Microplastic-antifouling paint particle contamination alters microbial communities in surrounding marine sediment

Paint used to coat surfaces in aquatic environments often contain biocides to prevent biofouling, and as these coatings degrade, antifouling paint particles (APPs) end up in aquatic, and especially marine, sediments. However, it is currently unclear what further influence APPs in the sediment have on biotic communities or processes. This study investigates how a variety of commercially-available APPs effect the marine microbial community by spiking different laboratory-manufactured APPs to sediment. Following exposure for 30 and 60 days, APPs caused a clear and consistent effect on the bacterial community composition as determined by 16S metabarcoding. This effect was strongest between 0 and 30 days, but continues to a lesser extent between 30 and 60 days. APPs appear to inhibit the highly diverse, but in general rarer, fraction of the community and/or select for specific community members to become more dominant. 71 antifouling-presence and 454 antifouling-absence indicator taxa were identified by indicator analysis. The difference in the level of classification in these two indicator groups was highly significant, with the antifouling-presence indicators having much higher percentage sequence identity to cultured taxa, while the antifouling-absence indicators appear to be made up of undescribed taxa, which may indicate that APPs act as a proxy for general anthropogenic influence or that APP contamination selects for taxa capable of being cultured. Given the clear and consistent effect APPs have on the surrounding sediment microbial community, further research into how APPs affect sediment functional processes and how such effects scale with concentration is recommended to better assess the wider consequences of these pollutants for marine biogeochemical cycles in the future. SYNOPSIS: Microplastic-paint particles are commonly found in marine sediment but little is known about how these, especially antifouling, paint particles affect sediment microbial communities. This study demonstrates that antifouling paint particles fundamentally alter sediment microbial communities.

Unlocking the potential of bacterioplankton-mediated microcystin degradation and removal: A bibliometric analysis of sustainable water treatment strategies

Microcystins (MCs) constitute a significant threat to human and environmental health, urging the development of effective removal methods for these toxins. In this review, we explore the potential of MC-degrading bacteria as a solution for the removal of MCs from water. The review insights into the mechanisms of action employed by these bacteria, elucidating their ability to degrade and thus remove MCs. After, the review points out the influence of the structural conformation of MCs on their removal, particularly their stability at different water depths within different water bodies. Then, we review the crucial role played by the production of MCs in ensuring the survival and safeguarding of the enzymatic activities of Microcystis cells. This justifies the need for developing effective and sustainable methods for removing MCs from aquatic ecosystems, given their critical ecological function and potential toxicity to humans and animals. Thereafter, challenges and limitations associated with using MC-degrading bacteria in water treatment are discussed, emphasizing the need for further research to optimize the selection of bacterial strains used for MCs biodegradation. The interaction of MCs-degrading bacteria with sediment particles is also crucial for their toxin removal potential and its efficiency. By presenting critical information, this review is a valuable resource for researchers, policymakers, and stakeholders involved in developing sustainable and practical approaches to remove MCs. Our review highlights the potential of various applications of MC-degrading bacteria, including multi-soil-layering (MSL) technologies. It emphasizes the need for ongoing research to optimize the utilization of MC-degrading bacteria in water treatment, ultimately ensuring the safety and quality of water sources. Moreover, this review highlights the value of bibliometric analyses in revealing research gaps and trends, providing detailed insights for further investigations. Specifically, we discuss the importance of employing advanced genomics, especially combining various OMICS approaches to identify and optimize the potential of MCs-degrading bacteria.

Microbial community and antimicrobial resistance niche differentiation in a multistage, surface flow constructed wetland

Free-living (FL) and particulate-associated (PA) communities are distinct bacterioplankton lifestyles with different mobility and dissemination routes. Understanding spatio-temporal dynamics of PA and FL fractions will allow improvement to wastewater treatment processes including pathogen and AMR bacteria removal. In this study, PA, FL and sediment community composition and antimicrobial resistance gene (ARG; tetW, ermB, sul1, intI1) dynamics were investigated in a full-scale municipal wastewater free-water surface polishing constructed wetland. Taxonomic composition of PA and FL microbial communities shifted towards less diverse communities (Shannon, Chao1) at the CW effluent but retained a distinct fraction-specific composition. Wastewater treatment plant derived PA communities introduced the bulk of AMR load (70 %) into the CW. However, the FL fraction was responsible for exporting over 60 % of the effluent AMR load given its high mobility and the effective immobilization (1-3 log removal) of PA communities. Strong correlations (r2>0.8, p < 0.05) were observed between the FL fraction, tetW and emrB dynamics, and amplicon sequence variants (ASVs) of potentially pathogenic taxa, including Bacteroides, Enterobacteriaceae, Aeromonadaceae, and Lachnospiraceae. This study reveals niche differentiation of microbial communities and associated AMR in CWs and shows that free-living bacteria are a primary escape route of pathogenic and ARG load from CWs under low-flow hydraulic conditions.

Analysis of differences in microorganisms and aroma profiles between normal and off-flavor pit mud in Chinese strong-flavor Baijiu

The unique cellar fermentation process of Chinese strong-flavor Baijiu is the reason for its characteristic cellar aroma flavor. The types, abundance, community structure and metabolic activity of microorganisms in the pit mud directly affect the microbial balance in the white spirit production environment, promoting the formation of typical aromas and influencing the quality of CFSB. During the production process, the production of off-flavor in the cellar may occur. The aim of this study is to elucidate the differences in microbiota and flavor between normal pit mud and abnormal pit mud (pit mud with off-flavor). A total of 46 major volatile compounds were identified, and 24 bacterial genera and 21 fungal genera were screened. The esters, acids, and alcohols in the abnormal pit mud were lower than those in the normal pit mud, while the aldehydes were higher. 3-Methyl indole, which has been proven to be responsible for the muddy and musty flavors, was detected in both types of pit mud, and for the first time, high levels of 4-methylanisole was detected in the pit mud. The microbial composition of the two types of pit mud showed significant differences in the bacterial genera of Sporosarcina, Lactobacillus, Garciella, Anaerosalibacter, Lentimicrobium, HN-HF0106, Petrimonas, Clostridium_sensu_stricto_12 and Bacillus, and the fungal genera of Millerozyma, Penicillium, Mortierella, Monascus, Saccharomyces, Issatchenkia, Pithoascus, Pseudallescheria, and Wickerhamomyces. Additionally, we speculate that Sporosarcina is the predominant bacterial genus responsible for the imbalance of microbiota in pit mud.

Microcosm study reveals the microbial and environmental effects on tributyltin degradation in an estuarine sediment

Tributyltin (TBT) is one of the most harmful contaminants ever released into the aquatic environment. Despite being banned, it is still present at many locations throughout the world. Its degradation in sediment mainly occurs through microbial biodegradation, a process that remains unclear. This study therefore aimed at better understanding TBT biodegradation in estuarine sediment and the microbial community associated with it. Microcosm experiments were set up, embracing a range of environmental control parameters. Major community shifts were recorded, mainly attributed to the change in oxygen status. The highest percentage of degradation (36,8%) occurred at 4°C in anaerobic conditions. These results are encouraging for the in-situ bioremediation of TBT contaminated muddy sediment in temperate ports worldwide. However, with TBT able to persist in the coastal environment for decades when undisturbed in anoxic sediment, further research is needed to fully understand the mechanisms that triggered this biodegradation observed in the microcosms.

Mechanisms of microbial coexistence in a patchy ecosystem: Differences in ecological niche overlap and species fitness between rhythmic and non-rhythmic species

Resource patchiness caused by external events breaks the continuity and homogeneity of resource distribution in the original ecosystem. For local organisms, this leads to drastic changes in the availability of resources, breaks down the co-existence of species, and reshuffles the local ecosystem. West Lake is a freshwater lake with resource patchiness caused by multiple exogenous disturbances that has strong environmental heterogeneity that prevents clear observation of seasonal changes in the microbial communities. Despite this, the emergence of rhythmic species in response to irregular changes in the environment has been helpful for observing microbial communities dynamics in patchy ecosystems. We investigated the ecological mechanisms of seasonal changes in microbial communities in West Lake by screening rhythmic species based on the ecological niche and modern coexistence theories. The results showed that rhythmic species were the dominant factors in microbial community changes and the effects of most environmental factors on the microbial community were indirectly realised through the rhythmic species. Random forest analyses showed that seasonal changes in the microbial community were similarly predicted by the rhythmic species. In addition, we incorporated species interactions and community phylogenetic patterns into stepwise multiple regression analyses, the results of which indicate that ecological niches and species fitness may drive the coexistence of these subcommunities. Thus, this study extends our understanding of seasonal changes in microbial communities and provides new ways for observing seasonal changes in microbial communities, especially in ecosystems with resource patches. Our study also show that combining community phylogenies with co-occurrence networks based on ecological niches and modern coexistence theory can further help us understand the ecological mechanisms of interspecies coexistence.

Sucralose (C12H19Cl3O8) impact on microbial activity in estuarine and freshwater marsh soils

As the general population's diet has shifted to reflect current weight-loss trends, there has been an increase in zero-calorie artificial sweetener usage. Sucralose (C12H19Cl3O8), commonly known as Splenda® in the USA, is a primary example of these sweeteners. In recent years, sucralose has been identified as an environmental contaminant that cannot easily be broken down via bacterial decomposition. This study focuses on the impact of sucralose presence on microbial communities in brackish and freshwater systems. Microbial respiration and fluorescence were measured as indicators of microbial activity in sucralose-dosed samples taken from both freshwater and estuarine marsh environments. Results showed a significant difference between microbial concentration and respiration when dosed with varying levels of sucralose. Diatom respiration implied a negative correlation of community abundance with sucralose concentration. The freshwater cyanobacterial respiration increased in the presence of sucralose, implying a positive correlation of community abundance with sucralose concentration. This was in direct contrast to its brackish water counterpart. However, further investigation is necessary to confirm any potential utility of these communities in the breakdown of sucralose in the marsh environment.

Spatial distribution characteristics and interaction effects of DOM and microbial communities in kelp cultivation areas

The influence of macroalgae cultivation on aquaculture carbon sinks is significant, with microbial carbon (C) pumps contributing to a stable inert dissolved carbon pool in this context. Concurrently, dissolved organic matter (DOM) exchange at the marine sediment-water interface profoundly affects global ecosystem element cycling. However, the interactions between DOM and bacterial communities at the sediment-water interface in kelp cultivation areas, especially regarding microbial function prediction, have not been fully explored. This study analyzed the DOM characteristics, environmental factors, and bacterial community structure in the Tahewan kelp--Saccharina japonica cultivated area and compared them with those in non-cultivated areas. The results indicated significantly higher dissolved organic carbon (DOC) concentrations in the kelp culture area, particularly in surface seawater and overlying water. The dominant bacterial phyla in both regions included Pseudomonadota, Actinomycetota, and Bacteroidota in both regions, while Desulfobacterota was more prevalent in the sediment environment of the cultivated region. Parallel factor analysis (EEM-PARAFAC) was used to identify DOM components, among which component C2 (a microbial humic-like substance DOM) was highly resistant to microbial degradation. We infer that C2 has similar properties to recalcitrant dissolved organic matter (RDOM). Analysis of the predicted functional genes based on 16S rRNA gene data showed that methanol oxidation, methylotrophy, and methanotrophy were significant in the bottom seawater of the cultivation area. The carbon (C), nitrogen (N), and sulfur (S) cycle functional genes in the sediment environment of the kelp cultivation area were more active than those in other areas, especially in which sulfate reduction and denitrification were the two main processes. Furthermore, a DOM priming effect was identified in the cultivated sediment environment, where kelp-released labile dissolved organic matter (LDOM) stimulates rapid degradation of the original RDOM, potentially enhancing C sequestration.

An approach to evaluating seasonal responses to acute toxicity of antibiotic nitrofurazone on periphytic ciliated protist communities in marine environments

Periphytic protists including ciliates are the primary components of microbial communities in which they play a vital role in the progression of food webs by moving resources from lower to higher trophic levels. However, the toxic effects of veterinary antibiotics on periphytic protists across four seasons are minimally understood. Therefore, in this study, a 1-year survey was conducted with the antibiotic nitrofurazone (NFZ) applied at concentrations of 0.0, 1.5, 3.0, 6.0, and 12.0 mg/L. Samples of protist communities were collected using microscope glass slides during four seasons in the coastal waters of the Yellow Sea, Qingdao, northern China. The abundance of protists dropped with an increase in NFZ concentrations, and almost all species were dead at a concentration of 12.0 mg/L. The 12 h-LC50 values of NFZ for the protist biota were similar among the four seasons, despite significant seasonal variability in the community structure. The present results suggest that the periphytic protist biota may be used as a biomarker for assessing the ecotoxicity of NFZ in marine environments regardless of the year season.

The ecological role of microbiome at community-, taxonomic - and genome-levels in black-odorous waters

Black-odorous waters (BOWs) are heavily polluted waters where microbial information remains elusive mechanistically. Based on gene amplicon and metagenomics sequencing, a comprehensive study was conducted to investigate the microbial communities in urban and rural BOWs. The results revealed that microbial communities' assembly in urban and rural BOWs was predominantly governed by stochastic factors at the community level. At the taxonomic level, there were 62 core species (58.48%) in water and 207 core species (44.56%) in sediment across urban and rural areas. Notably, significant differences were observed in the functional genetic composition of BOWs between urban and rural areas. Specifically, rural areas exhibited an enhanced abundance of genes involved in nitrogen fixation, Fe2+ transport, and sulfate reduction. Conversely, urban areas showed higher abundances of some genes associated with carbon fixation, nitrification and denitrification. A sulfur-centered ecological model of microbial communities was constructed by integrating data from the three levels of analysis, and 14 near-complete draft genomes were generated, representing a substantial portion of the microbial community (35.04% in rural BOWs and 29.97% in urban BOWs). This research provides significant insights into the sustainable management and preservation of aquatic ecosystems affected by BOWs.

Biochar imparted constructed wetlands (CWs) for enhanced biodegradation of organic and inorganic pollutants along with its limitation

The remediation of polluted soil and water stands as a paramount task in safeguarding environmental sustainability and ensuring a dependable water source. Biochar, celebrated for its capacity to enhance soil quality, stimulate plant growth, and adsorb a wide spectrum of contaminants, including organic and inorganic pollutants, within constructed wetlands, emerges as a promising solution. This review article is dedicated to examining the effects of biochar amendments on the efficiency of wastewater purification within constructed wetlands. This comprehensive review entails an extensive investigation of biochar's feedstock selection, production processes, characterization methods, and its application within constructed wetlands. It also encompasses an exploration of the design criteria necessary for the integration of biochar into constructed wetland systems. Moreover, a comprehensive analysis of recent research findings pertains to the role of biochar-based wetlands in the removal of both organic and inorganic pollutants. The principal objectives of this review are to provide novel and thorough perspectives on the conceptualization and implementation of biochar-based constructed wetlands for the treatment of organic and inorganic pollutants. Additionally, it seeks to identify potential directions for future research and application while addressing prevailing gaps in knowledge and limitations. Furthermore, the study delves into the potential limitations and risks associated with employing biochar in environmental remediation. Nevertheless, it is crucial to highlight that there is a significant paucity of data regarding the influence of biochar on the efficiency of wastewater treatment in constructed wetlands, with particular regard to its impact on the removal of both organic and inorganic pollutants.

Associations Between Walking Speed and Gut Microbiome Composition in Older Men From the MrOS Study

BACKGROUND

Gut dysbiosis has been linked to frailty, but its association with early mobility decline is unclear.

METHODS

First, we determined the cross-sectional associations between walking speed and the gut microbiome in 740 older men (84 ± 4 years) from the MrOS cohort with available stool samples and 400 m walking speed measured in 2014-2016. Then, we analyzed the retrospective longitudinal associations between changes in 6 m walking speed (from 2005-2006 to 2014-2016, calculated by simple linear equation) and gut microbiome composition among participants with available data (702/740). We determined gut microbiome composition by 16S sequencing and examined diversity, taxa abundance, and performed network analysis to identify differences in the gut microbiome network of fast versus slow walkers.

RESULTS

Faster 400 m walking speed (m/s) was associated with greater microbiome α-diversity (R = 0.11; p = .004). The association between a slower decline in 6 m walking speed and higher α-diversity (R = 0.07; p = .054) approached borderline significance. Faster walking speed and less decline in walking speed were associated with a higher abundance of genus-level bacteria that produce short-chain fatty acids, and possess anti-inflammatory properties, including Paraprevotella, Fusicatenibacter, and Alistipes, after adjusting for potential covariates (p < .05). The gut microbiome networks of participants in the first versus last quartile of walking speed (≤0.9 vs ≥1.2 m/s) exhibited distinct characteristics, including different centrality measures (p < .05).

CONCLUSIONS

Our findings suggest a possible relationship between gut microbiome diversity and mobility function, as indicated by the associations between faster walking speed and less decline in walking speed over 10 years with higher gut microbiome diversity in older men.

Rainfall-induced changes in aquatic microbial communities and stability of dissolved organic matter: Insight from a Fen river analysis

Microbial communities are pivotal in aquatic ecosystems, as they affect water quality, energy dynamics, nutrient cycling, and hydrological stability. This study explored the effects of rainfall on hydrological and photosynthetic parameters, microbial composition, and functional gene profiles in the Fen River. Our results demonstrated that rainfall-induced decreases in stream temperature, dissolved oxygen, pH, total phosphorus, chemical oxygen demand, and dissolved organic carbon concentrations. In contrast, rainfall increased total dissolved solids, salinity, and ammonia-nitrogen concentrations. A detailed microbial community structure analysis revealed that Cyanobacteria was the dominant microbial taxon in the Fen River, accounting for approximately 75% and 25% of the microalgal and bacterial communities, respectively. The abundance of Chlorophyta and Bacillariophyta increased by 47.66% and 29.92%, respectively, whereas the relative abundance of Bacteroidetes decreased by 37.55% under rainfall conditions. Stochastic processes predominantly affected the assembly of the bacterial community on rainy days. Functional gene analysis revealed variations in bacterial functions between sunny (Sun) and rainy (Rain) conditions, particularly in genes associated with the carbon cycle. The 3-oxoacyl-[acyl-carrier-protein] reductase gene was more abundant in the Fen River bacterial community. Particular genes involved in metabolism and environmental information processing, including the acetyl-CoA C-acetyltransferase (atoB), enoyl-CoA hydratase (paaF), and branched-chain amino acid transport system gene (livK), which are integral to environmental information processing, were more abundant in Sun than the Rain conditions. In contrast, the phosphate transport system gene, the galactose metabolic gene, and the pyruvate metabolic gene were more abundant in Rain. The excitation-emission matrix analysis with parallel factor analysis identified four fluorescence components (C1-C4) in the river, which were predominantly protein- (C1) and humic-like (C2-C4) substances. Rainfall affected organic matter production and transport, leading to changes in the degradation and stability of dissolved organic matter. Overall, this study offers insight into how rainfall affects aquatic ecosystems.

Molecular and next-generation sequencing analysis of tick-borne pathogens of Rhipicephalus ticks (Acari: Ixodidae) in cattle and dogs

Ticks are small and adaptable arachnid ectoparasites and global carriers of various pathogens that threaten both human and animal health. They are present in many parts of China. A total of 858 ticks were collected from various regions and hosts, then subjected to species identification based on morphological and molecular characteristics, as described in the authors' previous study. Eighty-three individual tick samples were selected for screening pathogens based on metagenomic next-generation sequencing (mNGS) and polymerase chain reaction (PCR) assays. The genomic DNA of tick species was extracted, and amplification of the bacterial 16S rRNA gene was carried out from DNA of individual ticks using V3-V4 hypervariable regions, before subjecting to metagenomic analysis. Each tick underwent specific PCR tests for identifying the bacterial species present, including Anaplasma, Ehrlichia, Coxiella, and Rickettsia, and also protozoans such as Babesia, Theileria, and Hepatozoon. Illumina NovaSeq sequencing results revealed that the dominant phylum and family in Rhipicephalus spp. were Bacteroidota and Muribaculaceae, respectively. Alpha diversity patterns varied depending on tick sex (R. linnaei only), species and location, but not on host. Furthermore, bacterial pathogens, including A. marginale (58 %, 29/50), A. platys (6 %, 3/50), E. minasensis (2 %, 1/50), Ehrlichia sp. (10 %, 5/50), T. sinensis (24 %, 12/50), T. orientalis (54 %, 27/50) and Coxiella-like bacteria (CLB) (80 %, 40/50) were detected in R. microplus, while E. canis (33.33 %, 10/30), H. canis (20 %, 6/30) and CLB (100 %, 30/30) were detected in R. linnaei. Also, Anaplasma sp. (33.33 %, 1/3), A. marginale (33.33 %, 1/3), R. felis (33.33 %, 1/3) and CLB (100 %, 3/3) were detected in R. haemaphysaloides. Dual and triple co-infections involving pathogens or CLB were detected in 84.00 % of R. microplus, 66.66 % of R. haemaphysaloides, and 33.00 % of R. linnaei. The report on microbial communities and pathogens, which found from Rhipicephalus spp. in Hainan Island, is an important step towards a better understanding of tick-borne disease transmission. This is the first report in the area on the presence of Anaplasma sp., A. marginale, R. felis and Coxiella, in R. haemaphysaloides.

Integrated system of electro-catalytic oxidation and microbial fuel cells for the treatment of recalcitrant wastewater

The emission of recalcitrant wastewater poses serious threats to the environment. In this study, an integrated approach combining electrocatalytic oxidation (EC) for pretreatment and microbial fuel cells (MFC) for thorough pollutant degradation is proposed to ensure efficient degradation of target substances, with low energy input and enhanced bioavailability of refractory organics. When phenol was used as the pollutant, an initial concentration of 2000 mg/L phenol solution underwent EC treatment under constant current-exponential attenuation power supply mode, resulting in a COD removal rate of 54.53%, and a phenol degradation rate of 99.83%. Intermediate products such as hydroquinone and para-diphenol were detected in the solution. After subsequent MFC treatment, only minor amounts of para-diphenol were left, and the degradation rate of phenol and its intermediate products reached 100%, with an output power density of 110.4 mW m-2. When coal chemical wastewater was used as the pollutant, further examination of the EC-MFC system performance showed a COD removal rate of 49.23% in the EC section, and a 76.21% COD removal rate in the MFC section, with an output power density of 181.5 mW m-2. Microbiological analysis revealed typical electrogenic bacteria (such as Pseudomonas and Geobacter), and specific degrading functional bacteria (such as Stenotrophomonas, Delftia, and Brevundimonas). The dominant microbial communities and their proportions adapted to environmental changes in response to the variation of carbon sources.

Simultaneous removal of antibiotic resistance genes and improved dewatering ability of waste activated sludge by Fe(II)-activated persulfate oxidation

Waste activated sludge properties vary widely with different regions due to the difference in living standards and geographical distribution, making a big challenge to developing a universally effective sludge dewatering technique. The Fe(II)-activated persulfate (S2O82-) oxidation process shows excellent ability to disrupt sludge cells and extracellular polymeric substances (EPS), and release bound water from sludge flocs. In this study, the discrepancies in the physicochemical characteristics of sludge samples from seven representative cities in China (e.g., dewaterability, EPS composition, surface charge, microbial community, relative abundance of antibiotic resistance genes (ARGs), etc.) were investigated, and the role of Fe(II)-S2O82- oxidation in enhancing removal of antibiotic resistance genes and dewatering ability were explored. The results showed significant differences between the EPS distribution and chemical composition of sludge samples due to different treatment processes, effluent sources, and regions. The Fe(II)-S2O82- oxidation pretreatment had a good enhancement of sludge dewatering capacity (up to 76 %). Microbial analysis showed that the microbial community in each sludge varied significantly depending on the types of wastewater, the wastewater treatment processes, and the regions, but Fe(II)-S2O82- oxidation was able to attack and rupture the sludge zoogloea indiscriminately. Genetic analysis further showed that a considerable number of ARGs were detected in all of these sludge samples and that Fe(II)-S2O82- oxidation was effective in removing ARGs by higher than 90 %. The highly active radicals (e.g., SO4-·, ·OH) produced in this process caused drastic damage to sludge microbial cells and DNA stability while liberating the EPS/cell-bound water. Co-occurrence network analysis highlighted a positive correlation between population distribution and ARGs abundance, while variations in microbial communities were linked to regional differences in living standards and level of economic development. Despite these variations, the Fe(II)-S2O82- oxidation consistently achieved excellent performance in both ARGs removal and sludge dewatering. The significant modularity of associations between different microbial communities also confirms its ability to reduce horizontal gene transfer (HGT) by scavenging microbes.

Enhancing aerobic composting performance of high-salt oily food waste with Bacillus safensis YM1

To alleviate the inhibitory effects of salt and oil on food waste compost, the compost was inoculated with salt-tolerant and oil-degrading Bacillus safensis YM1. The YM1 inoculation could effectively improve compost maturation index. Compared with uninoculated group, the oil content and Cl- concentration in the 0.5% YM1-inoculated compost decreased significantly by 19.7% and 8.1%, respectively. The addition of the YM1 inoculant substantially altered the richness and composition of the microbial community during composting, as evidenced by the identification of 47 bacterial and 42 fungal biomarker taxa. The enrichment of some oil-degrading salt-tolerant microbes (Bacillus, Haloplasma, etc.) enhanced nutrient conversion, which is crucial for the improved maturity of the YM1 compost. This study demonstrated that YM1 could regulate both abiotic and biotic processes to improve high-salt and oily food waste composting, which may be an effective inoculant in the industrial-scale composting.

Current status and future developments of assessing microbiome composition and dynamics in anaerobic digestion systems using metagenomic approaches

The metagenomic approach stands as a powerful technique for examining the composition of microbial communities and their involvement in various anaerobic digestion (AD) systems. Understanding the structure, function, and dynamics of microbial communities becomes pivotal for optimizing the biogas process, enhancing its stability and improving overall performance. Currently, taxonomic profiling of biogas-producing communities relies mainly on high-throughput 16S rRNA sequencing, offering insights into the bacterial and archaeal structures of AD assemblages and their correlations with fed substrates and process parameters. To delve even deeper, shotgun and genome-centric metagenomic approaches are employed to recover individual genomes from the metagenome. This provides a nuanced understanding of collective functionalities, interspecies interactions, and microbial associations with abiotic factors. The application of OMICs in AD systems holds the potential to revolutionize the field, leading to more efficient and sustainable waste management practices particularly through the implementation of precision anaerobic digestion systems. As ongoing research in this area progresses, anticipations are high for further exciting developments in the future. This review serves to explore the current landscape of metagenomic analyses, with focus on advancing our comprehension and critically evaluating biases and recommendations in the analysis of microbial communities in anaerobic digesters. Its objective is to explore how contemporary metagenomic approaches can be effectively applied to enhance our understanding and contribute to the refinement of the AD process. This marks a substantial stride towards achieving a more comprehensive understanding of anaerobic digestion systems.

Distribution of mercury in modern bottom sediments of the Beaufort Sea in relation to the processes of early diagenesis: Microbiological aspect

This study investigated the contents of total mercury (THg), trace metals, and CH4 and determined the signature microbes involved in various biogeochemical processes in the sediment of the Canadian Beaufort Sea. The THg ranged between 32 and 63 μg/kg and the trace metals such as Fe, Al, Mn, and Zn were significant in distributions. The pH, SO42-, Fe2+, and redox proxy metals were crucial factors in the spatial and vertical heterogeneity of geochemical distributions. CH4 was detected only at the mud volcano site. Microbial analyses identified Clostridium, Desulfosporosinus, Desulfofustis, and Desulftiglans as the predominant Hg methylators and sulfate reducers; Nitrosopumilus and Hyphomicrobium as the major nitrifiers and denitrifiers; Methanosarcina and Methanosaeta as keystone methanogens; and Methyloceanibacter and Methyloprofundus as signature methanotrophs. Altogether, this study expands the current understanding of the microbiological and geochemical features and could be helpful in predicting ecosystem functions in the Canadian Beaufort Sea.

Soil type and moisture content alter soil microbial responses to manure from cattle administered antibiotics

Growing concerns about the global antimicrobial resistance crisis require a better understanding of how antibiotic resistance persists in soil and how antibiotic exposure impacts soil microbial communities. In agroecosystems, these responses are complex because environmental factors may influence how soil microbial communities respond to manure and antibiotic exposure. The study aimed to determine how soil type and moisture alter responses of microbial communities to additions of manure from cattle treated with antibiotics. Soil microcosms were constructed using two soil types at 15, 30, or 45% moisture. Microcosms received biweekly additions of manure from cattle given cephapirin or pirlimycin, antibiotic-free manure, or no manure. While soil type and moisture had the largest effects on microbiome structure, impacts of manure treatments on community structure and individual ARG abundances were observed across varying soil conditions. Activity was also affected, as respiration increased in the cephapirin treatment but decreased with pirlimycin. Manure from cattle antibiotics also increased NH4+ and decreased NO3- availability in some scenarios, but the effects were heavily influenced by soil type and moisture. Overall, this work demonstrates that environmental conditions can alter how manure from cattle administered antibiotics impact the soil microbiome. A nuanced approach that considers environmental variability may benefit the long-term management of antibiotic resistance in soil systems.

Combined effects of mulch film-derived microplastics and pesticides on soil microbial communities and element cycling

Pesticides and microplastics (MPs) derived from mulch film in agricultural soil can independently impact soil ecology, yet the consequences of their combined exposure remain unclear. Therefore, the effects of simultaneous exposure to commonly used pesticides (imidacloprid and flumioxazin) and aged mulch film-derived MPs on soil microorganisms and element cycles in cotton fields were investigated. The combined exposure influenced soil microorganisms, alongside processes related to carbon, nitrogen, and phosphorus cycles, exhibiting effects that were either neutralized or enhanced compared to individual exposures. The impact of pesticides in combined exposure was notably more significant and played a dominant role than that of MPs. Specifically, combined exposure intensified changes in soil bacterial community and symbiotic networks. The combined exposure neutralized NH4+, NO3-, DOC, and A-P contents, shifting from 0.33 % and 40.23 % increase in MPs and pesticides individually to a 40.24 % increase. Moreover, combined exposure resulted in the neutralization or amplification of the nitrogen-fixing gene nifH, nitrifying genes (amoA and amoB), and denitrifying genes (nirS and nirK), the carbon cycle gene cbbLG and the phosphorus cycle gene phoD from 0.48 and 2.57-fold increase to a 2.99-fold increase. The combined exposure also led to the neutralization or enhancement of carbon and nitrogen cycle functional microorganisms, shifting from a 1.53-fold inhibition and 10.52-fold increase to a 6.39-fold increase. These findings provide additional insights into the potential risks associated with combined pesticide exposure and MPs, particularly concerning soil microbial communities and elemental cycling processes.

Transition of organic matter from allochthonous to autochthonous alters benthic nutrient dynamics via microbial food webs

The impoundment of rivers by dams has significantly modified sedimentation patterns and trophic structures. As a result, the algal-derived organic matter (OM), as opposed to terrestrial-derived OM, plays an increasingly important role along the river-reservoir gradient. This study utilized water-sediment microcosms to explore the impacts of allochthonous and autochthonous OM deposition on benthic nutrient dynamics mediated by microbial food webs. Our results revealed that OM addition led to increased fluxes of NH4+ and CO2, with the highest flux induced by cyanobacteria OM, followed by diatom and allochthonous OM. N2 release flux was promoted by allochthonous and diatom OM deposition but inhibited by cyanobacteria OM deposition. The amendment of autochthonous OM increased the activity of dehydrogenase and urease, while allochthonous OM with a higher C/N ratio enhanced the catalytic abilities of polyphenol oxidase and β-glucosidase. Furthermore, OM deposition significantly reduced microbial community richness and diversity, except for eukaryotic richness, and induced pronounced changes in bacterial and eukaryotic community structures. Allochthonous OM deposition stimulated the utilization of bacteria and protozoan on native OM, resulting in a positive priming effect of 26.78 %. In contrast, diatom and cyanobacteria OM additions exerted negative priming effects of -44.53 % and -29.76 %, respectively. Bayesian stable isotope mixing models showed that diatom OM was primarily absorbed by protozoan and metazoan, while cyanobacteria OM was more easily decomposed by bacteria and transferred to higher trophic levels through microbial food webs. In addition, bacterial ammonification accounted for 74.5 % of NH4+ release in the allochthonous OM deposition treatment, whereas eukaryotic excretion contributed separately 83.3 % and 83.1 % to NH4+ release in the diatom and cyanobacteria OM addition treatments. These findings highlight the significance of accounting for the regulatory capacity of OM deposition when studying benthic metabolism within river-reservoir systems.

Ecotoxicity of five veterinary antibiotics on indicator organisms and water and soil communities

This study explores the environmental effects of five common veterinary antibiotics widely detected in the environment, (chlortetracycline,CTC; oxytetracycline,OTC; florfenicol,FF; neomycin, NMC; and sulfadiazine, SDZ) on four bioindicators: Daphnia magna, Vibrio fischeri, Eisenia fetida, and Allium cepa, representing aquatic and soil environments. Additionally, microbial communities characterized through 16 S rRNA gene sequencing from a river and natural soil were exposed to the antibiotics to assess changes in population growth and metabolic profiles using Biolog EcoPlates™. Tetracyclines are harmful to Vibrio fisheri (LC50 ranges of 15-25 µg/mL), and the other three antibiotics seem to only affect D. magna, especially, SDZ. None of the antibiotics produced mortality in E. fetida at concentrations below 1000 mg/kg. NMC and CTC had the highest phytotoxicities in A. cepa (LC50 = 97-174 µg/mL, respectively). Antibiotics significantly reduced bacterial metabolism at 0.1-10 µg/mL. From the highest to the lowest toxicity on aquatic communities: OTC > FF > SDZ ≈ CTC > NMC and on edaphic communities: CTC ≈ OTC > FF > SDZ > NMC. In river communities, OTC and FF caused substantial decreases in bacterial metabolism at low concentrations (0.1 µg/mL), impacting carbohydrates, amino acids (OTC), and polymers (FF). At 10 µg/mL and above, OTC, CTC, and FF significantly decreased metabolizing all tested metabolites. In soil communities, a more pronounced decrease in metabolizing ability, detectable at 0.1 µg/mL, particularly affected amines/amides and carboxylic and ketonic acids (p < 0.05). These new ecotoxicity findings underscore that the concentrations of these antibiotics in the environment can significantly impact both aquatic and terrestrial ecosystems.

Exploring the microbiome of coffee plants: Implications for coffee quality and production

Coffee stands as one of the world's most popular beverages, and its quality undergoes the influence of numerous pre- and post-harvest procedures. These encompass genetic variety, cultivation environment, management practices, harvesting methods, and post-harvest processing. Notably, microbial communities active during fermentation hold substantial sway over the ultimate quality and sensory characteristics of the final product. The interaction between plants and microorganisms assumes critical significance, with specific microbes assuming pivotal roles in coffee plant growth, fruit development, and, subsequently, the fruit's quality. Microbial activities can synthesize or degrade compounds that influence the sensory profile of the beverage. However, studies on the metabolic products generated by various coffee-related microorganisms and their chemical functionality, especially in building sensory profiles, remain scarce. The primary aim of this study was to conduct a literature review, based on a narrative methodology, on the current understanding of the plant-microorganism interaction in coffee production. Additionally, it aimed to explore the impacts of microorganisms on plant growth, fruit production, and the fermentation processes, directly influencing the ultimate quality of the coffee beverage. Articles were sourced from ScienceDirect, Scopus, Web of Science, and Google Scholar using specific search terms such as "coffee microorganisms", "microorganisms-coffee interactions", "coffee fermentation", "coffee quality", and 'coffee post-harvest processing". The articles used were published in English between 2000 and 2023. Selection criteria involved thoroughly examining articles to ensure their inclusion was based on results about the contribution of microorganisms to both the production and quality of the coffee beverage. The exploration of microorganisms associated with the coffee plant and its fruit presents opportunities for bioprospecting, potentially leading to targeted fermentations via starter cultures, consequently generating new profiles. This study synthesizes existing data on the current understanding of the coffee-associated microbiome, its functionalities within ecosystems, the metabolic products generated by microorganisms, and their impacts on fermentation processes and grain and beverage quality. It highlights the importance of plant-microorganism interactions in the coffee production chain.

Differences in greenhouse gas emissions and microbial communities between underground and conventionally constructed wastewater treatment plants

Large quantities of greenhouse gases (GHGs) are emitted into the atmosphere during wastewater treatment. In this study, GHG and microbial samples were collected from four wastewater treatment plants (WWTPs), and their differences and relationships were assessed. The study showed that, compared with conventionally constructed WWTPs, well-established gas collection systems in underground WWTPs facilitate comprehensive collection and accurate accounting of GHGs. In aboveground WWTPs, capped anoxic ponds promote methane production releasing it at 2-8 times the rate of uncapped emissions, in contrast to nitrous oxide emissions. Moreover, a stable subsurface environment allows for smaller fluctuations in daily GHG emissions and higher microbial diversity and abundance. This study highlights differences in GHG emission fluxes and microbial communities in differently constructed WWTPs, which are useful for control and accurate accounting of GHG emissions.

leachates from the Mexican Caribbean which are involved in their degradation in the environment, a tool to tackle the problem

The Sargassum phenomenon is currently affecting the Caribbean in several ways; one of them is the increase of greenhouse gases due to the decomposition process of this macroalgae; these processes also produce large amounts of pollutant leachates, in which several microbial communities are involved. To understand these processes, we conducted a 150-day study on the Sargassum spp environmental degradation under outdoor conditions, during which leachates were collected at 0, 30, 90, and 150 days. Subsequently, a metagenomic study of the microorganisms found in the leachates was carried out, in which changes in the microbial community were observed over time. The results showed that anaerobic bacterial genera such as Thermofilum and Methanopyrus were predominant at the beginning of this study (0 and 30 days), degrading sugars of sulfur polymers such as fucoidan, but throughout the experiment, the microbial communities were changed also, with the genera Fischerella and Dolichospermum being the most predominant at days 90 and 150, respectively. A principal component analysis (PCA) indicated, with 94% variance, that genera were positively correlated at 30 and 90 days, but not with initial populations, indicating changes in community structure due to sargassum degradation were present. Finally, at 150 days, the leachate volume decreased by almost 50% and there was a higher abundance of the genera Desulfobacter and Dolichospemum. This is the first work carried out to understand the degradation of Sargassum spp, which will serve, together with other works, to understand and provide a solution to this serious environmental problem in the Caribbean.

Microbial community dynamics and functional potentials in the conversion of oil palm wastes into biomethane

Oil palm processing generates substantial waste materials rich in organic content, posing various environmental challenges. Anaerobic digestion (AD), particularly for palm oil mill effluent (POME), offers a sustainable solution, by converting waste into valuable biomethane for thermal energy or electricity generation. The synergistic activities of the AD microbiota directly affect the biomethane production, and the microbial community involved in biomethane production in POME anaerobic digestion has been reported. The composition of bacterial and archaeal communities varies under different substrate and physicochemical conditions. This review discusses the characteristics of POME, explores the microbial members engaged in each stage of AD, and elucidates the impacts of substrate and physicochemical conditions on the microbial community dynamics, with a specific focus on POME. Finally, the review outlines current research needs and provides future perspectives on optimizing the microbial communities for enhanced biomethane production from oil palm wastes.

Revolutionizing early-stage green tide monitoring: eDNA metabarcoding insights into Ulva prolifera and microecology in the South Yellow Sea

Green tides, characterized by excessive Ulva prolifera blooms, pose significant ecological and economic challenges, especially in the South Yellow Sea. We successfully employed 18S environmental DNA (eDNA) metabarcoding to detect Ulva prolifera micropropagules, confirming the technique's reliability and introducing a rapid green tide monitoring method. Our investigation revealed notable disparities in the eukaryotic microbial community composition within Ulva prolifera habitats across different regions. Particularly, during the early stages of the South Yellow Sea green tide outbreak, potential interactions emerged between Ulva prolifera micropropagules and certain previously undocumented microorganisms from neighboring waters. These findings enhance our comprehension of early-stage green tide ecosystem dynamics, underscoring the value of merging advanced molecular techniques with conventional ecological methods to gain a comprehensive understanding of the impact of green tide on the local ecosystem. Overall, our study advances our understanding of green tide dynamics, offering novel avenues for control, ecological restoration, and essential scientific support for sustainable marine conservation and management.

Differential effects of tree species identity on rhizospheric bacterial and fungal community richness and composition across multiple trace element-contaminated sites

Soil microbial communities play a key role in plant nutrition and stress tolerance. This is particularly true in sites contaminated by trace metals, which often have low fertility and stressful conditions for woody plants in particular. However, we have limited knowledge of the abiotic and biotic factors affecting the richness and composition of microbial communities inhabiting the rhizosphere of plants in contaminated sites. Using high-throughput amplicon sequencing, we studied the rhizospheric bacterial and fungal community structures of 14 woody plant families planted in three contrasting sites contaminated by metals (Pb, Cd, Zn, Mn, Fe, S). The rhizospheric bacterial communities in the given sites showed no significant difference between the various woody species but did differ significantly between sites. The Proteobacteria phylum was dominant, accounting for over 25 % of the overall relative abundance, followed by Actinobacteria, Bacteroidetes and Gemmatimonadetes. Site was also the main driver of fungal community composition, yet unlike bacteria, tree species identity significantly affected fungal communities. The Betulaceae, Salicaceae and Fagaceae families had a high proportion of Basidiomycota, particularly ectomycorrhizal fungi, and the lowest diversity and richness. The other tree families and the unplanted soil harboured a greater abundance of Ascomycota and Mucoromycota. Consequently, for both bacteria and fungi, the site effect significantly impacted their community richness and composition, while the influence of plants on the richness and composition of rhizospheric microbial communities stayed consistent across sites and was dependent on the microbial kingdom. Finally, we highlighted the importance of considering this contrasting response of plant rhizospheric microbial communities in relation to their host identity, particularly to improve assisted revegetation efforts at contaminated sites.

Combined applications of UV and chlorine on antibiotic resistance control: A critical review

Environmental health problems caused by antibiotic-resistant bacteria (ARB) and antibiotic-resistant genes (ARGs) have become a global concern. ARB and ARGs have been continuously detected in various water environments, which pose a new challenge for water quality safety assurance. Disinfection is a key water treatment process to eliminate pathogenic microorganisms in water, and combined chlorine and UV processes (the UV/Cl2 process, the UV-Cl2 process, and the Cl2-UV process) are considered potential disinfection methods to control antibiotic resistance. This review documented the efficacy and mechanism of combined UV and chlorine processes for the control of antibiotic resistance, as well as the effects of chlorine dose, solution pH, UV wavelength, and water matrix on the effectiveness of the processes. There are knowledge gaps in research on the combined chlorine and UV processes for antibiotic resistance control, in particular the UV-Cl2 process and the Cl2-UV process. In addition, changes in the structure of microbial communities and the distribution of ARGs, which are closely related to the spread of antibiotic resistance in the water, induced by combined processes were also addressed. Whether these changes could lead to the re-transmission of antibiotic resistance and harm human health may need to be further evaluated.

The use of copper as plant protection product contributes to environmental contamination and resulting impacts on terrestrial and aquatic biodiversity and ecosystem functions

Copper-based plant protection products (PPPs) are widely used in both conventional and organic farming, and to a lesser extent for non-agricultural maintenance of gardens, greenspaces, and infrastructures. The use of copper PPPs adds to environmental contamination by this trace element. This paper aims to review the contribution of these PPPs to the contamination of soils and waters by copper in the context of France (which can be extrapolated to most of the European countries), and the resulting impacts on terrestrial and aquatic biodiversity, as well as on ecosystem functions. It was produced in the framework of a collective scientific assessment on the impacts of PPPs on biodiversity and ecosystem services in France. Current science shows that copper, which persists in soils, can partially transfer to adjacent aquatic environments (surface water and sediment) and ultimately to the marine environment. This widespread contamination impacts biodiversity and ecosystem functions, chiefly through its effects on phototrophic and heterotrophic microbial communities, and terrestrial and aquatic invertebrates. Its effects on other biological groups and biotic interactions remain relatively under-documented.

Microbial communities drive flux of acid orange 7 and crystal violet dyes in water-sediment system

Unchecked dye effluent discharge poses escalating environmental and economic concerns, especially in developing nations. While dyes are well-recognized water pollutants, the mechanisms of their environmental spread are least understood. Therefore, the present study examines the partitioning of Acid Orange 7 (AO7) and Crystal Violet (CV) dyes using water-sediment microcosms and reports that native microbes significantly affect AO7 decolorization and transfer. Both dyes transition from infused to pristine matrices, reaching equilibrium in a fortnight. While microbes influence CV partitioning, their role in decolorization is minimal, emphasizing their varied impact on the environmental fate of dyes. Metagenomic analyses reveal contrasting microbial composition between control and AO7-infused samples. Control water samples displayed a dominance of Proteobacteria (62%), Firmicutes (24%), and Bacteroidetes (9%). However, AO7 exposure led to Proteobacteria reducing to 57% and Bacteroidetes to 3%, with Firmicutes increasing to 34%. Sediment samples, primarily comprising Firmicutes (47%) and Proteobacteria (39%), shifted post-AO7 exposure: Proteobacteria increased to 53%, and Firmicutes dropped to 38%. At the genus level, water samples dominated by Niveispirillum (34%) declined after AO7 exposure, while Bacillus and Pseudomonas increased. Notably, Serratia and Sphingomonas, known for azo dye degradation, rose post-exposure, hinting at their role in AO7 decolorization. Conversely, sediment samples showed a decrease in the growth of Bacillus and an increase in that of Pseudomonas and Serratia. These findings emphasize the significant role of microbial communities in determining the environmental fate of dyes, providing insights on its environmental implications and management.

Microbial community of municipal drinking water in Hangzhou using metagenomic sequencing

While traditional culture-dependent methods can effectively detect certain microorganisms, the comprehensive composition of the municipal drinking water (DW) microbiome, including bacteria, archaea, and viruses, remains unknown. Metagenomic sequencing has opened the door to accurately determine and analyze the entire microbial community of DW, providing a comprehensive understanding of DW species diversity, especially in the context of public health concerns during the COVID-19 era. In this study, we found that most of the culturable bacteria and some fecal indicator bacteria, such as Escherichia coli and Pseudomonas aeruginosa, were non-culturable using culture-dependent methods in all samples. However, metagenomic analysis showed that the predominant bacterial species in the DW samples belonged to the phyla Proteobacteria and Planctomycetes. Notably, the genus Methylobacterium was the most abundant in all water samples, followed by Sphingomonas, Gemmata, and Azospirilum. While low levels of virulence-associated factors, such as the Esx-5 type VII secretion system (T7SS) and DevR/S, were detected, only the erythromycin resistance gene erm(X), an rRNA methyltransferase, was identified at low abundance in one sample. Hosts corresponding to virulence and resistance genes were identified in some samples, including Mycobacterium spp. Archaeal DNA (Euryarchaeota, Crenarchaeota) was found in trace amounts in some DW samples. Viruses such as rotavirus, coxsackievirus, human enterovirus, and SARS-CoV-2 were negative in all DW samples using colloidal gold and real-time reverse transcription polymerase chain reaction (RT‒PCR) methods. However, DNA encoding a new order of reverse-transcribing viruses (Ortervirales) and Herpesvirales was found in some DW samples. The metabolic pathways of the entire microbial community involve cell‒cell communication and signal secretion, contributing to cooperation between different microbial populations in the water. This study provides insight into the microbial community and metabolic process of DW in Hangzhou, China, utilizing both culture-dependent methods and metagenomic sequencing combined with bioinformatics tools during the COVID-19 pandemic era.

Broad environmental adaptation of abundant microbial taxa in Robinia pseudoacacia forests during long-term vegetation restoration

Vegetation restoration has significant impacts on ecosystems, and a comprehensive understanding of microbial environmental adaptability could facilitate coping with ecological challenges such as environmental change and biodiversity loss. Here, abundant and rare soil bacterial and fungal communities were characterized along a 15-45-year chronosequence of forest vegetation restoration in the Loess Plateau region. Phylogenetic-bin-based null model analysis (iCAMP), niche breadth index, and co-occurrence network analysis were used to assess microbial community assembly and environmental adaptation of a Robinia pseudoacacia plantation under long-term vegetation restoration. The drift process governed community assembly of abundant and rare soil fungi and bacteria. With increasing soil total phosphorus content, the relative importance of drift increased, while dispersal limitation and heterogeneous selection exhibited opposite trends for abundant and rare fungi. Rare soil fungal composition dissimilarities were dominated by species replacement processes. Abundant microbial taxa had higher ecological niche width and contribution to ecosystem multifunctionality than rare taxa. Node property values (e.g., degree and betweenness) of abundant microbial taxa were substantially higher than those of rare microbial taxa, indicating abundant species occupied a central position in the network. This study provides insights into the diversity and stability of microbial communities during vegetation restoration in Loess Plateau. The findings highlight that abundant soil fungi and bacteria have broad environmental adaptation and major implications for soil multifunctionality under long-term vegetation restoration.

Characteristics of microbial community structure and influencing factors of Yangcheng Lake and rivers entering Yangcheng Lake during the wet season

Yangcheng Lake, a typical fishery lake in the middle and lower reaches of the Yangtze River, is threatened by eutrophication. As the main performers of biogeochemical cycles, microorganisms affect the ecological stability of the lake. To study the structural characteristics of the microbial community in Yangcheng Lake and rivers entering Yangcheng Lake and the response relationship with environmental factors, the microbial community was categorized based on the contour of Yangcheng Lake, the major rivers entering Yangcheng Lake, and the pollution sources. The distribution characteristics of seven physicochemical indices were analyzed, including total organic carbon (TOC), total nitrogen (TN), total phosphorus (TP), water temperature (WT), pH, dissolved oxygen (DO), and ratio of total nitrogen to total phosphorus (TN/TP). Characterization of microbial community structure based on 16S rRNA high-flux sequencing technology and ANOSIM analysis were used to explore the differences in the relative abundance of microorganisms at each sampling point in the lake and rivers, and redundancy analysis (RDA) was used to analyze the relationship between the microbial community and physicochemical factors. The results showed that the dominant phyla, genera of microorganisms, and the total number of OTUs in the lake and rivers were similar. The dominant phyla included Proteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, and Verrucomicrobia; the dominant genera included the hgcI clade, CL500-29 marine group, Microcystis PCC-7914, Chloroplast_norank, Clade III_norank, and Flavobacterium. ANOSIM analyses revealed that the microbial community of Yangcheng Lake exhibited an association with geographical space, while the microbial community in the rivers that was linked to the type of pollution source. Redundancy analysis (RDA) indicated that dissolved oxygen (DO), total nitrogen (TN), and pH were significantly correlated with the dominant phyla in Yangcheng Lake (p < 0.05), while total nitrogen (TN), water temperature(WT), and the ratio of total nitrogen to total phosphorus (TN/TP) were significantly related with the dominant genera in Yangcheng Lake (p < 0.05). Total nitrogen (TN) was also significantly linked to the dominant phyla and genera of the tributaries (p < 0.05). Despite the structural similarities in microbial communities between Yangcheng Lake and its inflowing rivers, environmental factors demonstrated significant associations with these communities, providing crucial data support for pollution prevention and the ecological restoration of Yangcheng Lake.

The soil microbial necromass carbon and the carbon pool stability drive a stronge priming effect following vegetation restoration

The priming effect stands as a critical factor influencing the balance of soil organic carbon (SOC). Following vegetation restoration, the carbon (C) pool stability in Platycladus orientalis forests (PO) varies, and the priming effect resulting from exogenous C addition also differs significantly. Here, we selected PO with restoration ages of 10, 15, and 30 years in the rocky mountainous area in northern China and conducted measurements of soil properties, microbial communities, microbial necromass C (MNC), SOC fractions, and the priming effect characteristics to explore the main influencing factors of the priming effect, especially the microbiological mechanisms. Our results showed that the ratio of mineral-associated organic C to particulate organic C increased. The characteristics of the priming effect showed the same pattern, and there was a significant positive correlation between the C pool stability and the priming effect. The diversity of the fungal communities increased with increasing vegetation restoration age, and the content and proportion of fungal necromass C (FNC) also increased synchronously, reaching the maximum value in the soil of PO that had been restored for 30 years. In addition, the soil water content and total nitrogen indirectly affected the priming effect by influencing the microbial communities. In summary, the results suggested that vegetation restoration can enhance the C pool stability by promoting an increase in soil FNC, thereby producing a positive priming effect. This can help deepen our understanding of the SOC mineralization changes induced by fresh C input following vegetation restoration and provides a theoretical basis for better explaining the C cycle between soil and atmosphere under the vegetation restoration models in the future.

Effects of microbubble pretreatment on physiochemical and microbial properties of excess activated sludge

Fast increased amount of excess activated sludge (EAS) from wastewater treatment plants has aroused universal concerns on its environmental risks and demands for appropriate treatments, while effective treatment is dependent upon proper pretreatment. In this study, air-supplied microbubbles (air-MBs) with generated size of 25.18 to 28.25 μm were used for EAS pretreatment. Different durations (30, 60, 90, and 120 s) yielded sludge with varied physiochemical conditions, and 60 s decreased sludge oxidation status and significantly increased adenosine triphosphate (ATP) content. Soluble, loosely-bound, and tightly-bound extracellular polymeric substances (SEPS, LB-EPS, and TB-EPS) were extracted from the sludge through a stepwise approach and examined through three-dimensional excitation-emission matrix (3D-EEM) and quantitative analysis. The results showed that 60- and 120-s treatments generated stronger fluorescence intensities on dissolved organic matters (DOMs) of protein-like and fulvic acid in LB-EPS and TB-EPS, which indicated the decrease of counterparts in EAS, and therefore facilitated sludge dewaterability and reduction. The dominant microbial communities in EAS, including Proteobacteria, Bacteroidota, Chloroflexi, and Actinobacteriota, were not significantly affected by MB pretreatment. The results collectively revealed the effects of MB pretreatment on EAS and indicated that MBs could be an effective pretreatment technique for EAS treatment process.

Flux sampling in genome-scale metabolic modeling of microbial communities

BACKGROUND

Microbial communities play a crucial role in ecosystem function through metabolic interactions. Genome-scale modeling is a promising method to understand these interactions and identify strategies to optimize the community. Flux balance analysis (FBA) is most often used to predict the flux through all reactions in a genome-scale model; however, the fluxes predicted by FBA depend on a user-defined cellular objective. Flux sampling is an alternative to FBA, as it provides the range of fluxes possible within a microbial community. Furthermore, flux sampling can capture additional heterogeneity across a population, especially when cells exhibit sub-maximal growth rates.

RESULTS

In this study, we simulate the metabolism of microbial communities and compare the metabolic characteristics found with FBA and flux sampling. With sampling, we find significant differences in the predicted metabolism, including an increase in cooperative interactions and pathway-specific changes in predicted flux.

CONCLUSIONS

Our results suggest the importance of sampling-based approaches to evaluate metabolic interactions. Furthermore, we emphasize the utility of flux sampling in quantitatively studying interactions between cells and organisms.

Humic acid biosynthesis and bacterial community evolution during aerobic composting of rice straw

In this study, the effects of inoculum ratio, substrate particle size and aeration rate on humic acid (HA) biosynthesis during aerobic composting of rice straw were investigated, respectively. The contents of total organic carbon, total nitrogen and HA, as well as lignocellulose degradation in the composting were evaluated, respectively. It is found that the maximal HA yield of 356.9 g kg-1 was obtained at an inoculum ratio of 20%, a substrate particle size of 0.83 mm and an aeration rate of 0.3 L·kg-1 DM min-1 in the process of composting. The changes of microbial communities and metabolic functions at different stages of the composting were also analyzed through high-throughput sequencing. The result demonstrates that Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria were the dominant phyla and their relative abundance significantly varied over time (p < 0.05), and Rhizobium, Phenylobacterium, Pseudoxanthomonas and Paenibacillus were positively related to HA content in the compost. Furthermore, the metabolic function profiles of bacterial community indicate that these functional genes in carbohydrate metabolism and amino acid metabolism were involved in lignocellulose biodegradation and HA biosynthesis. This work may be conducive to explore new regulation strategy to improve bioconversion efficiency of agricultural residues to applicable biofertilizers. KEY POINTS: • Temperature, pH, TOC, TN and C/N caused a great influence on humic acids synthesis • The succession of the microbial community during the composting were evaluated • The metabolisms of carbohydrate and amino acids were involved in HA synthesis.

Machine learning modeling for the prediction of phosphorus and nitrogen removal efficiency and screening of crucial microorganisms in wastewater treatment plants

The effectiveness of wastewater treatment plants (WWTPs) is largely determined by the microbial community structure in their activated sludge (AS). Interactions among microbial communities in AS systems and their indirect effects on water quality changes are crucial for WWTP performance. However, there is currently no quantitative method to evaluate the contribution of microorganisms to the operating efficiency of WWTPs. Traditional assessments of WWTP performance are limited by experimental conditions, methods, and other factors, resulting in increased costs and experimental pollutants. Therefore, an effective method is needed to predict WWTP efficiency based on AS community structure and quantitatively evaluate the contribution of microorganisms in the AS system. This study evaluated and compared microbial communities and water quality changes from WWTPs worldwide by meta-analysis of published high-throughput sequencing data. Six machine learning (ML) models were utilized to predict the efficiency of phosphorus and nitrogen removal in WWTPs; among them, XGBoost showed the highest prediction accuracy. Cross-entropy was used to screen the crucial microorganisms related to phosphorus and nitrogen removal efficiency, and the modeling confirmed the reasonableness of the results. Thirteen genera with nitrogen and phosphorus cycling pathways obtained from the screening were considered highly appropriate for the simultaneous removal of phosphorus and nitrogen. The results showed that the microbes Haliangium, Vicinamibacteraceae, Tolumonas, and SWB02 are potentially crucial for phosphorus and nitrogen removal, as they may be involved in the process of phosphorus and nitrogen removal in sewage treatment plants. Overall, these findings have deepened our understanding of the relationship between microbial community structure and performance of WWTPs, indicating that microbial data should play a critical role in the future design of sewage treatment plants. The ML model of this study can efficiently screen crucial microbes associated with WWTP system performance, and it is promising for the discovery of potential microbial metabolic pathways.

Enhancement of nitrogen cycling and functional microbial flora by artificial inoculation of biological soil crusts in sandy soils of highway slopes

Biological soil crusts (BSCs) are common in arid and semi-arid ecosystems and enhance soil stability and fertility. Highway slopes severely deplete the soil ecological structure and soil nutrients, hindering plant survival. The construction of highway slope BSCs under human intervention is critical to ensure the long-term stable operation of the slope ecosystem. This study investigated the variation rules and interaction mechanisms between soil nutrients and microbial communities in the subsoil BSCs on highway slopes. Bacterial 16S rRNA high-throughput sequencing was employed to investigate the dynamic compositional changes in the microbial community and perform critical metabolic predictive analyses of functional bacteria. This study revealed that the total soil nitrogen increased significantly from 0.557 to 0.864 g/kg after artificial inoculation with desert Phormidium tenue and Scytonema javanicum. Actinobacteria (44-48%) and Proteobacteria (28-31%) were the dominant phyla in all samples. The abundance of Cyanobacteria, Cytophagaceae, and Chitinophagaceae increased significantly after inoculation. PICRUST analysis showed that the main metabolic pathways of soil microorganisms on highway slopes included cofactor and vitamin, nucleotide, and amino acid metabolisms. These findings suggest that the artificial inoculation with Phormidium tenue and Scytonema javanicum could alter soil microbial distribution to promote soil development on highway slopes toward nutrient accumulation.

Linking the impact of bacteria on phytoplankton growth with microbial community composition and co-occurrence patterns

The interactions between microalgae and bacteria have recently emerged as key control factors which might contribute to a better understanding on how phytoplankton communities assemble and respond to environmental disturbances. We analyzed partial 16S rRNA and 18S rRNA genes from a total of 42 antibiotic bioassays, where phytoplankton growth was assessed in the presence or absence of an active bacterial community. A significant negative impact of bacteria was observed in 18 bioassays, a significant positive impact was detected in 5 of the cases, and a non-detectable effect occurred in 19 bioassays. Thalasiossira spp., Chlorophytes, Vibrionaceae and Alteromonadales were relatively more abundant in the samples where a positive effect of bacteria was observed compared to those where a negative impact was observed. Phytoplankton diversity was lower when bacteria negatively affect their growth than when the effect was beneficial. The phytoplankton-bacteria co-occurrence subnetwork included many significant Chlorophyta-Alteromonadales and Bacillariophyceae-Alteromonadales positive associations. Phytoplankton-bacteria co-exclusions were not detected in the network, which contrasts with the negative effect of bacteria on phytoplankton growth frequently detected in the bioassays, suggesting strong competitive interactions. Overall, this study adds strong evidence supporting the key role of phytoplankton-bacteria interactions in the microbial communities.

Simultaneous selenite reduction and nitrogen removal using Paracoccus sp.: Reactor performance, microbial community, and mechanism

Selenium-containing wastewater has a high concentration of nitrogen compounds (ammonia nitrogen [NH4+-N]), leading to water pollution. Thus, the simultaneous reduction of selenium and removal of nitrogen compounds during wastewater treatment has become the top priority. However, the exogenous bacteria that can simultaneously reduce selenite and remove ammonia nitrogen and colonize in the wastewater treatment systems have not been reported. Additionally, the effects and the underlying mechanism of biofortification on the reduction and removal efficiency of the microorganisms remain unclear. In this study, we investigated the simultaneous selenite reduction and nitrogen removal efficiency of Paracoccus sp. (strain SSJ) isolated from selenium-contaminated soil and explored biofortification effects on the composition and structure of the microbial community. Using sequencing biofilm batch reactors (SBBRs), the structural and functional characteristics of the microbial community were systematically compared between the control (group A) and biofortified (group B) groups. Strain SSJ could simultaneously reduce 63.28% of selenite and remove 93.05% of NH4+-N within 24 h. Moreover, no accumulation of nitrate nitrogen (NO3--N) and nitrite nitrogen (NO2--N) was observed in the reaction process. The performance and stability of the SBBRs enhanced by strain SSJ were greatly improved. Illumina sequencing results showed that strain SSJ was surprisingly colonized, and Paracoccus was the predominant genus in group B (relative abundance: 13.93%). Moreover, PICRUSt2 analysis results suggested that the microbial community in group B demonstrated increased rates of ammonia nitrogen removal through ammonia assimilation and selenite reduction through sulfur metabolism and glutathione-mediated selenite reduction pathway. In summary, our findings shed light on the mechanism for simultaneous selenite reduction and nitrogen removal by biofortification and provide novel microbial resources for the treatment of selenite-containing wastewater.

Effect of bioturbation of the mitten crab on distribution of tire wear particles and their combined effect on sediment ecosystem

Tire wear particles (TWPs) are a major source of environmental microplastic pollution which gradually settle and accumulate in sediments after entering the aquatic environment, which can affect the behaviors of benthic organisms. Bioturbation of benthic species could affect the fate, impacts and potential risks of TWPs by altering the properties and structure of sediments. Therefore, in this study, the effect of TWPs on the burrowing activity of Chinese mitten crab (Eriocheir sinensis) was investigated. In addition, the effects of crab bioturbation on the distribution of TWPs and their additives were studied. The combined effects of TWPs and crab bioturbation on the microbial communities in the sediments were also explored. The results of this study showed that both TWPs and the leachate significantly inhibited the burrowing activity of crabs. TWPs in the surface layer of sediments were re-distributed by crab bioturbation and enriched mainly in the sediments near the burrow walls. Meanwhile, the heavy metals (i.e., Zn, Ca, Mg, Ba and Al) used as additives during the tire production in the burrow walls significantly increased as the accumulation of TWPs near burrow walls. In this study, TWP exposure decreased the bacterial diversity and abundance, as well as the functional genes related to carbon and nitrogen cycling process, but crab bioturbation increased them in the sediments of burrow walls by constructing a unique habitat. However, after TWPs entering into burrows, they were significantly decreased in the sediments near the burrow walls like the effects of TWPs, suggesting the negative effects of TWPs could play a dominant role in this combined system. Overall, this study is important for evaluating the distribution and effects of TWP pollution in the sediment ecosystem under biological factors such as bioturbation.

Unveiling the biogeochemical mechanism of nitrate in the vadose zone-groundwater system: Insights from integrated microbiology, isotope techniques, and hydrogeochemistry

Clarifying the biogeochemical mechanism of nitrate (NO3-) in the vadose zone-groundwater system, particularly in agricultural contexts, is crucial for mitigating groundwater NO3- pollution. However, comprehensive studies on the impacts of changes in chemical indicators and microbial communities on NO3- are still lacking. This paper aims to address this gap by employing hydrogeochemistry, stable isotopes, and microbial techniques to assess the NO3- biogeochemical processes in the vadose zone-groundwater system. The findings suggested that NO3- in upper soil layers was primarily influenced by plant root absorption, assimilation, and nitrification processes. The oxygen contents gradually decreased with the nitrification process, resulting in the occurrence of the denitrification. However, denitrification predominantly occurred in the 60-80 cm soil layer in the study area. The limited thickness of the denitrification layer results in less NO3- consumption, leading to increased NO3- leaching into groundwater. Hydrochemical and isotopic characteristics further indicated that groundwater NO3- concentrations were mainly controlled by nitrification, followed by denitrification and mixing processes. The 16S rRNA sequencing analysis revealed great influences of soil sampling depths and groundwater NO3- concentrations on the microbial community structure. Additionally, the PICRUSt2-based prediction results demonstrated a stronger potential for dissimilatory reduction of NO3- to ammonium (DNRA) in both soil and groundwater compared to the other processes, potentially due to the widespread presence of the nrfH functional genes. However, the chemical indicators and isotopes used in this study did not support the occurrence of DNRA process in the vadose zone-groundwater system. This finding highlights the importance of an integrated approach combining microbiological, isotopic, and hydrogeochemical data to comprehensive understanding biogeochemical processes. The study developed a conceptual model elucidating the NO3- biogeochemical processes in the vadose zone-groundwater system within an agricultural area, contributing to enhanced comprehension and advancement of sustainable management practices for groundwater nitrogen.

Forest swamp succession alters organic carbon composition and survival strategies of soil microbial communities

Forest swamp ecosystems plays crucial role in the global carbon cycle. However, the effects of forest swamp succession on soil organic matter (SOM) and microbial community structure remain unclear. To determine the drivers of SOM change and soil microbial communities in forest swamp succession, a 'space instead of time' approach was used. Soil samples from 0 to 40 cm were collected along forest swamp (early stage), dried-up forest swamp (middle stage), and forest (late stage) ecosystems. Our findings reveal that as succession progresses, the relative content of aromatics decreases and SOM undergoes a transition towards a more readily degradable form. These changes affect soil carbon sequestration and nutrient availability. Bacterial diversity was significantly influenced by succession and changes in soil depth, with fungi exhibiting higher resilience. Soil properties and environmental conditions exert influence over the structure and function of microorganisms. As succession occurred, microbial interactions shifted from cooperation to competition, with bacteria displaying a deterministic distribution pattern and fungi exhibiting a random distribution pattern. SOM quality plays a key role in shaping microbial communities and influencing their growth strategies. Microorganisms are the major drivers of soil respiration, with K-strategist dominated communities in early succession exhibiting slower degradation rates, whereas r-strategists dominated in later stages, leading to faster decomposition.

Soil aggregate-driven changes in nutrient redistribution and microbial communities after 10-year organic fertilization

Research studies on nutrient content and microbial communities after the application of organic manure have been reported, while available information about multi-interaction mechanisms of nutrient stoichiometry and microbial succession in soil aggregates remains limited. This work conducted a 10-year field experiment amended with cow manure (1.5 t/ha), during which the application of organic manure stimulated the fragmentation of soil macro-aggregates (>5 mm) and the agglomeration of soil micro-aggregates (<0.25 mm). Hence, the proportion of medium-size aggregates (0.25-5 mm) was increased in bulk soil, and there was an insignificant difference in the stability of soil aggregates. Meanwhile, the application of organic manure increased soil organic carbon (SOC), total nitrogen (TN) and phosphorus (TP) in all soil aggregate fractions. SOC, TN and TP were higher in micro-aggregates (<0.25 mm) after the application of organic manure, thus the dominating phylum of bacteria and fungi was more abundance in micro-aggregates due to the increase in nutrient level. During the organic fertilization process, fungal communities significantly changed because the variation of carbon-to-nitrogen ratio (C:N) in soil aggregates. Cultivated farmland in Northeast China showed a considerable capacity to sequestrate SOC during the organic fertilization process, but nitrogen may be a primary macro-element limiting soil productivity. Theoretically, organic manure amended with nitrogen fertilizer could be an effective measure to maintain microbial diversity and crop productivity in agro-ecosystems in Northeast China.

Vertical connectivity of microbiome and metabolome reveals depth-dependent variations across a deep cold-seep water column

Deciphering the vertical connectivity of oceanic microbiome and metabolome is crucial for understanding the carbon sequestration and achieving the carbon neutrality. However, we lack a systematic view of the interplay among particle transport, microbial community, and metabolic trait across depths. Through integrating the biogeochemical, microbial, and metabolic characteristics of a deep cold-seep water column (∼1989 m), we find the altered connectivity of microbial community and dissolved organic matter (DOM) across depths. Both the microbial communities (bacteria and protists) and DOM show a clear compositional connectivity from surface to the depth of 1000 m, highlighting the controls of sinking particle over microbial connectivity from the epipelagic to mesopelagic zone. However, due to the biological migration and ocean mixing, the fecal-associated bacteria and protistan consumers unexpectedly emerge and the degradation index of DOM substantially alters around 1000-1200 m. Collectively, we unveil the significance of multi-faceted particle dispersion, which supports the connectivity and variability of deep ocean microbial communities.

Metabolites and metagenomic analysis reveals the quality of Pu-erh "tea head"

Tea head, a derivative product of Pu-erh tea, are tight tea lumps formed during pile-fermentation. The aim of this study was to reveal the differences of quality-related metabolites and microbial communities between ripened Pu-erh tea (PE-21) and tea heads (CT-21). Compared with PE-21, CT-21 showed a more mellow and smooth taste with slight bitterness and astringency, and can withstand multiple infusions. Metabolites analysis indicated CT-21 had more abundant water-soluble substances (47.39%) and showed significant differences with PE-21 in the main compositions of amino acids, catechins and saccharides which contributed to the viscosity of tea liquor, mellow taste and the tight tea lumps formation. Microbial communities and COG annotation analysis revealed CT-21 had lower abundance of Bacteria (84.05%), and higher abundance of Eukaryota (15.10%), carbohydrate transport and metabolism (8.28%) and glycoside hydrolases (37.36%) compared with PE-21. The different microbial communities may cause metabolites changes, forming distinct flavor of Pu-erh.

Formation characteristics of bacteria and fungi in sewers: In terms of signal molecule generation

Bio-metabolism of diverse communities is the main reason of water quality variation in sewers, and the signal molecule generation of communities is dementated to be the key regulation procedure for community metabolism. To reveal the mechanism of pollutant biotransformation in complex sewer environment, this study explored the formation of bacteria and fungi and the signal molecule transduction characteristics in a pilot sewer. In this study, several kinds of signal molecules that produced by bacteria and fungi (C4-HSL, C6-HSL, C8-HSL, farnesol and tyrosol) were detected along the formation process of sewer biofilms. The results showed that, in the early stage, bacterial AHLs signaling molecules are beneficial to the synthesis of EPS, providing a good material basis for the growth of bacterial flora. In addition, tyrosol stimulates the formation of embryonic tubes in yeast cells, further promoting the growth of hyphae. At the later stage, AHLs signaling molecules and tyrosol jointly promoted the growth of biofilms. In conclusion, it is precisely because of the coexistence of bacteria and fungi in the sewer system that the generated signal molecules can jointly promote the synthesis and growth of biofilms through different pathways, and have positive feedback on the biodegradation of various pollutants. Based on the exploration, the ecological patterns of bacterial-fungal communities in urban sewer system were proposed and it could improve the understanding on the pollutant transformation behaviors in sewers.