorexia

BackgroundThis study aimed to explore the gut microbiota and inflammatory factor characteristics in major depressive disorder (MDD) patients with anorexia and to analyze the correlation between gut microbiota and inflammatory factors, anorexia, and HAMD scores.Methods46 MDD patients and 46 healthy controls (HC) were included in the study. The 46 MDD patients were divided into two groups according to whether they had anorexia:20 MDD without anorexia (MDA0 group) and 26 MDD with anorexia (MDA1 group). We used the Hamilton Depression Scale-24 (HAMD-24) to evaluate the depression status of all participants and 16 S ribosomal RNA (16 S rRNA)sequencing to evaluate the composition of the gut microbiota. Inflammatory factors in peripheral blood such as C-reactive protein (CRP) were detected using enzyme-linked immunosorbent assay (ELISA). Spearman’s correlation analysis was used to evaluate the correlation between gut microbiota and inflammatory factors, HAMD scores, and anorexia.Results1). CRP was significantly higher in the MDA0, MDA1, than HC. 2). An analysis of α-diversity shows: the Simpson and Pielou indices of the HC group are higher than the MDA1 group (P < 0.05). 3). The β-diversity analysis shows differences in the composition of microbial communities between the MDA0, MDA1, and HC group. 4). A correlation analysis showed that Blautia positively correlated with anorexia, HAMD scores, and CRP level, whereas Faecalibacterium, Bacteroides, Roseburia, and Parabacteroides negatively correlated with anorexia, HAMD scores, and CRP level. 5). The receiver operating characteristic (ROC) curve was drawn using the differential bacterial genera between MDD patients with or without anorexia as biomarkers to identify whether MDD patients were accompanied with anorexia, and its area under curve (AUC) was 0.85. The ROC curve was drawn using the differential bacterial genera between MDD patients with anorexia and healthy controls as biomarkers to diagnose MDD patients with anorexia, with its AUC was 0.97.ConclusionThis study suggested that MDD patients with anorexia had a distinct gut microbiota compared to healthy individuals, with higher level of CRP. Blautia was more abundant in MDD patients with anorexia and positively correlated with CRP, HAMD scores, and anorexia. The gut microbiota might have influenced MDD and anorexia through the inflammatory factor CRP.

Response of rhizosphere microbial community structure and production performance of corn and soybean to belt planting mode

Soybean and corn strip cropping takes full advantage of the root characteristics and plant height differences between soybean and corn, which can improve crop photosynthesis and nutrient uptake as well as capitalize on the marginal effect of corn. However, there is not enough in-depth research on the effects of soybean and corn strip cropping modes on inter-root microbial communities and crop yield traits and their correlations, and the functional genes of inter-root microbes. In this study, the structural composition and functional genes of soil inter-root microbial communities under different strip cropping patterns of soybean and maize, Mode 1, Mode 2, and Mode 3, were studied using macro-genome high-throughput sequencing, and the yield traits of soybean and maize were determined and the correlation was understood, taking Zhonglian Soybean 1505 and Tiyu 108 maize as test materials at the experimental base of the Research Institute of Agricultural and Livestock Sciences, Xing'anmeng, Inner Mongolia. correlation between the two. The following results were found. Redundancy analysis found that rhizosphere microorganisms are mainly bacteria, followed by viruses, followed by archaea, and fungi are the least. Relatively speaking, viruses and bacteria are more susceptible to the influence of planting patterns than fungi. Alpha diversity analysis shows that the diversity index changes significantly during the peak flowering period. There is no difference between the other two stages. The diversity of maize rhizosphere microorganisms under Mode 1 or Mode 2 modes is higher than that under Mode 3 modes, while the diversity of soybean rhizosphere microorganisms under Mode 3 modes is higher than the other two modes. Profiling analysis found that different growth periods and planting patterns lead to varying degrees of changes in community structure. The dominant bacterial phyla include Pseudomonas, Actinobacteria, Bacteroidetes, and Streptococcus. The dominant genera of bacteria are rhizobia, pseudomonas, erythrobacteria, and pseudomonas. The relative abundance of slow root rhizobia in the three growth stages of maize rhizosphere is relatively low. The results of yield traits showed that corn yield under Mode 1 and Mode 2 planting was significantly higher than that under pattern III; soybean yield under pattern III planting was significantly higher than that under the other two patterns, indicating that pattern I or II planting is suitable for corn production, while Mode 3 planting mode is more suitable for soybean production. Correlation analysis showed that S_Massilis_putida was significantly and positively correlated with maize yield, and S_lysobacter_capsici was highly significantly and significantly positively correlated with the number of soybean plants per square meter, and the number of plants in 2 square meters. This study contributes to our further understanding of the classification of inter-root microorganisms and their functional relationships in maize and soybean under different conditions.

Siderophores and competition for iron govern myxobacterial predation dynamics.

Bacterial predators are decisive organisms that shape microbial ecosystems. In this study, we investigated the role of iron and siderophores during the predatory interaction between two rhizosphere bacteria: Myxococcus xanthus, an epibiotic predator, and Sinorhizobium meliloti, a bacterium that establishes nitrogen-fixing symbiosis with legumes. The results show that iron enhances the motility of the predator and facilitates its predatory capability, and that intoxication by iron is not used by the predator to prey, although oxidative stress increases in both bacteria during predation. However, competition for iron plays an important role in the outcome of predatory interactions. Using combinations of predator and prey mutants (non-producers and overproducers of siderophores), we have investigated the importance of competition for iron in predation. The results demonstrate that the competitor that, via the production of siderophores, obtains sufficient iron for growth and depletes metal availability for the opponent will prevail in the interaction. Consequently, iron fluctuations in soils may modify the composition of microbial communities by altering the activity of myxobacterial predators. In addition, siderophore overproduction during predation can alter soil properties, affecting the productivity and sustainability of agricultural operations.

Analysis of Salt Stress on Soil Microbial Community Composition and Its Correlation with Active Components in the Rhizosphere of Acanthopanax senticosus.

Salt stress can adversely affect plant seed germination, growth and development, and eventually lead to slow growth and even death of plants. The purpose of this study was to investigate the effects of different concentrations of NaCl and Na2SO4 stress on the physicochemical properties, enzyme activities, rhizosphere microbial community and seven active components (L-phenylalanine, Protocatechuic acid, Eleutheroside B, Chlorogenic acid, Caffeic acid, Eleutheroside E, Isofraxidin) of Acanthopanax senticosus rhizosphere soil. Statistical analysis was used to explore the correlation between the rhizosphere ecological factors of Acanthopanax senticosus and its active components. Compared with Acanthopanax senticosus under NaCl stress, Na2SO4 generally had a greater effect on Acanthopanax senticosus, which reduced the richness of fungi in rhizosphere soil and adversely affected the content of multiple active components. Pearson analysis showed that pH, organic matter, ammonium nitrogen, available phosphorus, available potassium, catalase and urease were significantly correlated with active components such as Caffeic acid and Isofraxidin. There were 11 known bacterial genera, 12 unknown bacterial genera, 9 known fungal genera and 1 unknown fungal genus significantly associated with the active ingredient. Salt stress had great changes in the physicochemical properties, enzyme activities and microorganisms of the rhizosphere soil of Acanthopanax senticosus. In conclusion, different types and concentrations of salts had different effects on Acanthopanax senticosus, and the active components of Acanthopanax senticosus were regulated by rhizosphere soil ecological factors.

Structure and composition of microbial communities in the water column from Southern Gulf of Mexico and detection of putative hydrocarbon-degrading microorganisms.

This study assessed the bacterioplankton community and its relationship with environmental variables, including total petroleum hydrocarbon (TPH) concentration, in the Yucatan shelf area of the Southern Gulf of Mexico. Beta diversity analyses based on 16S rRNA sequences indicated variations in the bacterioplankton community structure among sampling sites. PERMANOVA indicated that these variations could be mainly related to changes in depth (5 to 180 m), dissolved oxygen concentration (2.06 to 5.93 mg L-1), and chlorophyll-a concentration (0.184 to 7.65 mg m3). Moreover, SIMPER and one-way ANOVA analyses showed that the shifts in the relative abundances of Synechococcus and Prochlorococcus were related to changes in microbial community composition and chlorophyll-a values. Despite the low TPH content measured in the studied sites (0.01 to 0.86 μL L-1), putative hydrocarbon-degrading bacteria such as Alteromonas, Acinetobacter, Balneola, Erythrobacter, Oleibacter, Roseibacillus, and the MWH-UniP1 aquatic group were detected. The relatively high copy number of the alkB gene detected in the water column by qPCR and the enrichment of hydrocarbon-degrading bacteria obtained during lab crude oil tests exhibited the potential of bacterioplankton communities from the Yucatan shelf to respond to potential hydrocarbon impacts in this important area of the Gulf Mexico.

A Comparative Analysis of Microbial Communities in the Rhizosphere Soil and Plant Roots of Healthy and Diseased Yuanyang Nanqi (Panax vietnamensis) with Root Rot

Microbial communities are not only an important indicator of soil status but also a determinant of plant nutrition and health levels. Loss of microbial community ecosystem control can directly lead to microbial disease occurrence. During the process of Yuanyang Nanqi wild imitation planting, root rot diseases frequently occur, seriously affecting their yield and quality. Via amplicon sequencing, this study mainly compared the microbial community composition between the rhizosphere soil and roots of healthy and diseased Yuanyang Nanqi with root rot. The α-diversity showed that the microbial community diversity and abundance in the roots of diseased Yuanyang Nanqi were much lower than those of those in healthy specimens, while no significant difference was found in the rhizosphere soil. The β－diversity showed that the bacterial community in the Gejiu region and the fungal community in the Honghe region were significantly different from those in other regions. The species relative abundance map showed that there was no obvious difference in microbial community composition between the rhizosphere soil and roots of healthy and diseased Nanqi, but in diseased specimens with root rot, the proportions of Pseudomonas and Fusarium increased. Based on a functional prediction analysis of FUNGuild, the results showed that the Nanqi roots were mainly pathological saprophytic type and that their rhizosphere soil was mainly saprophytic type. The microorganisms in the roots of Yuanyang Nanqi tubers with root rot were also isolated and identified through the use of the culture method. The possible pathogenic strains were tested via anti－inoculation, and Fusarium oxysporum was identified as one of the main pathogenic fungi of Nanqi root rot, which was consistent with the amplicon sequencing results. These results will help us understand the change trend of microbial communities in healthy and diseased plants and analyze the pathogens involved, the pathogenesis, and the beneficial microorganisms, which would provide a theoretical basis for effective biological control.

In situ incubation of iron(II)-bearing minerals and Fe(0) reveals insights into metabolic flexibility of chemolithotrophic bacteria in a nitrate polluted karst aquifer

Groundwater nitrate pollution is a major reason for deteriorating water quality and threatens human and animal health. Yet, mitigating groundwater contamination naturally is often complicated since most aquifers are limited in bioavailable carbon. Since metabolically flexible microbes might have advantages for survival, this study presents a detailed description and first results on our modification of the BacTrap© method, aiming to determine the prevailing microbial community's potential to utilize chemolithotrophic pathways. Our microbial trapping devices (MTDs) were amended with four different iron sources and incubated in seven groundwater monitoring wells for ~3 months to promote growth of nitrate-reducing Fe(II)-oxidizing bacteria (NRFeOxB) in a nitrate-contaminated karst aquifer. Phylogenetic analysis based on 16S rRNA gene sequences implies that the identity of the iron source influenced the microbial community's composition. In addition, high throughput amplicon sequencing revealed increased relative 16S rRNA gene abundances of OTUs affiliated to genera such as Thiobacillus, Rhodobacter, Pseudomonas, Albidiferax, and Sideroxydans. MTD-derived enrichments set up with Fe(II)/nitrate/acetate to isolate potential NRFeOxB, were dominated by e.g., Acidovorax spp., Paracoccus spp. and Propionivibrio spp. MTDs are a cost-effective approach for investigating microorganisms in groundwater and our data not only solidifies the MTD's capacity to provide insights into the metabolic flexibility of the aquifer's microbial community, but also substantiates its metabolic potential for anaerobic Fe(II) oxidation.

Mechanisms and implications of bacterial-fungal competition for soil resources.

Elucidating complex interactions between bacteria and fungi that determine microbial community structure, composition, and functions in soil, as well as regulate carbon (C) and nutrient fluxes, is crucial to understand biogeochemical cycles. Among the various interactions, competition for resources is the main factor determining the adaptation and niche differentiation between these two big microbial groups in soil. This is because C and energy limitations for microbial growth are a rule rather than an exception. Here, we review the C and energy demands of bacteria and fungi - the two major kingdoms in soil - the mechanisms of their competition for these and other resources, leading to niche differentiation, and the global change impacts on this competition. The normalized microbial utilization preference showed that bacteria are 1.4-5 times more efficient in the uptake of simple organic compounds as substrates, whereas fungi are 1.1-4.1 times more effective in utilizing complex compounds. Accordingly, bacteria strongly outcompete fungi for simple substrates, while fungi take advantage of complex compounds. Bacteria also compete with fungi for the products released during the degradation of complex substrates. Based on these specifics, we differentiated spatial, temporal, and chemical niches for these two groups in soil. The competition will increase under the main five global changes including elevated CO2, N deposition, soil acidification, global warming, and drought. Elevated CO2, N deposition, and warming increase bacterial dominance, whereas soil acidification and drought increase fungal competitiveness.

Helicobacter pylori infection in infant rhesus macaque monkeys is associated with an altered lung and oral microbiome

It is estimated that more than half of the world population has been infected with Helicobacter pylori. Most newly acquired H. pylori infections occur in children before 10 years of age. We hypothesized that early life H. pylori infection could influence the composition of the microbiome at mucosal sites distant to the stomach. To test this hypothesis, we utilized the infant rhesus macaque monkey as an animal model of natural H. pylori colonization to determine the impact of infection on the lung and oral microbiome during a window of postnatal development. From a cohort of 4–7 month-old monkeys, gastric biopsy cultures identified 44% of animals infected by H. pylori. 16S ribosomal RNA gene sequencing of lung washes and buccal swabs from animals showed distinct profiles for the lung and oral microbiome, independent of H. pylori infection. In order of relative abundance, the lung microbiome was dominated by the phyla Proteobacteria, Firmicutes, Bacteroidota, Fusobacteriota, Campilobacterota and Actinobacteriota while the oral microbiome was dominated by Proteobacteria, Firmicutes, Bacteroidota, and Fusobacteriota. In comparison to the oral cavity, the lung was composed of more genera and species that significantly differed by H. pylori status, with a total of 6 genera and species that were increased in H. pylori negative infant monkey lungs. Lung, but not plasma IL-8 concentration was also associated with gastric H. pylori load and lung microbial composition. We found the infant rhesus macaque monkey lung harbors a microbiome signature that is distinct from that of the oral cavity during postnatal development. Gastric H. pylori colonization and IL-8 protein were linked to the composition of microbial communities in the lung and oral cavity. Collectively, these findings provide insight into how H. pylori infection might contribute to the gut-lung axis during early childhood and modulate future respiratory health.

Performance and microbial community composition of full-scale high-rate cascade sludge digestion system via pie-shaped reactor configuration

A full-scale high-rate cascade anaerobic digestion (CAD) system was evaluated for its ability to enhance enzymatic sludge hydrolysis. The system included a newly built digester, innovatively divided into three pie-shaped compartments (500 m3 each), followed by an existing, larger digester (1500 m3). The system treated a mixture of waste activated sludge and primary sludge, achieving a stable total chemical oxygen demand reduction efficiency (56.1 ± 6.8 %), and enhanced sludge hydrolytic enzyme activities at a 14.5-day total solids retention time (SRT). High-throughput sequencing data revealed a consistent microbial community across reactors, dominated by consortia that govern hydrolysis and acidogenesis. Despite relatively short SRTs in the initial reactors of the CAD system, acetoclastic methanogens belonging to Methanosaeta became the most abundant archaea. ‬‬‬‬‬‬‬‬‬‬‬‬‬ This study proves that the CAD system achieves stable sludge reduction, accelerates enzymatic hydrolysis at full-scale, and paves the way for its industrialization in municipal waste sewage sludge treatment

Exploring the role of gut microbiota in human health

The study explores the intricate relationship between the human gut microbiota and health. It analyzes the gut microbiota’s roles in digestion, metabolism, immune responses, and overall well-being. The review discusses the composition and diversity of gut microbial communities, emphasizing their symbiotic relationship with the host. It also examines how gut dysbiosis, or microbial imbalance, relates to health conditions like inflammatory bowel diseases and metabolic disorders. The review highlights research methodologies like metagenomics and metabolomics that deepen our understanding of gut microbiota function. It also explores external factors, such as diet and antibiotic use, in shaping the gut microbiome. The review discusses potential therapeutic interventions like probiotics and fecal microbiota transplantation, suggesting a future for personalized medicine. By synthesizing existing knowledge, the review aims to advance understanding of the gut microbiota’s role in health and suggest future research and interventions.

Control of phosphorus release from sediment by iron/aluminum co-modified zeolite: efficiency, mechanism, and response of microbial communities in sediment.

The efficiency of iron/aluminum co-modified zeolite (FeAl-Z) covering and amendment for controlling the internal loading of phosphorus (P) from sediment to the overlying water (OW) and its controlling mechanism were explored. The response of the composition of sedimentary microbial communities in sediment and their function to the FeAl-Z capping and amendment was also examined. FeAl-Z showed good removal performance for phosphate in aqueous solution. The maximum phosphate adsorption quantity for FeAl-Z at pH 7 attained 11.2mg P/g. The release of sediment endogenous phosphorus to OW can be successfully restrained by the FeAl-Z covering and amendment, and the suppression ability of FeAl-Z covering was stronger than that of FeAl-Z amendment. Under the capping or amendment condition, FeAl-Z can effectively inactivate the labile phosphorus measured by diffusion gradient in thin film (DGT-LP) in the overlying water and surface sediment. The added FeAl-Z transformed redox-sensitive phosphorus (BD-P) to metal oxide-bound phosphorus (NaOH-IP) and residual phosphorus (Res-P) in sediment, which increased the stability of inorganic phosphorus in the sediment. The passivation of soluble reactive phosphorus (SRP) and DGT-LP in the surface sediment by FeAl-Z significantly contributed to the inhibition of sediment endogenous phosphorus release to OW by the FeAl-Z capping, and the passivation of SRP, DGT-LP and mobile phosphorus in the surface sediment played a pivotal role in the control of sediment internal phosphorus release by the FeAl-Z amendment. The FeAl-Z amendment and capping did not increase the liberation risk of Fe from sediment, and the microorganisms in the sediments under the conditions of FeAl-Z amendment and covering still can perform good ecological functions. Results of this research demonstrate that FeAl-Z capping has high application potential in the control of phosphorus transfer from sediment to OW.

Microbial community structure and carbon transformation characteristics of different aggregates in black soil.

Previous research on whole-soil measurements has failed to explain the spatial distribution of soil carbon transformations, which is essential for a precise understanding of the microorganisms responsible for carbon transformations. The microorganisms involved in the transformation of soil carbon were investigated at the microscopic scale by combining 16S rDNA sequencing technology with particle-level soil classification. In this experiment,16S rDNA sequencing analysis was used to evaluate the variations in the microbial community structure of different aggregates in no-tillage black soil. The prokaryotic microorganisms involved in carbon transformation were measured before and after the freezing and thawing of various aggregates in no-tillage black soil. Each sample was divided into six categories based on aggregate grain size: >5, 2-5, 1-2, 0.5-1, 0.25-0.5, <0.25 mm, and bulk soil. The relative abundance of Actinobacteria phylum in <0.25 mm aggregates was significantly higher compared to that in other aggregates. The Chao1 index, Shannon index, and phylogenetic diversity (PD) whole tree index of <0.25 mm aggregates were significantly smaller than those of in bulk soil and >5 mm aggregates. Orthogonal partial least-squares discrimination analysis showed that the microbial community composition of black soil aggregates was significantly different between <1 and >1 mm. The redundancy analysis (RDA) showed that the organic carbon conversion rate of 0.25-0.5 mm agglomerates had a significantly greater effect on their bacterial community structure. Moreover, humic acid conversion rates on aggregates <0.5 mm had a greater impact on community structure. The linear discriminant analysis effect size (LEfSe) analysis and RDA analysis were combined. Bradyrhizobium, Actinoplane, Streptomyces, Dactylosporangium, Yonghaparkia, Fleivirga, and Xiangella in <0.25 mm aggregates were positively correlated with soil organic carbon conversion rates. Blastococcus and Pseudarthrobacter were positively correlated with soil organic carbon conversion rates in 0.25-0.5 mm aggregates. In aggregates smaller than 1 mm, the higher the abundance of functional bacteria that contributed to the soil's ability to fix carbon and nitrogen. There were large differences in prokaryotic microbial community composition between <1 and >1 mm aggregates. The <1 mm aggregates play an important role in soil carbon transformation and carbon fixation. The 0.25-0.5 mm aggregates had the fastest organic carbon conversion rate and increased significantly more than the other aggregates. Some genus or species of Actinobacteria and Proteobacteria play a positive role in the carbon transformation of <1 mm aggregates. Such analyses may help to identify microbial partners that play an important role in carbon transformation at the micro scale of no-till black soils.

Interplay between green-synthesized nanoparticles and plant performance is mediated by the microbial community in the rhizocompartments

Numerous green-synthesized nanoparticles are being evaluated for their potential application in soil, yet understanding their influence on plant performance and their rhizocompartments associated microbes is a gap that needs to be addressed. In this study, we investigated how applying iron oxide nanoparticles (control 0, low 25 and high 50 mg/kg) impacted the rhizocompartments associated microbial communities and plant secondary metabolites grown in natural soil microcosm. The transcriptional analysis showed that the majority of artemisinin and flavonoid biosynthetic pathway genes were significantly upregulated in plants with the application of low concentration of green-synthesized iron oxide nanoparticles (FeO.NPs) when compared with control plants, suggesting a fine collaboration between these metabolites’ pathways, as indicated by a remarkable increase in artemisinin content (2-fold), ferulic acid (7.6-fold), luteolin (4.3-fold) and syringic acid (6.2-fold). The response of rhizocompartments microbial communities and associated soil enzymes was investigated using high-throughput sequencing and profiler test kits, respectively. The soil microbial community structure was altered upon FeO.NPs exposure in both low and high treated soils as indicated by multivariate analysis. For instance, bacterial phyla Bacteroidetes and Gemmatimonadetes and fungal phyla Ascomycota demonstrated a significant rise in relative abundance in both the rhizosphere and rhizoplane in low and high treatments relative to the control. Moreover, genera level analysis revealed that Cupriavidus, Vibrionimonas, and Burkholderia displayed higher relative abundance (p < 0.05) in low FeO.NPs concentration while Giaella and Nonomuraea didn't show any noticeable response to FeO.NPs. In terms of fungal genera, Oidiodendron and Cryptococcus showed high relative abundance under low treatment. The altered microbiome profile is possibly associated with soil enzymes, for instance, urease and catalase activities were increased by 1.76 and 1.71-fold, respectively in low FeO.NPs. Thus, this study demonstrates the effects of FeO.NPs gradients on plant secondary metabolites and soil enzyme activities, while contributing new insights into their specific impacts on the microbial community composition in the rhizocompartments of plant root system.

Aquatic Bacterial Community Connectivity: The Effect of Hydrological Flow on Community Diversity and Composition

Microbial communities are vital components of freshwater ecosystems due to their role in nutrient cycling and energy flow; however, the mechanisms driving their variation are still being explored. In aquatic systems, water flow (hydrology) can impact microbial community composition through community connectivity; however, the details of hydrology’s effects on microbial connectivity remain unclear. To address this question, we used 16S rRNA metabarcoding to determine bacterial community composition and connectivity across flow transects in three connected Great Lakes waterbodies with very different water-flow regimes: the Little River (high flow), the Detroit River (moderate flow), and Lake Erie (low flow). Bacterial alpha diversity (Chao1) did not differ among the three locations or sample sites along the transects. Analyses of beta diversity using community dissimilarity matrices identified significant differences among the three locations and among sample sites within locations. Bacterial community connectivity varied among the three locations, with a significant distance–decay relationship observed only in the low-flow location, which is indicative of connectivity driven by spatial proximity. Directional analyses showed that the water-flow direction affected bacterial similarity, consistent with the expected hydrological effects on community connectivity and previous published work. Our results indicate that (1) microbial community composition varies within and among even geographically close sampling locations and (2) the specific water-flow regime appears to affect bacterial community connectivity. Including hydrology in models of bacterial community composition will improve our understanding of the relative roles of selection versus stochastic effects on bacterial community diversity and composition in freshwater ecosystems.