Bacterial Diversity Composition Research Articles

Increase in potato yield by the combined application of biochar and organic fertilizer: key role of rhizosphere microbial diversity.

The large-scale planting of potatoes leads to soil degradation, thus limiting the potato yield. An effective method of improving soil quality involves the combined application of biochar and organic fertilizer. However, the proportion of biochar and organic fertilizer at which potato yield can be improved, as well as the improvement mechanism, remain unclear. A combined application experiment involving biochar (B) and organic fertilizer (O) with four concentration gradients was conducted using the equal carbon ratio method. On this basis, rhizosphere soil fertility, bacterial community composition, and bacterial diversity in potato crops, as well as the potato yield difference under different combined application ratios, were investigated. Then, the direct and indirect effects of these factors on potato yield were analyzed. The results suggest that soil fertility was improved by the combined application of biochar and organic fertilizer, with the best effect being achieved at a ratio of B:O=1:2. The dominant bacterial communities in the potato rhizosphere included Proteobacteria, Actinobacteria, Gemmatimonadetes, Chloroflexi, and Bacteroidetes. When compared to the control, the relative abundance and diversity index of soil bacteria were significantly improved by the treatment at B:O=1:2, which exerted a stronger effect on improving the relative abundance of beneficial bacteria. Soil available phosphorus (AP), soil pH (SpH), and soil organic carbon (SOC) explained 47.52% of the variation in bacterial composition. Among them, the main factor was the content of soil available nutrients, while SpH generated the weakest effect. The bacterial diversity index showed a significant positive correlation with soil AP, SOC, available potassium (AK), total nitrogen (TN), and C/N ratio, and a significant negative correlation with SpH. Bacterial diversity directly affected the potato yield, while soil fertility indirectly affected potato yield by influencing the soil bacterial diversity. The combined application of biochar and organic fertilizer elevates potato yield mainly by improving the diversity of bacterial communities in potato rhizosphere soil, especially the combined application of biochar and organic fertilizer at a 1:2 ratio (biochar 0.66 t ha-1+organic fertilizer 4.46 t ha-1), which made the largest contribution to increasing potato yield.

Comparative Analysis of the Symbiotic Microbiota in the Chinese Mitten Crab (Eriocheir sinensis): Microbial Structure, Co-Occurrence Patterns, and Predictive Functions

Symbiotic microorganisms in the digestive and circulatory systems are found in various crustaceans, and their essential roles in crustacean health, nutrition, and disease have attracted considerable interest. Although the intestinal microbiota of the Chinese mitten crab (Eriocheir sinensis) has been extensively studied, information on the symbiotic microbiota at various sites of this aquatic economic species, particularly the hepatopancreas and hemolymph, is lacking. This study aimed to comprehensively characterize the hemolymph, hepatopancreas, and intestinal microbiota of Chinese mitten crab through the high-throughput sequencing of the 16S rRNA gene. Results showed no significant difference in microbial diversity between the hemolymph and hepatopancreas (Welch t-test; p > 0.05), but their microbial diversity was significantly higher than that in the intestine (p < 0.05). Distinct differences were found in the structure, composition, and predicted function of the symbiotic microbiota at these sites. At the phylum level, the hemolymph and hepatopancreas microbiota were dominated by Proteobacteria, Firmicutes, and Acidobacteriota, followed by Bacteroidota and Actinobacteriota, whereas the gut microbiota was mainly composed of Firmicutes, Proteobacteria, and Bacteroidota. At the genus level, Candidatus Hepatoplasma, Shewanella, and Aeromonas were dominant in the hepatopancreas; Candidatus Bacilloplasma, Roseimarinus, and Vibrio were dominant in the intestine; Enterobacter, norank_Vicinamibacterales, and Pseudomonas were relatively high-abundance genera in the hemolymph. The composition and abundance of symbiotic microbiota in the hemolymph and hepatopancreas were extremely similar (p > 0.05), and no significant difference in functional prediction was found (p > 0.05). Comparing the hemolymph in the intestine and hepatopancreas, the hemolymph had lower variation in bacterial composition among individuals, having a more uniform abundance of major bacterial taxa, a smaller coefficient of variation, and the highest proportion of shared genera. Network complexity varied greatly among the three sites. The hepatopancreas microbiota was the most complex, followed by the hemolymph microbiota, and the intestinal microbiota had the simplest network. This study revealed the taxonomic and functional characteristics of the hemolymph, hepatopancreas, and gut microbiota in Chinese mitten crab. The results expanded our understanding of the symbiotic microbiota in crustaceans, providing potential indicators for assessing the health status of Chinese mitten crab.

Variation in bacterial composition, diversity, and activity across different subglacial basal ice types

Abstract. Glaciers and ice sheets possess basal ice layers characterized by high amounts of entrained debris that can serve as sources of nutrients and organic matter, providing a habitat for microorganisms adapted to the frozen conditions. Basal ice forms through various mechanisms and is classified based on ice and debris content; however, little is known about variation in microbial composition, diversity, and activity across different basal ice types. We investigated these parameters in four different types of basal ice from a cold-based and temperate glacier and used a meta-analysis to compare our findings with microbiome studies from other frozen environments. We found basal ice environments harbor a diverse range of microbiomes whose composition and activity can vary significantly between basal ice types, even within adjacent facies from the same glacier. In some debris-rich basal ices, elevated ATP concentrations, isotopic gas signatures, and high 16S rRNA/rDNA amplicon ratios implicated certain bacterial taxa (e.g., Paenisporosarcina, Desulfocapsa, Syntrophus, and Desulfosporosinus) as being potentially active, with ice temperature appearing to be an important predictor for the diversity of inferred active taxa. Compared to those of other sympagic environments, the basal ice microbiomes more closely resemble those found in permafrost or perennial cave ice than glacial ice. In contrast, debris-poor basal ices harbored microbiomes more like those found in englacial ice. Collectively, these results suggest that different basal ice types contain distinct microbiomes that are actively structured by physicochemical properties of their habitat.

Bacterial communities of the oviduct of turkeys

Bacterial communities in the reproductive tract of avian species play an important role in keeping birds healthy and encouraging growth. Infection can occur during egg formation with pathogens that can be transmitted to the embryo. In this study, we investigated the bacterial composition in the turkey reproductive tract using a taxa identification based on the amplicon sequence of the V3–V4 region of the 16S rRNA gene. The microbial composition and relative abundance of bacteria differed between individual birds. Among the 19 phyla detected in turkey oviduct were unique taxa like Planctomycetes or Petescibacteria. Differences in composition of bacterial diversity were found at the family and genus level. Oviducts contained also several genus with well-recognized avian pathogens like Escherichia-Shigella, Enterococcus, Staphylococcus, and Ornithobacterium. Some of the bacteria described in this study have not been so far identified in turkeys. The objective of this study was to identify bacterial communities in the turkey oviduct and compared the composition of the oviduct with that in chickens broadening the knowledge of the microbial composition in the reproductive tract of poultry.

The carbon and nitrogen stoichiometry in litter-soil-microbe continuum rather than plant diversity primarily shapes the changes in bacterial communities along a tropical forest restoration chronosequence

Soil bacteria play core roles in mediating the functional linkage between above- and belowground components during forest restoration. However, the pattern and mechanism through which plants and soils influence bacterial communities remain unclear. This study aimed to quantify the contributions of plant community and soil characteristics to shifts in bacterial composition and diversity along a tropical forest restoration chronosequence in the Xishuangbanna. We found a negative effect of forest restoration on bacterial composition and a positive impact on the diversity. Forest restoration changed bacterial communities from being oligotrophic Acidobacteria and Actinobacteria dominatedto copiotrophic Proteobacteria and Firmicutes dominated. Forest restoration also induced a 1.5–1.6 fold increase in OTU richness and diversity of bacterial communities. Soil variables, including plant litter, contributed 46.3–58.1% to the variations in bacterial composition and diversity, while the contribution of plant community was 6.4–13.8%. Furthermore, the increase in plant richness and diversity had minor contribution to variations in bacterial diversity and composition during forest restoration. Soil bacterial diversity was primarily explained by the elevated levels of carbon and nitrogen stoichiometry in the litter-soil-microbe continuum, but litter was explained by the increased plant diversity. In contrast, soil bacterial composition was negatively correlated with biomass, nitrogen, and carbon:nitrogen of the litter, as well as the level of soil carbon and nitrogen pools. Our data suggested that the carbon and nitrogen stoichiometry in litter-soil-microbe continuum rather than plant diversity primarily shaped the changes in bacterial composition and diversity along tropical forest restoration.

The influence of culture-dependent native microbiota in Zika virus infection in Aedes aegypti

BackgroundEmerging and re-emerging vector-borne diseases (VBDs) pose a recurring threat to tropical countries, mainly due to the abundance and distribution of the Aedes aegypti mosquito, which is a vector of the Zika, dengue, chikungunya, and yellow fever arboviruses.MethodsFemale 3–5 day-old Ae. aegypti were distributed into two experimental groups: group I—survey of cultivable bacteria; sucrose group: fed only on sucrose, i.e., non-blood-fed (UF); blood-fed group: (i) fed with non-infected blood (BF); (ii) fed with blood infected with the Zika virus (BZIKV); (iii) pretreated with penicillin/streptomycin (pen/strep), and fed with non-infected blood (TBF); (iv) pretreated with pen/strep and fed blood infected with ZIKV, i.e., gravid with developed ovaries, (TGZIKV); group II—experimental co-infections: bacteria genera isolated from the group fed on sucrose, i.e., non-blood-fed (UF).ResultsUsing the cultivable method and the same mosquito colony and ZIKV strain described by in a previous work, our results reveled 11 isolates (Acinetobacter, Aeromonas, Cedecea, Cellulosimicrobium, Elizabethkingia, Enterobacter, Lysinibacillus, Pantoea, Pseudomonas, Serratia, and Staphylococcus). Enterobacter was present in all evaluated groups (i.e., UF, BF, BZIKV, TBF, and TGZIKV), whereas Elizabethkingia was present in the UF, BZIKV, and TBF groups. Pseudomonas was present in the BZIKV and TBF groups, whereas Staphylococcus was present in the TBF and TGZIKV groups. The only genera of bacteria that were found to be present in only one group were Aeromonas, Lysinibacillus, and Serratia (UF); Cedacea, Pantoea and Acinetobacter (BF); and Cellulosimicrobium (BZIKV). The mosquitoes co-infected with ZIKV plus the isolates group fed on sucrose (UF) showed interference in the outcome of infection.ConclusionsWe demonstrate that the distinct feeding aspects assessed herein influence the composition of bacterial diversity. In the co-infection, among ZIKV, Ae. aegypti and the bacterial isolates, the ZIKV/Lysinibacillus–Ae. aegypti had the lowest number of viral copies in the head-SG, which means that it negatively affects vector competence. However, when the saliva was analyzed after forced feeding, no virus was detected in the mosquito groups ZIKV/Lysinibacillus–Lu. longipalpis and Ae. aegypti; the combination of ZIKV/Serratia may interfere in salivation. This indicates that the combinations do not produce viable viruses and may have great potential as a method of biological control.Graphical

Molecular characterization of gut microbial structure and diversity associated with colorectal cancer patients in Egypt.

a large number of microbes colonizing the gut are highly diverse and complex in their structure, as this complex structure of gut microbiota acts as an indicator of a diseased state. Recently, there is a need for improved biomarkers for colorectal cancer (CRC) and advanced adenoma. Among the CRC associated organisms, bacteria are the most common causes of serious disease and deaths. To understand the dynamic interaction among bacteria colonizing the gut, different approaches have been implicated. in this study, faecal microbial markers were evaluated for detecting CRC. As most of these organisms are anaerobic, different molecular tools are of great values for rapid detection of these bacteria. Samples from Tumor Hospital were screened for the presence of different pathogens by both usual polymerase chain reaction (PCR) and a real-time assay. in a total of 34 samples, by PCR method, bifidobacterium, fusobacterium and Escherichia coli (E. coli) were mainly identified in almost all samples. However, a clear variation in bacterial composition could be observed in Porphyromonas gingivalis, Prevotella intermedia and Peptostreptococcus magnus, where positive results could be detected only in diseased samples. In addition, E. faecium and E. saphenum were mainly identified in diseased samples. In contrast, providencia could be detected mainly in control samples. In realtime assay, the relative abundance was higher for fusobacterium and bifidobacterium markers in CRC patients compared to control samples. However, such increased in abundance has never been observed in both fusobacterium and bifidobacterium in the same sample. these results demonstrated increased abundance of fusobacterium or bifidobacterium can be considered as a sign for impairment or a diseased condition and the possibility of use of the faecal microbiotain CRC patients as a marker for detecting the disease.

Antibiotic resistance genes of emerging concern in municipal and hospital wastewater from a major Swedish city

The spread of antibiotic resistance among bacterial pathogens is to a large extent mediated by mobile antibiotic resistance genes (ARGs). The prevalence and geographic distribution of several newly discovered ARGs, as well as some clinically important ARGs conferring resistance to last resort antibiotics, are largely unknown. Targeted analysis of wastewater samples could allow estimations of carriage in the population connected to the sewers as well as release to the environment. Here we quantified ARGs conferring resistance to linezolid (optrA and cfr(A)) and colistin (mcr-1, -2, -3, -4 and -5) and the recently discovered gar (aminoglycoside ARG) and sul4 (sulphonamide ARG) in raw hospital and municipal wastewater as well as treated municipal wastewater during five years in a low antibiotic resistance prevalence setting (Gothenburg, Sweden). Additionally, variations in bacterial composition of the wastewaters characterized by 16S rRNA sequencing were related to the variations of the ARGs in an attempt to reveal if the presence of known or suspected bacterial host taxa could explain the presence of the ARGs in wastewater. The mcr-1, mcr-3, mcr-4, mcr-5, sul4 and gar genes were detected regularly in all types of wastewater samples while optrA and cfr(A) were detected only in hospital wastewater. The most abundant genes were mcr-3 and mcr-5, especially in municipal wastewater. The detection of optrA was restricted to a peak during one year. Most of the ARGs correlated with taxa previously described as bacterial hosts and associated with humans. Although some of the tentative hosts may include bacteria also thriving in wastewater environments, detection of the ARGs in the wastewaters could reflect their presence in the gut flora of the contributing populations. If so, they could already today or in the near future hinder treatment of bacterial infections in a setting where they currently are rarely targeted/detected during clinical surveillance.

Bacterial structure and dynamics in mango (Mangifera indica) orchards after long term organic and conventional treatments under subtropical ecosystem

This study explores the comparative effect of conventional and organic treatments on the rhizosphere microbiome of Mangifera indica cv. Dashehari. The long-term exposures (about 20 years) were monitored under a subtropical ecosystem. Based on plant growth properties and acetylene reduction assay, 12 bacterial isolates (7 from G1-organic and 5 from G2-conventional systems) were identified as Pseudomonas and Bacillus spp. In the conventional system, dehydrogenase activity significantly decreased (0.053 µg TPF formed g−1 of soil h−1) and adversely affected the bacterial diversity composition. In comparison, organic treatments had a good impact on dehydrogenase activity (0.784 µg TPF formed g−1 of soil h−1), alkaline phosphatase (139.25 µg PNP g−1 soil h−1), and bacterial community composition. The Metagenomics approach targeted the V3 and V4 regions to see the impact in the phylum, order, family, genus, and species for both the treatments. Results showed that phylum Acidobacteria (13.6%), Firmicutes (4.84%), and Chloroflexi (2.56%) were dominating in the G2 system whereas phylum Bacteroides (14.55%), Actinobacteria (7.45%), and Proteobacteria (10.82%) were abundantly dominated in the G1 system. Metagenome sequences are at the NCBI-GenBank sequence read archive with SRX8289747 (G1) and SRX8289748 (G2) in the study PRJNA631113. Results indicated that conventional and organic conditions affect rhizosphere microbiome and their environment.

Bacterial communities of the upper respiratory tract of turkeys

The respiratory tracts of turkeys play important roles in the overall health and performance of the birds. Understanding the bacterial communities present in the respiratory tracts of turkeys can be helpful to better understand the interactions between commensal or symbiotic microorganisms and other pathogenic bacteria or viral infections. The aim of this study was the characterization of the bacterial communities of upper respiratory tracks in commercial turkeys using NGS sequencing by the amplification of 16S rRNA gene with primers designed for hypervariable regions V3 and V4 (MiSeq, Illumina). From 10 phyla identified in upper respiratory tract in turkeys, the most dominated phyla were Firmicutes and Proteobacteria. Differences in composition of bacterial diversity were found at the family and genus level. At the genus level, the turkey sequences present in respiratory tract represent 144 established bacteria. Several respiratory pathogens that contribute to the development of infections in the respiratory system of birds were identified, including the presence of Ornithobacterium and Mycoplasma OTUs. These results obtained in this study supply information about bacterial composition and diversity of the turkey upper respiratory tract. Knowledge about bacteria present in the respiratory tract and the roles they can play in infections can be useful in controlling, diagnosing and treating commercial turkey flocks.

Neonicotinoid Seed Treatments Have Significant Non-target Effects on Phyllosphere and Soil Bacterial Communities.

The phyllosphere and soil are dynamic habitats for microbial communities. Non-pathogenic microbiota, including leaf and soil beneficial bacteria, plays a crucial role in plant growth and health, as well as in soil fertility and organic matter production. In sustainable agriculture, it is important to understand the composition of these bacterial communities, their changes in response to disturbances, and their resilience to agricultural practices. Widespread pesticide application may have had non-target impacts on these beneficial microorganisms. Neonicotinoids are a family of systemic insecticides being vastly used to control soil and foliar pests in recent decades. A few studies have demonstrated the long-term and non-target effects of neonicotinoids on agroecosystem microbiota, but the generality of these findings remains unclear. In this study, we used 16S rRNA gene amplicon sequencing to characterize the effects of neonicotinoid seed treatment on soil and phyllosphere bacterial community diversity, composition and temporal dynamics in a 3-year soybean/corn rotation in Quebec, Canada. We found that habitat, host species and time are stronger drivers of variation in bacterial composition than neonicotinoid application. They, respectively, explained 37.3, 3.2, and 2.9% of the community variation. However, neonicotinoids did have an impact on bacterial community structure, especially on the taxonomic composition of soil communities (2.6%) and over time (2.4%). They also caused a decrease in soil alpha diversity in the middle of the growing season. While the neonicotinoid treatment favored some bacterial genera known as neonicotinoid biodegraders, there was a decline in the relative abundance of some potentially beneficial soil bacteria in response to the pesticide application. Some of these bacteria, such as the plant growth-promoting rhizobacteria and the bacteria involved in the nitrogen cycle, are vital for plant growth and improve soil fertility. Overall, our results indicate that neonicotinoids have non-target effects on phyllosphere and soil bacterial communities in a soybean-corn agroecosystem. Exploring the interactions among bacteria and other organisms, as well as the bacterial functional responses to the pesticide treatment, may enhance our understanding of these non-target effects and help us adapt agricultural practices to control these impacts.

Influence of Diet, Sex, and Viral Infections on the Gut Microbiota Composition of Spodoptera exigua Caterpillars.

The gut microbiota plays essential roles in processes related with metabolism, physiology, and immunity in all organisms, including insects. In the present work, we performed a broad analysis of the Spodoptera exigua gut microbiota, a major agricultural pest. We analyzed the influence of multiple parameters such as diet, geographic location, sex, or viral infections on S. exigua caterpillar gut microbiota composition. Our study revealed a high variability in bacterial composition among individuals, and a major influence of environmental bacteria (including those acquired through diet) on the gut microbiota composition, supporting previous studies that claim resident microbiota are lacking in caterpillars. Previous studies with laboratory-reared insects showed that changes in caterpillar gut bacterial composition affect the insecticidal properties of entomopathogenic viruses and bacteria. Our study revealed different microbiota composition in field insects carrying a natural viral infection with Spodoptera exigua nucleopolyhedrovirus (SeMNPV) and/or Spodoptera exigua iflavirus 1 (SeIV1). Few taxa can be specifically associated with the infection, suggesting microbiota influence the infective process of these natural pathogens, and providing new strategies for insect pest management.

Viable and Total Bacterial Populations Undergo Equipment- and Time-Dependent Shifts during Milk Processing.

We set out to identify the viable and total bacterial content in milk as it passes through a large-scale, dairy product manufacturing plant for pasteurization, concentration, separation, blending, and storage prior to cheese manufacture. A total of 142 milk samples were collected from up to 10 pieces of equipment for a period spanning 21 h on two collection dates in the spring and late summer of 2014. Bacterial composition in the milk was determined by 16S rRNA marker gene, high-throughput DNA sequencing. Milk samples from the late summer were paired such that half were treated with propidium monoazide (PMA) to enrich for viable cells prior to quantification by PCR and identification by DNA sequence analysis. Streptococcus had the highest median relative abundance across all sampling sites within the facility on both sampling dates. The proportions of Anoxybacillus, Thermus, Lactococcus, Lactobacillus, Micrococcaceae, and Pseudomonas were also elevated in some samples. Viable cells detected by PMA treatment showed that Turicibacter was enriched after high-temperature short-time pasteurization, whereas proportions of Staphylococcus were significantly reduced. Using clean-in-place (CIP) times as a reference point, Bacillus, Pseudomonas, and Anoxybacillus were found in high relative proportions in several recently cleaned silos (<19 h since CIP). At later times (>19 h after CIP), 10 of 11 silos containing elevated viable cell numbers were enriched in Acinetobacter and/or Lactococcus These results show the tremendous point-to-point and sample-dependent variations in bacterial composition in milk during processing.IMPORTANCE Milk undergoes sustained contact with the built environment during processing into finished dairy products. This contact has the potential to influence the introduction, viability, and growth of microorganisms within the milk. Currently, the population dynamics of bacteria in milk undergoing processing are not well understood. Therefore, we measured for total and viable bacterial composition and cell numbers in milk over time and at different processing points in a cheese manufacturing facility in California. Our results provide new perspectives on the dramatic variations in microbial populations in milk during processing even over short amounts of time. Although some of the changes in the milk microbiota were predictable (e.g., reduced viable cell numbers after pasteurization), other findings could not be easily foreseen based on knowledge of bacteria contained in raw milk or when the equipment was last cleaned. This information is important for predicting and controlling microbial spoilage contaminants in dairy products.

The drivers of soil bacterial communities in rubber plantation at local and geographic scales

ABSTRACTAccording to traditional biogeographic theory, historical contingency can influence soil microbial communities. Thus, we ask: are historical contingencies (soil profiles and geographic sampling locations), or other factors (seasonal changes and soil nutrients), important drivers of soil bacterial communities? This study used high throughput sequencing technology to investigate the soil bacterial compositions of rubber plantations at the local and geographic scales. Significant differences were detected in bacterial compositions between two study locations, Xishuangbanna and Hainan Island. Redundancy analysis showed that the most important factor driving bacterial composition was site location and total nitrogen, which explained 38.2 and 38.4% the total variance, respectively; this indicates that historical contingencies drive distinct bacterial communities in rubber plantation soils. At the local scale, there were also distinct differences in soil bacterial compositions between the dry and rainy season in both the Xishuangbanna and Hainan sites. Seasonal changes explained 13.6 and 41.4% of the total variation of soil bacterial composition in Xishuangbanna and on Hainan Island, respectively, whereas other factors had little effect on soil bacterial communities (p < 0.001). In conclusion, our results demonstrate that historical contingencies drive variation in bacterial composition at the geographic scale, whereas seasonal changes influence variation at the local scale.

Hindgut microbiota in laboratory-reared and wild Triatoma infestans.

Triatomine vectors transmit Trypanosoma cruzi, the etiological agent of Chagas disease in humans. Transmission to humans typically occurs when contaminated triatomine feces come in contact with the bite site or mucosal membranes. In the Southern Cone of South America, where the highest burden of disease exists, Triatoma infestans is the principal vector for T. cruzi. Recent studies of other vector-borne illnesses have shown that arthropod microbiota influences the ability of infectious agents to colonize the insect vector and transmit to the human host. This has garnered attention as a potential control strategy against T. cruzi, as vector control is the main tool of Chagas disease prevention. Here we characterized the microbiota in T. infestans feces of both wild-caught and laboratory-reared insects and examined the relationship between microbial composition and T. cruzi infection using highly sensitive high-throughput sequencing technology to sequence the V3-V4 region of the 16S ribosomal RNA gene on the MiSeq Illumina platform. We collected 59 wild (9 with T. cruzi infection) and 10 lab-reared T. infestans (4 with T. cruzi infection) from the endemic area of Arequipa, Perú. Wild T. infestans had greater hindgut bacterial diversity than laboratory-reared bugs. Microbiota of lab insects comprised a subset of those identified in their wild counterparts, with 96 of the total 124 genera also observed in laboratory-reared insects. Among wild insects, variation in bacterial composition was observed, but time and location of collection and development stage did not explain this variation. T. cruzi infection in lab insects did not affect α- or β-diversity; however, we did find that the β-diversity of wild insects differed if they were infected with T. cruzi and identified 10 specific taxa that had significantly different relative abundances in infected vs. uninfected wild T. infestans (Bosea, Mesorhizobium, Dietzia, and Cupriavidus were underrepresented in infected bugs; Sporosarcina, an unclassified genus of Porphyromonadaceae, Nestenrenkonia, Alkalibacterium, Peptoniphilus, Marinilactibacillus were overrepresented in infected bugs). Our findings suggest that T. cruzi infection is associated with the microbiota of T. infestans and that inferring the microbiota of wild T. infestans may not be possible through sampling of T. infestans reared in the insectary.

Intra-event variability of bacterial composition in stormwater runoff from mixed land use and land cover catchment

Microbial community and composition in stormwater runoff from mixed land use land cover (LULC) catchment with ongoing land development was diverse across the hydrological stage due different environmental parameters (hydrometeorological and physicochemical) and source of runoff. However, limited studies have been made for bacterial composition in this catchment. Therefore, this study aims to: (1) quantify the concentration of fecal indicator bacteria (FIB), stormwater quality and bacterial composition and structure according to hydrological stage; and (2) determine their correlation to environmental parameters. The 454 pyrosequencing was used to determine the bacterial community and composition; while Pearson\'s correlation was used to determine the correlation among parameters—FIB, stormwater quality, bacterial composition and structure-to environmental parameters. Results demonstrated that the initial and peak runoff has the highest concentration of FIB, stormwater quality and bacterial composition and structure. Proteobacteria, Bacteroidetes, Actinobacteria and Firmicutes were dominant bacteria identified in this catchment. Furthermore, the 20 most abundant genera were correlated with runoff duration, average rainfall intensity, runoff volume, runoff flow, temperature, pH, organic matter, nutrients, TSS and turbidity. An increase of FIB and stormwater quality concentration, diversity and richness of bacterial composition and structure in this study was possibly due to leakage from septic tanks, cesspools and latrines; feces of domestic and wild animals; and runoff from forest, destroyed septic system in land development site and urban LULC. Overall, this study will provide an evidence of hydrological stage impacts on the runoff microbiome environment and public health perspective.

Interpersonal Variations in Gut Microbiota Profiles Supersedes the Effects of Differing Fecal Storage Conditions

Due to ease of acquisition, fecal samples are often used in studies investigating gut microbiota. Improper handling of these samples can lead to bacterial growth and alter bacterial composition. While freezing samples at −80 °C is considered gold standard, this is not suitable for studies utilizing self-sampling by lay participants or field studies. Thus to effectively prevent bacterial growth, techniques that allow efficient fecal storage outside laboratory facilities are needed. Fecal samples were collected from three donors. From each donor feces, 45 samples were collected and stored either freshly frozen at −80 or −20 °C, or in three separate storage buffers at room temperature or 4 °C for 24 or 72 hours. Bacterial composition was analyzed using Illumina amplicon sequencing of the V4 region of the 16 S rRNA gene. While storage conditions did affect bacterial composition and diversity compared to storage at −80 °C, the variation between donors superseded the variations introduced by storage. Samples stored at −20 °C most closely resembled those stored at −80 °C. When investigating variations in bacterial composition between separate study populations, fecal samples can efficiently be stored in −20 °C freezers or in one of the presented storage buffers, without severe alterations in bacterial composition.

Deciphering the bacterial composition in the rhizosphere of Baphicacanthus cusia (NeeS) Bremek

Rhizobacteria is an important ingredient for growth and health of medicinal herbs, and synthesis of pharmacological effective substances from it. In this study, we investigated the community structure and composition of rhizobacteria in Baphicacanthus cusia (NeeS) Bremek via 16S rRNA amplicon sequencing. We obtained an average of 3,371 and 3,730 OTUs for bulk soil and rhizosphere soil samples respectively. Beta diversity analysis suggested that the bacterial community in the rhizosphere was distinctive from that in the bulk soil, which indicates that B.cusia can specifically recruit microbes from bulk soil and host in the rhizosphere. Burkholderia was significantly enriched in the rhizosphere. Burkholderia is a potentially beneficial bacteria that has been reported to play a major role in the synthesis of indigo, which was a major effective substances in B. cusia. In addition, we found that Bacilli were depleted in the rhizosphere, which are useful for biocontrol of soil-borne diseases, and this may explain the continuous cropping obstacles in B. cusia. Our results revealed the structure and composition of bacterial diversity in B. cusia rhizosphere, and provided clues for improving the medicinal value of B. cusia in the future.

Biological and chemical compositions of atmospheric particulate matter during hazardous haze days in Beijing

Particulate matter (PM), a major air pollutant in Beijing in recent years, poses a formidable public health threat. Even through many studies have documented the chemical and biological characteristics of PM, less is known about these characteristics on hazardous haze days (Air Quality Index, AQI 301–500) and the difference with sunny or unhealthy haze day (AQI 151–200) characteristics. Herein, studies were performed during a red alert air pollution event (continuous hazardous haze days) and the first few days following the event (sunny days first and then unhealthy haze days) in Beijing from December 19 to 25, 2016. A laser particle counter and an ANDERSEM-6 sampler were used to study the concentration and size distributions dynamics of the PM and the culturable airborne bacteria and fungi, respectively. PM2.5 was sampled by a high-volume air sampler and the chemical compositions, bacterial and fungal community structures, and endotoxin levels were analyzed. The results showed that the PM concentrations on the hazardous haze days and unhealthy haze days were 10.7 and 8.0 times higher, respectively, than those on the sunny days. The chemical composition of PM2.5 was highly correlated with the AQI. The concentration and percentage of water-soluble inorganic ions (WSII), which dominated the PM2.5 constituents, as well as the levels of endotoxin were higher on hazardous haze days than on unhealthy haze days and sunny days. Interestingly, the abundances of bacteria and fungi demonstrated the following order: unhealthy haze days> sunny days> hazardous haze days. Most culturable bacteria and fungi were distributed in particles with aerodynamic diameters of 2.1–4.7 μm. Redundancy analysis found total organic carbon explained 30.0% and 27.1% of total variations in bacterial composition and fungal composition at the genera level, respectively. Our results facilitate a better understanding of the biological and chemical composition dynamics of PM in Beijing.

Dysbiosis of the buccal mucosa microbiome in primary Sjögren's syndrome patients.

Environmental factors in the aetiology of primary Sjögren's syndrome (pSS) are largely unknown. Host-microbiome interaction at mucosal surfaces is presumed to be involved in the aetiopathogenesis of pSS. Here, we assessed whether the microbiome of the buccal mucosa is specific for pSS compared with symptom-controls. The bacterial composition of buccal swab samples from 37 pSS patients, 86 non-SS sicca patients (with similar dryness symptoms to pSS patients, but not fulfilling the classification criteria) and 24 healthy controls (HCs) was determined with 16S rRNA sequencing. Multivariate Association with Linear Models was used to find associations between individual taxa and pSS, taking into account smoking and dental status. Associations were replicated in a general population cohort (n = 103). The buccal mucosa microbiome of pSS and non-SS sicca patients both differed from HCs. A higher Firmicutes/Proteobacteria ratio was characteristic for both pSS and non-SS sicca patients. Disease status (pSS, non-SS sicca, HCs) and salivary secretion rate contributed almost equally to the variation in bacterial composition between individuals (3.8 and 4.3%, respectively). Two taxa were associated with pSS compared with non-SS sicca patients and 19 compared with HCs. When salivary secretion rate was taken into account, no taxon was associated with pSS compared with non-SS sicca. Twelve of the 19 pSS-associated taxa were correlated with salivary secretion. Dysbiosis of the buccal mucosa microbiome in pSS patients resembles that of symptom-controls. The buccal mucosa microbiome in pSS patients is determined by a combination of reduced salivary secretion and disease-specific factors.