Carcass decay deteriorates water quality and modifies the nirS denitrifying communities in different degradation stages

Environmental impacts of organic residues from livestock management on soil and groundwater

Leaching nitrogenous compounds and total organic carbon (TOC) from livestock waste can contribute to long-term soil and groundwater quality degradation, particularly under rainfall-driven infiltration. This study investigates the behavior of these contaminants using a combination of laboratory-scale leaching, adsorption, and desorption experiments alongside pilot-scale field monitoring. Results indicate that organic residues derived from livestock waste processing release high concentrations of ammonium (NH₄+-N) and TOC even after extended rainfall exposure (up to 1600 mm). Subsequent desorption phases show nitrate (NO₃--N) emerging as the dominant leached species over time, suggesting microbial transformation and increased subsurface mobility. Field observations confirm these trends, with gradual accumulation of NO₃--N and TOC observed in groundwater near storage areas. This study addresses a significant knowledge gap regarding the long-term dynamics of contaminants originating from livestock waste. The findings underscore the importance of effective containment, consistent monitoring, and appropriate site management strategies to reduce potential impacts on water resources.

Determination of putrefactive amine and ammonia concentrations around decomposed corpses

The surface of a rotting corpse is covered with liquid decomposition products that have flowed out of the body that include putrefactive amines produced via putrefaction and decarboxylation reactions of proteins. Ammonia generated by deamination is also present around the corpse as a liquid or gas. As these putrefactive substances are toxic to humans, we attempted to measure the concentration of putrefactive substances in decomposed corpses in this study. Liquid putrefaction products were collected from the surface of a corpse, and the concentrations of putrefactive amines such as histamine, tyramine, phenethylamine, and tryptamine were analyzed by LC-MS/MS. Ammonia in the liquid and air around the corpse was also measured. Putrefactive amines and ammonia were present on all corpse surfaces. The highest concentrations and postmortem days in parentheses were as follows: histamine 2.26 mg/g (15 days), tyramine 1.77 mg/g (16 days), phenethylamine 4.90 mg/g (24 days), tryptamine 1.58 mg/g (17 days) and ammonia 25.6 mg/g (24 days postmortem). The highest concentration of ammonia in the air was 1310 ppm at 24 days postmortem. The ammonia level in the air around a corpse is toxic to humans. Inhalation of putrefactive amines and ammonia can cause chemical irritation to the respiratory tract and the skin and damage the mucous membrane of the eye. Oral ingestion can also cause poisoning symptoms such as blood pressure changes and headaches. Adequate protection against putrefactive substances is required when in contact with decaying corpses.

Temporal dynamics of the diazotrophic community during corpse decomposition

Corpse decomposition affects soil organisms through the formation of "cadaver decomposition islands." Soil diazotrophic microbes possess essential ecological functions on nitrogen input and nutrient cycling in the terrestrial ecosystem. However, our knowledge about how soil diazotrophic communities respond to corpse decomposition is lacking. In this study, we focused on the succession patterns and biological interaction of nitrogen-fixing microorganisms during animal (Ochotona curzoniae) corpse decomposition in terrestrial ecosystems by targeting nifH gene with high-throughput sequencing. Our results revealed that corpse decomposition of pikas reduced the α diversity and significantly impacted the β diversity of diazotrophic community across different decomposition stages. The divergent succession of diazotrophic community occurred under corpse pressure. Furthermore, the relative importance of stochasticity to the community assembly was improved by corpse decomposition, while the importance decreased over decomposition time. Cadaver decay also simplified the diazotrophic networks and weakened the biological interactions among diazotrophic populations. Notably, NH4-N was the most important factor affecting diazotrophic community, followed by time and total carbon. This work emphasized that corpse decomposition perhaps influences the process of biological nitrogen fixation by altering soil diazotrophic communities, which is of great significance for understanding the terrestrial ecosystems' nitrogen cycle functions. KEY POINTS: • Corpse decomposition reduced the α diversity of diazotrophic community. • Corpse decomposition improved the stochasticity of diazotrophic community assembly. • Corpse decomposition weakened the interactions among diazotrophic populations.

Cadaverine and putrescine exposure influence carbon and nitrogen cycling genes in water and sediment of the Yellow River

The response patterns of microbial functional genes involved in biogeochemical cycles to cadaver decay is a central topic of recent environmental sciences. However, the response mechanisms and pathways of the functional genes associated with the carbon (C) and nitrogen (N) cycling to cadaveric substances such as cadaverine and putrescine remain unclear. This study explored the variation of functional genes associated with C fixation, C degradation and N cycling and their influencing factors under cadaverine, putrescine and mixed treatments. Our results showed only putrescine significantly increased the alpha diversity of C fixation genes, while reducing the alpha diversity of N cycling genes in sediment. For the C cycling, the mixed treatment significantly decreased the total abundance of reductive acetyl-CoA pathway genes (i.e., acsB and acsE) and lig gene linked to lignin degradation in water, while only significantly increasing the hydroxypropionate-hydroxybutylate cycle (i.e., accA) gene abundance in sediment. For the N cycling, mixed treatment significantly decreased the abundance of the nitrification (i.e., amoB), denitrification (i.e., nirS3) genes in water and the assimilation pathway gene (i.e., gdhA) in sediment. Environmental factors (i.e., total carbon and total nitrogen) were all negatively associated with the genes of C and N cycling. Therefore, cadaverine and putrescine exposure may inhibit the pathway in C fixation and N cycling, while promoting C degradation. These findings can offer some new insight for the management of amine pollution caused by animal cadavers.

Effect of ferrous ions combined with zeolite on humification degree during food waste composting

The research aims to clarify role of ferrous sulfate (FeSO4) combined with zeolite (Z) on humification degree based on investigation of concentration and structural stability of humic acid (HA) during food waste composting. Four treatments were set up, namely CK (control), Fe (5 %), Z (5 %) and Fe + Z (2.5 %+2.5 %). Results demonstrated that concentration and polymerization degree of HA were 53.4 % and 97.3 % higher in composting amended with Fe + Z than in the control, respectively. Meanwhile, formation of aromatic functional groups and recalcitrant fluorescent components (HAC3) was significantly promoted, indicating that Fe + Z treatment enhanced HA structure stability. The bacterial networks became tighter, and the proportion of core bacteria in dominant modules increased at Fe + Z treatment. Additionally, key factors affecting HAC3 and product quality were identified by structural equation models, which verified potential mechanism of humification enhancement. Overall, this study provided theoretical support for improving humification degree and product quality.

Homogeneous environmental selection mainly determines the denitrifying bacterial community in intensive aquaculture water

Nitrate reduction by napA (encodes periplasmic nitrate reductase) bacteria and nitrous oxide reduction by nosZ (encodes nitrous oxide reductase) bacteria play important roles in nitrogen cycling and removal in intensive aquaculture systems. This study investigated the diversity, dynamics, drivers, and assembly mechanisms of total bacteria as well as napA and nosZ denitrifiers in intensive shrimp aquaculture ponds over a 100-day period. Alpha diversity of the total bacterial community increased significantly over time. In contrast, the alpha diversity of napA and nosZ bacteria remained relatively stable throughout the aquaculture process. The community structure changed markedly across all groups over the culture period. Total nitrogen, phosphate, total phosphorus, and silicate were identified as significant drivers of the denitrifying bacterial communities. Network analysis revealed complex co-occurrence patterns between total, napA, and nosZ bacteria which fluctuated over time. A null model approach showed that, unlike the total community dominated by stochastic factors, napA and nosZ bacteria were primarily governed by deterministic processes. The level of determinism increased with nutrient loading, suggesting the denitrifying community can be manipulated by bioaugmentation. The dominant genus Ruegeria may be a promising candidate for introducing targeted denitrifiers into aquaculture systems to improve nitrogen removal. Overall, this study provides important ecological insights into aerobic and nitrous oxide-reducing denitrifiers in intensive aquaculture, supporting strategies to optimize microbial community structure and function.

Metabolomic profiles reveals the dose-dependent effects of rice grain yield and nutritional quality upon exposure zero-valent iron nanoparticles

Zero-valent iron nanoparticles (nZVI) were widely used material in environmental remediation, which has attracted increasing concern for their safety. Previous studies have shown that the addition of nZVI could inhibit rice seedling growth. However, the effect of nZVI on the soil-rice system during the entire life cycle was not reported. Furthermore, the effect of nZVI on the quality of rice grain has also not been studied. Therefore, we investigated the effects of rice grain yield and nutritional quality upon exposure nZVI. The results showed that the soil pH value, redox potential and Fe (II) content in the nZVI-treated group were decreased in a dose-dependent manner. Interestingly, 2500 mg/kg nZVI significantly decreased the relative abundance of several functional microbial communities (10.52-73.53 %) associated with carbon and nitrogen cycles in response to plants compared to the control. Meanwhile, the nZVI treatment clearly reduced grain yield (8.71-18.21 %). Furthermore, the content of protein (51.72-57.79 %) and several essential nutrients (Zn, Cu, Mn and Mo) in the nZVI-treated grains was also decreased in a dose-dependent manner. The results of grain metabolomics indicated that nZVI could interfere with the relative expression of lysine and glutathione by regulating the metabolic pathways of antioxidant and protein synthesis in rice.

Mammalian carcass decay increases carbon storage and temporal turnover of carbon-fixing microbes in alpine meadow soil

Corpse decomposition is of great significance to the carbon cycle of natural ecosystem. Carbon fixation is a carbon conversion process that converts carbon dioxide into organic carbon, which greatly contributes to carbon emission reduction. However, the effects of wild animal carcass decay on carbon-fixing microbes in grassland soil environment are still unknown. In this research, thirty wild mammal (Ochotona curzoniae) corpses were placed on alpine meadow soil to study the carbon storage and carbon-fixing microbiota succession for a 94-day decomposition using next-generation sequencing. Our results revealed that 1) the concentration of total carbon increased approximately 2.24-11.22% in the corpse group. 2) Several carbon-fixing bacterial species (Calothrix parietina, Ancylobacter rudongensis, Rhodopseudomonas palustris) may predict the concentration of total carbon. 3) Animal cadaver degradation caused the differentiation of carbon-fixing microbiota structures during succession and made the medium-stage networks of carbon-fixing microbes more complicated. 4) The temporal turnover rate in the experimental groups was higher than that in the control groups, indicating a quick change of gravesoil carbon-fixing microbiota. 5) The deterministic process dominates the assembly mechanism of experimental groups (ranging from 53.42% to 94.94%), which reflects that the carbon-fixing microbial community in gravesoil can be regulated. Under global climate change, this study provides a new perspective for understanding the effects of wild animal carcass decay on soil carbon storage and carbon-fixing microbes.

Metagenomics reveals elevated temperature causes nitrogen accumulation mainly by inhibiting nitrate reduction process in polluted water

Determining the response of functional genes and microbiota involved in the nitrogen (N) cycle to warming in the face of global climate change is a hotpot topic. However, whether and how elevated temperature affects the N-cycle genes in polluted water remains unclear. Based on metagenomics, we investigated the responses of the whole N-cycling genes and their microbial communities to the temperature gradients (23, 26, 29, 32, and 35 °C) using animal cadavers as an N-pollution model. We found that the abundance of gene families involved in glutamate metabolism, assimilatory nitrate reduction to nitrite (ANRN), and denitrification pathways decreased with temperature. Moreover, warming reduced the diversity of N-cycling microbial communities. Ecological network analysis indicated that elevated temperature intensified the mutual competition of N-cycle genes. The partial least squares path model (PLS-PM) showed that warming directly suppressed most N-cycle pathways, especially glutamate metabolism, denitrification, and ANRN pathways. Corpse decay also indirectly inhibited N-cycling via regulating N content and microbial communities. Our results highlight warming leads to N accumulation by inhibiting the ANRN and denitrification pathways, which may jeopardize ecological environment security. Our study is expected to provide valuable insights into the complex N-cycle process and N-pollution in warmer aquatic ecosystems.

Metagenomics reveals that temperature predicts a small proportion of antibiotic resistomes and mobile genetic elements in polluted water

Climate warming multiplies the threat of antibiotic resistance genes (ARGs) to public health, but whether temperature may predict antibiotic resistomes in water environment remain unknown. Here, by metagenomic sequencing, we investigated the changes of resistome at five different temperature gradients (23, 26, 29, 32, and 35 °C) in polluted water by animal cadaver. Thirty ARG types including 668 subtypes were observed in our samples. Temperature significantly influenced ARG profiles and showed a negative correlation with ARG diversity. The ARG assembly process was dominated by a deterministic process (63.32%-95.08%) but showed a peak pattern with temperature. Notably, temperature may predict approximately 21% of ARGs and 36% of mobile genetic elements (MGEs), while most other ARGs or MGEs were insensitive to temperature. Three types (carbapenem, dicyclomycin, and diaminopyrimidine antibiotic) and 63 subtypes of ARGs that positively correlated with temperature were identified in the polluted water. Notably, we screened 21 subtypes of high-risk ARGs (bacA, mdtA, tetM, etc.) and 22 opportunistic pathogens (Aeromonas, Clostridium, Bacteroides, etc.) and found their positive co-occurrence with temperature, implying these potential biological or genetic pollutants may probably go up under global warming. Our study reveals the predictability of temperature on antibiotic resistance genes, providing a suitable approach to track the fate and spread of ARGs in water environment under climate warming.

Heavy rainfall accelerates the temporal turnover but decreases the deterministic processes of buried gravesoil bacterial communities

The influences of global climatic change require an understanding of changes in soil microbial communities under precipitation. However, little is known about how soil ("gravesoil") microbial communities associated with corpse decay respond to precipitation. Here, we explored the variations of temporal turnover and assembly in gravesoil bacterial communities in the Qinghai-Tibet Plateau ecosystem via controlled rainfall simulation experiments. In our experiments, rainfall intensity was set to 2.5 and 5 mm/3 days to simulate moderate and heavy rainfall, respectively, and sampling was conducted on the 4th, 11th, 18th, 32nd, 46th and 60th day. Our results showed precipitation significantly altered bacterial abundances and community structures. Analysis of time-decay relationships revealed that precipitation resulted in a divergent succession of gravesoil bacterial community structure and abundance changes of dominant phyla, such as Chloroflexi. Moreover, in the experimental groups, our results suggested that moderate rainfall increased the deterministic processes in the initial and mid periods, whereas heavy rainfall decreased these processes of gravesoil microbial community assembly in every period compared with those in the control group. The dispersal capacity induced by stochastic processes of gravesoil microbial communities decreased over time under moderate rainfall, whereas it initially increased and then decreased under heavy rainfall. This study highlights the influence of heavy rainfall on bacterial communities during corpse decay, which can provide some inferences for predicting changes in soil microbial communities under global climatic change.

Corpse decay of wild animals leads to the divergent succession of nrfA-type microbial communities

Animal carcasses introduce large amounts of nitrates and ammonium into the soil ecosystem. Some of this ammonium is transformed from nitrite through the nrfA-type microbial community. However, it is unclear how nrfA-type microorganisms respond to the decomposition of corpses. This study applied high-throughput sequencing to characterize the ecological succession of nrfA-type microbial communities in grassland soil. Our results showed that Cyclobacterium and Trueperella were the predominant genera for nrfA-type communities in soil with a decomposing corpse (experimental group), while Cyclobacterium and Archangium were dominant in soil without a corpse (control group). The alpha diversity indexes and the resistance and resilience indexes of the microbial communities initially increased and then decreased during decomposition. Compared with the control group, nrfA-encoding community structure in the experimental group gradually became divergent with succession and temporal turnover accelerated. Network analysis revealed that the microbial communities of the experimental group had more complex interactions than those of the control groups. Moreover, the bacterial community assembly in the experimental group was governed by stochastic processes, and the communities of the experimental group had a weaker dispersal capacity than those of the control group. Our results reveal the succession patterns of the nrfA-type microbial communities during degradation of wild animal corpses, which can offer references for demonstrating the ecological mechanism underlying the changes in the nrfA-type microbial community during carcass decay. KEY POINTS: • Corpse decay accelerates the temporal turnover of the nrfA-type community in soil. • Corpse decay changes the ecological succession of the nrfA-type community in soil. • Corpse decay leads to a complex co-occurrence pattern of the nrfA-type community in soil.

A review on nirS-type and nirK-type denitrifiers via a scientometric approach coupled with case studies

The denitrification process plays an important role in improving water quality and is a source/sink of nitrous oxide to the atmosphere. The second important rate-limiting step of the denitrification process is catalyzed by two enzymes with different structures and unrelated evolutionary relationships, namely, the Cu-type nitrite reductase encoded by the nirK gene and the cytochrome cd1-type nitrite reductase encoded by the nirS gene. Although some relevant reviews have been published on denitrifiers, most of these reviews do not include statistical analysis, and do not compare the nirS and nirK communities in-depth. However, a systematic study of the nirS-type and nirK-type denitrifying communities and their response to environmental factors in different ecosystems is needed. In this review, a scientometric approach combined with case studies was used to study the nirS-type and nirK-type denitrifiers. The scientometric approach demonstrated that Pseudomonas, Paracoccus, and Thauera are the most frequently mentioned nirS-type denitrifiers, while Pseudomonas and Bradyrhizobium are the top two most frequently mentioned nirK-type denitrifiers. Among various environmental factors, the concentrations of nitrite, nitrate and carbon sources were widely reported factors that can influence the abundance and structure of nirS-type and nirK-type denitrifying communities. Case studies indicated that Bradyrhizobium was the major genus detected by high-throughput sequencing in both nirS and nirK-type denitrifiers in soil systems. nirS-type denitrifiers are more sensitive to the soil type, soil moisture, pH, and rhizosphere effect than nirK. To clarify the relationships between denitrifying communities and environmental factors, the DNA stable isotope probe combined with metagenomic sequencing is needed for new denitrifier detections.

Heavy metals and microbiome are negligible drivers than mobile genetic elements in determining particle-attached and free-living resistomes in the Yellow River

Suspended particles in water can shelter both microorganisms and contaminants. However, the emerging pollutants antibiotic resistance genes (ARGs) in free-living (FL) or particle-attached (PA) bacteria in aquatic environments are less explored. In this study, we compared the free-living and particle-attached ARGs during four seasons in the Yellow River using high-throughput quantitative PCR techniques and 16S rRNA gene sequencing. Our results demonstrated that both the free-living water and particles were dominated by tetracycline and beta-lactamase resistance genes. The PA-ARGs had a higher absolute abundance than FL-ARGs in the Yellow River, regardless of the season. Both PA-ARGs and FL-ARGs had the highest absolute abundance and diversity during winter. Mobile genetic elements (MGEs) were the dominant driver for both size-fractionated ARGs. However, the microbiome had less influence on PA-ARG profiles than the FL-ARG profiles, while the effects of the heavy metals on ARGs were negligible. The community assembly of both FL-ARG and PA-ARG can be explained by neutral processes. Several opportunistic pathogens (e.g., Escherichia coli) associated with human health exhibited a higher relative abundance in the particles than during a free-living lifestyle. Parts of these pathogens were potential ARG hosts. As such, it is important to monitor the ARGs and opportunistic pathogens from size-fractionated bacteria and develop targeted strategies to manage ARG dissemination and opportunistic pathogens to ensure public health.

Microbial explanation to performance stratification along up-flow solid-phase denitrification column packed with polycaprolactone

In this study, the fluctuating profiles of physicochemical and microbial characterizations along different filling heights of continuously up-flow solid-phase denitrification (SPD) columns packed with polycaprolactone (PCL) were investigated. It was found both the PCL filling area and non-filling area made significant contributions to treatment performance and denitrification mainly occurred near the bottom of the filling column. Nitrate displayed a high proportional removal (≥98.7%) among all the cases except the one with the lowest filling ratio (FR30) and highest NLR (3.99 ± 0.12 gN/(L·d)), while nitrite and ammonium displayed a weak accumulation in final effluents (nitrite ≤ 0.40 mg/L; ammonium ≤ 0.98 mg/L). The intensity of PCL hydrolysis in the top substrate was stronger than those in the middle or bottom. Both dissimilatory nitrate reduction to ammonium (DNRA) and microbial lysis contributed to ammonium accumulation, and nitrate was mainly removed via traditional denitrification and DNRA. JGI_0000069-P22_unclassified and Gracilibacteria_unclassified might contribute to denitrification.