Microbial Community Structure Research Articles

Microbiome structure and function in parallel full-scale aerobic granular sludge and activated sludge processes.

Aerobic granular sludge (AGS) and conventional activated sludge (CAS) are two different biological wastewater treatment processes. AGS consists of self-immobilised microorganisms that are transformed into spherical biofilms, whereas CAS has floccular sludge of lower density. In this study, we investigated the treatment performance and microbiome dynamics of two full-scale AGS reactors and a parallel CAS system at a municipal WWTP in Sweden. Both systems produced low effluent concentrations, with some fluctuations in phosphate and nitrate mainly due to variations in organic substrate availability. The microbial diversity was slightly higher in the AGS, with different dynamics in the microbiome over time. Seasonal periodicity was observed in both sludge types, with a larger shift in the CAS microbiome compared to the AGS. Groups important for reactor function, such as ammonia-oxidising bacteria (AOB), nitrite-oxidising bacteria (NOB), polyphosphate-accumulating organisms (PAOs) and glycogen-accumulating organisms (GAOs), followed similar trends in both systems, with higher relative abundances of PAOs and GAOs in the AGS. However, microbial composition and dynamics differed between the two systems at the genus level. For instance, among PAOs, Tetrasphaera was more prevalent in the AGS, while Dechloromonas was more common in the CAS. Among NOB, Ca. Nitrotoga had a higher relative abundance in the AGS, while Nitrospira was the main nitrifier in the CAS. Furthermore, network analysis revealed the clustering of the various genera within the guilds to modules with different temporal patterns, suggesting functional redundancy in both AGS and CAS. KEY POINTS: • Microbial community succession in parallel full-scale aerobic granular sludge (AGS) and conventional activated sludge (CAS) processes. • Higher periodicity in microbial community structure in CAS compared to in AGS. • Similar functional groups between AGS and CAS but different composition and dynamics at genus level.

Screening of enhanced biohydrogen production from anaerobic fermentation amended with nano-sized barium ferrite supported by aluminum oxide

Anaerobic fermentation has attracted wide attention to effectively reduce carbon footprint and alleviate potential energy shortages, which is being regarded as a sustainable and promising technology to obtain high biohydrogen production from widespread organic wastes. However, biohydrogen commercial uptake is now dominantly inhibited by the low hydrogen yield and process instability. In this work, Al2O3/BaFe2O4 nanoparticles (NPs) are successfully applied to anaerobic fermentation for investigating their effects on hydrogen yield, activity of bacteria and microbial community structure. The benefits of Al2O3/BaFe2O4 NPs with respect to microbial metabolism, reactivity of enzymes and process optimization are systematically researched through batch experiments. In addition, various characterizations are used to verify the physical and chemical properties of Al2O3/BaFe2O4 NPs. The results show that the activity of hydrogenases and microbe metabolism can be significantly inhibited by excess addition of Al2O3/BaFe2O4 NPs (150 mg/L and 200 mg/L) while the optimum addition 100 mg/L of Al2O3/BaFe2O4 NPs can boost the biohydrogen yield by 49% via facilitating microorganism growth and enhancing key enzymatic activities, which indicate that the Al2O3/BaFe2O4 NPs display a beneficial influence on electron transfer efficiency and process stability. The existence of Fe3+, Al3+and Ba2+ derived from the corrosion of Al2O3/BaFe2O4 NPs by organic acids synergistically improve the microbial transmembrane transportation and substrate utilization, which contribute to higher conversion rate of glucose into acetate, butyrate and H2. Meanwhile, the complementary functions of Fe3+ and Al3+ can powerfully shorten the lag phase and promote the glycolysis, which finally accelerate the dark fermentation process. Compared with the control group, Clostridium_sensu_stricto_1 is selectively enriched by the addition of Al2O3/BaFe2O4 NPs, which keep heavily involved in the synthesis of H2. On balance, this study provides an effective strategy to enhance hydrogen productivity and maintain process stability, which offer the valuable information for the sustainable utilization of sewage sludge.

Study on microbial diversity of washing machines.

Health and environmental protection are the development trend of household appliances, coupled with the impact of the COVID-19 epidemic in the past few years. Consumers have unprecedented concerns and expectations about the sterilization and disinfection functions of household appliances. As a washing and nursing equipment for household clothes, the anti-bacterial technology of washing machine has developed rapidly. The new models of washing machines in the market have basically added the function of sterilization. In order to thoroughly solve the problem of sterilization and bacteriostasis of washing machines from the source, the distribution of microbial contamination in washing machines should be fully investigated. At present, there is almost no systematic study on the microbial community structure in washing machines in China. Therefore, the purpose of this study is to analyze the bacterial community structure in Chinese household washing machines. To explore the key factors affecting the bacterial community structure of washing machines. Bacterial communities were comprehensively analyzed by high throughput sequencing. Using chao and shannon indexes as indicators, one-way ANOVA was used to explore the key factors affecting the bacterial community structure of washing machines. A total of 2,882,778 tags and 21,265 OTUs from 522 genera were sequenced from 56 washing machine samples. Genus Mycobacterium, Pseudomonas, Brevundimonas, Sphingomonas, Sphingobium, Enhydrobacter, Methylobacterium, Pseudoxanthomonas, Stenotrophomonas and Sphingopyxis were the top ten bacteria genera in abundance. The effects of sources, types, frequency of utilization, sampling locations and service life of washing machines on bacterial diversity in washing machine were systematically analyzed. The statistical analysis showed that service life was an important factor affecting bacterial diversity in washing machine. Our study lays a foundation for directional screening of characteristic microorganisms with targeted characters including malodor-producing, fouling, pathogenic and stress-resistance, the antibacterial evaluation, metabolic mechanism of key characteristic microorganisms as well as antibacterial materials development. At present, the sterilization technology of washing machines has not been fully in combination with the distribution survey of microorganisms in washing machines. According to the specific microorganism distribution condition of the washing machine, the key distribution positions and the types of specific microorganisms contained in different positions, conduct more targeted sterilization treatment. This will help to completely solve the problem of microbial growth in washing machines from the source.

Conversion of boreal forests to agricultural systems: soil microbial responses along a land-conversion chronosequence

BackgroundBoreal regions are warming at more than double the global average, creating opportunities for the northward expansion of agriculture. Expanding agricultural production in these regions will involve the conversion of boreal forests to agricultural fields, with cumulative impacts on soil microbial communities and associated biogeochemical cycling processes. Understanding the magnitude or rate of change that will occur with these biological processes will provide information that will enable these regions to be developed in a more sustainable manner, including managing carbon and nitrogen losses. This study, based in the southern boreal region of Canada where agricultural expansion has been occurring for decades, used a paired forest-adjacent agricultural field approach to quantify how soil microbial communities and functions were altered at three different stages post-conversion (< 10, > 10 and < 50, and > 50 years). Soil microbial functional capacity was assessed by quantitative PCR of genes associated with carbon (C), nitrogen, and phosphorous (P) cycling; microbial taxonomic diversity and community structure was assessed by amplicon sequencing.ResultsFungal alpha diversity did not change, but communities shifted from Basidiomycota to Ascomycota dominant within the first decade. Bacterial alpha diversity increased, with Gemmatimonadota groups generally increasing and Actinomycetota groups generally decreasing in agricultural soils. These altered communities led to altered functional capacity. Functional genes associated with nitrification and low molecular weight C cycling potential increased after conversion, while those associated with organic P mineralization potential decreased. Stable increases in most N cycling functions occurred within the first decade, but C cycling functions were still changing 50 years post conversion.ConclusionsMicrobial communities underwent a rapid shift in the first decade, followed by several decades of slower transition until stabilizing 50 years post conversion. Understanding how the microbial communities respond at different stages post-conversion improves our ability to predict C and N losses from emerging boreal agricultural systems, and provides insight into how best to manage these soils in a way that is sustainable at the local level and within a global context.

Ca(H2PO4)2 and MgSO4 activated nitrogen-related bacteria and genes in thermophilic stage of compost

This study was conducted to investigate the effects of Ca(H2PO4)2 and MgSO4 on the bacterial community and nitrogen metabolism genes in the aerobic composting of pig manure. The experimental treatments were set up as control (C), 1% Ca(H2PO4)2 + 2% MgSO4 (CaPM1), and 1.5% Ca(H2PO4)2 + 3% MgSO4 (CaPM2), which were used at the end of composting for potting trials. The results showed that Ca(H2PO4)2 and MgSO4 played an excellent role in retaining nitrogen and increasing the alkali-hydrolyzed nitrogen (AN), available phosphorus (AP), and available potassium (AK) contents of the composts. Adding Ca(H2PO4)2 and MgSO4 changed the microbial community structure of the compost. The microorganisms associated with nitrogen retention were activated. The complexity of the microbial network was enhanced. Genetic prediction analysis showed that the addition of Ca(H2PO4)2 and MgSO4 reduced the accumulation of nitroso-nitrogen and the process of denitrification. At the same time, despite the reduction of genes related to nitrogen fixation, the conversion of ammonia to nitrogenous organic compounds was promoted and the stability of nitrogen was increased. Mantel test analysis showed that Ca(H2PO4)2 and MgSO4 can affect nitrogen transformation-related bacteria and thus indirectly affect nitrogen metabolism genes by influencing the temperature, pH, and organic matter (OM) of the compost and also directly affected nitrogen metabolism genes through PO43− and Mg2+. The pot experiment showed that composting with 1.5% Ca(H2PO4)2 + 3% MgSO4 produced the compost product that improved the growth yield and nutrient content of cilantro and increased the fertility of the soil. In conclusion, Ca(H2PO4)2 and MgSO4 reduces the loss of nitrogen from compost, activates nitrogen-related bacteria and genes in the thermophilic phase of composting, and improves the fertilizer efficiency of compost products.Key points• Ca(H2PO4)2 and MgSO4 reduced the nitrogen loss and improved the compost effect• Activated nitrogen-related bacteria and altered nitrogen metabolism genes• Improved the yield and quality of cilantro and fertility of soil

Rumen fluid pretreatment promotes anaerobic methane production: revealing microbial dynamics driving increased acid yield from different concentrations of corn straw.

In this work, the corn straw (CS) with concentrations of 3%, 6%, and 9% (w/v) were pretreated by rumen fluid (RF) and then used for batched mesophilic biogas production. The results showed that after a 6-day pretreatment, volatile fatty acid (VFAs) production of 3.78, 8.27, and 10.4 g/L could be found in 3%, 6%, and 9%, respectively. When concerning with biogas production, the highest accumulative methane production of 149.1 mL CH4/g volatile solid was achieved by 6% pretreated CS, which was 22% and 45% higher than 3% and 9%, respectively. Also, it was 3.6 times higher than the same concentration of unpretreated CS. The results of the microbial community structure analysis revealed that the 6% CS pretreatment not only maintained a microbial community with the highest richness and diversity, but also exhibited the highest relative abundance of Firmicutes (45%) and Euryarchaeota (3.9%). This high abundance was conducive to its elevated production of VFAs and methane. These findings provide scientific reference for the utilization of CS and support the development of agricultural waste resource utilization and environmental protection.

FastCCLasso: a fast and efficient algorithm for estimating correlation matrix from compositional data.

The composition and structure of microbial communities on the body surface are closely related to human health. The interaction relationship among microbes can help us understand the formation of the microecological environment and the biological mechanism by which microorganisms influence host health. With the help of high-throughput sequencing technologies, microbial abundances in a natural environment can be directly measured without the isolation of microorganisms in culture. Sequencing experiments in microbiome studies can measure the relative abundance of microbes, which is called compositional data. Although there are already many methods for correlation analysis for compositional data, the computation time or accuracy still needs to be improved for current microbiome studies. We develop a fast and efficient algorithm, called fastCCLasso, based on a penalized weighted least squares for inferring the correlation structure of microbes from compositional data in microbiome studies. We perform a large number of numerical experiments and the simulation results show that fastCCLasso outperforms its competitors in edge detection for inferring the correlation network. We also apply fastCCLasso for estimating microbial networks in microbiome studies and fastCCLasso provides a conservative network with comparable false discovery counts that are derived from shuffled data. FastCCLasso is open source and freely available from https://github.com/ShenZhang-Statistics/fastCCLasso under GNU LGPL v3.

A Continuous Plug-Flow Anaerobic-Multistage Anoxic/Aerobic Process Treating Low-C/N Domestic Sewage: Nutrient Removal, Greenhouse Gas Emissions, and Microbial Community Analysis

The anaerobic-multistage anoxic/aerobic (A-MAO) process has shown good potential for advanced nitrogen removal in recent years, but its greenhouse gas emissions still need to be fully explored. The effects of the influent distribution and external carbon source sodium acetate on nutrient removal, greenhouse gas emissions, and the microbial community structure in a continuous plug-flow A-MAO reactor fed with real low C/N ratio domestic sewage were investigated. The results showed that altering the allocation of carbon source resulted in average chemical oxygen demand (COD) and total nitrogen (TN) concentration in effluent reduced to 26.10 ± 4.86 and 6.65 ± 1.73 mg/L, respectively. Both operations reduced the emission rate of greenhouse gas. While the addition of external car-bon sources leaded to lower N2O emission rates and higher CO2 and CH4 emission rates. The addition of sodium acetate facilitated nitrification and denitrification processes, thereby leading to a reduction in N2O production. Meanwhile, it spurred the growth of methanogenic bacteria and heterotrophic microorganisms, thus boosting the production of CO2 and CH4. Influent distribution promoted the increase of Bacteroidota, Chloroflexi and Acidobacteriota of the reactor. The enrichment of typical hydrolytic bacteria and glycogen accumulating organisms (GAOs) increased the utilization efficiency of carbon sources in the system after the addition of sodium acetate. The significant increase of typical denitrifying bacteria (DNBs) Azospira reduced the N2O emission during heterotrophic denitrification process, which was considered to be an important functional genus for increasing nitrogen loss in this system. The rational utilization of carbon source makes the difference in metabolism function. The study provides a valuable strategy for comprehensively evaluating the pollutant removal and greenhouse gas emission reduction from the A-MAO process.

Microbial community response to hydrocarbon exposure in iron oxide mats: an environmental study

Hydrocarbon pollution is a widespread issue in both groundwater and surface-water systems; however, research on remediation at the interface of these two systems is limited. This interface is the oxic–anoxic boundary, where hydrocarbon pollutant from contaminated groundwaters flows into surface waters and iron mats are formed by microaerophilic iron-oxidizing bacteria. Iron mats are highly chemically adsorptive and host a diverse community of microbes. To elucidate the effect of hydrocarbon exposure on iron mat geochemistry and microbial community structure and function, we sampled iron mats both upstream and downstream from a leaking underground storage tank. Hydrocarbon-exposed iron mats had significantly higher concentrations of oxidized iron and significantly lower dissolved organic carbon and total dissolved phosphate than unexposed iron mats. A strong negative correlation between dissolved phosphate and benzene was observed in the hydrocarbon-exposed iron mats and water samples. There were positive correlations between iron and other hydrocarbons with benzene in the hydrocarbon-exposed iron mats, which was unique from water samples. The hydrocarbon-exposed iron mats represented two types, flocculent and seep, which had significantly different concentrations of iron, hydrocarbons, and phosphate, indicating that iron mat is also an important context in studies of freshwater mats. Using constrained ordination, we found the best predictors for community structure to be dissolved oxygen, pH, and benzene. Alpha diversity and evenness were significantly lower in hydrocarbon-exposed iron mats than unexposed mats. Using 16S rDNA amplicon sequences, we found evidence of three putative nitrate-reducing iron-oxidizing taxa in microaerophile-dominated iron mats (Azospira, Paracoccus, and Thermomonas). 16S rDNA amplicons also indicated the presence of taxa that are associated with hydrocarbon degradation. Benzene remediation-associated genes were found using metagenomic analysis both in exposed and unexposed iron mats. Furthermore, the results indicated that season (summer vs. spring) exacerbates the negative effect of hydrocarbon exposure on community diversity and evenness and led to the increased abundance of numerous OTUs. This study represents the first of its kind to attempt to understand how contaminant exposure, specifically hydrocarbons, influences the geochemistry and microbial community of freshwater iron mats and further develops our understanding of hydrocarbon remediation at the land–water interface.

Dynamic interplay between soil microbial communities, enzyme activities, and pear quality across planting years

Few studies have been reported on the effect of planting years on fruit quality and soil of pear trees. In this study, four planting years (T5, T20, T30, and T40) of Cuiguan pears were used to analyze fruit quality, rhizosphere soil enzymes, and microbial diversity of pear trees, and their correlations. The results showed that the content of sucrose, reducing sugar and ascorbic acid in Cuiguan Pear showed a tendency of increasing and then decreasing with the increase of planting years, in which the highest content was found in 20- and 30-year-old fruits, and the highest content of total acid was found in 5-year-old fruits. Rhizosphere soil enzyme activities varied with planting year, with the highest protease activity in 20-year-old soil, phosphatase and urease in 30-year-old soil, polyphenol oxidase in 5-year-old soil, and sucrase in 40-year-old soil. The microbial diversity index and the number of OTUs showed an increasing and decreasing trend with the increase of planting years. Among the top 11 bacteria in pear rhizosphere soil average relative abundance, with Bradyrhizobium decreasing in relative abundance at the peak pear fruiting stages (T20 and T30), while Acidothermus showed an increasing trend in relative abundance with increasing planting years. RDA analysis showed that there were differences in the microbial community structure of pear trees at different planting years, and that both sucrose and reducing sugar contents in pears were positively correlated with T20 and T30, ascorbic acid content was positively correlated with T40, whereas the total acid content was positively correlated with T5, and that T20 was positively correlated with soil protease and phosphate mono esterase activities, and that T30 was positively correlated with polyphenol oxidase and urease activities, whereas T40 was positively correlated with sucrase activity. In summary, with the increase of planting years, changes in soil microbial community structure and soil enzyme activity have a significant impact on pear quality formation, and the results of the study provide a theoretical basis for scientific management of pear orchards.

Bacterial–fungal interactions and response to heavy metal contamination of soil in agricultural areas

IntroductionLong-term heavy metal contamination of soil affects the structure and function of microbial communities. The aim of our study was to investigate the effect of soil heavy metal contamination on microorganisms and the impact of different heavy metal pollution levels on the microbial interactions.MethodsWe collected soil samples and determined soil properties. Microbial diversity was analyzed in two groups of samples using high-throughput sequencing technology. Additionally, we constructed microbial networks to analyze microbial interactions.ResultsThe pollution load index (PLI) &amp;lt; 1 indicates that the area is not polluted. 1 &amp;lt; PLI &amp;lt; 2 represents moderate pollution. PLI was 1.05 and 0.14 for the heavy metal contaminated area and the uncontaminated area, respectively. Cd, Hg, Pb, Zn, and Cu were identified as the major contaminants in the contaminated area, with the contamination factors were 30.35, 11.26, 5.46, 5.19, and 2.46, respectively. The diversities and compositions of the bacterial community varied significantly between the two groups. Compared to the uncontaminated area, the co-occurrence network between bacterial and fungal species in the contaminated area was more complex. The keystone taxa of the co-occurrence network in the contaminated area were more than those in the uncontaminated area and were completely different from it.DiscussionHeavy metal concentrations played a crucial role in shaping the difference in microbial community compositions. Microorganisms adapt to long-term and moderate levels of heavy metal contamination through enhanced interactions. Bacteria resistant to heavy metal concentrations may play an important role in soils contaminated with moderate levels of heavy metals over long periods of time.

Metagenomic comparison of gut communities between wild and captive Himalayan griffons

IntroductionHimalayan griffons (Gyps himalayensis), known as the scavenger of nature, are large scavenging raptors widely distributed on the Qinghai-Tibetan Plateau and play an important role in maintaining the balance of the plateau ecosystem. The gut microbiome is essential for host health, helping to maintain homeostasis, improving digestive efficiency, and promoting the development of the immune system. Changes in environment and diet can affect the composition and function of gut microbiota, ultimately impacting the host health and adaptation. Captive rearing is considered to be a way to protect Himalayan griffons and increase their population size. However, the effects of captivity on the structure and function of the gut microbial communities of Himalayan griffons are poorly understood. Still, availability of sequenced metagenomes and functional information for most griffons gut microbes remains limited.MethodsIn this study, metagenome sequencing was used to analyze the composition and functional structures of the gut microbiota of Himalayan griffons under wild and captive conditions.ResultsOur results showed no significant differences in the alpha diversity between the two groups, but significant differences in beta diversity. Taxonomic classification revealed that the most abundant phyla in the gut of Himalayan griffons were Fusobacteriota, Proteobacteria, Firmicutes_A, Bacteroidota, Firmicutes, Actinobacteriota, and Campylobacterota. At the functional level, a series of Kyoto Encyclopedia of Genes and Genome (KEGG) functional pathways, carbohydrate-active enzymes (CAZymes) categories, virulence factor genes (VFGs), and pathogen-host interactions (PHI) were annotated and compared between the two groups. In addition, we recovered nearly 130 metagenome-assembled genomes (MAGs).DiscussionIn summary, the present study provided a first inventory of the microbial genes and metagenome-assembled genomes related to the Himalayan griffons, marking a crucial first step toward a wider investigation of the scavengers microbiomes with the ultimate goal to contribute to the conservation and management strategies for this near threatened bird.

Cultivars and Production Environments Shape Shoot Endophyte Profiles of Boxwood with Different Blight Resistance

Phyllosphere colonizers, including bacteria and fungi, are critical for plant growth and health. Yet, how they are affected simultaneously by host plant cultivar, local environment and agricultural practices was not well understood. We used boxwood, an iconic landscape plant and a major evergreen shrub crop in the U.S. nursery industry, as a model plant, and sequenced 16S rRNA and ITS amplicons to examine the assemblages of endophytic bacteria and fungi in the shoots of four cultivars representing three levels of boxwood blight resistance under two distinct climates and production systems in Oregon and Virginia. Cultivar and local environment were the two main drivers shaping the composition and structure of the boxwood endophytic microbial community, particularly the fungal community. Three bacterial and seven fungal genera were consistently identified with high prevalence and abundance as the core taxa from four cultivars and two locations across three sampling times. The microbial composition varied among the levels of boxwood blight resistance and taxa specific to the tolerant cultivar were fewer compared to the susceptible one. Identification of these microbial indicators, along with the core taxa, is foundational for developing a microbiome-based plant breeding program and a systems approach to improve boxwood health and production under a changing climate.

A New Strategy for the Treatment of Old Corrugated Container Pulping Wastewater by the Ozone-Catalyzed Polyurethane Sponge Biodegradation Process

Old Corrugated Container (OCC) pulping wastewater has a complex organic composition and high levels of biotoxicity. The presence of dissolved and colloidal substances (DCSs) is a major limiting factor for pulp and paper companies to achieve closed-water recycling. In order to solve this problem, the coupled ozone-catalyzed oxidation and biodegradation (OCB) method was used to treat OCC pulping wastewater in this study. A polyurethane sponge was used as the basic skeleton, loaded with nano TiO2 and microorganisms, respectively, and then put into a reactor. After an 8-min ozone-catalyzed oxidation reaction, a 10-h biological reaction was carried out. The process was effective in removing organic pollutants such as COD and BOD5 from OCC paper whitewater. The removal rates of COD and BOD5 were 81.5% and 85.1%, respectively. By using the polyurethane sponge to construct a microenvironment suitable for microbial growth and metabolism, this study successfully applied and optimized engineered bacteria—white rut fungi (WRF)—in the system to achieve practical degradation of OCC pulping wastewater. Meanwhile, the biocompatibility of different microbial communities on the polyurethane sponge was analyzed by examining the degradation performance of OCC pulping wastewater. The structure of microbial communities loaded on the polyurethane sponge was analyzed to understand the degradation mechanism and microbial reaction behavior. White-rot fungi (Phanerochaete) contributed more to the degradation of OCC wastewater, and new strains adapted to OCC wastewater degradation were generated.

Mechanisms of partial denitrification in an integrated fixed-film activated sludge (IFAS) system: From progressive startup to stabilization

The rapid startup and long-term stability of partial denitrification (PD) processes are essential prerequisites for successful PD/Anammox systems. Bioaggregates play a significant role in impacting mass transfer efficiency and shaping the microbial community structure within the PD process. Thus, the startup and stable operation of the PD process were investigated in an integrated fixed-film activated sludge (IFAS) by inoculating activated sludge and biofilm from anoxic tanks of a wastewater treatment plant. During the initial stage of startup, a sudden increase in NO3−-N concentration induced a rapid enzyme stress response, leading to a significant increase in total NaR activity (1.38 ± 0.0 μmol·(L·min)−1 to 25.94 ± 0.23 μmol·(L·min)−1), concomitant with the inhibition of total NiR activity (13.93 ± 0.48 μmol·(L·min)−1 to 4.25 ± 0.26 μmol·(L·min)−1), thereby inducing the rapid accumulation of NO2−-N (13.39 mg·L−1) within 6 days. During the later stage of startup, enzyme stress response was subsided but the partial denitrifiers were gradually enriched, consequently leading to continuous accumulation of NO2−-N. The results of ex-situ activity showed that flocs exhibit superior PD performance in contrast to biofilm throughout the entire operational period. Meanwhile, the total extracellular polymeric substances (EPS) content and community structure in both flocs and biofilm indicated that the migration of EPS-secreted partial denitrifiers (Thauera) from flocs to biofilm was obliged by substrate deficiency during the stable operating stage (days 35–100). Therefore, the startup of PD may be sequentially mediated by two distinct mechanisms, enzyme stress response and functional bacterial enrichment, with microbial community migration occurring during the stable phase.

From Residue to Resource: A Physicochemical and Microbiological Analysis of Soil Microbial Communities through Film Mulch-Enhanced Rice Straw Return Strategies

Promoting rice straw in situ return is an important strategy for improving soil quality. From 2018 to 2021, we investigated the effects of rice straw return with microbial agents and film covering technology on soil physical and chemical properties at different layer depths, as well as the soil microbial community structure, in Hunan, southern China. This study was designed to evaluate the effects of microbial agents (T1), film mulch covering (T2), and the application of microbial agents combined with film mulch (T3) on the soil physicochemical properties and microbial community after rice straw in situ return. The results show that, after three years of continuous treatment, T3 significantly increased the soil temperature by 17.76–22.97%, T2 significantly increased the water content by 34.27–46.23%, and T1 and T3 significantly increased the soil pH. The addition of microbial agents combined with film mulch resulted in a notable increase in both the number of OTUs and the Chao1 index of soil microorganisms. Additionally, the model of promoting rice straw in situ return (the application of a microbial agent combined with film mulch) was shown to promote the growth of beneficial soil microorganisms. RDA was used for the investigation, and the findings showed that soil microorganisms were significantly influenced by the TOC content, pH, and water content. These findings provide evidence of an effective method for accelerating the decomposition of late rice straw and guiding soil improvement in tobacco–rice rotation regions.

Microbiological Mechanisms of Collaborative Remediation of Cadmium-Contaminated Soil with Bacillus cereus and Lawn Plants

Severe cadmium contamination poses a serious threat to food security and human health. Plant–microbial combined remediation represents a potential technique for reducing heavy metals in soil. The main objective of this study is to explore the remediation mechanism of cadmium-contaminated soil using a combined approach of lawn plants and microbes. The target bacterium Bacillus cereus was selected from cadmium-contaminated soil in mining areas, and two lawn plants (Festuca arundinacea A‘rid III’ and Poa pratensis M‘idnight II’) were chosen as the target plants. We investigated the remediation effect of different concentrations of bacterial solution on cadmium-contaminated soil using two lawn plants through pot experiments, as well as the impact on the soil microbial community structure. The results demonstrate that Bacillus cereus promotes plant growth, and the combined action of lawn plants and Bacillus cereus improves soil quality, enhancing the bioavailability of cadmium in the soil. At a bacterial suspension concentration of 105 CFU/mL, the optimal remediation treatment was observed. The removal efficiency of cadmium in the soil under Festuca arundinacea and Poa pratensis treatments reached 33.69% and 33.33%, respectively. Additionally, the content of bioavailable cadmium in the rhizosphere soil increased by up to 13.43% and 26.54%, respectively. Bacillus cereus increased the bacterial diversity in the non-rhizosphere soil of both lawn plants but reduced it in the rhizosphere soil. Additionally, the relative abundance of Actinobacteriota and Firmicutes, which have potential for heavy metal remediation, increased after the application of the bacterial solution. This study demonstrates that Bacillus cereus can enhance the potential of lawn plants to remediate cadmium-contaminated soil and reshape the microbial communities in both rhizosphere and non-rhizosphere soils.

[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.

[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.

[Characteristics of Microorganisms and Antibiotic Resistance Genes of the Riparian Soil in the Lanzhou Section of the Yellow River].

Riparian soil is a critical area of watersheds. The characteristics of biological contaminants in riparian soil affect the pollution control of the watershed water environment. Thus, the microbial community structure, antibiotic resistance genes (ARGs), and mobile genetic elements (MGEs) in the riparian soil of the Lanzhou section of the Yellow River were investigated by analyzing the characteristics of soil samples collected from farmland, mountains, and industrial land. The results showed that the Proteobacteria, Bacteroidetes, and Actinobacteria were the dominant phyla in the riparian soil of Lanzhou section of the Yellow River. The microbial structure in the riparian soil was significantly correlated with the land use type (P &lt; 0.05). The α diversity index of bacterial communities in land types was in the order of farmland &gt; mountain &gt; industry. Sulfonamide-typed ARGs were the most dominant genes in the soil of the Lanzhou section of the Yellow River Basin, among which the sul1 gene had the highest abundance, 20-36 000 times that of other detected ARGs. Moreover, the total absolute abundance of ARGs in industrial soil was the highest. Principal coordinate analysis (PCoA) displayed that the ARGs characteristics had a significant correlation with land types (P &lt; 0.05), and intl1 and tnpA-04 drove the diffuseness of sulfonamide and tetracycline ARGs, respectively. Redundancy analysis (RDA) demonstrated that the content of inorganic salt ions and total phosphorus in the soil of the riparian zone of the Yellow River Lanzhou section were the main environmental factors, modifying the distribution of the microbial structure. Halobacterota and Acidobacteriota were the main microflora that drove the structural change in ARGs.