Disturbance of the human gut microbiota in patients with Myotonic Dystrophy type 1

Myotonic dystrophy type 1 (DM1) is a rare autosomal dominant genetic disorder. Although DM1 is primarily characterized by progressive muscular weakness, it exhibits many multisystemic manifestations, such as cognitive deficits, cardiac conduction abnormalities, and cataracts, as well as endocrine and reproductive issues. Additionally, the gastrointestinal (GI) tract is frequently affected, encompassing the entire digestive tract. However, the underlying causes of these GI symptoms remain uncertain, whether it is biomechanical problems of the intestine, involvement of bacterial communities, or both. The primary objective of this study is to investigate the structural changes in the gut microbiome of DM1 patients. To achieve this purpose, 35 patients with DM1 were recruited from the DM-Scope registry of the neuromuscular clinic in the Saguenay-Lac-St-Jean region of the province of Québec, Canada. Stool samples from these 35 patients, including 15 paired samples with family members living with them as controls, were collected. Subsequently, these samples were sequenced by 16S MiSeq and were analyzed with DADA2 to generate taxonomic signatures. Our analysis revealed that the DM1 status correlated with changes in gut bacterial community. Notably, there were differences in the relative abundance of Bacteroidota, Euryarchaeota, Fusobacteriota, and Cyanobacteria Phyla compared to healthy controls. However, no significant shift in gut microbiome community structure was observed between DM1 phenotypes. These findings provide valuable insights into how the gut bacterial community, in conjunction with biomechanical factors, could potentially influence the gastrointestinal tract of DM1 patients.

Evaluating the impact of biochar amendment on antibiotic resistance genes and microbiome dynamics in soil, rhizosphere, and endosphere at field scale

Biochar amendment is a promising strategy for mitigating antibiotic resistance genes (ARGs) in soil and plants, but its effects on ARGs at field scale are not fully understood. Here, field trials were executed utilizing two plant varieties, Brassica juncea and Lolium multiflorum, with four types of biochar to investigate changes in ARGs and microbiome in soil, rhizosphere, root endophytes, and leaf endophytes. Results showed that biochar altered ARG distribution in soil and plant, and restrained their transmission from soil and rhizosphere to endophytes. A reduction of 1.2-2.2 orders of magnitude in the quantity of ARGs was observed in root and leaf endophytes following biochar addition, while no significant changes were observed in soil and rhizosphere samples. Procrustes and network analyses revealed significant correlations between microbial communities and mobile genetic elements with ARGs (P < 0.05). Besides, redundancy and variation partitioning analysis indicated that bacterial communities may play a dominant role in shaping the ARGs profile, contributing to 43 % of the variation observed in ARGs. These field results suggest that biochar amendment alone may not fully alleviate ARGs in soil, but it has a significant beneficial impact on food safety and human health by effectively reducing ARGs in plant endophytes.

Using ozone nanobubbles, and microalgae to promote the removal of nutrients from aquaculture wastewater: Insights from the changes of microbiomes

Integrated aquaculture wastewater treatment systems (IAWTSs) are widely used in treating aquaculture wastewater with the aeration-microalgae unit serving as an important component. In this study, we artificially constructed an IAWTS and applied two aeration-microalgae methods: ordinary aeration or ozone nanobubbles (ONBs) with microalgae (Nannochloropsis oculata). The impact of N.oculata and ONBs on the removal performance of nutrients and the underlying micro-ecological mechanisms were investigated using 16S rRNA gene amplicon sequencing. The results demonstrated that the combined use of ONBs and N.oculata exhibited superior purification effects with 78.25%, 76.59% and 86.71% removal of CODMn, TN and TP. N.oculata played a pivotal role as the primary element in wastewater purification, while ONBs influenced nutrient dynamics by affecting both N.oculata and bacterial communities. N.oculata actively shaped bacterial communities, with a specific focus on nitrogen and phosphorus cycling in the micro-environment remodeled by ONBs. Rare bacterial communities displayed heightened activity in response to the changes in N.oculata, ONBs, and nutrient levels. These findings provide a novel approach to improve the technological processes the IAWTS, contributing to the advancement of sustainable aquaculture practices by offering valuable insights into wastewater purification efficiency and micro-ecological mechanisms.

Effects of acid mine drainage and sediment contamination on soil bacterial communities, interaction patterns, and functions in alkaline desert grassland

Acid mine drainage and sediments (AMD-Sed) contamination pose serious ecological and environmental problems. This study investigated the geochemical parameters and bacterial communities in the sediment layer (A) and buried soil layer (B) of desert grassland contaminated with AMD-Sed and compared them to an uncontaminated control soil layer (CK). The results showed that soil pH was significantly lower and iron, sulfur, and electroconductivity levels were significantly higher in the B layer compared to CK. A and B were dominated by Proteobacteria and Actinobacteriota, while CK was dominated by Firmicutes and Bacteroidota. The pH, Fe, S, and potentially toxic elements (PTEs) gradients were key influences on bacterial community variability, with AMD contamination characterization factors (pH, Fe, and S) explaining 48.6 % of bacterial community variation. A bacterial co-occurrence network analysis showed that AMD-Sed contamination significantly affected topological properties, reduced network complexity and stability, and increased the vulnerability of desert grassland soil ecosystems. In addition, AMD-Sed contamination reduced C/N-cycle functioning in B, but increased S-cycle functioning. The results highlight the effects of AMD-Sed contamination on soil bacterial communities and ecological functions in desert grassland and provide a reference basis for the management and restoration of desert grassland ecosystems in their later stages.

Exploring seasonal variations, assembly dynamics, and relationships of bacterial communities in different habitats of marine ranching

Offshore coastal marine ranching ecosystems provide habitat for diverse and active bacterial communities. In this study, 16S rRNA gene sequencing and multiple bioinformatics methods were applied to investigate assembly dynamics and relationships in different habitats. The higher number of edges in the water network, more balanced ratio of positive and negative links, and more keystone species included in the co-occurrence network of water. Stochastic processes dominated in shaping gut and sediment community assembly (R2 < 0.5), while water bacterial community assembly were dominated by deterministic processes (R2 > 0.5). Dissimilarity-overlap curve model indicated that the communities in different habitats have general dynamics and interspecific interaction (P < 0.001). Bacterial source-tracking analysis revealed that the gut was more similar to the sediment than the water bacterial communities. In summary, this study provides basic data for the ecological study of marine ranching through the study of bacterial community dynamics.

Integrating experiments with modeling to understand key bacterial taxa dynamics after episodic mixing of a stratified water column

Hydraulic mixing of stratified reservoirs homogenizes physicochemical gradients and microbial communities. This has potential repercussions for microbial metabolism and water quality, not least in dams and hydraulically controlled waters. A better understanding of how key taxa respond to mixing of such stratified water bodies is needed to understand and predict the impact of hydraulic operations on microbial communities and nutrient dynamics in reservoirs. We studied taxa transitions between cyanobacteria and sulfur-transforming bacteria following mixing of stratified water columns in bioreactors and complemented the experimental approach with a biogeochemical model. Model predictions were consistent with experimental observations, suggesting that stable stratification of DO is restored within 24 h after episodic and complete mixing, at least in the absence of other more continuous disturbances. Subsequently, the concentration of S2- gradually return to pre-mixing states, with higher concentration at the surface and lower in the bottom waters, while the opposite pattern was seen for SO42-. The total abundance of sulfate-reducing bacteria and phototrophic sulfur bacteria increased markedly after 24h of mixing. The model further predicted that the rapid re-oxygenation of the entire water column by aeration will effectively suppress the water stratification and the growth of sulfur-transforming bacteria. Based on these results, we suggest that a reduction of thermocline depth by optimal flow regulation in reservoirs may also depress sulfur transforming bacteria and thereby constrain sulfur transformation processes and pollutant accumulation. The simulation of microbial nutrient transformation processes in vertically stratified waters can provide new insights about effective environmental management measures for reservoirs.

Variations in bacterial community succession and assembly mechanisms with mine age across various habitats in coal mining subsidence water areas

Microorganisms play a pivotal role as catalysts in the biogeochemical cycles of aquatic ecosystems within coal mining subsidence areas. Despite their importance, the succession of microbial communities with increasing mine age, particularly across different habitats, and variations in phylogenetically-based community assembly mechanisms are not well understood. To address this knowledge gap, we collected 72 samples from lake sediments, water, and surrounding topsoil (0-20 cm) at various mining stages (early: 16 years, middle: 31 years, late: 40 years). We analyzed these samples using 16S rRNA gene sequencing and multivariate statistical methods to explore the dynamics and assembly mechanisms of bacterial communities. Our findings reveal that increases in phosphorus and organic matter in sediments, correlating with mining age, significantly enhance bacterial alpha diversity while reducing species richness (P < 0.001). Homogenizing selection (49.9 %) promotes species asynchrony-complementarity, augmenting the bacterial community's ability to metabolize sulfur, phosphorus, and organic matter, resulting in more complex-stable co-occurrence networks. In soil, elevated nitrogen and organic carbon levels markedly influence bacterial community composition (Adonis R2 = 0.761), yet do not significantly alter richness or diversity (P > 0.05). The lake's high connectivity with surrounding soil leads to substantial species drift and organic matter accumulation, thereby increasing bacterial richness in later stages (P < 0.05) and enhancing the ability to metabolize dissolved organic matter, including humic-like substances, fulvic acids, and protein-like materials. The assembly of soil bacterial communities is largely governed by stochastic processes (79.0 %) with species drift (35.8 %) significantly shaping these communities over a broad spatial scale, also affecting water bacterial communities. However, water bacterial community assembly is primarily driven by stochastic processes (51.2 %), with a substantial influence from habitat quality (47.6 %). This study offers comprehensive insights into the evolution of microbial community diversity within coal mining subsidence water areas, with significant implications for enhancing environmental management and protection strategies for these ecosystems.

Saturated constructed wetlands for the remediation of cylindrospermopsin and microcystin-LR: Plants, microbes, and biodegradation pathways

Harmful cyanobacterial blooms will be more intense and frequent in the future, contaminating surface waters with cyanotoxins and posing a threat to communities heavily reliant on surface water usage for crop irrigation. Constructed wetlands (CWs) are proposed to ensure safe crop irrigation, but more research is needed before implementation. The present study operated 28 mesocosms in continuous mode mimicking horizontal sub-surface flow CWs. Mesocosms were fed with synthetic lake water and spiked periodically with two cyanotoxins, microcystin-LR (MC-LR) and cylindrospermopsin (CYN), at environmentally relevant cyanotoxins concentrations (10 μg L-1). The influence of various design factors, including plant species, porous media, and seasonality, was explored. The mesocosms achieved maximum MC-LR and CYN mass removal rates of 95 % and 98 %, respectively. CYN removal is reported for the first time in CWs mimicking horizontal sub-surface flow CWs. Planted mesocosms consistently outperformed unplanted mesocosms, with Phragmites australis exhibiting superior cyanotoxin mass removal compared to Juncus effusus. Considering evapotranspiration, J. effusus yielded the least cyanotoxin-concentrated effluent due to the lower water losses in comparison with P. australis. Using the P-kC* model, different scaling-up scenarios for future piloting were calculated and discussed. Additionally, bacterial community structure was analyzed through correlation matrices and differential taxa analyses, offering valuable insights into their removal of cyanotoxins. Nevertheless, attempts to validate microcystin-LR biotransformation via the known mlrA gene degradation pathway were unfruitful, indicating alternative enzymatic degradation pathways occurring in such complex CW systems. Further investigation into the precise molecular mechanisms of removal and the identification of transformation products is needed for the comprehensive understanding of cyanotoxin mitigation in CW. This study points towards the feasibility of horizontal sub-surface flow CWs to be employed to control cyanotoxins in irrigation or recreational waters.

Investigating the lignocellulolytic gut microbiome of huhu grubs (Prionoplus reticularis) using defined diets and dietary switch

The huhu beetle (Prionoplus reticularis) is the largest endemic beetle found throughout Aotearoa New Zealand, and is characterised by feeding on wood during its larval stage. It has been hypothesised that its gut microbiome plays a fundamental role in the degradation of wood. To explore this idea we examined the fungal and bacterial community composition of huhu grubs' frass, using amplicon sequencing. Grubs were reared on an exclusive diet of either a predominantly cellulose source (cotton) or lignocellulose source (pine) for 4 months; subsequently a diet switch was performed and the grubs were grown for another 4 months. The fungal community of cellulose-reared huhu grubs was abundant in potential cellulose degraders, contrasting with the community of lignocellulose-reared grubs, which showed abundant potential soft rot fungi, yeasts, and hemicellulose and cellulose degraders. Cellulose-reared grubs showed a less diverse fungal community, however, diet switch from cellulose to lignocellulose resulted in a change in community composition that showed grubs were still capable of utilising this substrate. Conversely, diet seemed to have a limited influence on huhu grub gut bacterial communities.

Unraveling the effect of micro/nanoplastics on the occurrence and horizontal transfer of environmental antibiotic resistance genes: Advances, mechanisms and future prospects

Microplastics can not only serve as vectors of antibiotic resistance genes (ARGs), but also they and even nanoplastics potentially affect the occurrence of ARGs in indigenous environmental microorganisms, which have aroused great concern for the development of antibiotic resistance. This article specifically reviews the effects of micro/nanoplastics (concentration, size, exposure time, chemical additives) and their interactions with other pollutants on environmental ARGs dissemination. The changes of horizontal genes transfer (HGT, i.e., conjugation, transformation and transduction) of ARGs caused by micro/nanoplastics were also summarized. Further, this review systematically sums up the mechanisms of micro/nanoplastics regulating HGT process of ARGs, including reactive oxygen species production, cell membrane permeability, transfer-related genes expression, extracellular polymeric substances production, and ARG donor-recipient adsorption/contaminants adsorption/biofilm formation. The underlying mechanisms in changes of bacterial communities induced by micro/nanoplastics were also discussed as it was an important factor for structuring the profile of ARGs in the actual environment, including causing environmental stress, providing carbon sources, forming biofilms, affecting pollutants distribution and environmental factors. This review contributes to a systematical understanding of the potential risks of antibiotic resistance dissemination caused by micro/nanoplastics and provokes thinking about perspectives for future research and the management of micro/nanoplastics and plastics.

Insight into spatial variations of DOM fractions and its interactions with microbial communities of shallow groundwater in a mesoscale lowland river watershed

Dissolved organic matter (DOM) plays a crucial role in driving biogeochemical processes and determining water quality in shallow groundwater systems, where DOM could be susceptible to dynamic influences of surface water influx. This study employed fluorescence excitation-emission matrix (EEM) spectroscopy combined with principal component coefficients, parallel factor analysis (PARAFAC), co-occurrence network analysis and structural equation modeling (SEM) to examine changes of DOM fractions from surface water to shallow groundwater in a mesoscale lowland river basin. Combining stable isotope and hydrochemical parameters, except for surface water (SW), two groups of groundwater samples were defined, namely, deeply influenced by surface water (IGW) and groundwater nearly non-influenced by surface water (UGW), which were 50.34 % and 19.39 % recharged by surface water, respectively. According to principal component coefficients, reassembled EEM data of these categories highlighted variations of the tyrosine-like peak in DOM. EEMs coupled with PARAFAC extracted five components (C1-C5), i.e. C1, protein-like substances, C2 and C4, humic-like substances, and C3 and C5, microbial-related substances. The abundance of the protein-like was SW > IGW > UGW, while the order of the humic-like was opposite. The bacterial communities exhibited an obvious cluster across three regions, which hinted their sensitivity to variations in environmental conditions. Based on co-occurrence, SW represented the highest connectivity between bacterial OTUs and DOM fractions, followed by IGW and UGW. SEM revealed that microbial activities increased bioavailability of the humic-like in the SW and IGW, whereas microbial compositions promoted the evolution of humic-like substances in the UGW. Generally, these results could be conducive to discern dissimilarity in DOM fractions across surface water and shallow groundwater, and further trace their interactions in the river watershed.

Determination of the variations in the metabolic profiles and bacterial communities during traditional craftsmanship Liupao tea processing

In this study, the metabolic profiles of traditional craftsmanship (TC) Liupao tea presented great changes at different processing stages. The contents of flavonoids and their glycosides generally exhibited a continuing downward trend, resulting in the sensory quality of TC-Liupao tea gradually improved. However, the taste of TC-Liupao tea faded when piling exceeded 12 h, as a result of the excessive degradation of some key flavor substances. Therefore, it could be deduced that piling for 10 h might be optimum for the quality formation of TC-Liupao tea. Sphingomonas, Acrobacter, Microbacterium, and Methylobacterium were the dominant bacteria during piling. The correlation analysis between differential metabolites and bacteria showed that only Sphingomonas and Massilia were significantly correlated to metabolites, demonstrating that the bacteria had less effect on the transformation of metabolites. Thus, the metabolic structure change during the process of TC-Liupao tea might be mainly attributed to the high temperature and humidity environment.

Biomass acid pretreatment impacts on metabolic routes and bacterial composition of dark fermentation process

Complex organic matter represents a suitable substrate to produce hydrogen through dark fermentation (DF) process. To increase H2 yields, pretreatment technology is often required. The main objective of the present work was to investigate thermo-acid pretreatment impact on sugar solubilization and biotic parameters of DF of sorghum or organic fraction of municipal solid waste (OFMSW). Biochemical hydrogen potential tests were carried out without inoculum using raw or thermo-acid pretreated substrates. Results showed an improvement in sugar solubilization after thermo-acid pretreatments. Pretreatments led to similar DF performances (H2 and total metabolite production) compared to raw biomasses. Nevertheless, they were responsible for bacterial shifts from Enterobacteriales towards Clostridiales and Bacillales as well as metabolic changes from acetate towards butyrate or ethanol. The metabolic changes were attributed to the biomass pretreatment impact on indigenous bacteria as no change in the metabolic profile was observed after performing thermo-acid pretreatments on irradiated OFMSW (inactivated indigenous bacteria and inoculum addition). Consequently, acid pretreatments were inefficient to improve DF performances but led to metabolic and bacterial community changes due to their impact on indigenous bacteria.

Deciphering the removal of antibiotics and the antibiotic resistome from typical hospital wastewater treatment systems

Hospital wastewater treatment systems (HWTSs) are a significant source and reservoir of antibiotic resistance genes (ARGs) and a crucial hub for transmitting ARGs from clinical to natural environments. However, there is a lack of research on the antibiotic resistome of clinical wastewater in HWTSs. In this study, we used metagenomics to analyze the prevalence and abundance of ARGs in five typical HWTSs. A total of 17 antibiotics from six categories were detected in the five HWTSs; β-lactam antibiotics were found at the highest concentrations, with up to 4074.08 ng·L-1. We further found a total of 21 ARG types and 1106 subtypes of ARGs with the highest percentage of multi-drug resistance genes (evgS, msbA, arlS, and baeS). The most abundant last-resort ARGs were mcr, which were detected in 100 % of the samples. HWTSs effluent is a major pathway for the transmission of last-resort ARGs into urban wastewater networks. The removal of antibiotics, antibiotic-resistant bacteria, and ARGs from HWTSs was mainly achieved by tertiary treatment, i.e., chlorine disinfection, but antibiotics and ARGs were still present in the HWTSs effluent or even increased after treatment. Moreover, antibiotics and heavy metals (especially mercury) in hospital effluents can exert selective pressure for antibiotic resistance, even at low concentrations. Qualitative analyses based on metagenome-assembled genome analysis revealed that the putative hosts of the identified ARGs are widely distributed among Pseudomonas, Acidovorax, Flavobacterium, Polaromonas, and Arcobacter. Moreover, we further assessed the clinical availability of ARGs and found that multidrug ARGs had the highest clinical relevance values. This study provides new impulses for monitoring and removing antibiotics and ARGs in the hospital sewage treatment process.

Geographic distribution of bacterial communities of inland waters in China

Microorganisms are integral to freshwater ecological functions and, reciprocally, their activity and diversity are shaped by the ecosystem state. Yet, the diversity of bacterial community and its driving factors at a large scale remain elusive. To bridge this knowledge gap, we delved into an analysis of 16S RNA gene sequences extracted from 929 water samples across China. Our analyses revealed that inland water bacterial communities showed a weak latitudinal diversity gradient. We found 530 bacterial genera with high relative abundance of hgcI clade. Among them, 29 core bacterial genera were identified, that is strongly linked to mean annual temperature and nutrient loadings. We also detected a non-linear response of bacterial network complexity to the increasing of human pressure. Mantel analysis suggested that MAT, HPI and P loading were the major factors driving bacterial communities in inland waters. The map of taxa abundance showed that the abundant CL500-29 marine group in eastern and southern China indicated high eutrophication risk. Our findings enhance our understanding of the diversity and large-scale biogeographic pattern of bacterial communities of inland waters and have important implications for microbial ecology.

Bacterial microbiota shifts in vacuum-packed beef during storage at different temperatures: Impacts on blown pack spoilage

We aimed to evaluate the bacterial growth and diversity in vacuum-packed beef bags stored at different temperatures and to monitor blown-pack spoilage. We used culture-based methods and high-throughput sequencing to study the development of the main bacterial groups naturally present in beef stored at 4 and 15 °C for 28 days. The growth of sulfite-reducing clostridium (SRC) was impaired in beef bags stored at 4 °C; significant differences among SRC counts were observed in beef bags stored at 4 and 15 °C on days 14, 21, and 28 (P = 0.001). Blown pack was observed in most beef bags stored at 15 °C, from day 14 to day 28, but not in beef bags stored at 4 °C. A storage temperature of 4 °C was able to maintain a stable bacterial microbiota (most prevalent: Photobacterium, Hafnia-Obesumbacterium, and Lactococcus). Remarkable changes in microbial abundance occurred at 15 °C from day 14 to day 28, with a predominance of strict anaerobes (Bacteroides) and the presence of Clostridium spp. The relative frequencies of strict anaerobes and Clostridium were statistically higher in the beef bags stored at 15 °C (P < 0.001 and P = 0.004, respectively). The temperature influenced the microbial counts and relative abundance of spoilage bacteria, leading to blown pack spoilage.

The biocontrol potentials of rhizospheric bacterium Bacillus velezensis K0T24 against mulberry bacterial wilt disease

Mulberry bacterial wilt disease, caused by Ralstonia pseudosolanacearum, is a devastating soil-borne disease in the silk-mulberry-related industry. In this study, through high-throughput sequencing, we compared the rhizosphere bacterial composition of the mulberry-resistant cultivar (K10) and susceptible cultivar (G12), confirming Bacillus as a genus-level biomarker for K10. Next, twelve Bacillus spp. isolates, derived from the rhizosphere of K10, were screened for their antagonistic activity against R. pseudosolanacearum. The isolate showing strong antagonism was identified as B. velezensis K0T24 and selected for further analysis. The fermentation supernatant of B. velezensis K0T24 significantly inhibited the growth of R. pseudosolanacearum (82.47%) and the expression of its pathogenic genes. Using B. velezensis K0T24 in mulberry seedlings also increased defense enzyme activities and achieved a control efficacy of up to 55.17% against mulberry bacterial wilt disease. Collectively, our findings demonstrate the potential of B. velezensis K0T24 in suppressing mulberry bacterial wilt disease.

Effects of environmentally relevant concentrations of oxytetracycline and sulfadiazine on the bacterial communities, antibiotic resistance genes, and functional genes are different between maize rhizosphere and bulk soil

Antibiotic contamination in soil has become a major concern worldwide. At present, it is not clear how two co-existed antibiotics with environmentally relevant concentrations would affect soil bacterial community structure, the abundances of antibiotic resistance genes (ARGs) and functional genes, and whether the effects of antibiotics would differ between rhizosphere and bulk soil. We conducted a greenhouse pot experiment to grow maize in a loess soil treated with oxytetracycline (OTC) or sulfadiazine (SDZ) or both at an environmentally relevant concentration (1 mg kg-1) to investigate the effects of OTC and SDZ on the rhizosphere and bulk soil bacterial communities, abundances of ARGs and carbon (C)-, nitrogen (N)-, and phosphorus (P)-cycling functional genes, and on plant growth and plant N and P nutrition. The results show that the effects of environmentally relevant concentrations of OTC and SDZ on bacterial communities and abundances of ARGs and functional genes differ between maize rhizosphere and bulk soil. The effects of two antibiotics resulted in a higher absolute abundances of accA, tet(34), tnpA-04, and sul2 in the rhizosphere soil than in the bulk soil and different bacterial community compositions and biomarkers in the rhizosphere soil and the bulk soil. However, OTC had a stronger inhibitory effect on the abundances of a few functional genes in the bulk soil than SDZ did, and their combination had no synergistic effect on plant growth, ARGs, and functional genes. The role of co-existed OTC and SDZ decreased shoot height and increased root N concentration. The results demonstrate that environmentally relevant concentrations of antibiotics shift soil microbial community structure, increase the abundances of ARGs, and reduce the abundances of functional genes. Furthermore, soil contamination with antibiotics can diminish agricultural production via phytotoxic effects on crops, and combined effects of antibiotics on plant growth and nutrient uptake should be considered.

Antibiotics and antibiotic resistance change bacterial community compositions in marine sediments

Emerging contaminants, including antibiotics, antibiotic-resistant bacteria (ARB), and extracellular antibiotic resistance genes (eARGs), have been detected in large numbers in the aquatic environment. The effects of emerging contaminants on bacterial communities in marine sediments are not well studied. In this study, the effects of emerging contaminants (antibiotics, ARB, and eARGs) on the variations of bacterial populations in marine sediments of the Bohai Sea, Yellow Sea, East China Sea, and South China Sea were investigated. The results showed that the abundance of the host bacterial phylum Probacteria in the marine sediments of the Bohai Sea was the lowest among the four seas after exposure to different antibiotics, ARB, and eARGs. The inputs of exogenous antibiotics and resistance genes significantly affected the community function, resulting in significant differences in community abundance at the genus level. The abundance of Halomonas, Sulfitobacter, and Alcanivorax in the four sea areas displayed noteworthy differences in response to the addition of exogenous antibiotics and eARGs. These findings contribute to a more comprehensive understanding of the intricate interplay between emerging contaminants and the dynamics of bacterial communities in natural ecosystems.

Temporal dynamics of bacterial colonization on five types of microplastics in a freshwater lake

Microplastics (MPs), as a new substrate, provide a unique niche for microbial colonization in the freshwater ecosystems; however, the impacts of long-term MP exposure on colonized bacteria are still unclear. In this study, five MP types were exposed in a freshwater lake for approximately one year, and the MP particles, together with the surrounding water, were collected on days 60, 150, 250 and 330 during the in situ field experiment. Bacteria on the MP surface, as well as free-living bacteria in the surrounding water, were analyzed to evaluate the temporal dynamics of these bacterial communities. Results show that all five MP types exhibited signs of degradation during the exposure process. Additionally, the alpha diversity, community structure and composition of MP-attached bacteria significantly differed from that of the free-living bacteria in the surrounding water, indicating that the five MP types could provide a preferable niche for bacterial colonization in a freshwater environment. Proteobacteria, Chloroflexi, Verrucomicrobiota, Actinobacteriota and Firmicutes were the top five dominant phyla. Some plastic-degrading bacteria included in these phyla were detected, verifying that MP-attached biofilms had a certain degree of MP degradation potential. Some potentially pathogenic bacteria were also detected, suggesting an ecological threat for spreading disease in the aquatic ecosystem. Furthermore, the bacterial community and some metabolic pathways were significantly affected by the MP type (P < 0.01) and exposure time (P < 0.01), indicating that the presence of MPs not only alters the bacterial community structure and composition, but also influences their potential functional properties in freshwater ecosystems. Multiple factors, including the physicochemical properties related to MPs and the environmental parameters of the surrounding water, affect the community composition and the function of MP-attached bacteria to different degrees. Our findings indicate that the presence of MPs has a potential ecological impact on freshwater ecosystems.

Insight into bacterial role attribution in dissolved organic matter humification during rice straw composting with microbial inoculation

This study aims to investigate the effect of microbial role distribution in microbial carbon pumps on dissolved organic matter (DOM) humification during rice straw composting with microbial inoculation. Three composting groups were designed, named CK (control), B4 (with Bacillus subtilis, OR058594) and Z1 (with Aspergillus fumigatus, AF202956.1). As a result of inoculation, the composition of microbial communities was changed, so that the microorganisms that promoted DOM humification were concentrated in the responders in the microbial carbon pump. DOM was divided into three components in three composting treatments: C1, C2 and C3. After inoculation with Bacillus subtilis, the C2 component was significantly affected, while after inoculation with Aspergillus fumigatus, the C3 component was significantly affected. The results of physicochemical factors affecting the transformation of DOM fluorescence components indicated that C1, C2 and C3 were related to the abundance of the cellulose-degrading enzyme-encoding gene GH7 in CK and B4 composting. However, the C2 was susceptible to organic matter in Z1 composting. This study explored the distribution of microbial communities from a new perspective, which provided new information for analyzing DOM humification and treating agricultural straws to achieve clean conditions for environmental friendliness.

Integrating molecular microbial methods to improve faecal pollution management in rivers with designated bathing waters

Rivers are at risk from a variety of pollution sources. Faecal pollution is of particular concern since it disperses pathogenic microorganisms in the aquatic environment. Currently, faecal pollution levels in rivers is monitored using faecal indicator bacteria (FIB) that do not offer information about pollution sources and associated risks. This study used a combined molecular approach, along with measurements of water quality, to gain information on pollution sources, and risk levels, in a newly designated recreational bathing site in the River Wharfe (UK). Physico-chemical parameters were monitored in situ, with water quality multiparameter monitoring sondes installed during the 2021 bathing season. The molecular approach was based on quantitative PCR (qPCR)-aided Microbial Source Tracking (MST) and 16S rRNA gene metabarcoding to obtain a fingerprint of bacterial communities and identify potential bioindicators. The analysis from the water quality sondes showed that ammonium was the main parameter determining the distribution of FIB values. Lower faecal pollution levels were detected in the main river when compared to tributaries, except for samples in the river located downstream of a wastewater treatment plant. The faecal pollution type (anthropogenic vs. zoogenic) changed the diversity and the structure of bacterial communities, giving a distinctive fingerprint that can be used to inform source. DNA-based methods showed that the presence of human-derived bacteria was associated with Escherichia coli spikes, coinciding with higher bacterial diversity and the presence of potential pathogenic bacteria mainly of the genus Mycobacterium, Aeromonas and Clostridium. Samples collected after a heavy rainfall event were associated with an increase in Bacteroidales, which are markers of faecal pollution, including Bacteroides graminisolvens, a ruminant marker associated with surface run-off from agricultural sources. The combined use of qPCR and 16S rRNA sequencing was able to identify pollution sources, and novel bacterial indicators, thereby aiding decision-making and management strategies in recreational bathing rivers.

Influence of rapid vertical mixing on bacterial community assembly in stratified water columns

Water column mixing homogenizes thermal and chemical gradients which are known to define distribution of microbial communities and influence the prevailing biogeochemical processes. Little is however known about the effects of rapid water column mixing on the vertical distribution of microbial communities in stratified reservoirs. To address this knowledge gap, physicochemical properties and microbial community composition from 16 S rRNA amplicon sequencing were analyzed before and after mixing of vertically stratified water-column bioreactors. Our results showed that α-diversity of bacterial communities decreased from bottom to surface during periods of thermal stratification. After an experimental mixing event, bacterial community diversity experienced a significant decrease throughout the water column and network connectivity was disrupted, followed by slow recovery. Significant differences in composition were seen for both total (DNA) and active (RNA) bacterial communities when comparing surface and bottom layer during periods of stratification, and when comparing samples collected before mixing and after re-stratification. The dominant predicted community assembly processes for stratified conditions were deterministic while such processes were less important during recovery from episodic mixing. Water quality characteristics of stratified water were significantly correlated with bacterial community diversity and structure. Furthermore, structural equation modeling analyses showed that changes in sulfur may have the greatest direct effect on bacterial community composition. Our results imply that rapid vertical mixing caused by episodic weather extremes and hydrological operations may have a long-term effect on microbial communities and biogeochemical processes.

Comparative analysis of hydrogen production and bacterial communities in mesophilic and thermophilic consortia using multiple inoculum sources

This study investigates the hydrogen (H2) production performance and bacterial communities in mesophilic (37 °C) and thermophilic (50 °C) H2-producing consortia derived from different inoculum sources and utilizing food waste as a substrate. This study found notable variations in H2 production characteristics among these consortia. Among the mesophilic consortia (MC), the W-MC obtained with wetland (W) as the inoculum source exhibited the highest hydrogen production (3900 mL·L-1 and 117 mL·L-1·h-1), while among the thermophilic consortia (TC), the FP-TC obtained with forest puddle sediment (FP) as the inoculum source showed the highest performance (2112 mL·L-1 and 127 mL·L-1·h-1). This study reveals that the choice of inoculum source plays a crucial role in determining hydrogen production efficiency. Furthermore, the bacterial community analysis demonstrated varying microbial diversity and richness in different inoculum sources. Clostridium, a well-known H2-producing bacterium, was found in both mesophilic and thermophilic consortia and showed a positive correlation with H2 production. Other bacteria, such as Sporanaerobacter, Caproiciproducens, and Caldibacillus, also exhibited significant correlations with H2 production, suggesting their potential roles in the process. The study highlights the complex interactions between bacterial communities and hydrogen production performance, shedding light on the critical factors influencing this renewable energy source. Overall, this study contributes to our understanding of the microbial ecology and the factors affecting hydrogen production in different temperature conditions, which can have practical implications for optimizing biohydrogen production processes using organic waste substrates.

Structures and diversities of bacterial communities in oil-contaminated soil at shale gas well site assessed by high-throughput sequencing

Currently, there is limited understanding of the structures and variabilities of bacterial communities in oil-contaminated soil within shale gas development. The Changning shale gas well site in Sichuan province was focused, and high-throughput sequencing was used to investigate the structures of bacterial communities and functions of bacteria in soil with different degrees of oil pollution. Furthermore, the influences of the environmental factors including pH, moisture content, organic matter, total nitrogen, total phosphorus, oil, and the biological toxicity of the soil on the structures of bacterial communities were analyzed. The results revealed that Proteobacteria and Firmicutes predominated in the oil-contaminated soil. α-Proteobacteria and γ-Proteobacteria were the main classes under the Proteobacteria phylum. Bacilli was the main class in the Firmicutes phylum. Notably, more bacteria were only found in CN-5 which was the soil near the storage pond for abandoned drilling mud, including Marinobacter, Balneola, Novispirillum, Castellaniella, and Alishewanella. These bacteria exhibited resilience to higher toxicity and demonstrated proficiency in oil degradation. The functions including carbohydrate transport and metabolism, energy metabolism, replication, recombination and repair replication, signal transduction mechanisms, and amino acid transport and metabolism responded differently to varying concentrations of oil. The disparities in bacterial genus composition across samples stemmed from a complex play of pH, moisture content, organic matter, total nitrogen, total phosphorus, oil concentration, and biological toxicity. Notably, bacterial richness correlated positively with moisture content, while bacterial diversity showed a significant positive correlation with pH. Acidobacteria exhibited a significant positive correlation with moisture content. Litorivivens and Luteimonas displayed a significant negative correlation with pH, while Rhizobium exhibited a significant negative correlation with moisture content. Pseudomonas, Proteiniphilum, and Halomonas exhibited positive correlations not only with organic matter but also with oil concentration. Total nitrogen exhibited a significant positive correlation with Taonella and Sideroxydans. On the other hand, total phosphorus showed a significant negative correlation with Sphingomonas. Furthermore, Sphingomonas, Gp6, and Ramlibacter displayed significant negative correlations with biological toxicity. The differential functions exhibited no significant correlation with environmental factors but displayed a significant positive correlation with the Proteobacteria phylum. Aridibacter demonstrated a significant positive correlation with cell motility and cellular processes and signaling. Conversely, Pseudomonas, Proteiniphilum, and Halomonas were negatively correlated with differential functions, particularly in amino acid metabolism, carbohydrate metabolism, and membrane transport. Compared with previous research, more factors were considered in this research when studying structural changes in bacterial communities, such as physicochemical properties and biological toxicity of soil. In addition, the correlations of differential functions of communities with environmental factors, bacterial phyla, and genera were investigated.