Changes In Microbial Community Composition Research Articles

Structure and composition of microbial communities in the water column from Southern Gulf of Mexico and detection of putative hydrocarbon-degrading microorganisms.

This study assessed the bacterioplankton community and its relationship with environmental variables, including total petroleum hydrocarbon (TPH) concentration, in the Yucatan shelf area of the Southern Gulf of Mexico. Beta diversity analyses based on 16S rRNA sequences indicated variations in the bacterioplankton community structure among sampling sites. PERMANOVA indicated that these variations could be mainly related to changes in depth (5 to 180 m), dissolved oxygen concentration (2.06 to 5.93 mg L-1), and chlorophyll-a concentration (0.184 to 7.65 mg m3). Moreover, SIMPER and one-way ANOVA analyses showed that the shifts in the relative abundances of Synechococcus and Prochlorococcus were related to changes in microbial community composition and chlorophyll-a values. Despite the low TPH content measured in the studied sites (0.01 to 0.86 μL L-1), putative hydrocarbon-degrading bacteria such as Alteromonas, Acinetobacter, Balneola, Erythrobacter, Oleibacter, Roseibacillus, and the MWH-UniP1 aquatic group were detected. The relatively high copy number of the alkB gene detected in the water column by qPCR and the enrichment of hydrocarbon-degrading bacteria obtained during lab crude oil tests exhibited the potential of bacterioplankton communities from the Yucatan shelf to respond to potential hydrocarbon impacts in this important area of the Gulf Mexico.

Effects of denitrification on speciation and redistribution of arsenic in estuarine sediments

Microbially-mediated redox processes involving arsenic (As) and its host minerals significantly contribute to the mobilization of As in estuarine sediments. Despite its significance, the coupling between As dynamics and denitrification processes in these sediments is not well understood. This study employed sequential sediment extractions and simultaneous monitoring of dissolved iron (Fe), nitrogen (N), and sulfur (S) to investigate the impact of nitrate (NO3−) on the speciation and redistribution of As, alongside changes in microbial community composition. Our results indicated that NO3− additions significantly enhance anaerobic arsenite (As(III)) oxidation, facilitating its immobilization by increased adsorption onto sediment matrices in As-contaminated estuarine settings. Furthermore, NO3− promoted the conversion of As bound to troilite (FeS) and pyrite (FeS2) into forms associated with Fe oxides, challenging the previously assumed stability of FeS/FeS2-bound As in such environments. Continuous NO3− additions ensured As and Fe oxidation, thereby preventing their reductive dissolution and stabilizing the process that reduces As mobility. Changes in the abundance of bacterial communities and correlation analyses revealed that uncultured Anaerolineaceae and Thioalkalispira may be the main genus involved in these transformations. This study underscores the critical role of NO3− availability in modulating the biogeochemical cycle of As in estuarine sediments, offering profound insights for enhancing As immobilization techniques and informing environmental management and remediation strategies in As-contaminated coastal regions.

Spontaneous fermentation mitigates the frequency of genes encoding antimicrobial resistance spreading from the phyllosphere reservoir to the diet

The phyllosphere microbiome of vegetable products constitutes an important reservoir for multidrug resistant bacteria and Antibiotic Resistance Genes (ARG). Vegetable products including fermented products such as Paocai therefore may serve as a shuttle for extrinsic microorganisms with ARGs into the gut of consumers. Here we study the effect of fermentation on Paocai ARG dissemination by metagenomic analysis. Microbial abundance and diversity of the Paocai microbiome were diminished during fermentation, which correlated with the reduction of abundance in ARGs. Specifically, as fermentation progressed, Enterobacterales overtook Pseudomonadales as the predominant ARG carriers, and Lactobacillales and Enterobacteriales became the determinants of Paocai resistome variation. Moreover, the dual effect of microbes and metal resistance genes (MRGs) was the major contributor driving Paocai resistome dynamics. We recovered several metagenome-assembled genomes (MAGs) carrying acquired ARGs in the phyllosphere microbiome. ARGs of potential clinical and epidemiological relevance such as tet M and emrB-qacA, were mainly hosted by non-dominant bacterial genera. Overall, our study provides evidence that changes in microbial community composition by fermentation aid in constraining ARG dispersal from raw ingredients to the human microbiome but does not eliminate them.

The Effects of Mine Waste and Rain Water on the Structure of Bacteria Community of Paddy Soils

ABSTRACT Heavy metal contamination of soil has become one of the most important environmental problems worldwide. Heavy metals can affect growth and lead to changes in microbial community composition, which could influence the growth of crops in the soil. In this study, we conducted an experiment to investigate the distribution profile of heavy metals and bacterial communities in soil with the effects of slag and/or water on the top of the soil. Extra heavy metals, acting as selective pressure, led to the loss of sensitive taxa, with tolerant or less sensitive taxa being more abundant in the community. The results showed that the addition of slag on the top of soils did not change the diversity of bacteria but influenced the relative abundance of indigenous members in the community. Water addition, however, improved the homogeneity of the environment vertically in the soil, which consequently led to a lower variation in the bacterial community. This study mimicked the scenario of tailings and abandoned mines in nature, and aimed to study the effects of mines on the soil microbial community with the influence of precipitation on the distribution of heavy metals in the soil. With the effect of precipitation, the transportation of heavy metals in the slag may influence the local bacterial community and subsequently undermine the quality of soil for agriculture. These observations provide evidence of the effects of heavy metals on the soil around abandoned mines without any treatment. Mining causes both heavy metal and water pollution, which may lead to the accumulation of heavy metals in plants and agricultural production. Therefore, it is necessary to take care of tailings with proper procedures instead of exposing them to nature.

Redox mediator chlorophyll accelerates low-temperature biological denitrification with responses of extracellular polymers and changes in microbial community composition

Low temperatures limit the denitrification wastewater in activated sludge systems, but this can be mitigated by addition of redox mediators (RMs). Here, the effects of chlorophyll (Chl), 1,2-naphthoquinone-4-sulfonic acid (NQS), humic acid (HA), and riboflavin (RF), each tested at three concentrations, were compared for denitrification performance at low temperature, by monitoring the produced extracellular polymeric substances (EPS), and characterizing microbial communities and their metabolic potential. Chl increased the denitrification rate most, namely 4.12-fold compared to the control, followed by NQS (2.62-fold increase) and HA (1.35-fold increase), but RF had an inhibitory effect. Chl promoted the secretion of tryptophan-like and tyrosine-like proteins in the EPS and aided the conversion of protein from tightly bound EPS into loosely bound EPS, which improved the material transfer efficiency. NQS, HA, and RF also altered the EPS components. The four RMs affected the microbial community structure, whereby both conditionally abundant taxa (CAT) and conditionally rare or abundant taxa (CRAT) were key taxa. Among them, CRAT members interacted most with the other taxa. Chl promoted Flavobacterium enrichment in low-temperature activated sludge systems. In addition, Chl promoted the abundance of nitrate reduction genes narGHI and napAB and of nitrite reduction genes nirKS, norBC, and nosZ. Moreover, Chl increased abundance of genes involved in acetate metabolism and in the TCA cycle, thereby improving carbon source utilization. This study increases our understanding of the enhancement of low-temperature activated sludge by RMs, and demonstrates positive effects, in particular by Chl.

Consecutive Fertilization-Promoted Soil Nutrient Availability and Altered Rhizosphere Bacterial and Bulk Fungal Community Composition

Fertilization is an important measure to quickly supplement the soil nutrients required for plantation productivity. However, the response patterns of the microbial community and functional taxa in Larix plantation root, rhizosphere, and bulk soil to short-term and consecutive fertilization have rarely been reported. In this study, we assessed Larix root, rhizosphere, and bulk soil microbial community on days 0, 5, 15, and 30 after the first inorganic fertilization and after three consecutive years of fertilization. The bacterial 16S and fungal ITS high-throughput sequencing technology were used to monitor changes in microbial community composition and potential functional groups, as well as changes in soil nutrient content and enzyme activity to evaluate the status of plantation soil productivity. Consecutive fertilization treatment significantly increased the available nitrogen, phosphorus, and potassium (NPK) content and soil enzyme activity. The nonmetric multidimensional scaling (NMDS) and analysis of similarities (ANOSIM) results showed that there were significant differences in microbial community composition in root samples, rhizosphere soil, and bulk soil samples. The dominant microbial taxa were different between root and soil microbial community composition. Consecutive fertilization treatment had little effect on endophytic microbial community but significantly increased the abundance of Gaiellales in rhizosphere soil and Mortierella in bulk soil. The redundancy analysis (RDA) and co-occurrence network analyses showed that Gaiellales and Mortierellales had significant positive correlations with soil nutrient content and enzyme activity. The fungal functional group compositions were significantly affected by consecutive fertilization treatment and the proportions of ectomycorrhizal and saprotroph significantly decreased, but the proportion of endophyte significantly increased in bulk soil samples. Our results suggested that consecutive fertilization may promote soil nutrient availability by increasing the abundance of Gaiellales and Mortierella. Consecutive fertilization maintained the balance of the soil microbiota under Larix plantation and had a positive effect on promoting soil nutrient availability. This study provided a theoretical basis for consecutive fertilization to promote soil nutrient availability through specific microbial groups.

Impact of dry density and incomplete saturation on microbial growth in bentonite clay for nuclear waste storage.

Many countries are in the process of designing a deep geological repository (DGR) for long-term storage of used nuclear fuel. For several designs, used fuel containers will be placed belowground, with emplacement tunnels being backfilled using a combination of highly compacted powdered bentonite clay buffer boxes surrounded by a granulated "gapfill" bentonite. To limit the potential for microbiologically influenced corrosion of used fuel containers, identifying conditions that suppress microbial growth is critical for sustainable DGR design. This study investigated microbial communities in powdered and gapfill bentonite clay incubated in oxic pressure vessels at dry densities between 1.1g cm-3 (i.e. below repository target) and 1.6g cm-3 (i.e. at or above repository target) as a 1-year time series. Our results showed an initial (i.e. 1 month) increase in the abundance of culturable heterotrophs associated with all dry densities <1.6g cm-3, which reveals growth during transient low-pressure conditions associated with the bentonite saturation process. Following saturation, culturable heterotroph abundances decreased to those of starting material by the 6-month time point for all 1.4 and 1.6g cm-3 pressure vessels, and the most probable numbers of culturable sulfate-reducing bacteria (SRB) remained constant for all vessels and time points. The 16S rRNA gene sequencing results showed a change in microbial community composition from the starting material to the 1-month time point, after which time most samples were dominated by sequences associated with Pseudomonas, Bacillus, Cupriavidus, and Streptomyces. Similar taxa were identified as dominant members of the culture-based community composition, demonstrating that the dominant members of the clay microbial communities are viable. Members of the spore-forming Desulfosporosinus genus were the dominant SRB for both clay and culture profiles. After initial microbial growth while bentonite was below target pressure in the early phases of saturation, microbial growth in pressure vessels with dry densities of at least 1.4g cm-3 was eventually suppressed as bentonite neared saturation.

Fecal microbiome composition and diversity of cryopreserved canine stool at different duration and storage conditions.

Fresh-frozen stool banks intended for humans with gastrointestinal and metabolic disorders have been recently established and there are ongoing efforts to establish the first veterinary fresh-frozen stool bank. Fresh frozen stored feces provide an advantage of increased availability and accessibility to high-quality optimal donor fecal material. The stability of frozen canine feces regarding fecal microbiome composition and diversity has not been reported in dogs, providing the basis for this study. We hypothesized that fecal microbial composition and diversity of healthy dogs would remain stable when stored at -20°C and -80°C for up to 12 months compared to baseline samples evaluated before freezing. Stool samples were collected from 20 apparently healthy dogs, manually homogenized, cryopreserved in 20% glycerol and aliquoted, frozen in liquid nitrogen and stored at -20°C or -80°C for 3, 6, 9, and 12 months. At baseline and after period of storage, aliquots were thawed and treated with propidium monoazide before fecal DNA extraction. Following long-read 16S-rRNA amplicon sequencing, bacterial community composition and diversity were compared among treatment groups. We demonstrated that fresh-frozen canine stools collected from 20 apparently healthy dogs could be stored for up to 12 months at -80°C with minimal change in microbial community composition and diversity and that storage at -80°C is superior to storage at -20°C. We also found that differences between dogs had the largest effect on community composition and diversity. Relative abundances of certain bacterial taxa, including those known to be short-chain fatty acid producers, varied significantly with specific storage temperatures and duration. Further work is required to ascertain whether fecal donor material that differs in bacterial community composition and diversity across storage conditions and duration could lead to differences in clinical efficacy for specific clinical indications of fecal microbiota transplantation.

Microbial assemblages in Arctic coastal thermokarst lakes and lagoons.

Several studies have investigated changes in microbial community composition in thawing permafrost landscapes, but microbial assemblages in the transient ecosystems of the Arctic coastline remain poorly understood. Thermokarst lakes, abrupt permafrost thaw features, are widespread along the pan-Arctic coast and transform into thermokarst lagoons upon coastal erosion and sea-level rise. This study looks at the effect of marine water inundation (imposing a sulfate-rich, saline environment on top of former thermokarst lake sediments) on microbial community composition and the processes potentially driving microbial community assembly. In the uppermost lagoon sediment influenced from marine water inflow, the microbial structures were significantly different from those deeper in the lagoon sediment and from those of the lakes. In addition, they became more similar along depth compared with lake communities. At the same time, the diversity of core microbial consortia community decreased compared with the lake sediments. This work provides initial observational evidence that Arctic thermokarst lake to lagoon transitions do not only substantially alter microbial communities but also that this transition has a larger effect than permafrost thaw and lake formation history.

Herbicide application impacted soil microbial community composition and biochemical properties in a flooded rice field

Herbicide application is a common practice in intensive agriculture. However, accumulating herbicide residues in the ecosystem affects important soil attributes. The effect of two herbicides, pendimethalin and pretilachlor, on soil biochemical properties and microbial community composition was studied in a transplanted paddy field. Results reveal a gradual decline in herbicide residue up to 60 days after application. Changes in soil microbiological and biochemical properties (microbial biomass, enzymes, respiration, etc.) showed an inconsistent pattern across the treatments. Quantitative polymerase chain reaction analysis showed the archaeal, bacterial and fungal populations to be of higher order in control soil compared to the treated one. Amplicon sequencing (16S rRNA and ITS genes) exhibited that besides the unclassified genera, ammonia-oxidizing Crenarchaeota and the group represented by Candidatus Nitrososphaera were dominant in both the control and treated samples. Other archaeal genera viz. Methanosarcina and Bathyarchaeia showed a slight decrease in relative abundance of control (0.5 %) compared to the treated soil (0.7 %). Irrespective of treatments, the majority of bacterial genera comprised unclassified and uncultured species, accounting for >64–75 % in the control group and over 78.29 % in the treated samples. Members of Vicinamibacteraceae, Bacillus and Bryobacter were dominant in control samples. Dominant fungal genera belonging to unclassified groups comprised Curvularia, Aspergillus, and Emericellopsis in the control group, whereas Paraphysoderma and Emericellopsis in the herbicide-treated groups. Inconsistent response of soil properties and microbial community composition is evident from the present study, suggesting that the recommended dose of herbicides might not result in any significant change in microbial community composition. The findings of this investigation will help in the formulation of a framework for risk assessment and maintaining sustainable rice cultivation in herbicide- amended soils.

Process conditions affect microbial diversity and activity in a haloalkaline biodesulfurization system.

Biodesulfurization (BD) systems that treat sour gas employ mixtures of haloalkaliphilic sulfur-oxidizing bacteria to convert sulfide to elemental sulfur. In the past years, these systems have seen major technical innovations that have led to changes in microbial community composition. Different studies have identified and discussed the microbial communities in both traditional and improved systems. However, these studies do not identify metabolically active community members and merely focus on members' presence/absence. Therefore, their results cannot confirm the activity and role of certain bacteria in the BD system. To investigate the active community members, we determined the microbial communities of six different runs of a pilot-scale BD system. 16S rRNA gene-based amplicon sequencing was performed using both DNA and RNA. A comparison of the DNA- and RNA-based sequencing results identified the active microbes in the BD system. Statistical analyses indicated that not all the existing microbes were actively involved in the system and that microbial communities continuously evolved during the operation. At the end of the run, strains affiliated with Alkalilimnicola ehrlichii and Thioalkalivibrio sulfidiphilus were confirmed as the most active key bacteria in the BD system. This study determined that microbial communities were shaped predominantly by the combination of hydraulic retention time (HRT) and sulfide concentration in the anoxic reactor and, to a lesser extent, by other operational parameters.IMPORTANCEHaloalkaliphilic sulfur-oxidizing bacteria are integral to biodesulfurization (BD) systems and are responsible for converting sulfide to sulfur. To understand the cause of conversions occurring in the BD systems, knowing which bacteria are present and active in the systems is essential. So far, only a few studies have investigated the BD system's microbial composition, but none have identified the active microbial community. Here, we reveal the metabolically active community, their succession, and their influence on product formation.

Year-round activity of microbial communities in cold-climate peatlands treating mining-affected waters

Pristine peatlands are typically low in nitrogen, sulfur and metal compounds. Thus, input of high concentrations of those compounds as a result of anthropogenic activity pose a huge challenge to peatland ecosystems. At a mine site in Finnish Lapland, mining-affected waters are purified in two treatment peatlands (TPs) before they are released into downstream waters. The TPs experience long winters and are snow- and partly ice-covered from October to May. Contaminants in inflow waters include nitrogen compounds, sulfate, metals and metalloids. The TPs were intensively monitored for >10 years, and monitoring data was complemented with laboratory experiments. High levels of multiple contaminants, often in the mM range, were measured in TP inflow. Removal of some contaminants such as nitrogen compounds and sulfate was higher in summer months while removal of other contaminants such as arsenic and antimony was similar throughout the year. Potential process rates as assessed in laboratory incubations were generally higher at higher incubation temperatures and decreased with decreasing temperatures, but processes still occurred at 0 °C. The composition of the potentially active microbial community as assessed by 16S rRNA amplicon sequencing varied more strongly between the two TPs and the two layers, while seasonal variability was minor. Potentially active microorganisms included genera known for nitrification, denitrification, sulfate reduction, iron reduction as well as arsenate and antimonate reduction. The collective results indicate that (i) microbial communities in mining-affected peatlands were exposed to high concentrations of multiple contaminants, (ii) microbially mediated processes contributed to contaminant removal throughout the year, and (iii) differences in process rates and contaminant removal likely stem from overall lower activities rather than from changes in microbial community composition.

Response of microbial communities in the phyllosphere ecosystem of tobacco exposed to the broad-spectrum copper hydroxide.

Copper hydroxide is a broad-spectrum copper fungicide, which is often used to control crop fungal and bacterial diseases. In addition to controlling targeted pathogens, copper hydroxide may also affect other non-targeted microorganisms in the phyllosphere ecosystem. At four time points (before spraying, and 5, 10 and 15 days after fungicide application), the response of diseased and healthy tobacco phyllosphere microorganisms to copper hydroxide stress was studied by using Illumina high-throughput sequencing technology, and Biolog tools. The results showed that the microbiome communities of the healthy group were more affected than the disease group, and the fungal community was more sensitive than the bacterial community. The most common genera in the disease group were Alternaria, Boeremia, Cladosporium, Pantoea, Ralstonia, Pseudomonas, and Sphingomonas; while in the healthy group, these were Alternaria, Cladosporium, Symmetrospora, Ralstonia, and Pantoea. After spraying, the alpha diversity of the fungal community decreased at 5 days for both healthy and diseased groups, and then showed an increasing trend, with a significant increase at 15 days for the healthy group. The alpha diversity of bacterial community in healthy and diseased groups increased at 15 days, and the healthy group had a significant difference. The relative abundance of Alternaria and Cladosporium decreased while that of Boeremia, Stagonosporopsis, Symmetrospora, Epicoccum and Phoma increased in the fungal communities of healthy and diseased leaves. The relative abundance of Pantoea decreased first and then increased, while that of Ralstonia, Pseudomonas and Sphingomonas increased first and then decreased in the bacterial communities of healthy and diseased leaves. While copper hydroxide reduced the relative abundance of pathogenic fungi Alternaria and Cladosporium, it also resulted in the decrease of beneficial bacteria such as Actinomycetes and Pantoea, and the increase of potential pathogens such as Boeremia and Stagonosporopsis. After treatment with copper hydroxide, the metabolic capacity of the diseased group improved, while that of the healthy group was significantly suppressed, with a gradual recovery of metabolic activity as the application time extended. The results revealed changes in microbial community composition and metabolic function of healthy and diseased tobacco under copper hydroxide stress, providing a theoretical basis for future studies on microecological protection of phyllosphere.

Effects of Fe(III) (hydr)oxide mineralogy on the development of microbial communities originating from soil, surface water, groundwater, and aerosols

Microbial Fe(III) reduction is a key component of the iron cycle in natural environments. However, the susceptibility of Fe(III) (hydr)oxides to microbial reduction varies depending on the mineral's crystallinity, and the type of Fe(III) (hydr)oxide in turn will affect the composition of the microbial community. We created microcosm reactors with microbial communities from four different sources (soil, surface water, groundwater, and aerosols), three Fe(III) (hydr)oxides (lepidocrocite, goethite, and hematite) as electron acceptors, and acetate as an electron donor to investigate the shaping effect of Fe(III) mineral type on the development of microbial communities. During a 10-month incubation, changes in microbial community composition, Fe(III) reduction, and acetate utilization were monitored. Overall, there was greater reduction of lepidocrocite than of goethite and hematite, and the development of microbial communities originating from the same source diverged when supplied with different Fe(III) (hydr)oxides. Furthermore, each Fe(III) mineral was associated with unique taxa that emerged from different sources. This study illustrates the taxonomic diversity of Fe(III)-reducing microbes from a broad range of natural environments.

Freshwater mussels promote functional redundancy in sediment microbial communities under different nutrient regimes

Abstract Animals are a critical component of biogeochemical cycles. While animal mediated fluxes of nutrients and energy have received considerable attention, the impacts of these fluxes on microbial community structure and function are comparatively understudied. Here, we investigated if freshwater mussel influences on biogeochemical cycling in stream sediment are accompanied by changes in sediment microbial community composition and ecoenzymatic activity, and if these relationships change under different nutrient regimes. We predicted that mussel effects on ecosystem function are reflected by modified sediment microbial communities. We hypothesized that if changes in either sediment ecoenzymatic function or microbial community composition are driven by mussel‐derived nutrient amendments, we should see muted changes in microbial community assemblages or function when a given nutrient is abundant. However, if microbial communities and function are influenced by other mussel functions, then we should see uniform changes regardless of nutrient availability. We transplanted freshwater mussels and natural river sediment to flow‐through mesocosms and monitored changes in microbial community composition over 1 week. Our results indicate that mussels always changed sediment microbial community composition, but the way communities changed was dependent on ambient nutrient concentrations. On the final day we measured the activity of ecoenzymes known to correlate to microbial function and nutrient availability. Mussels homogenized the stoichiometric ratios of ecoenzyme activities, indicating a consistent function of sediment microbes associated with freshwater mussels. Our results suggest that mussels may promote functional redundancy in sediment microbial communities and highlight the importance of animals in controlling biogeochemical transformations under changing nutrient conditions. Read the free Plain Language Summary for this article on the Journal blog.

Impact of corrosion inhibitors on antibiotic resistance, metal resistance, and microbial communities in drinking water.

Corrosion inhibitors, including zinc orthophosphate, sodium orthophosphate, and sodium silicate, are commonly used to prevent the corrosion of drinking water infrastructure. Metals such as zinc are known stressors for antibiotic resistance selection, and phosphates can increase microbial growth in drinking water distribution systems (DWDS). Yet, the influence of corrosion inhibitor type on antimicrobial resistance in DWDS is unknown. Here, we show that sodium silicates can decrease antibiotic resistant bacteria (ARB) and antibiotic-resistance genes (ARGs), while zinc orthophosphate increases ARB and ARGs in source water microbial communities. Based on controlled bench-scale studies, zinc orthophosphate addition significantly increased the abundance of ARB resistant to ciprofloxacin, sulfonamides, trimethoprim, and vancomycin, as well as the genes sul1, qacEΔ1, an indication of resistance to quaternary ammonium compounds, and the integron-integrase gene intI1. In contrast, sodium silicate dosage at 10 mg/L resulted in decreased bacterial growth and antibiotic resistance selection compared to the other corrosion inhibitor additions. Source water collected from the drinking water treatment plant intake pipe resulted in less significant changes in ARB and ARG abundance due to corrosion inhibitor addition compared to source water collected from the pier at the recreational beach. In tandem with the antibiotic resistance shifts, significant microbial community composition changes also occurred. Overall, the corrosion inhibitor sodium silicate resulted in the least selection for antibiotic resistance, which suggests it is the preferred corrosion inhibitor option for minimizing antibiotic resistance proliferation in DWDS. However, the selection of an appropriate corrosion inhibitor must also be appropriate for the water chemistry of the system (e.g., pH, alkalinity) to minimize metal leaching first and foremost and to adhere to the lead and copper rule. IMPORTANCE Antibiotic resistance is a growing public health concern across the globe and was recently labeled the silent pandemic. Scientists aim to identify the source of antibiotic resistance and control points to mitigate the spread of antibiotic resistance. Drinking water is a direct exposure route to humans and contains antibiotic-resistant bacteria and associated resistance genes. Corrosion inhibitors are added to prevent metallic pipes in distribution systems from corroding, and the type of corrosion inhibitor selected could also have implications on antibiotic resistance. Indeed, we found that sodium silicate can minimize selection of antibiotic resistance while phosphate-based corrosion inhibitors can promote antibiotic resistance. These findings indicate that sodium silicate is a preferred corrosion inhibitor choice for mitigation of antibiotic resistance.

Leachate leakage enhances the microbial diversity and richness but decreases Proteobacteria and weakens stable microbial ecosystem in landfill groundwater.

Sanitary landfill is the most prevalent and economic method for municipal solid waste disposal, and the resultant groundwater pollution has become an environmental problem due to leachate leakage. The pollution characteristics in groundwater near landfill sites have been extensively investigated, although the succession characteristics and driving mechanisms of microbial communities in leachate-contaminated groundwater and the sensitive microbial indicators for leachate leakage identification remain poorly studied. Herein, results showed that leachate leakage enhanced the microbial diversity and richness and transferred endemic bacteria from landfills into groundwater, producing an average decrease of 17.73% in the relative abundance of Proteobacteria. The key environmental factor driving the evolution of microbial communities in groundwater due to leachate pollution was organic matter, which can explain 16.13% of the changes in microbial community composition. The |βNTI| values of the bacterial communities in all six landfills were <2, and the assembly process of microbial communities was primarily dominated using stochastic processes. Leachate pollution changed the assembly mechanism, transforming the community assembly process from an undominated process to a dispersal limitation process. Leachate pollution reduced the efficiency and stability of microbial communities in groundwater, increasing the vulnerability of the stable microbial ecosystems in groundwater. Notably, microbial indicators are more sensitive to leachate leakage and could accurately identify landfills where leachate leakage occurred and other extraneous pollutants. The phylum Proteobacteria and mcrA could act as appropriate indicators for the identification of leachate leakage. These results provide a novel insight into the monitoring, identification of groundwater pollution and the scientific guidance for appropriate remediation strategies for leachate-contaminated groundwater.

Remediation Effect and Mechanism of Biochar in Combination with Nitrogen Fertilizer on Cd-contaminated Paddy Soil

Cadmium (Cd) heavy metal pollution has posed serious threats to soil health and the safe production utilization of agricultural products. A pot experiment was conducted to study the effects of biochar (BC) and nitrogen fertilizer with three levels, namely 2.6 g·pot-1 (N1), 3.5 g·pot-1 (N2), 4.4 g·pot-1 (N3) biochar combined with nitrogen fertilizer (BCN1, BCN2, and BCN3), on soil Cd fractions, Cd enrichment, the transport of rice, and soil enzyme activity, as well as the changes in microbial community composition and complex interactions between microorganisms through high-throughput sequencing. The results showed that biochar combined with nitrogen fertilizer led to the transformation of Cd from the exchangeable state to the residue state, and the proportion of the exchangeable state was significantly reduced by 6.2%-14.7%; by contrast, the proportion of the residue state increased by 18.6%-26.4% relative to that in CK. In addition, singular treatments of nitrogen fertilizer enhanced the accumulation capacities of Cd in roots, which increased by 22%-33.5% compared with that in CK. By contrast, the BC and BCN treatments reduced Cd accumulation in roots and the transfer capacity from stems to rice husks and husk to rice. Furthermore, the BCN treatments promoted soil enzyme activities (urease, acid phosphatase, invertase, and catalase). MiSeq sequencing showed that BCN treatments increased the abundance of the main species of soil bacterial microbes (such as Acidobacteriales, Solibacterales, Pedosphaerales, and Nitrospirales). Moreover, co-occurrence network analysis showed that the complexity of the soil bacterial network was enhanced under the N, BC, and BCN treatments. Overall, biochar combined with nitrogen fertilizer reduced soil Cd availability, inhibited the capacity of Cd accumulation and the transport of rice, and improved the soil eco-environmental quality. Thus, using BCN could be a feasible practice for the remediation of Cd-polluted agricultural soil.

Succession of bacterial community structure in response to a one-time application of biochar in barley rhizosphere and bulk soils

Biochar is often used as an amendment to enhance soil fertility by directly increasing soil pH and nutrient availability. However, biochar may also improve soil fertility indirectly by altering the succession of bacterial communities that, in turn, may alter nutrient supply and availability. To determine how biochar affects soil bacterial richness and diversity, as well as how bacterial communities respond to biochar across space and time, we studied the rhizosphere and bulk soils of potted barley plants for 2 years. Adding biochar significantly increased bacterial community richness (Chao 1 richness index) by the end of the second year in the rhizosphere (P = 0.037), but in bulk soils, we observed an increase in richness in Year 1 that dissipated by Year 2. In contrast to richness, adding biochar only had a significant effect on bacterial community diversity (Shannon diversity index) in Year 1 seedling stage (P &amp;lt; 0.001), but the effect dissipated thereafter. We also found that adding biochar increased the relative abundances of Actinobacteria and Proteobacteria but decreased the relative abundances of Acidobacteria and Chloroflexi, suggesting these communities were sensitive to biochar inputs. The biochar-sensitive genera belonging to Actinobacteria and Proteobacteria made up 45%–58% of sensitive taxa in both rhizosphere and bulk soils. Of the Proteobacteria sensitive to adding biochar, Nitrosospira and Sphingomonas were most abundant in the rhizosphere relative to bulk soils. However, despite the initial increase of biochar sensitive responders in the rhizosphere, their numbers decreased after 2 years and had 179 fewer genera than bulk soils. Our findings suggest the effect of adding biochar was relatively short-lived and that the influence of the plant phenology was a stronger driver of bacterial community change than biochar inputs 2 years after its application. Altogether, the succession of soil bacterial community structure reflected changes in the soil environment induced by the combined effect of biochar, rhizospheric inputs, and plant phenology, suggesting that changes in microbial community composition observed after amending soils with biochar, may also contribute to changes in soil fertility.

The Effect of Commonly Used Organic Acids on the Microbiota of Cured Deli-Style Turkey Breast

The purpose of this study was to investigate changes in the microbial community structure consisting of spoilage lactic acid bacteria (LAB) when sodium lactate (SL) and SL + sodium diacetate (SD) are included in RTE meat product formulations at concentrations commonly used for controlling Listeria monocytogenes. Sliced cooked, vacuum-packaged turkey breast samples containing no SD or SL (control [C]), 0.125% SD, and the combination of 2.5% SL + 0.125%SD (SLSD) were inoculated with a target of 3 log colony-forming units (CFU)/g of 5 different LAB species (Lactobacillus sakei, Leuconostoc mesenteroides [bacon and deli-shaved ham isolates], Lactococcus lactis, and Enterococcus faecium) and stored at 4°C for 35 d. Microbial community changes were analyzed utilizing 16S ribosomal RNA (rRNA) gene sequencing for the V4 region from the samples collected at days 0, 7, 14, 21, and 35. No significant difference (P&amp;gt;0.05) was observed between the richness of microbial community for all treatments. According to Bray-Curtis dissimilarity matrix and permutational analysis of variance, a significant difference in β-diversity was observed only between C and SLSD (P&amp;lt;0.05) because of the antimicrobial effect of the addition of SL that slowed down changes in microbial community composition until day 14. L. sakei remained a dominant strain throughout 35 d of storage regardless of treatment, whereas L. mesenteroides existed with a very low abundance. Two of the five strains were not seen after day 7. No significant effect (P&amp;gt;0.05) was observed for the SD treatment compared with C in the microbiota. According to the results from this study, only SLSD affected the microbial community structure at the beginning of the storage. This study demonstrated that the incorporation of SL in the formulation slowed down the microbial spoilage and the changes in the microbiota of RTE meat products.