Characterization Of Microbial Communities Research Articles

Compositional, genetic and functional characterization of soil culturable microbial communities in polychlorinated dibenzo-p-dioxins/furans contaminated soil

Dioxins (PCDD/Fs) are one of the most toxic environmental pollutants known to date. Due to their structural stability and extreme hydrophobicity dioxins persist in the ecosystems and can be bioaccumulated to critical levels in both human and animal food chains. Soils are the most important reservoirs of dioxins, thus soil microbes are highly exposed to dioxins, impacting their diversity, genetics and functional characteristics. To experimentally evaluate these effects, the diversity and functionality of soil microbes were assessed in seven local sites potentially exposed to PCDD/Fs.Concentration of dioxins in soils samples was firstly determined and the soils cultivable microbes were identified and molecularly characterized as a function of their in vitro ability to degrade the TCDD. Our results revealed that the diversity of microbial communities largely varied among the sites and was likely inversely proportional to their level of contamination with PCDD/Fs. Furthermore, the genetics profiling of dioxin-degrading bacteria revealed that the Cytochrome P450 CYPBM3-positive species largely belong to the genus Bacillus and were randomly distributed among the soils samples, while the angular dioxygenase (AD)-positive species were mainly found in highly polluted soils with a major presence of the genus Pseudomonas. Finally, the functionality of dioxin-biodegrading genes (AD or CYPBM3), was confirmed by the ability of bacteria to consume 2,3,7,8-TCDD, and this was synchronized with an induced level of both pathways. Our results suggest that different dioxin-metabolizing pathways exist under the same environmental conditions and work differentially for an effective removal of PCDD/Fs.

Long-term exposure to microplastics induces intestinal function dysbiosis in rare minnow (Gobiocypris rarus)

Microplastics are ubiquitous in the natural environment, especially in waters, and their potential impact is also a key issue of concern. In this study, we used 1 µm, 1000 μg/L, polystyrene (PS-MPs) particles to analyze the effects after exposure for 14 and 28 days in rare minnow (Gobiocypris rarus). Results indicated that PS-MPs induce structural alterations in the intestinal tissue, including epithelial damage, villi damage and the inflammatory cell infiltration, while the changes were severer after exposure for 28 days. Polystyrene microplastics also significantly increased the activities of catalase (CAT, increased 142 % and 385 % in 14d and 28d), superoxide dismutase (SOD, increased 17.76 % and 23.43 % in the 14d and 28d) and the content of malondialdehyde (MDA, increased 14.5 % and 442 % in the 14d and 28d), glutathione (GSH, increased 146 % and 298 % in the 14d and 28d). The results not only showed the characterization of gut microbial communities in rare minnow, but also indicated that microbial diversity and composition were altered in gut of fish exposed to PS-MPs. In the control groups, Proteobacteria (31.36–54.54 %), Actinobacteriota (39.99–52.54 %), Fusobacteriota (1.43–1.78 %), Bacteriadota (0.31–0.57 %) were the four dominant bacterial phyla in the intestinal of rare minnow. After exposure to microplastics, In the gut microbiota, the proportion of Proteobacteria increased 9.27 % and 30 % with exposure time, while Actinobacteria decreased 37.89 % and significantly different after 28 days. In addition, metabolomic analysis suggested that exposure to PS-MPs induced alterations of metabolic profiles in rare minnow and differential metabolites were involved in energy metabolism, inflammatory responsible secretion, oxidative stress, nucleotide and its metabolomics. In conclusion, our findings suggest that long-term exposure to microplastics could induce intestinal inflammation, oxidative stress, microbiota dysbiosis and metabolic disorder in rare minnow, and the alterations and severity were exacerbated by prolonged exposure. This study has extended our cognition of the toxicity of polystyrene, and enriched theoretical data for exploring the toxicological mechanism of microplastics.

Synergistic effect of hydrogen and nanoscale zero-valent iron on ex-situ biogas upgrading and acetate recovery

Hydrogen (H2) assisted ex-situ biogas upgrading and liquid chemicals production can augment the fossil fuel-dominated energy market, and alleviate CO2-induced global warming. Recent investigations confirmed that nanoscale zero-valent iron (nZVI) enabled the enhancement of anaerobic digestion for biogas production. However, little is known about the effect of nZVI on the downstream ex-situ biogas upgrading. Herein, different levels (0 mg L−1, 100 mg L−1, 200 mg L−1, 500 mg L−1, 1000 mg L−1, 2000 mg L−1) of nZVI were added for H2-assisted ex-situ biogas upgrading, to study whether nZVI could impact the biomethane purity and acetate yield for the first time. Results showed that all tested nZVI levels were favorable for biogas upgrading in the presence of H2, the highest biomethane content (94.1 %, v/v), the CO2 utilization ratio (95.9 %), and acetate yield (19.4 mmol L−1) were achieved at 500 mg L−1 nZVI, respectively. Further analysis indicated that increased biogas upgrading efficiency was related to an increase in extracellular polymeric substances, which ensures the microbial activity and stability of the ex-situ biogas upgrading. Microbial community characterization showed that the Petrimonas, Romboutsia, Acidaminococcus, and Clostridium predominated the microbiome during biogas upgrading at 500 mg L−1 nZVI with H2 supply. These results suggested that nZVI and H2 contributed jointly to promoting the bioconversion of CO2 in biogas to acetate. The findings could be helpful for paving a new way for efficient simultaneous ex-situ biogas upgrading and liquid chemicals recovery.

Deep metagenomic characterization of gut microbial community and function in preeclampsia.

Preeclampsia (PE) is a pregnancy complication characterized by severe hypertension and multiple organ damage. Gut microbiota has been linked to PE by previous amplicon sequencing studies. To resolve the PE gut microbiota in a higher taxonomy resolution, we performed shotgun metagenomic sequencing on the fecal samples from 40 early-onset PE and 37 healthy pregnant women. We recovered 1,750 metagenome-assembled genomes (representing 406 species) from the metagenomic dataset and profiled their abundances. We found that PE gut microbiota had enriched in some species belonging to Blautia, Pauljensenia, Ruminococcus, and Collinsella and microbial functions such as the bacitracin/lantibiotics transport system, maltooligosaccharide transport system, multidrug efflux pump, and rhamnose transport system. Conversely, the gut microbiome of healthy pregnant women was enriched in species of Bacteroides and Phocaeicola and microbial functions including the porphyrin and chlorophyll metabolism, pyridoxal-P biosynthesis, riboflavin metabolism, and folate biosynthesis pathway. PE diagnostic potential of gut microbial biomarkers was developed using both species and function profile data. These results will help to explore the relationships between gut bacteria and PE and provide new insights into PE early warning.

Novel technologies to characterize and engineer the microbiome in inflammatory bowel disease

ABSTRACT We present an overview of recent experimental and computational advances in technology used to characterize the microbiome, with a focus on how these developments improve our understanding of inflammatory bowel disease (IBD). Specifically, we present studies that make use of flow cytometry and metabolomics assays to provide a functional characterization of microbial communities. We also describe computational methods for strain-level resolution, temporal series, mycobiome and virome data, co-occurrence networks, and compositional data analysis. In addition, we review novel techniques to therapeutically manipulate the microbiome in IBD. We discuss the benefits and drawbacks of these technologies to increase awareness of specific biases, and to facilitate a more rigorous interpretation of results and their potential clinical application. Finally, we present future lines of research to better characterize the relation between microbial communities and IBD pathogenesis and progression.

Characterization of the core microbial community governing acidogenic processes for the production of valuable bioproducts

Volatile fatty acids (VFAs) and alcohols generated from acidogenic processes are valuable bioresources. However, how the diversity of acidogenic microorganisms and environmental factors affect their generation are still poorly understood. In this study, 18 different inocula and 42 sludges from acidogenic lab-scale reactors were collected to analyze the microbial communities and their metabolic potential using 16S rRNA genes high throughput sequencing coupled with PICRUSt2. 23 out of 30732 distinctive amplicon sequence variants were identified as the core features and 34.8% of them (e.g., Clostridium spp.) were positively correlated with the generation of the most common product acetate. PICRUSt2 shows that an average of 27% of predicted fermentation-pathway genes was assigned to the core features, suggesting their crucial roles in acidogenesis. From the network aspect, the acidogenic network had a slightly higher number of nodes (12%), but significantly lower numbers of edges (109%) and neighbors (132%) compared with the inoculum network. A total of 28 independent subnetworks from large to small scales were extracted from the acidogenic network. The decentralized distribution of core features in these subnetworks emphasized their non-co-occurring relationships. The electrode potential was the most significant environmental variable (48.2–49.3% of the explanation), positively affecting the distribution of more than 50% of the core features and fermentation pathways. Results of this study emphasized the importance of core features rather than microbial diversity in acidogenic performance and highlighted the response of the core microbial community to environmental changes, which may be applied in practical applications to optimize acidogenic performance.

Characterization of Microbial Communities and Naturally Occurring Radionuclides in Soilless Growth Media Amended with Different Concentrations of Biochar

Biochar, derived from the pyrolysis of plant materials has the potential to enhance plant growth in soilless media. Howevetar, little is known about the impact of biochar amendments to soilless growth media, microbial community composition, and fate of chemical constituents in the media. In this study, different concentrations of biochar were added to soilless media and microbial composition, and chemical constituents were analyzed using metagenomics and gamma spectroscopy techniques, respectively. Across treatments, carboxyl-C, phenolic-C, and aromatic-C were the main carbon sources that influenced microbial community composition. Flavobacterium (39.7%), was the predominantly bacteria genus, followed by Acidibacter (12.2%), Terrimonas (10.1%), Cytophaga (7.5%), Ferruginibacter (6.0%), Lacunisphaera (5.9%), Cellvibrio (5.8%), Opitutus (4.8%), Mucilaginibacter (4.0%) and Bryobacter (4.0%). Negative relationships were found between Cytophaga and 226Ra (r = −0.84, p = 0.0047), 40K (r = −0.82, p = 0.0069) and 137Cs (r = −0.93, p = 0.0002). Similarly, Mucilaginibacter was negatively correlated with 226Ra (r = −0.83, p = 0.0054) and 137Cs (r = −0.87, p = 0.0021). Overall, the data suggest that high % biochar amended samples have high radioactivity concentration levels. Some microorganisms have less presence in high radioactivity concentration levels.

Biogeographical Patterns and Assembly of Bacterial Communities in Saline Soils of Northeast China

Increasing salinity undermines soil fertility and imposes great threats to soil ecosystem productivity and ecological sustainability. Microbes with the ability to adapt to environmental adversity have gained increasing attention for maintenance and restoration of the salt-affected soil ecosystem structure and functioning; however, the characterization of microbial communities in saline–sodic soils remains limited. This study characterized the bacterial community composition and diversity in saline–sodic soils along a latitude gradient across Northeast China, aiming to reveal the mechanism of physicochemical and geographic characteristics shaping the soil bacterial communities. Our results showed that the bacterial community composition and diversity were significantly impacted by soil pH, electrical conductivity, Na+, K+, Cl−, and CO32−. Significant differences in bacterial diversity were revealed along the latitude gradient, and the soil factors accounted for 58.58% of the total variations in bacterial community composition. Proteobacteria, Actinobacteria, Gemmatimonadetes, Chloroflexi, and Bacteroidetes were dominant across all samples. Actinobacteria and Gemmatimonadetes were significantly enriched in high soil sodicity and salinity, while Acidobacteria and Proteobacteria were suppressed by high pH and salt stress in the saline–sodic soils. Increase in soil pH and salinity significantly decreased bacterial species richness and diversity. Community composition analysis indicated that bacterial taxonomic groups (e.g., Bacillus, Egicoccus, Truepera, Halomonas, and Nitrolancea) that may adapt well to high salinity were greatly enriched in the examined soils. The findings collectively evidenced that bacterial community composition and diversity in a broad biographic scale were determined by niche-based environmental characteristics and biotic interactions. The profiling of the soil bacterial communities along the latitude gradient will also provide a basis for a better understanding of the salt-affected soil ecosystem functioning and restoration of these soil ecosystems.

Removal of H2S in an extremely acidic-biotrickling filter: Evaluation of removal performance and characterization of microbial communities

A cost-efficient, environmentally friendly, and extremely acidic biotrickling filter is essential for desulfurization to recover elemental sulfur and sulfate for extensively remediating H2S. The present study investigated the H2S removal capacity, accumulation of desulfurization products, sulfur balance, microbial community, and the H2S biodegradation kinetics. The results showed that when the empty bed retention time (EBRT) decreased from 180 s to 60 s, the removal efficiency of H2S decreased from 100% to 95.4%, and the elimination capacity increased from 18.0 ± 1.3–51.5 ± 3.2 gH2S m–3 h–1. Furthermore, with the increase of EBRT, the proportion of SO42–-S in the biodesulfurization products gradually decreased from 74.83% to 38.71%, whereas that of S0-S increased from 16.04% to 53.30%. The content of polysaccharide (PS), protein (PN), and the change of PN/PS values during the H2S removal process were studied. Moreover, 16 S rRNA high-throughput sequencing analysis showed that Acidithiobacillus, Thiobacillus, Sulfuricurvum, and Sulfobacillus were the main genera in the removal of H2S, and their total abundance was higher than 68.00%. In addition, the system viability and robustness were proved by shock loads and starvation regimes.

Characterization of microbial communities in anaerobic acidification reactors fed with casein and/or lactose

Protein-rich agro-industrial waste streams are high in organic load and represent a major environmental problem. Anaerobic digestion is an established technology to treat these streams; however, retardation of protein degradation is frequently observed when carbohydrates are present. This study investigated the mechanism of the retardation by manipulating the carbon source fed to a complex anaerobic microbiota and linking the reactor performance to the variation of the microbial community. Two anaerobic acidification reactors were first acclimated either to casein (CAS reactor) or lactose (LAC reactor), and then fed with mixtures of casein and lactose. Results showed that when lactose was present, the microbial community acclimated to casein shifted from mainly Chloroflexi to Proteobacteria and Firmicutes, the degree of deamination in the CAS reactor decreased from 77 to 15%, and the VFA production decreased from 75 to 34% of the effluent COD. A decrease of 75% in protease activity and 90% in deamination activity of the microbiota was also observed. The microorganisms that can ferment both proteins and carbohydrates were predominant in the microbial community, and from a thermodynamical point of view, they consumed carbohydrates prior to proteins. The frequently observed negative effect of carbohydrates on protein degradation can be mainly attributed to the substrate preference of these populations.Keypoints• The presence of lactose shifted the microbial community and retarded anaerobic protein degradation.• Facultative genera were dominant in the presence and absence of lactose.• Substrate-preference caused retardation of anaerobic protein degradation.

Cecal microbiota of feedlot cattle fed a four-species Bacillus supplement.

As commercial fed cattle consume large amounts of concentrate feedstuffs, hindgut health can be challenged. The objective of this study was to evaluate the effects of a commercially available Bacillus feed additive on cattle health outcomes and cecal microbiota of fed cattle at the time of harvest. Commercial cattle from a single feedlot were identified for characterization of cecal microbial communities using 16S ribosomal ribonucleic acid gene sequencing. All cattle were fed a common corn-based finishing diet. Control cattle (CON) were administered no treatment while treated cattle (TRT) were supplemented daily with 0.050 g of MicroSaf 4C 40 (2 billion colony forming units of Bacillus spp.; Phileo by Lesaffre, Milwaukee, WI). Immediately after harvest and evisceration, the cecal contents of cattle were sampled. After DNA extraction, amplification, and sequencing, reads from CON samples (N = 12) and TRT samples (N = 12) were assigned taxonomy using the SILVA 138 database. Total morbidity, first treatment of atypical interstitial pneumonia, and early shipments for harvest were decreased among TRT cattle compared to CON cattle (P ≤ 0.021). On average, cecal microbiota from TRT cattle had greater alpha diversity than microbiota from CON cattle as measured by Shannon diversity, Pielou's evenness, and feature richness (P < 0.010). Additionally, TRT microbial communities were different (P = 0.001) and less variable (P < 0.001) than CON microbial communities when evaluated by unweighted UniFrac distances. By relative abundance across all samples, the most prevalent phyla were Firmicutes (55.40%, SD = 15.97) and Bacteroidetes (28.17%, SD = 17.74) followed by Proteobacteria (6.75%, SD = 10.98), Spirochaetes (4.54%, SD = 4.85), and Euryarchaeota (1.77%, SD = 3.00). Spirochaetes relative abundance in TRT communities was greater than that in CON communities and was differentially abundant between treatments by ANCOM testing (W = 11); Monoglobaceae was the only family-level taxon identified as differentially abundant (W = 59; greater mean relative abundance in TRT group by 2.12 percentage points). Half (N = 6) of the CON samples clustered away from all other samples based on principal coordinates and represented cecal dysbiosis among CON cattle. The results of this study indicated that administering a four-species blend of Bacillus positively supported the cecal microbial communities of finishing cattle. Further research is needed to explore potential mechanisms of action of Bacillus DFM products in feedlot cattle.

Characterization of phosphorus sorption and microbial community in lake sediments during overwinter and recruitment periods of cyanobacteria.

The release of endogenous phosphorus from lacustrine sediment is a key element of freshwater eutrophication. The microbes in sediments may affect phosphorus migration and transformation during the growth of cyanobacteria, which may lead to the release of phosphorus from sediments and contribute to water eutrophication. To study phosphorus sorption and the microbial community structure in the overlying water and the vertical depth of sediments, samples in Meiliang Bay were collected during the dormancy and resuscitation phases of cyanobacteria. The results showed that there were high total phosphorus (TP) concentrations in the overlying water and sediment, with maximum values reached 0.24 mg L−1 and 1059 mg kg−1, respectively. Fitting by modified Langmuir model indicated that the partitioning coefficients (KP) was, from greatest to least: bottom sediment (maximum of 0.923 L g−1) > middle sediment (0.571 L g−1) > surface sediment (0.262 L g−1). During the cyanobacteria resuscitation stage, the relative abundance of Proteobacteria (18.37%–33.56%), Chloroflexi (9.57%–17.76%), Cyanobacteria (0.38%–2.62%), and the Nitrospirota phylum Thermodesulfovibrionia (4.61%–10.14%) were higher than the dormant period of cyanobacteria, and bacteria with phosphorus-solubilizing (27.27%–52.01%) accounted for the majority. The redundancy analysis (RDA) found that the structure of the microbial communities in sediments was significant correlation with organic phosphorus (OP) (P = 0.002) during recruitment period of cyanobacteria, which would accelerate the conversion of OP into soluble inorganic phosphorus and then gets released from sediment to water. The most predominant phylum among phosphorus-solubilizing bacteria (PSB) is Proteobacteria, followed by Actinobacteriota, which were positively correlated with equilibrium phosphorus concentration (EPC0) (P < 0.05) during the cyanobacterial resuscitation phase. The sediments from the cyanobacteria resuscitation phase had phosphorus release risk and highlighted the significant role of the bacterial community.

Binning long reads in metagenomics datasets using composition and coverage information

BackgroundAdvancements in metagenomics sequencing allow the study of microbial communities directly from their environments. Metagenomics binning is a key step in the species characterisation of microbial communities. Next-generation sequencing reads are usually assembled into contigs for metagenomics binning mainly due to the limited information within short reads. Third-generation sequencing provides much longer reads that have lengths similar to the contigs assembled from short reads. However, existing contig-binning tools cannot be directly applied on long reads due to the absence of coverage information and the presence of high error rates. The few existing long-read binning tools either use only composition or use composition and coverage information separately. This may ignore bins that correspond to low-abundance species or erroneously split bins that correspond to species with non-uniform coverages. Here we present a reference-free binning approach, LRBinner, that combines composition and coverage information of complete long-read datasets. LRBinner also uses a distance-histogram-based clustering algorithm to extract clusters with varying sizes.ResultsThe experimental results on both simulated and real datasets show that LRBinner achieves the best binning accuracy in most cases while handling the complete datasets without any sampling. Moreover, we show that binning reads using LRBinner prior to assembly reduces computational resources required for assembly while attaining satisfactory assembly qualities.ConclusionLRBinner shows that deep-learning techniques can be used for effective feature aggregation to support the metagenomics binning of long reads. Furthermore, accurate binning of long reads supports improvements in metagenomics assembly, especially in complex datasets. Binning also helps to reduce the resources required for assembly. Source code for LRBinner is freely available at https://github.com/anuradhawick/LRBinner.

Characterization of the belowground microbial community and co-occurrence networks of tobacco plants infected with bacterial wilt disease.

Characterizing the microbial communities associated with soil-borne disease incidence is a key approach in understanding the potential role of microbes in protecting crops from pathogens. In this study, we compared the soil properties and microbial composition of the rhizosphere soil and roots of healthy and bacterial wilt-infected tobacco plants to assess their potential influence on plant health. Our results revealed that the relative abundance of pathogens was higher in diseased plants than in healthy plants. Moreover, compared with healthy plants, there was a significantly higher microbial alpha diversity in the roots and rhizosphere soil of diseased plants. In addition, we detected a lower abundance of certain plant microbiota, including species in the genera Penicillium, Trichoderma, and Burkholderia in the rhizosphere of diseased plants, which were found to be significantly negatively associated with the relative abundance of Ralstonia. Indeed, compared with healthy plants, the co-occurrence networks of diseased plants included a larger number of associations linked to plant health. Furthermore, structural equation modeling revealed that these specific microbes were correlated with disease suppression, thereby implying that they may play important roles in maintaining plant health. In conclusion, our findings provide important insights into the relationships between soil-borne disease incidence and changes in the belowground microbial community. These findings will serve as a basis for further research investigating the use of specific plant-associated genera to inhibit soil-borne diseases.

In-depth characterization of denitrifier communities across different soil ecosystems in the tundra

BackgroundIn contrast to earlier assumptions, there is now mounting evidence for the role of tundra soils as important sources of the greenhouse gas nitrous oxide (N2O). However, the microorganisms involved in the cycling of N2O in this system remain largely uncharacterized. Since tundra soils are variable sources and sinks of N2O, we aimed at investigating differences in community structure across different soil ecosystems in the tundra.ResultsWe analysed 1.4 Tb of metagenomic data from soils in northern Finland covering a range of ecosystems from dry upland soils to water-logged fens and obtained 796 manually binned and curated metagenome-assembled genomes (MAGs). We then searched for MAGs harbouring genes involved in denitrification, an important process driving N2O emissions. Communities of potential denitrifiers were dominated by microorganisms with truncated denitrification pathways (i.e., lacking one or more denitrification genes) and differed across soil ecosystems. Upland soils showed a strong N2O sink potential and were dominated by members of the Alphaproteobacteria such as Bradyrhizobium and Reyranella. Fens, which had in general net-zero N2O fluxes, had a high abundance of poorly characterized taxa affiliated with the Chloroflexota lineage Ellin6529 and the Acidobacteriota subdivision Gp23.ConclusionsBy coupling an in-depth characterization of microbial communities with in situ measurements of N2O fluxes, our results suggest that the observed spatial patterns of N2O fluxes in the tundra are related to differences in the composition of denitrifier communities.

The real-time monitoring system strategy for stable long-term operation of pilot-scale single-stage deammonification (SSD) process treating moderate-strength NH4+

Single-stage deammonification (SSD) processes have been successfully operated to treat high-strength NH4+-N, but often fail to treat moderate-strength NH4+-N (100–300 mg/L). Moderate-strength NH4+-N causes deterioration of process efficiency to occur NO2−-N oxidizing bacteria (NOB) due to free ammonia (FA) reduction and maintenance limits. The optimal FA (>0.1 mg/L) control focusing on real-time monitoring pH and NH4+-N under controlling low DO was integrated to enhance the SSD process stability operational treating moderate-strength NH4+-N wastewater. The average NRE and NRR were still high as 82 ± 1% and 0.22 ± 0.01 kg/m3/d. A real-time monitoring system strategy that directly uses DO, NH4+-N and pH was effective in stably providing optimal DO (<0.1 mg/L) and sufficient FA (>0.1 mg/L) that capable in inhibiting selective NOB activity. Microbial community characterization revealed that denitrifying bacteria indicate their important role in the improved nitrogen removal performance using in organic matter of reject-water without another anoxic period under long-term low DO with optimal FA conditions. The research results are expected to prevent the problem of unstable due to the substrate competition of major microorganisms and to reduce the deterioration within the SSD process due to excessive NOB activity.

A review of the emergence of antibiotic resistance in bioaerosols and its monitoring methods.

Despite significant public health concerns regarding infectious diseases in air environments, potentially harmful microbiological indicators, such as antibiotic resistance genes (ARGs) in bioaerosols, have not received significant attention. Traditionally, bioaerosol studies have focused on the characterization of microbial communities; however, a more serious problem has recently arisen due to the presence of ARGs in bioaerosols, leading to an increased prevalence of horizontal gene transfer (HGT). This constitutes a process by which bacteria transfer genes to other environmental media and consequently cause infectious disease. Antibiotic resistance in water and soil environments has been extensively investigated in the past few years by applying advanced molecular and biotechnological methods. However, ARGs in bioaerosols have not received much attention. In addition, ARG and HGT profiling in air environments is greatly limited in field studies due to the absence of suitable methodological approaches. Therefore, this study comprehensively describes recent findings from published studies and some of the appropriate molecular and biotechnological methods for monitoring antibiotic resistance in bioaerosols. In addition, this review discusses the main knowledge gaps regarding current methodological issues and future research directions.

Characterization of Microbial Communities in Wastewater Treatment Plants Containing Heavy Metals Located in Chemical Industrial Zones.

Water pollution caused by heavy metals (HMs) poses a serious risk to human health and the environment and can increase the risk of diabetes, cancer, and hypertension in particular. In this study, two full-scale wastewater treatment plants (WWTPs) in industrial zones in southern China were selected to analyze the microbial community structure, diversity, similarity, and differentiation in the anoxic/oxic (AO) and anoxic/oxic membrane bioreactor (AO-MBR) units under the stress of HMs. High-throughput sequencing showed that microbial diversity and abundance were higher in the AO process than in the AO-MBR process. In the two WWTPs, the common dominant phyla were Proteobacteria and Bacteroidetes, while the common dominant genera were Gemmatimonadaceae, Anaerolineaceae, Saprospiraceae, and Terrimonas. Manganese (Mn) and zinc (Zn) positively correlated with Saccharimonadales, Nakamurella, Micrococcales, and Microtrichales, whereas copper (Cu) and iron (Fe) positively correlated with Longilinea and Ferruginibacter. Additionally, the relative abundances of Chloroflexi, Patescibacteria, and Firmicutes differed significantly (p < 0.05) between the two processes. These results may provide comprehensive outlooks on the characterization of microbial communities in WWTPs, which could also help to reduce the potential environmental risks of the effluent from WWTPs located in industrial zones.

Monocot diet sources drive diversity of gut bacterial communities in Spodoptera frugiperda (Lepidoptera: Noctuidae) larvae

AbstractMicrobiome research is currently gaining tremendous interest on the impact of diets and environment to influence life traits of several hosts. Full understanding of the insect ecology and characterization of gut microbial community including their natural enemies is vital for development of novel insect pest management strategies. This study examined the gut bacterial communities of Fall armyworm (FAW) Spodoptera frugiperda reared in the laboratory with three monocot plant diets (Sugarcane [M1], maize [M2] and onion [M3]) using 16S rRNA gene sequencing. The study revealed variations in the structure and community of the gut bacterial biota of FAW larvae reared with three monocot plants. Diet sources greatly altered the structure of the gut bacterial community. Three alpha diversity indices (observed species richness Chao1 and ACE) showed significant differences among the various diet groups. The principal component analysis revealed a moderate distinction in bacterial communities of the FAW larvae reared with the three monocot plants. Higher numbers of operational taxonomic units (OTUs) were observed in sugarcane diet (M1). The bacterial communities of all the larvae groups were dominated by phylum Firmicutes. A redundancy analysis (RDA) indicated that neutral detergent fibre (NDF) (p &lt; 0.0005) was the most significant factors influencing the community distribution of gut bacteria of FAW larvae. Functional Annotation of Prokaryotic Taxa (FAPROTAX) analysis predicted that chemoheterotrophy, fermentation, aerobic chemoheterotrophy and aromatic compound degradation were the prominent putative functions of FAW larvae gut bacteria communities. Chemoheterotrophy was the most dominant putative functions predicted and was higher in sugarcane diet. Furthermore, the complexity of the network structure was higher in M1 while the modularity was higher in maize diet. The different monocot diets had a considerable impact on bacterial composition in the gut of Fall armyworm larvae and their ecological and functional relevance are discussed.

Dynamic changes in fecal bacterial microbiota of dairy cattle across the production line

BackgroundMicrobiota play important roles in the gastrointestinal tract (GIT) of dairy cattle as the communities are responsible for host health, growth, and production performance. However, a systematic characterization and comparison of microbial communities in the GIT of cattle housed in different management units on a modern dairy farm are still lacking. We used 16S rRNA gene sequencing to evaluate the fecal bacterial communities of 90 dairy cattle housed in 12 distinctly defined management units on a modern dairy farm.ResultsWe found that cattle from management units 5, 6, 8, and 9 had similar bacterial communities while the other units showed varying levels of differences. Hutch calves had a dramatically different bacterial community than adult cattle, with at least 10 genera exclusively detected in their samples but not in non-neonatal cattle. Moreover, we compared fecal bacteria of cattle from every pair of the management units and detailed the number and relative abundance of the significantly differential genera. Lastly, we identified 181 pairs of strongly correlated taxa in the community, showing possible synergistic or antagonistic relationships.ConclusionsThis study assesses the fecal microbiota of cattle from 12 distinctly defined management units along the production line on a California dairy farm. The results highlight the similarities and differences of fecal microbiota between cattle from each pair of the management units. Especially, the data indicate that the newborn calves host very different gut bacterial communities than non-neonatal cattle, while non-neonatal cattle adopt one of the two distinct types of gut bacterial communities with subtle differences among the management units. The gut microbial communities of dairy cattle change dramatically in bacterial abundances at different taxonomic levels along the production line. The findings provide a reference for research and practice in modern dairy farm management.