Grain size distribution drives microbial communities vertically assemble in nascent lake sediments

Sediment microbes are crucial for maintaining biogeochemical cycles in aquatic ecosystems, yet the influence of sediment geophysical structure on microbial communities remains unclear. In this study, we collected sediment cores from a nascent reservoir in its initial stage of deposition and utilized the multifractal model to comprehensively characterize the heterogeneity of sediment grain size and pore space. Our results demonstrate that both environmental physiochemistry and microbial community structures varied significantly with depth, with the grain size distribution (GSD) being the key driver of sediment microbial diversity, as revealed by the partial least squares path model (PLS-PM) method. GSD can potentially impact microbial communities and biomass by controlling pore space and organic matter. Overall, this study represents the first attempt to apply soil multifractal models into the integrated description of physical structure in sediment. Our findings provide valuable insights into the vertical distribution of microbial communities.

Effect of the lignocellulolytic Psychrotroph Lelliottia sp. on bacterial community succession in corn straw compost

This study aimed to explore the effect of an inoculation, Lelliottia sp., on the corn straw compost's physico-chemical properties, composition, and the succession of bacterial community structure. The compost community composition and succession changed after Lelliottia sp. inoculation. Inoculation increased the bacterial community diversity and abundance in the compost to promote composting. The inoculated group entered the thermophilic stage on the first day, lasting 8 days. Judging the pile maturity based on the carbon:nitrogen ratio and germination index values, the inoculated group reached the maturity standard, which was 6 days faster than the control group. The relationship between environmental factors and bacterial communities was comprehensively analyzed using redundancy analysis. Temperature and carbon:nitrogen ratio were the main environmental factors driving the succession of bacterial communities, to provide basic information on the changes of physicochemical indexes and bacterial community succession in Lelliottia sp. inoculated maize straw composting, providing assistance for practical composting applications of this strain.

Effects of Mn2+ and humic acid on microbial community structures, functional genes for nitrogen and phosphorus removal, and heavy metal resistance genes in wastewater treatment

Considering the wide occurrence of Mn²⁺ and humic acid (HA) in environmental media, the effects of Mn²⁺ (5-16 mg/L) and HA (10 mg/L) on microbial community structures, functional genes for nitrogen and phosphorus removal, and heavy metal resistance genes (HMRGs) were investigated in wastewater treatment using sequencing batch bioreactors (SBRs). The treatment efficiencies of influent chemical oxygen demands (COD), NH₄⁺-N, and PO₄^3--P were unaffected during the entire operational processes irrespective of whether Mn²⁺ and HA were supplied. Although the functional prediction of genetic information via sequencing analysis showed that the microbial activity was not influenced by Mn²⁺ and HA from different SBRs, the abundance of dominant phyla (Proteobacteria, Actinobacteriota, Firmicutes, and Bacteroidota), classes (Saccharimonadia, Gammaproteobacteria, and Bacilli), and genera (unidentified_Chloroplast, TM7a, Micropruina, Candidatus_Competibacter, Lactobacillus, OLB12, and Pediococcus) was different. Compared to the SBR without Mn²⁺ and HA supplementation, the abundance of functional genes for nitrogen and phosphorus removal (narG, nirS, nosZ, ppk, and phoD) and HMRGs (corA and mntA) significantly increased under Mn²⁺ stress, but significantly decreased with the addition of HA except for genes nirS and ppk. The abundance of genes corA and mntA was related to the partially dominant microbes and functional genes, and might be reduced by supplying HA. This study provides insight into the effects of Mn²⁺ and HA on functional genes for nitrogen and phosphorus removal and HMRGs in wastewater treatment.

Rice washing drainage (RWD) embedded in poly(vinyl alcohol)/sodium alginate as denitrification inoculum for high nitrate removal rate with low biodiversity

Immobilization technology with low maintenance is a promising alternative to enhance nitrate removal from water. In this study, washing rice drainage (RWD) was immobilized by poly(vinyl alcohol)/sodium alginate (PVA/SA) to obtain RWD-PVA/SA gel beads as inoculum for denitrification. When initial nitrate concentration was 50 mg N/L, nitrate was effectively removed at rates of 50-600 mg/(L∙d) using acetate as carbon source (C/N = 1.25). Arrhenius activation energy (Ea) of nitrate oxidoreductase was 28.64 kJ/mol for the RWD-PVA/SA gel beads. Temporal and spatial variation in microbial community structures were revealed along with RWD storage and in the reactors by Illumina high-throughput sequencing technology. RWD-PVA/SA gel beads has a simple (operational taxonomic units (OTUs) 〈100). Dechloromonas, Pseudomonas, Flavobacterium and Acidovorax were the most four dominant genera in the denitrification reactors inoculated with RWD-PVA/SA gel beads. This study provides an inoculum for denitrification with high nitrate removal performance and simple microbial community structures.

Effects of combined 4-chlorophenol and Cu2+ on functional genes for nitrogen and phosphorus removal and heavy metal resistance genes in sequencing batch bioreactors

The effects of combined 4-chlorophenol (4-CP) and Cu²⁺ on microbial community structures, functional genes for nitrogen and phosphorus removal, and heavy metal resistance genes (HMRGs) were explored in wastewater treatment using sequencing batch bioreactors (SBRs). Compared to influent 4-CP (2.3-4.5 mg/L), the removal of pollutants including chemical oxygen demands (COD), NH₄⁺-N, PO₄^3--P, and 4-CP was inhibited under Cu²⁺ stress (5 mg/L). The effects of Cu²⁺ on microbial community structures were more significant than those of 4-CP with respect to operational time, while the dominant function from gene information was not affected with or without influent 4-CP and Cu²⁺ via sequencing analysis. The influent 4-CP and Cu²⁺ largely influenced the dynamic changes of functional genes and HMRGs, and the abundance of partial HMRGs was correlated to the functional genes and dominant genera. This study provides insights into the treatment of combined chlorophenols and Cu²⁺ in wastewater.

Achieving stable nitrogen removal performance of mainstream PN-ANAMMOX by combining high-temperature shock for selective recovery of AOB activity

This paper describes the new concept of the mainstream partial nitritation (PN)-anaerobic ammonium oxidation (ANAMMOX) combined with a high-temperature shock strategy for the selective recovery of ammonia-oxidizing bacteria (AOB) activity. In the preliminary test, the temperature shock condition for PN was optimized (60 °C and > 20 min). Based on this, the implementation strategy in a continuous stirred tank reactor (CSTR) system was studied further, and the polyvinyl alcohol (PVA)/sodium alginate carrier exposure ratio (ER) and dissolved oxygen (DO) concentration were considered as primary variables. The AOB activity was recovered selectively when the ER of the carrier ranged from 20 to 40%, and the DO was higher than 2.3 mg O₂/L. This was not the case for nitrite-oxidizing bacteria (NOB) (AOB: 1.17±0.1 gNH₄⁺-N/L_Carrier/d, NOB: 0.34±0.1 gNO₃^--N/L_Carrier/d). As a result, the activity of AOB was recovered selectively with a decrease in Nitrospira spp., which was verified by kinetic and microbial analyses for the AOB (K_{S, DO} = 3.89 mgO₂/L) and NOB (K_{S, DO} = 1.14 mgO₂/L). Eventually, the mainstream PN-ANAMMOX was achieved with a nitrogen removal efficiency of 81.5±3.3% for 95 days. The findings provide insight to establishing a stable mainstream PN-ANAMMOX process using a high-temperature shock strategy.

Response of extracellular polymeric substances and microbial community structures on resistance genes expression in wastewater treatment containing copper oxide nanoparticles and humic acid

The extracellular polymeric substances (EPS) and microbial community structures were investigated in wastewater treatment containing copper oxide nanoparticles (CuO NPs) (reactor R1) and CuO NPs and humic acid (HA) (reactor R2) using both sequencing batch bioreactors (SBRs), and their response on resistance genes expression was analyzed. The removal of influent chemical oxygen demands (COD) and NH₄⁺-N was moderately influenced under CuO NPs (5 mg/L) stress, while the function of HA (10 mg/L) was not reflected. However, the EPS production and microbial community were affected by the HA addition. The expression of different antibiotic resistance genes (ARGs), metal-resistance genes (MRGs), and intI1 was related to the primary compositions of polysaccharides and proteins in EPS and different microbial communities at the genus level. Furthermore, the expression of resistance genes was not stimulated under CuO NPs stress, and supplying HA was suggested to reduce their expression in wastewater treatment.

Shifts in enzymatic activities and microbial community structures in the bioenhanced treatment of ship domestic sewage under microaerobic conditions

A bioenhancement strategy for improving the anaerobic degradation efficiency of ship domestic sewage under microaerobic conditions was proposed in this study. Strains Stenotrophomonas sp. MSPP05 and Prevotella sp. MSPP07 with high organic-degrading efficiency and extracellular hydrolase yield were used for the bioenhancement of activated sludge. In batch experiments, the removal rates of chemical oxygen demand and total nitrogen reached 94.5% and 66.9% after 72 h of degradation. The activities of dehydrogenase, extracellular amylase, and protease in the treatment group were 1.2, 1.4, and 2.0 times higher than those in the control group. Microbial community analysis showed that exogenous enhanced strains competed with original microorganisms and became dominant. One-stage continuous stirred tank reactor with bioenhanced activated sludge ran steadily for 90 days with average effluent COD and TN concentrations of 87.5 and 14.6 mg/L. The feasibility of improving organic-degrading efficiency through bioenhancement by using exogenous hydrolase-producing strains was confirmed under microaerobic conditions. This work provided a theoretical basis for improving treatment effects and developing a new technique for ship domestic sewage treatment.

Anaerobic biodegradation of four sulfanilamide antibiotics: Kinetics, pathways and microbiological studies

Large amounts of sulfanilamide antibiotics (SAs) have been excreted into the manure. In this study, the anaerobic biodegradation of four kinds of SAs including sulfaquinoxaline (SQX), sulfamethoxazole (SMX), sulfamethoxine (SMD) and sulfathiazole (STZ) was investigated. The degradation rates of SQX and STZ decreased with the increase of the concentrations of other organics, but those of SMX and SMD were less affected. The average degradation rates of SAs were in the order of SMX >SMD ≈QX >STZ, with the best degradation rate constants of 0.30125, 0.14752, 0.16696, and 0.06577 /d, respectively. STZ had the greatest effect on the population richness of microbes, whereas SQX had the largest impact on the population diversity. The degradation rates of SAs were positively correlated with the abundances of Proteobacteria and Bacteroidetes, and negatively correlated with the abundance of Firmicutes. The common degradation pathways of SAs were S-N cleavage and substitution. The specific functional groups of SQX, SMX and SMD, including quinoxaline, isoxazole and pyrimidine rings, could be opened, but the thiazole ring of STZ was difficult to be decomposed. After the rings of the specific functional groups were opened, they would be further substituted or decomposed to be products with small molecules.

Archaeal and bacterial community structures of rural household biogas digesters with different raw materials in Qinghai Plateau

The present study aims to investigate microbial community structures household biogas digesters with different raw materials in Qinghai Plateau rural. High-throughput 16S rRNA gene sequencing analysis revealed that Firmicutes, Bacteroidetes, and Proteobacteria are the most abundant bacterial phyla (64.08%). Prevotella group 7 was the most abundant genus in digester YL9 and YL10 (69.72% and 26.96%, respectively) using vegetable waste raw materials. Trichococcus exhibited the highest abundance (14.55%) in YL1 digester using sheep and pig manure. Clostridium sensu stricto 1 (13.89%) and Synergistaceae_uncultured (15.52%) comprised the highest abundances in digester YL5 with mixed raw materials (i.e., dairy manure, sheep manure, and human feces). In addition, Proteiniphilum and Pseudomonas exhibited the highest abundances among bacterial genera in YL4 digester using pig manure. Methanomicrobiales was the most dominant archaeal communities, ranging from 13.35% to 81.34% in abundance. Methanocorpusculum exhibited dominant abundances in all digesters using various raw materials. Methanogenium was the most abundant archaeal genera in YL4 and YL6 digesters, which consume pig manure as primary raw material. In addition, Methanosarcina and Methanosaeta exhibited the highest abundances in digester YL1 (55.03%) and YL9 (51.40%), respectively. Moreover, fermentation temperatures and pH both contributed to the archaeal and bacterial community structures in all the investigated digesters. Specially, fermentation temperature showed positive correlation with the abundances of Synergistaceae_uncultured, Methanogenium, and Methanosaeta, and pH was positively correlated with the abundances of Prevotella group 7 and Methanosarcina abundances.

Succession of the bacterial community structure and functional prediction in two composting systems viewed through metatranscriptomics

In this work, Illumina MiSeq sequencing of cDNA from metatranscriptomics RNA reverse transcription were employed in combination with phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) to estimate the dynamic variations of bacterial community structures and metabolic functions in a bioreactor and traditional composting process. Results showed that the change of bacterial α-diversity in the first three stages exhibit opposite trends in the two composting systems. The four most abundant phyla were the same in both systems (Firmicutes, Proteobacteria, Bacteroidetes and Actinobacteria), but the most abundant genera were different. The five most abundant genus-level groups in the bioreactor were Psychrobacter, Galbibacter, Pseudomonas, Staphylococcus and Flavobacterium. Within the same phase, the functional bacteria were dramatically different in the two composting processes. In the bioreactor system both bacterial community structure and metabolism function were greatly affected by available phosphorus.

Combined effects of maize straw biochar and oxalic acid on the dissipation of polycyclic aromatic hydrocarbons and microbial community structures in soil: A mechanistic study

Whether the rhizodegradation of organic contaminants occurs in biochar- amended soil and its potential mechanisms have rarely been reported. Therefore, a study was conducted to investigate the combined effects of root exudates and biochar on the dissipation of polycyclic aromatic hydrocarbons (PAHs) and on the microbial community structures in soil. As a major component of the root exudates of ryegrass, oxalic acid (OA) significantly enhanced the dissipation of high- and low-ring PAHs in the studied soil with or without maize straw biochar amendment (p < 0.05). However, biochar alone enhanced only the dissipation of high-ring PAHs. The activities of three enzymes (urease, polyphenol oxidase and dehydrogenase) were the highest in soil amended with both maize straw biochar and 0.5 mg kg^-1 of OA. Moreover, soil microbial biomass and the abundances of genera and genes associated with PAH degradation were significantly enhanced with the tandem application of biochar and OA (p < 0.05). These changes led to a synergetic effect of biochar and OA on the shifts in microbial community structures and on the dissipation of PAHs, especially for high-ring PAHs. The results in this study suggested that a combined biochar-rhizosphere approach should be a feasible remediation strategy for PAH-contaminated soil.

Succession of the functional microbial communities and the metabolic functions in maize straw composting process

Illumina MiSeq sequencing and phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) were applied to study the dynamic changes and effects of microbial community structures as well as the metabolic function of bacterial community in maize straw composting process. Results showed that humic acid contents in loosely combined humus (HA1) and stably combined humus (HA2) increased after composting and Staphylococcus, Cellulosimicrobium and Ochrobactrum possibly participated in the transformation of the process. The bacterial communities differed in different stages of the composting. Firmicutes, Proteobacteria, Bacteroidetes and Actinobacteria were reported the dominant phyla throughout the process and the relative abundance of the dominant phyla varied significantly (p < 0.05) over time. Moreover, the total phosphorus (TP) had the greatest influence on the microbial community structure among C/N ratio, available phosphorus (AP) and humic substances. Metabolism, cellular processes and environmental information processing might be the primary functions of microbial community during the composting.

Effect of hydraulic retention time on microbial community in biochemical passive reactors during treatment of acid mine drainage

The effect of hydraulic retention time (HRT) on the microbial community during acid mine drainage (AMD) treatment was investigated. Physicochemical and molecular (illumina and qPCR) analyses were performed on reactive mixtures collected from seven bioreactors in three-operation period (8, 17 and 36weeks). Long HRT (4day) favored the relative abundance of SRB, causing the increase of residual sulfides and short HRT (1day) affected the anaerobic conditions of the bioreactors and favored the presence the acidophilic chemolithotrophic microorganisms. Besides qPCR indicated that genes related to cellulose degradation were present in low copy numbers and were affected by the HRT. Finally, environmental factors (pH, organic source, metal sulfides, and sulfate concentrations) had significant impact on relative abundance of the phylogenetic lineages, rather than the types of lineages present in the reactive mixture. The findings of this study indicate that HRT affects the stability of passive bioreactors and their microbial communities.

Anaerobic ammonium oxidation-denitrification synergistic interaction of mature landfill leachate in aged refuse bioreactor: Variations and effects of microbial community structures

In this work, anammox-denitrification process was verified by ¹⁵N stable isotopic tracing methods and variations and effects of microbial community structures were studied using Illumina MiSeq sequencing and Quantitative Polymerase Chain Reaction (qPCR). The results showed that higher nitrogen removal efficiency and richer microbial consortia was observed at hydraulic loading rate (HLR) of 15L/m³·d, BOD₅/TN ratio of 0.4:1, respectively. Proteobacteria, Chloroflexi, Acidobacteria and Firmicutes were the dominant phyla in the anamox-denitrification biomass. The number of amx gene changed significantly during the HLR downshift and BOD₅/TN ratio upshift period. The obtained results enhance understanding regarding the microbial community structures of anammox-denitrification bacteria in aged refuse, leading to a more effective controlling of anammox-denitrification process.

Performance and microbial community structures of hydrolysis acidification process treating azo and anthraquinone dyes in different stages

In this study, performance of hydrolysis acidification process treating simulated dyeing wastewater containing azo and anthraquinone dyes in different stages was investigated. The decolorization ratio, COD_Cr removal ratio, BOD₅/COD_Cr value, and volatile fatty acids (VFAs) production were almost better in stage 1 than that in stage 2. Fourier transform infrared spectroscopy (FTIR) and gas chromatography-mass spectrometry (GC-MS) confirmed the biodegradation of Reactive Black 5 (RB5) and Remazol Brilliant Blue R (RBBR) in hydrolysis acidification process. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analyses revealed that significant difference of microbial community structures existed in stage 1 and 2. The dominant species in stage 1 was related to Bacteroidetes group, while the dominant species in stage 2 was related to Bacteroidetes and Firmicutes groups. From the results, it could be speculated that different dyes' structures might have significant influence on the existence and function of different bacterial species, which might supply information for bacteria screening and acclimation in the treatment of actual dyeing wastewater.

Microbial structures and community functions of anaerobic sludge in six full-scale wastewater treatment plants as revealed by 454 high-throughput pyrosequencing

The microbial communities and abundance in anaerobic sludge from 4 industrial and 2 municipal wastewater treatment plants were investigated using 454 pyrosequencing technology in this study. A total of 5482-8692 high-quality reads of 16S rRNA V3-V5 regions were obtained. Taxonomic analysis using QIIME and RDP classifier found that Proteobacteria, Bacteroidetes, Chloroflexi and Firmicutes were the most abundant phyla in these samples. Furthermore, real-time PCR was used to validate the absolute abundance of these 16S rRNAs and some functional genes, including total bacteria, anammox bacteria, NOB (Nitrobacter, Nitrospira), AOA amoA, AOB amoA, nosZ, nirS, nirK, narG, napA, nrfA, mcrA and dsrA. Multivariate linear regression analysis indicated that AOA might be mixotrophic. Finally, redundancy analysis was used to reveal the relationships between operation parameters and microbial communities. Results showed that the coexistence of anammox, denitrification and DNRA could be useful for the simultaneous removal of nitrogen and organic matter.