Environmental Bacterial Communities Research Articles

Flooding Promotes the Coalescence of Microbial Community in Estuarine Habitats

Microbial community coalescence describes the mixing of microbial communities and their integration with the surrounding environment, which is common in natural ecosystems and has potential impacts on ecological processes. However, few studies have focused on microbial community coalescence between different habitats in estuarine regions. In this study, we comprehensively investigated the environmental characteristics and bacterial community changes of different habitats (water body (Water), subtidal sediments (SS) and intertidal salt marsh sediments (SM)) in Luanhe estuary during flood and normal flow periods. The results showed that flood event significantly reduced the salinity of the estuarine habitats, changed the nutrient structure and intensified the eutrophication of estuarine water. By calculating the proportion of overlapping groups and applying the ‘FEAST’ algorithm, we revealed that flood event facilitated the migration of bacterial communities along alternative pathways across habitats, markedly enhanced the cross-habitat mobility of bacterial communities, which underscores the pivotal role of flood event in driving bacterial community coalescence. Flood-induced community coalescence not only increased the α-diversity of bacterial communities within habitats, but also increased the proportion of overlapped species between habitats, ultimately leading to homogenization between habitats. Canonical correlation analysis combined co-occurrence network analysis revealed that flood event attenuated the role of environmental filtration in microbial assembly, while increased the impact of dispersal processes and intensified interspecific competition among microorganisms, led to the change of keystone species and reduced the complexity and stability of bacterial communities. In conclusion, this study demonstrates the complex effects of flood events on estuarine microbial communities from the perspective of multi-habitat interactions in the estuary, and emphasizes the key role of river hydrodynamic conditions in facilitating the coalescence of estuarine microbial communities. We look forward to further attention and research on estuarine microbial coalescence, which will provide new insights into assessing the stability and resilience of estuarine ecosystems under flood challenges and the sustainable management of estuarine wetlands.

The impact of host development and density stress on the diversity of microbial communities in the gut and its surrounding environment of the Chinese alligator

AbstractThe Chinese alligator (Alligator sinensis) is currently an endangered species due to a combination of factors, including climate change, anthropogenic activities, and habitat fragmentation. Captivity plays a crucial role in mitigating the decline of the Chinese alligator population. Currently, there is a lack of clarity regarding the influence of host development and captive conditions on the gut microbiota of Chinese alligators. The aim of the study was to investigate the gut bacterial communities of Chinese alligators and their surrounding environmental bacterial communities using 16S rRNA sequencing. The primary gut flora of Chinese alligators consists of Proteobacteria, Bacteroidetes, and Firmicutes. Proteobacteria is the most abundant and efficient settler in the gut, water, and sediment. PCoA and Adonis test revealed significant differences in bacterial communities across these habitats. Venn analysis revealed overlap in OTUs among the gut, water, and sediment, varying with growth stage and density stress. Different growth stages of Chinese alligator guts harbor distinct pathogenic bacteria, requiring attention. Density stress leads to an increase in pathogenic bacteria, a decrease in gut absorption efficiency. PICRUst2 predicts more abundant metabolic pathways related to gut function during high‐density stress, possibly linked to Roseburia. SourceTracker Analysis indicated that water bacteria have a greater impact on Chinese alligator gut bacteria than sediment, and density stress significantly affects the contribution of environmental microorganisms to the gut microbes of Chinese alligator. BugBase analysis identified water body microbes as the main source of “potentially pathogenic” phenotypes in the gut microbiota. RDA analysis found dissolved oxygen (DO) in water to be the most significant factor influencing water microorganisms, positively correlated with certain pathogenic strains. These findings enhance our understanding of the significance of microbial communities in the gut and surrounding aquatic environment of the Chinese alligator. Furthermore, they provide theoretical support for environmental regulation, disease control, and healthy breeding.

Effect of rainfall in shaping microbial community during Microcystis bloom in Nakdong River, Korea

Various environmental factors play a role in the formation and collapse of Microcystis blooms. This study investigates the impact of heavy rainfall on cyanobacterial abundance, microbial community composition, and functional dynamics in the Nakdong River, South Korea, during typical and exceptionally rainy years. The results reveal distinct responses to rainfall variations, particularly in cyanobacterial dominance and physicochemical characteristics. In 2020, characterized by unprecedented rainfall from mid-July to August, Microcystis blooms were interrupted significantly, exhibiting lower cell densities and decreased water temperature, compared to normal bloom patterns in 2019. Moreover, microbial community composition varied, with increases in Gammaproteobacteria and notably in genera of Limnohabitans and Fluviicola. These alterations in environmental conditions and bacterial community were similar to those of the post-bloom period in late September 2019. It shows that heavy rainfall during summer leads to changes in environmental factors, consequently causing shifts in bacterial communities akin to those observed during the autumn-specific post-bloom period in typical years. These changes also accompany shifts in bacterial functions, primarily involved in the degradation of organic matter such as amino acids, fatty acids, and terpenoids, which are assumed to have been released due to the significant collapse of cyanobacteria. Our results demonstrate that heavy rainfall in early summer induces changes in the environmental factors and subsequently microbial communities and their functions, similar to those of the post-bloom period in autumn, leading to the earlier breakdown of Microcystis blooms.

Biochar reduces gaseous emissions during poultry manure composting: Evidence from the evolution of associated functional genes

Biochar has demonstrated the potential in mitigating pollutant gaseous emission during composting. However, little is known about the difference among biochars derived from different plant feedstocks on the critical genes' expression and microbial communities’ succession for gaseous emissions. In this study, the effects of biochar (from wood chips, cornstalks, and rice husks) on gaseous emissions during chicken manure composting were investigated. Environmental factors, bacterial communities, and functional genes related to CH4, N2O, NH3, and H2S emissions were analyzed to reveal the reduction pathways of different biochar amendments during composting. Results showed that all biochar treatments improved the seed germination index of the compost from unmature (55.74%) to mature (70.28–75.23%). The CH4, N2O, NH3, and H2S emissions from all biochar-treated composts were reduced by 18.93–27.47%, 35.74–52.82%, 1.26–36.38%, and 8.57–24.14%, respectively, and the cornstalk biochar had the highest emission reduction performance. Temperature, pH, and NH4+ were the major environmental factors that affected Lactobacillus and Bacillus activities, which critically influenced the CH4, N2O, NH3, and H2S emissions during composting. Furthermore, cornstalk biochar mainly improved pmoA for CH4 reduction, whereas wood chip biochar increased amoA for NH3 oxidation. Rice husk biochar mostly decreased nirS and nirK and increased norB, narG, and nosZ during N2O reduction. Cornstalk biochar also increased dsrB and decreased aprA during H2S reduction. Overall, cornstalk biochar was determined to be an optimal additive for simultaneously improving compost maturity and reducing gaseous pollutant emissions during chicken manure composting. This study verified the mechanisms of three plant derived biochars in pollutant gas control in composting, and thus provided evidence for facilitating the sustainable development of composting technologies.

Identifying environmental factors affecting the microbial community composition on outdoor structural timber

Timber wood is a building material with many positive properties. However, its susceptibility to microbial degradation is a major challenge for outdoor usage. Although many wood-degrading fungal species are known, knowledge on their prevalence and diversity causing damage to exterior structural timber is still limited. Here, we sampled 46 decaying pieces of wood from outdoor constructions in the area of Hamburg, Germany; extracted their DNA; and investigated their microbial community composition by PCR amplicon sequencing of the fungal ITS2 region and partial bacterial 16S rRNA genes. In order to establish a link between the microbial community structure and environmental factors, we analysed the influence of wood species, its C and N contents, the effect of wood-soil contact, and the importance of its immediate environment (city, forest, meadow, park, respectively). We found that fungal and bacterial community composition colonising exterior timber was similar to fungi commonly found in forest deadwood. Of all basidiomycetous sequences retrieved, some, indicative for Perenniporia meridionalis, Dacrymyces capitatus, and Dacrymyces stillatus, were more frequently associated with severe wood damage. Whilst the most important environmental factor shaping fungal and bacterial community composition was the wood species, the immediate environment was important for fungal species whilst, for the occurrence of bacterial taxa, soil contact had a high impact. No influence was tangible for variation of the C or N content. In conclusion, our study demonstrates that wood colonising fungal and bacterial communities are equally responsive in their composition to wood species, but respond differently to environmental factors.Key points• Perenniporia meridionalis and Dacrymyces are frequently associated with wood damage• Fungal community composition on timber is affected by its surrounding environment• Bacterial community composition on structural timber is affected by soil contact

Branched GDGT source shift identification allows improved reconstruction of an 8,000-year warming trend on Sumatra

Branched Glycerol Dialkyl Glycerol Tetraethers (brGDGTs) in sedimentary archives are increasingly used for paleotemperature reconstructions due to their strong correlation with mean annual air temperature. However, environmental factors can influence the brGDGT producing bacterial community, potentially affecting the brGDGT-temperature relationship and introducing fundamental errors in reconstructions. Here we assess the reliability of the methylation index of brGDGTs (MBT′5ME) in sediments as a paleotemperature proxy by tracking provenance differences based on brGDGT fractional abundances in a short lake core, two peat cores and surface soils on Sumatra (n = 333 in total). Then, we attempt to reconstruct the Holocene paleotemperatures on Sumatra using the two peat cores. Our results indicate distinct brGDGT and H-shaped brGDGT (H-GDGT) compositions in soil, lake and peat environments, suggesting production by different bacterial communities. We introduce a new index, the isomerization of H-GDGTs (IRH) that can distinguish between these environments. In an 11,000-year long peat core from Diatas, we find that brGDGT composition changes are dominated by bacterial community shifts rather than temperature changes. In contrast, a core from the nearby Padang peatland can be robustly used for a brGDGT-based paleotemperature reconstruction since there are no signs of past environmental or brGDGT source shifts. The results from Padang indicate a gradual warming trend over the past 8,000 years, consistent with climate model simulations and nearby sea surface temperature reconstructions. However, current MBT′5ME calibrations yield larger warming trends compared to simulations and other proxy studies, suggesting the need for tropical and/or peat-specific brGDGT temperature calibrations. Our findings demonstrate the importance of assessing environmental shifts and bacterial source community changes when employing brGDGT paleothermometry. The methodological framework outlined in this study can be used in future research for reliable down-core brGDGT temperature reconstructions. Our proxy reconstruction over the past 8,000 years offers novel insights into the Holocene temperature evolution from a region with low climate seasonality.

Deciphering antibiotic resistome variations during nitrogen removal process transition under mixed antibiotics stress: Assembly process and driving factors

Antibiotic resistome, which encompasses all types of antibiotic resistance genes (ARGs) in a given environment, has received increasing attention in research on different wastewater treatment processes. However, the variation in antibiotic resistome during the transition from the full nitrification–denitrification to the shortcut nitrification–denitrification process remains unclear. In this study, a total of 269 targeted gene subtypes were identified, along with 108 genes were consistently present in all samples. The introduction of mixed antibioticsrapidly increased the abundance of corresponding and non-corresponding ARGs, as well as that of mobile genetic elements.The variations in of the antibiotic resistome were primarily driven by dissolved oxygen and nitrite accumulation rate. Moreover, 34 bacterial genera were identified as potential ARG hosts, with most denitrifiers considered as potential antibiotic-resistant bacteria, including Branchymonas, Rhodobacter, and Thauera. This study provides a method for controlling antibiotic resistance by regulating the changes in environmental variables and bacterial communities.

Effect of the lignocellulolytic Psychrotroph Lelliottia sp. on bacterial community succession in corn straw compost.

This study aimed to explore the effect of an inoculation, Lelliottia sp., on the corn straw compost's physico-chemical properties, composition, and the succession of bacterial community structure. The compost community composition and succession changed after Lelliottia sp. inoculation. Inoculation increased the bacterial community diversity and abundance in the compost to promote composting. The inoculated group entered the thermophilic stage on the first day, lasting 8 days. Judging the pile maturity based on the carbon:nitrogen ratio and germination index values, the inoculated group reached the maturity standard, which was 6 days faster than the control group. The relationship between environmental factors and bacterial communities was comprehensively analyzed using redundancy analysis. Temperature and carbon:nitrogen ratio were the main environmental factors driving the succession of bacterial communities, to provide basic information on the changes of physicochemical indexes and bacterial community succession in Lelliottia sp. inoculated maize straw composting, providing assistance for practical composting applications of this strain.

Surfaces of gymnastic equipment as reservoirs of microbial pathogens with potential for transmission of bacterial infection and antimicrobial resistance.

Gymnastic equipment surfaces are shared by many people, and could mediate the transfer of bacterial pathogens. To better understand this detrimental potential, investigations on the reservoirs of bacterial pathogens and antimicrobial resistance on the surfaces of gymnastic equipment were performed by analyzing the bacterial community structures, prevalence of viable bacteria, and presence of antimicrobial resistance on both indoor and outdoor gymnastic facilities. The results of high-throughput 16S rDNA amplicon sequencing showed that Gram-positive bacteria on the surfaces of indoor gymnastic equipment significantly enriched, including the opportunistic pathogen Staphylococcus strains, while Enterobacteriaceae significantly enriched on surfaces of outdoor gymnastic equipment. The analysis of α-diversities showed a higher richness and diversity for bacterial communities on the surfaces of gymnastic equipment than the environment. Analysis of β-diversities showed that the bacterial communities on the surfaces of gymnastic equipment differ significantly from environmental bacterial communities, while the bacterial communities on indoor and outdoor equipment are also significantly different. Thirty-four bacterial isolates were obtained from the surfaces of gymnastic equipment, including three multidrug Staphylococcus and one multidrug resistant Pantoea. In particular, Staphylococcus hemolyticus 5-6, isolated from the dumbbell surface, is a multidrug resistant, hemolytic, high- risk pathogen. The results of quantitative PCR targeting antibiotic resistance related genes (intI1, sul1 and bla TEM) showed that the abundances of sul1 and bla TEM genes on the surfaces of gymnastic equipment are higher than the environment, while the abundances of sul1 gene on indoor equipment are higher than outdoor equipment. These results lead to the conclusion that the surfaces of gymnastic equipment are potential dissemination pathways for highly dangerous pathogens as well as antimicrobial resistance, and the risks of indoor equipment are higher than outdoor equipment.

Polyethylene Microplastic Particles Alter the Nature, Bacterial Community and Metabolite Profile of Reed Rhizosphere Soils

With the wide use of polyethylene film, the influence of polyethylene microplastic particles produced by its weathering on the rhizosphere soil microenvironment has attracted more and more attention from scientific research circles. In this study, the effects of low (0.2% w/w), medium (1% w/w), and high (2% w/w) doses of polyethylene particles and the combined reed biomass (2% w/w) on soil environmental factors and bacterial communities and metabolites in the reed rhizosphere were evaluated by a 90-day pot microscopic simulation system. The shape and surface microstructure of polyethylene particles in each treatment group changed obviously. A high (2% w/w) dose of microplastics significantly increased the TKN, TOC, and TP in reed root soil. The addition of the biomass significantly improved the activities of urease and sucrase in the soil. The α diversity of bacteria was not significantly affected by the addition of LDPE microplastics and biomass, but the β diversity of the bacterial community and the relative abundance of the Candidatus_Roku Bacteria, Chloroflexi, Unclassified_Blastocatella_Genus were significantly changed by the addition of middle (1% w/w) and high (2% w/w) doses of microplastics. In addition, the spectrum analysis of the soil metabolites showed that the abundance of soil metabolites was changed in each treatment group, and the differential metabolites were significantly up-regulated or down-regulated. Our findings provide a scientific reference to elucidate the impact of LDPE microplastic particles on the inter-rooted soil microenvironment and improve our understanding of the potential risks of microplastics in soil ecosystems.

Climate Warming Does Not Override Eutrophication, but Facilitates Nutrient Release from Sediment and Motivates Eutrophic Process.

The climate is changing. The average temperature in Wuhan, China, is forecast to increase by at least 4.5 °C over the next century. Shallow lakes are important components of the biosphere, but they are sensitive to climate change and nutrient pollution. We hypothesized that nutrient concentration is the key determinant of nutrient fluxes at the water-sediment interface, and that increased temperature increases nutrient movement to the water column because warming stimulates shifts in microbial composition and function. Here, twenty-four mesocosms, mimicking shallow lake ecosystems, were used to study the effects of warming by 4.5 °C above ambient temperature at two levels of nutrients relevant to current degrees of lake eutrophication levels. This study lasted for 7 months (April-October) under conditions of near-natural light. Intact sediments from two different trophic lakes (hypertrophic and mesotrophic) were used, separately. Environmental factors and bacterial community compositions of overlying water and sediment were measured at monthly intervals (including nutrient fluxes, chlorophyll a [chl a], water conductivity, pH, sediment characteristics, and sediment-water et al.). In low nutrient treatment, warming significantly increased chl a in the overlying waters and bottom water conductivity, it also drives a shift in microbial functional composition towards more conducive sediment carbon and nitrogen emissions. In addition, summer warming significantly accelerates the release of inorganic nutrients from the sediment, to which microorganisms make an important contribution. In high nutrient treatment, by contrast, the chl a was significantly decreased by warming, and the nutrient fluxes of sediment were significantly enhanced, warming had considerably smaller effects on benthic nutrient fluxes. Our results suggest that the process of eutrophication could be significantly accelerated in current projections of global warming, especially in shallow unstratified clear-water lakes dominated by macrophytes.

Insights into remediation effects and bacterial diversity of different remediation measures in rare earth mine soil with SO4 2- and heavy metals.

The increased demand for rare earth resources has led to an increase in the development of rare earth mines (REMs). However, the production of high-concentration leaching agents (SO4 2-) and heavy metals as a result of rare earth mining has increased, necessitating the removal of contaminants. Here, a series of experiments with different remediation measures, including control (CK), sulfate-reducing bacteria (SRB) alone (M), chemicals (Ca(OH)2, 1.5 g/kg) plus SRB (CM-L), chemicals (Ca(OH)2, 3.0 g/kg) plus SRB (CM-M), and chemicals (Ca(OH)2, 4.5 g/kg) plus SRB (CM-H), were conducted to investigate the removal effect of SO4 2-, Pb, Zn, and Mn from the REM soil. Then, a high-throughput sequencing technology was applied to explore the response of bacterial community diversity and functions with different remediation measures. The results indicated that CM-M treatment had a more efficient removal effect for SO4 2-, Pb, Zn, and Mn than the others, up to 94.6, 88.3, 98.7, and 91%, respectively. Soil bacterial abundance and diversity were significantly affected by treatments with the inoculation of SRB in comparison with CK. The relative abundance of Desulfobacterota with the ability to transform SO4 2- into S2- increased significantly in all treatments, except for CK. There was a strong correlation between environmental factors (pH, Eh, SO4 2-, Pb, and Zn) and bacterial community structure. Furthermore, functional prediction analysis revealed that the SRB inoculation treatments significantly increased the abundance of sulfate respiration, sulfite respiration, and nitrogen fixation, while decreasing the abundance of manganese oxidation, dark hydrogen oxidation, and denitrification. This provides good evidence for us to understand the difference in removal efficiency, bacterial community structure, and function by different remediation measures that help select a more efficient and sustainable method to remediate contaminants in the REM soil.

Uncovering Bacterial Hosts of Class 1 Integrons in an Urban Coastal Aquatic Environment with a Single-Cell Fusion-Polymerase Chain Reaction Technology.

Horizontal gene transfer (HGT) is a key driver of bacterial evolution via transmission of genetic materials across taxa. Class 1 integrons are genetic elements that correlate strongly with anthropogenic pollution and contribute to the spread of antimicrobial resistance (AMR) genes via HGT. Despite their significance to human health, there is a shortage of robust, culture-free surveillance technologies for identifying uncultivated environmental taxa that harbor class 1 integrons. We developed a modified version of epicPCR (emulsion, paired isolation, and concatenation polymerase chain reaction (PCR)) that links class 1 integrons amplified from single bacterial cells to taxonomic markers from the same cells in emulsified aqueous droplets. Using this single-cell genomic approach and Nanopore sequencing, we successfully assigned class 1 integron gene cassette arrays containing mostly AMR genes to their hosts in coastal water samples that were affected by pollution. Our work presents the first application of epicPCR for targeting variable, multigene loci of interest. We also identified the Rhizobacter genus as novel hosts of class 1 integrons. These findings establish epicPCR as a powerful tool for linking taxa to class 1 integrons in environmental bacterial communities and offer the potential to direct mitigation efforts toward hotspots of class 1 integron-mediated dissemination of AMR.

Using a batch test to derive sorption data of fluoroquinolone antibiotics in humic acids

Fluoroquinolone antibiotics (FQs) are of concern due to their disrupting effects on environmental bacterial communities. Evaluating FQ sorption by soil components is important to understand their interaction with soils and to address their environmental (bio)availability. However, data in soil organic components, especially humic acids, are scarce. Batch experiments following OECD guidelines are suitable for testing the sorption of pollutants in solid matrices. Here, we applied this methodology, with specific changes in the experimental setup, to derive sorption data and to identify the factors affecting sorption of four common FQs in seven humic acids with contrasting properties. The effect of shaking time, pH, calcium concentration in solution and dissolved organic carbon (DOC) content on the quantification of the solid-liquid distribution coefficient (Kd) of norfloxacin in three reference humic acids was evaluated. Sorption reversibility and sorption analogy of four FQs were additionally assessed in these three reference materials, whereas the effect of initial norfloxacin concentration was evaluated in the overall set of seven humic acids. Sorption was fast, strong, non-linear, irreversible and affected by changes in the pH and calcium levels in solution. The bell-shaped sorption trend at varying pH values confirmed the key role of FQ speciation in sorption and the high Kd values indicated a positive effect of soil organic matter components on FQ sorption in bulk soils at environmentally relevant pH values.•Relevant factors affecting sorption of pollutants in environmental matrices must be considered to derive Kd values with low variability and high representativeness.•In this article we modify the experimental conditions of standard batch tests to identify the factors that affect the sorption of FQs in humic acids.•The methodological approach followed can be extrapolated to the evaluation of other combinations of pollutant and environmental matrix.

Determination of antibiotic resistance profile of bacterial community from environmental water using antibiotic-resistant bacterial contamination detection (ABCD) kit

Quick and easy monitoring approaches are needed to assess sources, clinical relevance, and incidences of antibiotic resistance in environmental bacterial communities. In the present work, antibiotic-resistant bacterial contamination detection (ABCD) kits were developed for the same. The method was standardized with strains of Escherichia coli TS7, Staphylococcus arlettae HWI8, Enterococcus faecalis HWI19, and Aerococcus viridans HWII16 with known antibiogram using six clinically important antibiotics. The method was verified with different water sources having different physicochemical parameters successfully. Only 1 ml of sample water is required to be mixed with an optimized concentration of the antibiotic solution and incubated for 6h; subsequently, a color change to pink may be observed within a specified amount of time upon the addition of the bacterial detection PVDF membrane to monitor the presence of resistant bacteria. There is no color change in the case of antibiotic-susceptible bacterial communities or the absence of a resistant community. Moreover, the time taken for color change is inversely related to the magnitude of the antibiotic-resistant communities in terms of enumeration. Up to our understanding, this is the 1st report which can determine an antibiotic-resistance profile of any water source by observing only color change within a maximum of 7 h (6 h for co-culture of bacteria and antibiotics + 1 h for color change detection) time without the aid of any microbiology laboratory or skilled manpower.

Effect of Wastewater on the Composition of Bacterial Microbiota of Phragmites australis Used in Constructed Wetlands for Phytodepuration.

Phytodepuration occurs in the plant-mediated remediation processes exploited to remove pollutants from wastewater, and Phragmites australis is one of the most used plants. This goal is achieved using constructed wetlands (CW), which are engineered systems designed to mimic the natural processes of pollutants removal. The aim of this work was to characterize the bacterial communities associated to P. australis, soils, and permeates of the CW of Calice (Prato, Italy), to evaluate the possible effect of wastewaters on the CW bacterial communities, through a next-generation sequencing-based approach. A total of 122 samples were collected from different tissues of P. australis (i.e., roots, aerial parts, and stem), soil (i.e., rhizospheric and bulk soil), and permeates, and analyzed. All samples were collected during five sampling campaigns, with the first one performed before the activation of the plant. Obtained results highlighted a specific microbiota of P. australis, conserved among the different plant tissues and during time, showing a lower alpha diversity than the other samples and not influenced by the more complex and variable environmental (soils and permeates) bacterial communities. These data suggest that P. australis is able to select and maintain a defined microbiota, a capacity that could allow the plant to survive in hostile environments, such as that of CW.

Geographic patterns and determinants of antibiotic resistomes in coastal sediments across complex ecological gradients.

Coastal areas are highly influenced by terrestrial runoffs and anthropogenic disturbances, commonly leading to ecological gradients from bay, nearshore, to offshore areas. Although the occurrence and distribution of sediment antibiotic resistome are explored in various coastal environments, little information is available regarding geographic patterns and determinants of coastal sediment antibiotic resistomes across ecological gradients at the regional scale. Here, using high-throughput quantitative PCR, we investigated the geographic patterns of 285 antibiotic resistance genes (ARGs) in coastal sediments across a ~ 200 km scale in the East China Sea. Sediment bacterial communities and physicochemical properties were characterized to identify the determinants of sediments antibiotic resistome. Higher richness and abundance of ARGs were detected in the bay samples compared with those in nearshore and offshore samples, and significant negative correlations between the richness and/or abundance of ARGs and the distance to coastline (DTC) were identified, whereas different types of ARGs showed inconsistency in their relationships with DTC. The composition of antibiotic resistome showed significant correlations with nutrition-related variables (including NH4 +-N, NO3 --N, and total phosphorus) and metals/metalloid (including As, Cu, Ni, and Zn), suggesting that terrestrial disturbances largely shape the antibiotic resistome. The Bipartite network showed strong associations between ARGs and mobile genetic elements (MGEs), and Partial Least Squares Path Modeling further revealed that terrestrial disturbance strength (as indicated by DTC) directly affected abiotic environmental conditions and bacterial community composition, and indirectly affected antibiotic resistome via MGEs. These findings provide insights into regional variability of sediment antibiotic resistome and its shaping path across complex ecological gradients, highlighting terrestrial disturbances as determinative forces in shaping coastal sediment antibiotic resistomes.

Conjugative transfer of multi-drug resistance IncN plasmids from environmental waterborne bacteria to Escherichia coli.

Watersheds contaminated with municipal, hospital, and agricultural residues are recognized as reservoirs for bacteria carrying antibiotic resistance genes (ARGs). The objective of this study was to determine the potential of environmental bacterial communities from the highly contaminated La Paz River basin in Bolivia to transfer ARGs to an Escherichia coli lab strain used as the recipient. Additionally, we tested ZnSO4 and CuSO4 at sub-inhibitory concentrations as stressors and analyzed transfer frequencies (TFs), diversity, richness, and acquired resistance profiles. The bacterial communities were collected from surface water in an urban site close to a hospital and near an agricultural area. High transfer potentials of a large set of resistance factors to E. coli were observed at both sites. Whole-genome sequencing revealed that putative plasmids belonging to the incompatibility group N (IncN, IncN2, and IncN3) were predominant among the transconjugants. All IncN variants were verified to be mobile by a second conjugation step. The plasmid backbones were similar to other IncN plasmids isolated worldwide and carried a wide range of ARGs extensively corroborated by phenotypic resistance patterns. Interestingly, all transconjugants also acquired the class 1 integron intl1, which is commonly known as a proxy for anthropogenic pollution. The addition of ZnSO4 and CuSO4 at sub-inhibitory concentrations did not affect the transfer rate. Metal resistance genes were absent from most transconjugants, suggesting a minor role, if any, of metals in the spread of multidrug-resistant plasmids at the investigated sites.

Microbiome analysis reveals microecological advantages of emerging ditchless rice-crayfish co-culture mode

Ditchless rice-crayfish co-culture is an emerging model of rice-crayfish farming that circumvents the potential hazards of digging ditches in traditional rice-crayfish farming. However, due to the complex interactions among crayfish, ambient microbiota, and environmental variables, it is necessary to assess the differences in bacterial structure between ditchless and traditional rice-crayfish culture. In this study, the crayfish culture area in the Sichuan basin was selected as the study area, and the bacterial communities of two rice-crayfish culture systems were compared by high-throughput sequencing of 16S rDNA. The results showed that the ditchless system had lower water depth, higher dissolved oxygen, lower total ammonia nitrogen and lower morbidity. There are intuitive differences in the composition of environmental bacterial communities due to environmental changes, even if they are similar in composition at the phylum level. Microbiota in sediments from ditchless systems appear to produce less ammonia nitrogen. The abundance of the pathogens colonizing the intestine of ditchless crayfish was lower than ditched one, and the composition was similar to water. Ditch-farmed crayfish appear to be more susceptible to environmental microbes and have a more fragile intestinal structure. Water depth and dissolved oxygen are the main environmental factors that determine the distribution of microbiota. This study is the first to investigate the bacterial ecology of a ditchless rice- crayfish farming system. The results show that the ditchless rice-crayfish culture model has a more superior bacterial system than the traditional rice-crayfish culture.

Evolution of antibiotic resistance genes and bacterial community during erythromycin fermentation residue composting

The removal efficiency of antibiotic resistance genes (ARGs) is the biggest challenge for the treatment of erythromycin fermentation residue (EFR). In the current research, 0% (control), 10% (T1), and 30% (T2) spray-dried EFR were composted with bulking materials, consisting of cattle manure and maize straw, for 30 days. Environmental factors and bacterial community on the behaviors of ARGs were further investigated. Apart from the high levels of erythromycin, the electrical conductivities were also increased by 66.7% and 291.7% in the samples of T1 and T2, respectively. After 30 days of composting, total ARGs in the samples of control were decreased by 78.1%–91.2%, but those of T1 and T2 were increased 14.5–16.7- and 38.5–68.7-fold. ARGs related to ribosomal protection (erm) dominated the samples of T1 and T2 at D 13 and 30, especially that ermF accounted for more than 80% of the total ARGs. Furthermore, the results of bacterial community revealed that EFR promoted the growth of Proteobacteria and Bacteroidetes, but inhibited that of Actinobacteria, Verrucomicrobia and Chloroflexi. Network analysis revealed that the enriched ARGs had strong correlation with seven bacterial genera, including Halomonas, Oceanobacillus, and Alcaligenes, most of which are halotolerant. Above all, erythromycin combined with high salinity can have synergistic effect on the enrichment of ARGs and their hosts.