Changes In Microbial Communities Research Articles

Remote sensing ecological index (RSEI) affects microbial community diversity in ecosystems of different qualities

Soil microorganisms are key to ecological environment stability, but climate change and human activities exacerbate ecological environment changes. Therefore, assessment of ecological environment quality impacts on microbial diversity is needed. The Tarim River is the largest inland river in China and plays a crucial role in supporting regional biodiversity, maintaining ecological balance, and preventing desertification. In this study, we used the Remote Sensing-based Ecological Index (RSEI) to assess the ecological quality of habitats in the Tarim River Basin and explore the effects of habitat quality (extreme, semi-extreme, and general) on the structural diversity of microbial (bacterial and fungal) communities, biogeographic patterns, co-occurrence networks, and community assembly processes. Study results show that soil physicochemical characteristics varied significantly with habitat quality; highly resilient microorganisms are more abundant in habitats with low ecological quality. RSEI affects changes in microbial communities, and the positive correlation ratio of the network is inversely proportional to RSEI. The interspecific relationships of microbial communities in the Tarim River Basin are dominated by positive correlations, and community assembly is strongly influenced by stochastic processes. RSEI directly affects soil microbial diversity, with its contribution to both bacterial and fungal diversity being 0.27. Total nitrogen (TN) also directly affects microbial diversity, with effects of 0.11 on bacteria and 0.07 on fungi, respectively. This study provides scientific evidence and technical support for understanding microbial diversity in environments and for the development of regional sustainable development policies.

Field study on the dynamics of microbial communities following biostimulation at organochlorine-contaminated sites

Chlorinated ethenes (CEs) have become widespread contaminants in soils, sediments, and groundwater due to extensive historical use, improper handling, and disposal. At many sites, biostimulation is an effective remediation strategy for treating CEs, involving the addition of electron donors to support bacteria capable of degrading these compounds. This study aimed to understand how microbial communities adapt to environmental changes induced by biostimulation interventions. We investigated changes in microbial communities on biomass carriers transferred from a non-biostimulated, CE-contaminated environment to a previously biostimulated environment at two sites. In the non-biostimulated wells, a predominance of bacteria with nitrate-reducing or iron-reducing metabolisms was evident. Some of which are known to aerobically degrade CEs or other organic pollutants. Following the transfer of the carriers, these bacteria were outcompeted by anaerobic microorganisms with respiratory and fermentative metabolisms. The newly formed microbial community on the transferred biomass carriers exhibited greater diversity and higher abundance of organohalide-respiring bacteria. This rapid adaptability indicates the potential for these bacteria to flourish in favorable conditions, particularly at Site 2, where five days after carrier transfer, Dehalococcoides abundance increased 14,200-fold, and the biomarker vcrA increased 28,500-fold. PCoA revealed that that greater differences in hydrogeochemical conditions between biostimulated and non-biostimulated wells resulted in accelerated changes in bacterial community composition and diversity. In conclusion, our study demonstrates a rapid proliferation of CE-degrading bacteria after the transfer of biomass carriers into biostimulated wells at two different sites. The transfer stimulated shifts toward organohalide-respiring and other anaerobic bacteria in biostimulated environment and increased microbial diversity.

Nanoplastics indirectly compromise lettuce growth in hydroponic systems via microbial extracellular vesicles derived from Curvibacter fontanus

Recent studies confirm that nanoplastics (NP) cause severe microbial imbalances in various ecosystems, significantly affecting microbial diversity and abundance. Hydroponic systems vital for lettuce production are increasingly threatened by NP contamination in irrigation water and this issue is gaining global attention. This study investigates microbial species in hydroponic irrigation water altered by NP exposure and their impact on lettuce growth. While NP (108-1010 particles/L) did not directly harm or accumulate in lettuce, significant changes in water parameters and microbial communities were observed, particularly an increase in Curvibacter fontanus abundance. Inoculation of sterile irrigation water with NP and C. fontanus led to lettuce mortality, suggesting C. fontanus as a critical mediator. Furthermore, extracellular vesicles (EVs) isolated from C. fontanus, treated with NP, were shown to suppress leaf development, growth, antioxidant defenses, and lettuce survival. This study concludes that NP-induced microbial shifts, particularly involving C. fontanus EVs, indirectly harm hydroponic lettuce production.

Dynamics and biodiversity of microbial community among seasons in Shanxi mature vinegar fermentation by semisolid-solid process.

Understanding the changes in microbial communities across different seasons is crucial for ensuring the quality of Shanxi mature vinegar (SMV) by the semisolid-solid process. In a complete seasonal cycle, the richness and diversity of fungi were higher than those of bacteria. The microbial community in summer fermentation was significantly different compared to the other three seasons. For example, the dominant microorganisms such as Acetobacter and Lactobacillus decreased in summer. Screening or modifying this group of bacteria to enhance their tolerance to high fermentation temperature is an approach to improve industrial SMV fermentation. Through co-occurrence network analysis, eight highly connected genera were identified, which may play important roles in ecosystem stability. These results also lay a theoretical foundation for the further development of multi-microbial co-fermentation. This work provides an understanding of SMV fermentation from a seasonal perspective and offers new guidance for the process control of grain vinegar brewing.

Aggregate Size Mediated the Changes in Soil Microbial Communities After the Afforestation of a Former Dryland in Northwestern China

Although the afforestation of former arable lands is a common global land-use conversion, its impact on soil microbial communities at the aggregate scale has not been adequately addressed. In this study, soil samples were categorized into large macroaggregates (LM, >2 mm), small macroaggregates (SM, 2–0.25 mm), and microaggregates (MI, <0.25 mm) to assess the changes in microbial composition, diversity, network complexity, and network stability within soil aggregates after the afforestation of a former dryland in northwestern China. The results revealed that afforestation enhanced the relative abundance of Actinobacteriota, Chloroflexi, Ascomycota, and Mortierellomycota within the soil aggregates, suggesting that these phyla may have greater advantages in microbial communities post-afforestation. The Shannon–Wiener and Pielou indices for bacterial communities showed no significant differences between land-use types across all aggregate fractions. However, the alpha diversity of fungal communities within the LM and SM significantly increased after afforestation. Bray–Curtis dissimilarity indices showed that afforestation altered bacterial beta diversity within the LM and MI but had a minimal impact on fungal beta diversity across all three aggregate fractions. The topological features of cross-kingdom microbial co-occurrence networks within the soil aggregates generally exhibited a decreasing trend post-afforestation, indicating a simplification of microbial community structure. The reduced robustness of microbial networks within the LM and SM fractions implies that afforestation also destabilized the structure of microbial communities within the macroaggregates. The composition of the soil microbial communities correlated closely with soil carbon and nitrogen contents, especially within the two macroaggregate fractions. The linkages suggests that improved resource conditions could be a key driver behind the shifts in microbial communities within soil aggregates following afforestation. Our findings indicate that the impact of afforestation on soil microbial ecology can be better understood by soil aggregate fractionation.

Atractylodes macrocephala Root Rot Affects Microbial Communities in Various Root-Associated Niches

Atractylodes macrocephala, a perennial herb widely used in traditional Chinese medicine, is highly prone to root rot, which significantly reduces its yield and quality. This study compared the physicochemical properties of soil from healthy and diseased A. macrocephala plants and analyzed the microbial diversity in the endophytic, rhizosphere, and root zone soils. The results showed that the diseased plants had higher levels of available potassium and electrical conductivity in the rhizosphere, both positively correlated with the severity of root rot, while soil pH was negatively correlated. The diversity and richness of endophytic bacterial and fungal communities were significantly reduced in diseased plants. Additionally, root rot led to major changes in the rhizosphere microbial community, with an increased abundance of Proteobacteria and Ascomycota, and a decrease in Firmicutes, Bacteroidetes, Actinobacteria, and Basidiomycota. Fusarium oxysporum, Fusarium solani, and Fusarium fujikuroi were identified as key pathogens associated with root rot. This study enhances our understanding of the microbial interactions in soils affected by root rot, offering a foundation for developing soil improvement and biological control strategies to mitigate this disease in A. macrocephala cultivation.

Biochar-induced changes in soil microbial communities: a comparison of two feedstocks and pyrolysis temperatures

BackgroundThe application of a biochar in agronomical soil offers a dual benefit of improving soil quality and sustainable waste recycling. However, utilizing new organic waste sources requires exploring the biochar’s production conditions and application parameters. Woodchips (W) and bone-meat residues (BM) after mechanical deboning from a poultry slaughterhouse were subjected to pyrolysis at 300 °C and 500 °C and applied to cambisol and luvisol soils at ratios of 2% and 5% (w/w).ResultsInitially, the impact of these biochar amendments on soil prokaryotes was studied over the course of one year. The influence of biochar variants was further studied on prokaryotes and fungi living in the soil, rhizosphere, and roots of Triticum aestivum L., as well as on soil enzymatic activity. Feedstock type, pyrolysis temperature, application dose, and soil type all played significant roles in shaping both soil and endophytic microbial communities. BM treated at a lower pyrolysis temperature of 300 °C increased the relative abundance of Pseudomonadota while causing a substantial decrease in soil microbial diversity. Conversely, BM prepared at 500 °C favored the growth of microbes known for their involvement in various nutrient cycles. The W biochar, especially when pyrolysed at 500 °C, notably affected microbial communities, particularly in acidic cambisol compared to luvisol. In cambisol, biochar treatments had a significant impact on prokaryotic root endophytes of T. aestivum L. Additionally, variations in prokaryotic community structure of the rhizosphere depended on the increasing distance from the root system (2, 4, and 6 mm). The BM biochar enhanced the activity of acid phosphatase, whereas the W biochar increased the activity of enzymes involved in the carbon cycle (β-glucosidase, β-xylosidase, and β-N-acetylglucosaminidase).ConclusionsThese results collectively suggest, that under appropriate production conditions, biochar can exert a positive influence on soil microorganisms, with their response closely tied to the biochar feedstock composition. Such insights are crucial for optimizing biochar application in agricultural practices to enhance soil health.

Subtle changes in topsoil microbial communities of drained forested peatlands after prolonged drought.

A major consequence of anthropogenic climate change is the intensification and extension of drought periods. Prolonged drought can alter conditions in drained peatlands and cause disturbances in microbial communities in the topsoil layer of the peat. Varying environmental conditions throughout the growing season, such as the availability of organic matter and nutrients, temperature and water table, further impact these communities and consequently affect carbon and nutrient cycles. The impact of drought and new forestry practices is largely unknown in drained peatland forests. We examined how microbial communities change over a growing season in different harvesting intensities (continuous cover forestry, clear-cut and uncut) in a drained peatland site using bacterial 16S and fungal ITS2 rRNA analysis. We found seasonal differences in bacterial and fungal diversity and species richness, and subtle changes in microbial communities at the phylum and genus levels when comparing various environmental factors. Diversity, species richness and relative abundance differed in spring compared to summer and autumn. However, significant differences in the microbial community structure were not detected. Understanding the responses of microbial communities to disturbances like drought and other environmental factors provides new insights into the consequences of climate change on drained forested peatlands.

The strength of interspecies interaction in a microbial community determines its susceptibility to invasion.

Previous work shows that a host's resident microbial community can provide resistance against an invading pathogen. However, this community is continuously changing over time due to adaptive mutations, and how these changes affect the invasion resistance of these communities remains poorly understood. To address this knowledge gap, we used an experimental evolution approach in synthetic communities of Escherichia coli and Salmonella Typhimurium to investigate how the invasion resistance of this community against a bacterium expressing a virulent phenotype, i.e., colicin secretion, changes over time. We show that evolved communities accumulate mutations in genes involved in carbon metabolism and motility, while simultaneously becoming less resistant to invasion. By investigating two-species competitions and generating a three-species competition model, we show that this outcome is dependent on the strength of interspecies interactions. Our study demonstrates how adaptive changes in microbial communities can make them more prone to the detrimental effects of an invading species.

Spider waste enhances soil nutrient content, soil respiration, and plant growth

Abstract Predators can alter the movement of nutrients through ecosystems by depositing waste products following predation. Whilst the benefits of predator waste for large predators (e.g. bears) or dense accumulations of predators (e.g. seabirds on islands) seem clear, less is known about whether smaller, solitary predators can have measurable effects on local ecosystem processes. In separate experiments with web‐building and wandering spiders, we tested if the presence of predators affected soil nutrient content, soil respiration, soil microbial communities, and plant growth. In the first experiment with black widow spiders, total nitrogen and nitrate were not affected by spider presence, but ammonia and phosphorus were higher from soil under the edge of the spider web than soil away from the spider. Soil respiration and plant growth were both higher in soil collected from under the spider retreat compared with soil collected away from the spider web. In a second experiment with wolf spiders, we tested for interactions between spiders and soil microbial communities. There were positive effects of wolf spider presence on all soil nutrients and there were interactions between spiders and soil type (i.e. field‐collected versus autoclaved) for total carbon, total nitrogen, nitrate, and pH. Spider presence and soil type also affected soil respiration and spider presence had a large effect on the composition of the microbial community of the soil. There were also positive effects of wolf spider presence on plant biomass and plant height, with a significant interaction between spiders and soil type for plant height. Overall, our results show that two spiders with different life histories (i.e. web‐building and wandering) both have significant positive effects on plant growth through the deposition of their waste products. These effects may occur through the direct deposition of nutrients and changes in soil microbial communities. Although, further work is needed to resolve these interactions. Read the free Plain Language Summary for this article on the Journal blog.

Features of the oropharyngeal microbiota of healthy children and those with acute respiratory infections. A prospective single-center randomized study

Background. The oropharyngeal microbiota is involved in the development of colonization resistance, affecting viral adhesion and metabolism. Any deviations in the stability of the environmental microbial niches of the oropharynx alter the local immune response and can trigger severe chronic somatic disorders. Aim. To compare the composition of the microbiota of children during an episode of respiratory infection and healthy volunteers examined in different periods of convalescence. The obtained data can be used to predict the course of the disease, analyze the risk of complications, and assess the frequency of the diseases in the future. Materials and methods. From 20.01.2022 to 23.12.2022, an open-label prospective single-center randomized comparative study was conducted, which included 120 children aged 5-10 who presented with symptoms of acute respiratory infection. The control group consisted of 15 asymptomatic children examined at different periods of convalescence. The study compared changes in the oral microbiota composition of patients and healthy children. The evaluation was performed using complete 16S rRNA gene sequencing on the Oxford Nanopore platform. Taxonometric analysis at the species and genera level was performed using the Knomics-Biota platform. The R programming language was used for statistical processing. In addition, the parameters of α- and β-diversity of the microbiota were assessed. The Chao1 and Shannon indices were calculated to assess α-diversity (diversity within one community). The Chao1 index is based on the number of species found in the sample and also rare species that are found only 1 or 2 times, thus preventing underestimation of diversity. The Shannon index includes both the number of species and their uniformity in the community. A change in the index indicates the dominance of one or more species. The following indicators were used to assess the β-diversity describing the differences between two microbiota samples at the species and genera level: Bray–Curtis dissimilarity (characterizing the ratios of common and different microorganisms between the samples) and the Aitchison distance (reflecting the differences in the proportions of microorganisms). In addition, the balance between the two groups of microorganisms was evaluated using the NearesBalance method, which characterizes the differences between the microbiota of the main and control groups. Results. The results of our study show that during respiratory infection, the state of the oropharyngeal microbiota is characterized by an increase in α-diversity, which is associated with an increase in the proportion of species of Streptococcus salivarius, Streptococcus pneumoniae, Streptococcus pseudopneumoniae, Streptococcus pyogenes, Streptococcus thermophilus and A12 versus the proportion of Streptococcus mitis, Streptococcus oralis, Streptococcus gwangjuense, Streptococcus sanguinis, Streptococcus gordonii and FDAARGOS_192. In the control group, the oropharyngeal microbiota was divided into two clusters. The dominance of streptococci was observed in the first group (control), while the second group had a more uniform representation. Analysis of the changes in microbial communities in the main and control groups can show the stages of oral microbiota recovery after an acute respiratory infection episode. Conclusion. More research is needed in the field of the oropharyngeal microbiome on a larger sample of healthy children, to standardize the communities of the oropharyngeal microbiota, to study the interaction within communities and with the body as a whole. Analysis of the impact of the microbiota on the frequency and course of respiratory infections and the rate of complications opens up new prospects in treating, rehabilitating, and preventing diseases. These research areas can contribute to improving children's health and quality of life and introducing new approaches into clinical practice.

Effects of different quorum sensing signal molecules on alleviation of ammonia inhibition during biomethanation

Anaerobic digestion (AD) is a promising technology for achieving both organic wastes treatment and energy recovery. However, challenges such as ammonia inhibition still remain. Quorum sensing (QS) system is relevant with the regulation of microbial community behaviors by releasing and sensing signal molecules, which could improve methane production during AD process. Therefore, the current study explored the effects of different quorum sensing signal molecules on alleviation of ammonia inhibition. The results showed that both secretion of N-butyryl-DL-homoserine lactone (C4-HSL) and N-(β-ketocaproyl)-DL-homoserine lactone (3OC6-HSL) could be inhibited by high ammonia stress while stimulation of N-hexanoyl-L-homoserine lactone (C6-HSL) and N-octanoyl-DL-homoserine lactone (C8-HSL) secretion might be triggered by ammonia toxicity. Moreover, the alleviation of ammonia inhibition could be achieved by both introducing 3OC6-HSL (0.5 μM) and combination of 3OC6-HSL (0.1 μM) and biochar (4 g/L). Exogenous 3OC6-HSL could regulate microbial social behaviors and enhance the secretion of extracellular polymeric substances (EPS) to promote anaerobic digestion. In addition, the mitigation of ammonia inhibition through exogenous 3OC6-HSL and biochar were confirmed by microbial community changes (Methanobacterium, Propionicicella and Petrimonas). Critical enzymes involved in both acidification and methanogenic steps were enhanced after adding the combination of 3OC6-HSL and biochar. The combination of low levels of 3OC6-HSL and biochar could promote both direct interspecies electron transfer (DIET) process and communication between different anaerobic microorganisms to mitigate ammonia inhibition. The current study will provide primary insights for conquering ammonia inhibition during biomethanation.

Livestock grazing strengthens the effect of vole activity on the soil microbial community

Livestock grazing may affect small mammalian herbivore-soil microbe interactions and their association with the structure and functions of the ecosystem. However, the role of factors such as vegetation and soil nutrients in regulating these impacts is not clear. Here we conducted a 9-year experiment in temperate steppe to study how Brandt’s vole (Lasiopodomys brandtii) affects the soil microbial community under different livestock grazing intensities. This experiment contained 12 field enclosures with three livestock grazing intensities: control (CK), light grazing (LG), and moderate grazing (MG). We found that vole activity does not significantly change soil microbial diversity under non-grazing conditions. However, under livestock grazing conditions, vole activity led to a significant reduction in soil bacterial diversity and an increase in fungal diversity, demonstrating the impacts of livestock grazing on rodents-soil microbe interactions. The activity of voles significantly altered soil bacterial community composition, with changes primarily attributed to variations in the relative abundance of the phyla Actinobacteria, Bacteroidetes, Firmicutes, Gemmatimonadetes, and Proteobacteria. The soil fungal community remained relatively stable despite vole activity, which can be attributed to the richness of fungal colonies in mycelium and their low sensitivity to changes in external conditions. Vole activity also influenced soil microbial functional groups, and the variations in these groups were further amplified by livestock grazing. Furthermore, the shift in the microbial community composition and diversity induced by vole activity were mainly associated with the reduction of plant aboveground biomass. Overall, our study suggested that livestock grazing enhanced the changes in the soil microbial community induced by rodents, underscoring the importance of managing livestock grazing regimes for grassland conservation.

Initial abiotic factors as key drivers in core microbe assembly: Regulatory effects on flavor profiles in light-flavor baijiu

Instability in initial abiotic factors of open solid-state fermentation systems can significantly alter Baijiu's flavor profile, but the mechanisms governing microbial interactions and flavor formation remain unclear. This study comprehensively monitored changes in abiotic factors, microbial communities, and flavor profiles across two distinct fermentation processes in a Baijiu distillery, which differed significantly in their management of initial abiotic factors. Our results revealed significant differences in abiotic factors between the two groups, including moisture, ethanol, acidity, glucose, and organic acid levels. The assembly of microbial communities in fermented grains was primarily driven by deterministic processes. The moisture content in the fermentation grains positively affected the growth and metabolism of core microbiota. The rapid proliferation and metabolism of core microbes led to a rapid increase in the acidity of the fermented grains, alongside a significant accumulation of ethyl lactate. This study provides technical support and theoretical guidance for Baijiu production.

Profiling the gut and oral microbiota of hormone receptor-positive, HER2-negative metastatic breast cancer patients receiving pembrolizumab and eribulin

Aim: Changes in host-associated microbial communities (i.e., the microbiota) may modulate responses to checkpoint blockade immunotherapy. In the KELLY phase II study (NCT03222856), we previously demonstrated that pembrolizumab [anti-programmed cell death protein 1 (PD-1)] combined with eribulin (plus microtubule-targeting chemotherapy) showed encouraging antitumor activity in patients with hormone receptor (HR)-positive/human epidermal growth factor receptor 2 (HER2)-negative metastatic breast cancer (mBC) who had received prior treatments. Methods: A total of 58 fecal and 67 saliva samples were prospectively collected from a subset of 28 patients at baseline (BL), after three treatment cycles, and end of treatment. Shotgun metagenomics, 16S rRNA gene amplicon sequencing, and bioinformatics and statistical approaches were used to characterize fecal and oral microbiota profiles. Results: Treatment caused no substantial perturbations in gut or oral microbiota, suggesting minimal drug-related microbial toxicity. Bacteroides and Faecalibacterium were the dominant gut microbiota genera, while Prevotella and Streptococcus were present in both oral and gut samples, highlighting potential gut-oral microbial interactions. Additionally, clinical benefit (CB) appeared to be associated with gut-associated Bacteroides fragilis (B. fragilis ) and a BL oral abundance of Streptococcus ≥ 30%. Notably, B. fragilis NCTC 9343 supernatant induced dose-dependent lactate dehydrogenase (LDH) release from the MCF-7 (HR-positive/HER2-negative) BC cell line. Conclusion: These findings suggest that specific gut and oral microbiota may modulate the effectiveness of combinatory anti-BC therapies, potentially through the action of microbial metabolites.

Analysis of Physicochemical Properties, Enzyme Activity, Microbial Diversity in Rhizosphere Soil of Coconut (Cocos nucifera L.) Under Organic and Chemical Fertilizers, Irrigation Conditions

The application of chemical fertilizers and organic fertilizers, as well as irrigation, is an important agricultural practice that can increase crop yields and affect soil biogeochemical cycles. This study conducted coconut field experiments to investigate the effects of conventional fertilization (NCF), optimized fertilization (MCF), conventional fertilization + organic fertilizer (NOF), optimized fertilization + organic fertilizer (MOF), conventional fertilization + organic fertilizer + irrigation (NOFW), and optimized fertilization + organic fertilizer + irrigation (MOFW) treatments on soil physicochemical properties, soil enzyme activity, bacterial and fungal community structure and diversity, and compared the controls (CK, non-fertilizer and non-irrigation). The results showed that MOFW significantly increased soil electrical conductivity (EC), organic matter (OM), alkaline nitrogen (AN), available phosphorus (AP), available potassium (AK), available calcium (ACa), and available magnesium (AMg) levels. At the same time, it also significantly enhanced the activities of soil catalase (CE), polyphenol oxidase (POE), sucrase (SE), urease (UE), acid protease (APE), and acid phosphatase (APPE) (p < 0.05). The PCA analysis of soil microorganisms in the coconut rhizosphere soil showed indicated significant changes in bacteria and fungi community structure under fertilization treatments. The fertilization application leaded to an increase in the relative abundance and diversity of bacteria, but a decrease in fungi. Acidobacteriota, Proteobacteria, and Actinobacterota were the dominant bacterial phyla, and Ascomycota, Basidiomycota, Rozellomycota, and Mortierellomycota were the significant fungal phyla. Compared with CK, MOFW significantly increased the abundance of Acidobacteriota, Proteobacteria, Basidiomycota, and Mortierellomycota. Redundancy analysis (CCA) and Mantel test further revealed that pH, EC, OM, and AP were the main soil fertility factors driving changes in microbial communities. CE, SE, UE, APE, APPE were significantly correlated with microbial communities. Compared with NOFW, MOFW has a lower proportion of N, P, and K fertilizers in its fertilizer composition. The results indicated that MOFW can better improve the nutrient and enzyme status of the soil, which is a promising method for maintaining the balance of soil microorganisms in coconut orchards, and accordingly, reducing chemical fertilizers within a certain range can not only ensure consistency with conventional fertilizers, but also effectively improve soil conditions.

Multimodal Approaches Based on Microbial Data for Accurate Postmortem Interval Estimation

Accurate postmortem interval (PMI) estimation is critical for forensic investigations, aiding case classification and providing vital trial evidence. Early postmortem signs, such as body temperature and rigor mortis, are reliable for estimating PMI shortly after death. However, these indicators become less useful as decomposition progresses, making late-stage PMI estimation a significant challenge. Decomposition involves predictable microbial activity, which may serve as an objective criterion for PMI estimation. During decomposition, anaerobic microbes metabolize body tissues, producing gases and organic acids, leading to significant changes in skin and soil microbial communities. These shifts, especially the transition from anaerobic to aerobic microbiomes, can objectively segment decomposition into pre- and post-rupture stages according to rupture point. Microbial communities change markedly after death, with anaerobic bacteria dominating early stages and aerobic bacteria prevalent post-rupture. Different organs exhibit distinct microbial successions, providing valuable PMI insights. Alongside microbial changes, metabolic and volatile organic compound (VOC) profiles also shift, reflecting the body’s biochemical environment. Due to insufficient information, unimodal models could not comprehensively reflect the PMI, so a muti-modal model should be used to estimate the PMI. Machine learning (ML) offers promising methods for integrating these multimodal data sources, enabling more accurate PMI predictions. Despite challenges such as data quality and ethical considerations, developing human-specific multimodal databases and exploring microbial–insect interactions can significantly enhance PMI estimation accuracy, advancing forensic science.

Full-scale performance and microbial community evolution using dopamine modified ceramic membrane submerged membrane biological reactor in treating young landfill leachate

In this project, ceramic membrane submerged membrane biological reactor (SMBR) was integrated to dissolved air flotation (DAF)-up-flow anaerobic sludge blanket (UASB)-anoxic and aerobic (A/O) system in treating young landfill leachate with a capacity of 300 m3 /day over 185 days’ operation. High removal efficiencies of chemical oxygen demand (COD) (96.8 %), ammonia nitrogen (83.4 %) and total nitrogen (79.6 %) were achieved via DAF-UASB -A/O system. The membrane permeate COD was below 356 mg/L. The permeate turbidity was stable below 11 NTU, met the condition for further ultrafiltration treatment. The SMBR system was operated stability at the flux of 26 LMH because of excellent surface hydrophilicity of the dopamine modified ceramic membrane. Remarkably, immersed chemical cleaning can recover the filterability entirely, indicating the dopamine modified ceramic membrane SMBR can be recognized as fouling–free MBRs. The foulants removal after chemical cleaning on the ceramic membrane was detailly analyzed by scanning electron microscopy coupled with energy dispersive X-ray. The comparative microbial analysis between sludge Day-1 and Day-185 revealed that significant changes of microbial community occurred. Regarding the nitrifying and denitrifying bacteria, Thauera was identified as potential functional specie in simultaneous methanogensis and denitrification process in the UASB reactor. High populations of Proteobacteria, Planctomycetes, Bacteroidetes and Chloroflexi contributed the nitrification and denitrification in the A/O system. The anaerobic ammonia oxidation process might happen due to the identified Planctomycetes. At the genus level, genera, such as Thauera, Phycisphaerae and Betaproteobacteria, with high abundances were functional species ensuring the nitrogen removal in the A/O environment.

Soil microbial community composition by crop type under rotation diversification

BackgroundCrop rotation is an important agricultural practice that often affects the metabolic processes of soil microorganisms through the composition and combination of crops, thereby altering nutrient cycling and supply to the soil. Although the benefits of crop rotation have been extensively discussed, the effects and mechanisms of different crop combinations on the soil microbial community structure in specific environments still need to be analyzed in detail.Materials and methodsIn this study, six crop rotation systems were selected, for which the spring crops were mainly tobacco or gramineous crops: AT (asparagus lettuce and tobacco rotation), BT (broad bean and tobacco rotation), OT (oilseed rape and tobacco rotation), AM (asparagus lettuce and maize rotation), BM (broad bean and maize rotation), and OR (oilseed rape and rice rotation). All crops had been cultivated for > 10 years. Soil samples were collected when the rotation was completed in spring, after which the soil properties, composition, and functions of bacterial and fungal communities were analyzed.ResultsThe results indicate that spring cultivated crops play a more dominant role in the crop rotation systems than do autumn cultivated crops. Crop rotation systems with the same spring crops have similar soil properties and microbial community compositions. pH and AK are the most important factors driving microbial community changes, and bacteria are more sensitive to environmental responses than fungi. Rotation using tobacco systems led to soil acidification and a decrease in microbial diversity, while the number of biomarkers and taxonomic indicator species differed between rotation patterns. Symbiotic network analysis revealed that the network complexity of OT and BM was the highest, and that the network density of tobacco systems was lower than that of gramineous systems.ConclusionsDifferent crop rotation combinations influence both soil microbial communities and soil nutrient conditions. The spring crops in the crop rotation systems had stronger dominating effects, and the soil bacteria were more sensitive than the fungi were to environmental changes. The tobacco rotation system can cause soil acidification and thereby affect soil sustainability, while the complexity of soil microbial networks is lower than that of gramineous systems. These results provide a reference for future sustainable applications of rotation crop systems.

Healthy Dietary Pattern Cycling Affects Gut Microbiota and Cardiovascular Disease Risk Factors: Results from a Randomized Controlled Feeding Trial with Young, Healthy Adults.

Previous research demonstrates that adopting, abandoning, and re-adopting (i.e., cycling) a healthy dietary pattern (HDP) improved, reverted, and re-improved cardiovascular disease (CVD) risk factors. In addition, changes in CVD risk factors are associated with dietary modifications of gut microbiota. We sought to assess the effects of cycling an HDP on gut microbiota and CVD risk factors. Retrospectively, we used data from a randomized controlled, crossover trial with three 3-week controlled dietary interventions, each separated by a 5-week period of participant-chosen, uncontrolled food intake. Seventeen participants (10 males, 7 females, age 26 ± 4 years old, BMI 23 ± 3 kg/m2) all consumed intervention diets that followed healthy U.S.-style dietary patterns. Gut microbiota composition and cardiovascular risk factors were measured before and after each HDP. Repeatedly adopting and abandoning an HDP led to a cycling pattern of changes in the gut microbial community and taxonomic composition. During the HDP cycles, relative abundances of several bacterial taxa (e.g., Collinsella, Mediterraneibacter, Romboutsia, and Dorea) decreased and returned to baseline repeatedly. Similar HDP cycling occurred for multiple CVD risk factors (i.e., serum total cholesterol and LDL-C concentrations). Consistent negative associations were observed between changes in Mediterraneibacter or Collinsella and serum total cholesterol/HDL-C ratio. These results support previous findings that HDP cycling affected multiple CVD risk factors and expand the HDP cycling phenomenon to include several bacterial taxa. Young adults are encouraged to adopt and sustain a healthy dietary pattern to improve cardiovascular health, potentially through modifying gut microbiota composition.