Total Bacterial Community Research Articles

Grazing, liming, and fertilization: Shifts on soil fertility and microbial community in a no-till sheep-soybean integrated system

Integrated crop–livestock systems are recognized for intensifying food production as long as adequate management of grazing, fertilization, and liming is practiced. There is still a lack of information about the effect of these factors on the soil microbiological community. This study evaluated the effects of grazing, liming, and different P and K fertilization strategies on the soil microbial community and its relationship with soil chemical properties. For this purpose, a field experiment was established in 2017 on a subtropical Acrisol. Treatments consisted of two production systems: (i) integrated crop-livestock system (with winter sheep grazing) and (ii) specialized system (ungrazed), combined with two periods of P and K fertilization: (i) conventional fertilization (at soybean planting) and (ii) system fertilization (in the Italian ryegrass pasture). The effect of liming (with and without) was also evaluated. Eighteen months after lime application, the soil was sampled in the 0–5 and10–15 cm soil layers to evaluate soil chemical properties (pH, exchangeable Al, Ca, and Mg, available P and K, cation (Ca+Mg+K) saturation, and Al saturation) and soil microbial community composition. In the surface soil layer, a negative impact of lime application was observed for Gram+ bacteria (−29 %) and actinomycetes (−21 %), consequently decreasing the total bacterial community (−26 %) and total microbial biomass (−27 %). This negative impact of liming on Gram+ bacteria and actinomycetes was negatively related to the increase in soil pH, exchangeable Ca and Mg concentrations, and positively related to Al saturation and available K. The combination of an integrated system or system fertilization with lime increased arbuscular mycorrhizal fungi community 3.0-fold compared to a specialized system or conventional fertilization in the subsurface soil layer. In addition, sheep grazing increased saprophytic fungi biomass by 50 % in the subsurface soil layer compared to the specialized system. These positive impacts on the soil fungal community were probably associated with increased plant residue input. Sheep grazing and the fertilization strategy did not affect soil chemical properties or the microbial community at the soil surface. Liming, system fertilization, and sheep grazing benefitted the soil fungal community, thus improving soil health in highly weathered agricultural soils.

Insights into the mechanisms underlying the biodegradation of phenanthrene in biochar-amended soil: from bioavailability to soil microbial communities

The dynamic effect of biochar amendment in contaminated soil on the bioavailability of polycyclic aromatic hydrocarbons (PAHs) and microbial communities and how it comprehensively affects PAH biodegradation remain unclear. This study investigated the effects of wheat straw-derived biochars obtained at 300 and 500 °C at different amendment levels (0.03% and 0.3%) on the mineralization kinetics of phenanthrene with different initial concentrations (2 and 20 mg kg−1) in soil by indigenous microorganisms. The results revealed that the addition of biochar inhibited both the rates and extents of mineralization in low-concentration phenanthrene-contaminated soil (PLS) by 38.9–78.3% and 23.9–53.6%, respectively. This was because biochar amendment in the PLS greatly reduced the bioavailable fraction of phenanthrene for degradation owing to its strong sorption and also decreased that to specific degrading bacterial genera, which hindered their growth and reduced their abundances by 1.37–36.6%. However, biochar addition into the soil contaminated with high concentrations of phenanthrene (PHS) resulted in its effective mineralization and enhanced mineralization rates and extents at high amendment levels by 32.4–86.7% and 32.0–44.7%, respectively. This was because biochar amendment in the PHS significantly promoted the abundances of the total bacterial communities (29.9–80.4%) and potential degrading genera (1.89–25.9%) by providing nutrients and stimulated the specific PAH-degradative nidA gene abundance by 1–2 times. These findings will guide the use of biochar to remediate soils with different PAH pollution levels based on the two roles that they play (i.e., immobilizing PAHs or facilitating PAH degradation).Graphical

Similarities and differences in the rhizosphere biota among different ephemeral desert plants in Gurbantünggüt Desert

BackgroundThe interactions between rhizosphere microbial community and ephemeral desert plants strongly affect the ecological protection, restoration and reconstruction in deserts. Ephemeral desert plants as the pioneer plants in the succession are widely distributed in deserts. However, how the ephemeral desert plants assemble their rhizosphere microbiota to adapt to arid and semi-arid environments has been little explored. Here, we used high-throughput sequencing techniques to compare rhizosphere bacterial communities and functions with different ephemeral desert plants composition from Gurbantünggüt Desert in western China.ResultsThese plants had the same dominant bacterial phyla, which approximately counted 98% of the total bacterial communities. But the bacterial communities had significant differences (P < 0.05) in the composition, structure, diversity and functions of all groups. When comparing every two groups, similarities appeared in the composition, structure and functions of rhizosphere microbiota, and within each group, it is more likely that the rhizosphere bacterial communities of closely related ephemeral desert plants tend to be consistent. Additionally, the rhizosphere bacterial taxa had more similarities in predicted functions. And the predicted functions were correlated with the dominant bacterial phyla.ConclusionsOverall, to adapt to the arid and semi-arid environments, the rhizosphere bacterial communities of ephemeral desert plants appear similarities based on having differences. This finding will help to understand the importance of how plants and soil microorganisms cooperate in the process of adaption to arid and semi-arid environments.

Potential Exposure to Respiratory and Enteric Bacterial Pathogens among Wastewater Treatment Plant Workers, South Africa

Wastewater handling has been associated with an increased risk of developing adverse health effects, including respiratory and gastrointestinal illnesses. However, there is a paucity of information in the literature, and occupational health risks are not well quantified. Grab influent samples were analysed using Illumina Miseq 16S amplicon sequencing to assess potential worker exposure to bacterial pathogens occurring in five municipal wastewater treatment plants (WWTPs). The most predominant phyla were Bacteroidota, Campilobacterota, Proteobacteria, Firmicutes, and Desulfobacterota, accounting for 85.4% of the total bacterial community. Taxonomic analysis showed a relatively low diversity of bacterial composition of the predominant genera across all WWTPs, indicating a high degree of bacterial community stability in the influent source. Pathogenic bacterial genera of human health concern included Mycobacterium, Coxiella, Escherichia/Shigella, Arcobacter, Acinetobacter, Streptococcus, Treponema, and Aeromonas. Furthermore, WHO-listed inherently resistant opportunistic bacterial genera were identified. These results suggest that WWTP workers may be occupationally exposed to several bacterial genera classified as hazardous biological agents for humans. Therefore, there is a need for comprehensive risk assessments to ascertain the actual risks and health outcomes among WWTP workers and inform effective intervention strategies to reduce worker exposure.

Straw is more effective than biochar in mobilizing soil organic phosphorus mineralization in saline-alkali paddy soil

Fertilizer management can alter the availability and biological cycle of soil phosphorus (P). The objective of this study was to explore the relationship among soil P availability, organic phosphorus (Po) mineralization and soil bacteria characteristics under organic and inorganic fertilization in saline-alkali paddy soil. Four treatments were designed, namely no fertilizer (Control), mineral fertilizer (NPK), mineral fertilizer with rice straw (NPKS) or rice straw-derived biochar (NPKB). Compared with NPK treatment, straw and biochar addition greatly increased P uptake by rice while decreased soil organic P/total P ratio. The contents of soil available P (AP) and alkaline phosphatase (ALP) in NPKS treatment were higher than those in NPKB treatment. This was most likely due to the higher abundance of Streptomyces in NPKS treatment than that in NPKB treatment, which was known as a potential Po mineralizer. NPKS and NPKB treatments significantly increased diversity and abundance of phoD-harboring bacteria but have no significant effect on the total bacteria. Based on SEM analysis, the composition of phoD-harboring bacteria community was more important in ALP activity than the increased phoD-harboring bacterial abundance and diversity. Soil dissolved organic carbon (DOC) content and DOC: AP ratio were the key factors affecting the formation of total bacterial and phoD-harboring bacterial community, which were significantly increased in NPKS treatment. Compared with biochar application, straw was more efficient in increasing the abundance of some phoD-harboring bacteria, which preferred carbohydrate-rich environments, thereby improving the availability of P and its potential biological transformation in saline-alkali paddy soil.

Anthropogenic Nitrate Contamination Impacts Nitrous Oxide Emissions and Microbial Communities in the Marchica Lagoon (Morocco)

Lagoon systems are often confined, and their waters are poorly renewed, which makes them vulnerable to pollutants’ accumulation. Here, the impact of different sources of anthropogenic contamination (domestic, urban, industrial, and agricultural) on the nitrate (NO3−) content, emission of the greenhouse gas nitrous oxide (N2O), abundance of total bacterial archaeal, nitrifying, and denitrifying communities, and diversity and composition of bacterial communities in the sediments of the RAMSAR-protected Marchica lagoon (Nador, Morocco) was investigated. Six lake sites differing in NO3− concentration were selected. Wastewater coming from industrial activities results in the greatest concentration of NO3− in sediments and emissions of N2O. Increased carbon to nitrogen content in sites near domestic activities resulted in an increase in the abundance of total bacterial and archaeal communities, as well as nitrification and denitrification genes, but low N2O emissions due to a greater presence of microorganisms involved in N2O production over those able to reduce N2O. Significant differences in bacterial community composition between sites were observed, with the NO3− content being the main driver of these changes. Increased NO3− content in the sampling sites significantly reduced bacterial diversity. Bacterial genera involved in the degradation of organic and inorganic pollutants and nitrous oxide reduction, such as Robiginitalea, Symbiobacterium, Bacillus, Fusibacter, Neptunomonas, Colwellia, and Alteromonas, were the most abundant in the lagoon. The results suggest that the type of anthropogenic contamination directly impacts the nitrate content in the sediments of the Marchica lagoon, which determines variations in nitrous oxide emissions, nitrogen-cycling gene abundances, and bacterial diversity.

Nutritional additives dominance in driving the bacterial communities succession and bioremediation of hydrocarbon and heavy metal contaminated soil microcosms

Soil quality and microbial diversity are essential to the health of ecosystems. However, it is unclear how the use of eco-friendly natural additives can improve the quality and microbial diversity of contaminated soils. Herein, we used high-throughput 16 S rDNA amplicon Illumina sequencing to evaluate the stimulation and development of microbial diversity and concomitant bioremediation in hydrocarbon (HC) and heavy metal (HM)-rich waste disposal site soil when treated with meat and bone meal (MBM), cyclodextrin (Cdx), and MBM and cyclodextrin mixture (Cdx MBM) over a period of 3 months. Results showed that natural additive treatments significantly increased the soil bacterial diversity (higher Shannon index, Simpson index and evenness) in a time-dependent manner, with Cdx eliciting the greatest enhancement. The two additives influenced the bacterial community succession patterns differently. MBM, while it enhanced the enrichment of specific genera Chitinophaga and Terrimonas, did not significantly alter the total bacterial community. In contrast, Cdx or Cdx MBM promoted a profound change of the bacteria community over time, with the enrichment of the genera Parvibaculum, Arenimonas and unclassified Actinobacteria. These results provide evidence on the involvement of the two natural additives in coupling HC and HM bioremediation and bacterial community perturbations, and thus illustrates their potential application in ecologically sound bioremediation technologies for contaminated soils.

Effects of a Microbial Restoration Substrate on Plant Growth and Rhizosphere Microbial Community in a Continuous Cropping Poplar

In poplar cultivation, continuous cropping obstacles affect wood yield and soil-borne diseases, primarily due to structural changes in microbes and fungus infection. The bacterium Bacillus cereus BJS-1-3 has strong antagonistic properties against pathogens that were isolated from the rhizosphere soil of poplars. Poplar rhizospheres were investigated for the effects of Bacillus cereus BJS-1-3 on microbial communities. Three successive generations of soil were used to replant poplar seedlings. BJS-1-3 inoculated poplars were larger, had higher plant height and breast height diameter, and had a greater number of total and culturable bacteria than non-inoculated controls. B. cereus BJS-1-3 inoculated poplar rhizospheres were sequenced, utilizing the Illumina MiSeq platform to analyze changes in diversity and structure. The fungi abundance and diversity in the BJS-1-3 rhizosphere were significantly lower than in the control rhizosphere. In comparison to the control group, Bacillus sp. constituted 2.87% and 2.38% of the total bacterial community, while Rhizoctonia sp. constituted 2.06% and 6.00% of the total fungal community. Among the potential benefits of B. cereus BJS-1-3 in poplar cultivation is that it enhances rhizosphere microbial community structure and facilitates the growth of trees.

Carbon amendment rather than nitrate fertilization dominated the reassembly of the total, denitrifying, and DNRA bacterial community in the anaerobic subsoil

Carbon amendment rather than nitrate fertilization dominated the reassembly of the total, denitrifying, and DNRA bacterial community in the anaerobic subsoil

Changes in bacterial diversity, co-occurrence pattern, and potential pathogens following digestate fertilization: Extending pathogen management to field for anaerobic digestion of livestock manure

Digestate can spread pathogens into agroecosystem, posing serious threats to public health. However, the effect of digestate fertilization on digestate- or soil-borne pathogens has not been fully explored. Herein, two settings of microcosm experiment were performed with arable soil and digestate collected at two sites (Beilangzhong or Shunyi) to dissect the succession of the total and potential pathogenic bacterial communities following digestate fertilization. Each experimental setting consisted of three treatments, including digestate aerobically incubated in sterilized soil, and soil amended with sterilized or non-sterilized digestate. Digestate-borne potential pathogenic bacteria were enriched after the aerobic incubation, with Streptococcus sobrinus in the Beilangzhong setting, and Escherichia coli and Enterococcus faecium in the Shunyi setting. Potential soil-borne pathogenic bacteria, such as Acinetobacter lowffii and Pseudomonas fluorescens, were stimulated by the sterilized digestate in the Shunyi setting. Interestingly, S. sobrinus, E. coli, and Ent. faecium did not increase when digestate was amended into the non-sterilized soil, suggesting that soil microorganisms can inhibit the resurgence of these digestate-borne pathogens. A large-scale survey further revealed that organic fertilization exerted a site-dependent effect on different species of potential pathogen, but it did not enrich the total relative abundance of potential pathogenic bacteria in soils. Collectively, these results highlight that pathogen management of anaerobic digestion of livestock manure needs to be extended from anaerobic reactor to field.

Virus-Host Interactions Drive Contrasting Bacterial Diel Dynamics in the Ocean.

Marine organisms perform a sea of diel rhythmicity. Planktonic diel dynamics have been shown to be driven by light, energy resources, circadian rhythms, and the coordinated coupling of photoautotrophs and heterotrophic bacterioplankton. Here, we explore the diel fluctuation of viral production and decay and their impact on the total and active bacterial community in the coastal and open seawaters of the South China Sea. The results showed that the night-production diel pattern of lytic viral production was concurrent with the lower viral decay at night, contributing to the accumulation of the viral population size during the night for surface waters. The diel variations in bacterial activity, community composition, and diversity were found highly affected by viral dynamics. This was revealed by the finding that bacterial community diversity was positively correlated to lytic viral production in the euphotic zone of the open ocean but was negatively related to lysogenic viral production in the coastal ocean. Such distinct but contrasting correlations suggest that viral life strategies can not only contribute to diversifying bacterial community but also potentially piggyback their host to dominate bacterial community, suggesting the tightly synchronized depth-dependent and habitat-specific diel patterns of virus-host interactions. It further implies that viruses serve as an ecologically important driver of bacterial diel dynamics across the ocean, highlighting the viral roles in bacterial ecological and biogeochemical processes in the ocean.

Microbial Population Dynamics in Lemnaceae (Duckweed)-Based Wastewater Treatment System.

The dynamic microflora associated within, and in the surrounding aquatic environment, has been found to be responsible for the functional properties of many aquatic plants. The aim of the current work was to evaluate the effectiveness of Lemnaceae-based wastewater treatment system under tropical conditions and investigate the changes in the aquatic microflora upon plant growth. A biological wastewater treatment system was designed and investigated using mixed Lemnaceae culture comprising Lemna minor and Spirodela polyrhiza in a batch mode. A significant reduction in total solids (31.8%), biochemical oxygen demand (93.5%), and chemical oxygen demand (73.2%) was observed after seven days of duckweed growth using a low inoculum. A preliminary study on the change in the microbial population diversity and functionality, in the wastewater before and after treatment, revealed an increase in the denitrifying microflora in wastewater post-Lemnaceae treatment. Dominance of 10 bacterial phyla, contributing for 98.3% of the total bacterial communities, was recorded, and ~ 50.6% loss of diversity post-treatment of wastewater was revealed by the Shannon Index. Among 16 bacterial families showing relative abundance of ≥ 1% in untreated wastewater, Methylobacteriaceae, Pseudomonadaceae, Brucellaceae, Rhodobacteraceae, and Acetobacteraceae prevailed in the water post-treatment by duckweeds. This is a novel work done on the dynamics of aquatic microflora associated with Lemnaceae under tropical Indian conditions. It confirms the application of Lemnaceae-based wastewater treatment system as effective biofilter and calls for further studies on the active involvement of the endophytic and aquatic microflora in the functions of these plant.

Wheat genome architecture influences interactions with phytobeneficial microbial functional groups in the rhizosphere.

Wheat has undergone a complex evolutionary history, which led to allopolyploidization and the hexaploid bread wheat Triticum aestivum. However, the significance of wheat genomic architecture for beneficial plant-microbe interactions is poorly understood, especially from a functional standpoint. In this study, we tested the hypothesis that wheat genomic architecture was an overriding factor determining root recruitment of microorganisms with particular plant-beneficial traits. We chose five wheat species representing genomic profiles AA (Triticum urartu), BB {SS} (Aegilops speltoides), DD (Aegilops tauschii), AABB (Triticum dicoccon) and AABBDD (Triticum aestivum) and assessed by qPCR their ability to interact with free-nitrogen fixers, 1-aminocyclopropane-1-carboxylate deaminase producers, 2,4-diacetylphloroglucinol producers and auxin producers via the phenylpyruvate decarboxylase pathway, in combination with Illumina MiSeq metabarcoding analysis of N fixers (and of the total bacterial community). We found that the abundance of the microbial functional groups could fluctuate according to wheat genomic profile, as did the total bacterial abundance. N fixer diversity and total bacterial diversity were also influenced significantly by wheat genomic profile. Often, rather similar results were obtained for genomes DD (Ae. tauschii) and AABBDD (T. aestivum), pointing for the first time that the D genome could be particularly important for wheat-bacteria interactions. This article is protected by copyright. All rights reserved.

Characterizing potential pathogens from intracellular bacterial community of protists in wastewater treatment plants

Protists are a trophically diverse and biogeochemically significant component of water environments and are widely reported as hosts of bacteria. However, the potential role of protists in wastewater treatment plants (WWTPs) as reservoirs for human pathogens does not appear to have received adequate attention. Here, a combination of fluorescence-activated cell sorting and Illumina sequencing was applied to characterize the dynamics of the internalized bacterial community of the enriched protists from the influents and effluents of five WWTPs. The results showed that Proteobacteria (mainly Betaproteobacteria) dominate the intracellular bacterial communities of protists in both influents and effluents of WWTPs, accounting for 72.6% of the total intracellular bacterial communities. The most frequently detected genus was Sulfuricurvum in the influent samples, Chryseobacterium and Pseudomonas were most prevalent in the effluent samples. Compared with the influents, a more diverse and abundant intracellular bacterial community was observed in the effluents. Moreover, the potential intracellular bacterial pathogens were 26 times higher in effluents than in influents, with Pseudomonas fluorescens and Pseudomonas putida significantly enriched in effluents. This work provides insights into the dynamics of bacterial communities and potential pathogens harbored by protists in the influents and effluents from WWTPs, contributing to the improved evaluation of biosafety in WWTPs.

Bioprospecting for Novel Bacterial Sources of Hydrolytic Enzymes and Antimicrobials in the Romanian Littoral Zone of the Black Sea.

Marine microorganisms have evolved a large variety of metabolites and biochemical processes, providing great opportunities for biotechnologies. In the search for new hydrolytic enzymes and antimicrobial compounds with enhanced characteristics, the current study explored the diversity of cultured and uncultured marine bacteria in Black Sea water from two locations along the Romanian coastline. Microbial cell density in the investigated samples varied between 65 and 12.7 × 103 CFU·mL-1. The total bacterial community identified by Illumina sequencing of 16S rRNA gene comprised 185 genera belonging to 46 classes, mainly Gammaproteobacteria, Alphaproteobacteria, Flavobacteriia, and 24 phyla. The 66 bacterial strains isolated on seawater-based culture media belonged to 33 genera and showed variable growth temperatures, growth rates, and salt tolerance. A great fraction of these strains, including Pseudoalteromonas and Flavobacterium species, produced extracellular proteases, lipases, and carbohydrases, while two strains belonging to the genera Aquimarina and Streptomyces exhibited antimicrobial activity against human pathogenic bacteria. This study led to a broader view on the diversity of microbial communities in the Black Sea, and provided new marine strains with hydrolytic and antimicrobial capabilities that may be exploited in industrial and pharmaceutical applications.

Diversity and adaptation properties of actinobacteria associated with Tunisian stone ruins.

Stone surface is a unique biological niche that may host a rich microbial diversity. The exploration of the biodiversity of the stone microbiome represents a major challenge and an opportunity to characterize new strains equipped with valuable biological activity. Here, we explored the diversity and adaptation strategies of total bacterial communities associated with Roman stone ruins in Tunisia by considering the effects of geo-climatic regions and stone geochemistry. Environmental 16S rRNA gene amplicon was performed on DNA extracted from stones samples collected in three different sampling sites in Tunisia, along an almost 400km aridity transect, encompassing Mediterranean, semiarid and arid climates. The library was sequenced on an Illumina MiSeq sequencing platform. The cultivable Actinobacteria were isolated from stones samples using the dilution plate technique. A total of 71 strains were isolated and identified based on 16S rRNA gene sequences. Cultivable actinobacteria were further investigated to evaluate the adaptative strategies adopted to survive in/on stones. Amplicon sequencing showed that stone ruins bacterial communities were consistently dominated by Cyanobacteria, followed by Proteobacteria and Actinobacteria along the aridity gradient. However, the relative abundance of the bacterial community components changed according to the geo-climatic origin. Stone geochemistry, particularly the availability of magnesium, chromium, and copper, also influenced the bacterial communities' diversity. Cultivable actinobacteria were further investigated to evaluate the adaptative strategies adopted to survive in/on stones. All the cultivated bacteria belonged to the Actinobacteria class, and the most abundant genera were Streptomyces, Kocuria and Arthrobacter. They were able to tolerate high temperatures (up to 45°C) and salt accumulation, and they produced enzymes involved in nutrients' solubilization, such as phosphatase, amylase, protease, chitinase, and cellulase. Actinobacteria members also had an important role in the co-occurrence interactions among bacteria, favoring the community interactome and stabilization. Our findings provide new insights into actinobacteria's diversity, adaptation, and role within the microbiome associated with stone ruins.

Effect of fresh and aged biochar on electrogenic hydrocarbon degradation in soil microbial electrochemical remediation

The remediation of petroleum hydrocarbon-contaminated soil is a global problem. A bioelectrochemical system (BES) is an environmentally friendly technique. In BESs, microbes on the anode play central roles in electricity generation and pollutant degradation. Here, we utilized fresh and aged biochar (marked by FB and AB) as amendments to assess the spatial-temporal hydrocarbon removal, bacterial community shift and functional gene changes in the anode and cathode vicinity. After 78 days, an accumulated charge of 750 C for FB was gained, which was 12% and 98% higher than that of AB and the no-biochar control (CK), respectively. Moreover, the removal of total petroleum hydrocarbons was enhanced in the order of CK (17–26%) < AB (22–28%) < FB (24–29%) in the cathodic area, while in the anodic region, the removal was enhanced in the order CK (22–31%) < FB (24–30%) < AB (28–30%) on days 43–78. Additionally, the top six phyla were Proteobacteria, Desulfobacterota, Firmicutes, Chloroflexi, Actinobacteriota and Bacteroidota, accounting for > 92% of the total bacterial community, with a declining tendency over time. The cathode vicinity favoured Proteobacteria growth, whereas the anode region favoured Desulfobacterota and Firmicutes. Functional genes emphasized petroleum hydrocarbons as the carbon source and relationships with nitrogen, sulfur and iron compounds in soil. This study validated the aptitudes and application effects of fresh and aged biochar in BESs.

The devil is in the details: Variable impacts of season, BMI, sampling site temperature, and presence of insects on the post-mortem microbiome.

Post-mortem microbial communities are increasingly investigated as proxy evidence for a variety of factors of interest in forensic science. The reported predictive power of the microbial community to determine aspects of the individual's post-mortem history (e.g., the post-mortem interval) varies substantially among published research. This observed variation is partially driven by the local environment or the individual themselves. In the current study, we investigated the impact of BMI, sex, insect activity, season, repeat sampling, decomposition time, and temperature on the microbial community sampled from donated human remains in San Marcos, TX using a high-throughput gene-fragment metabarcoding approach. In the current study, we investigated the impact of BMI, sex, insect activity, season, repeat sampling, decomposition time, and temperature on the microbial community sampled from donated human remains in San Marcos, TX using a high-throughput gene-fragment metabarcoding approach. We found that season, temperature at the sampling site, BMI, and sex had a significant effect on the post-mortem microbiome, the presence of insects has a homogenizing influence on the total bacterial community, and that community consistency from repeat sampling decreases as the decomposition process progresses. Moreover, we demonstrate the importance of temperature at the site of sampling on the abundance of important diagnostic taxa. The results of this study suggest that while the bacterial community or specific bacterial species may prove to be useful for forensic applications, a clearer understanding of the mechanisms underpinning microbial decomposition will greatly increase the utility of microbial evidence in forensic casework.

Healthy adult gut microbiota sustains its own vitamin B12 requirement in an in vitro batch fermentation model.

Vitamin B12 (cobalamin) is present in the human lower gastrointestinal tract either coming from the unabsorbed dietary fraction or from in situ production of the gut microbiota. However, it is unclear whether the gut microbial communities need exogenous B12 for growth and metabolism, or whether B12 in low and high levels could affect gut community composition and metabolite production. Here, we investigated in vitro B12 production of human fecal microbiota and the effects of different levels of B12 (as cyanocobalamin) on composition and activity. Eight fecal communities from healthy human adults distributed over three enterotypes, dominated by Firmicutes (n = 5), Bacteroides (n = 1) or Prevotella (n = 2) were used to perform batch fermentations in Macfarlane medium supplemented with low B12 medium (Control, 5 ng/ml, within the tested fecal range), no B12 addition (NB12), and high B12 addition (ExtraB12, 2500 ng/ml). The microbiota community composition (qPCR, 16S rRNA metabarcoding), metabolic activity (HPLC-RI), and B12 levels (UHPLC-DAD) were measured after 24 h incubation at 37°C under strict anaerobic conditions. All fecal microbial communities produced B12 in the NB12 condition after 24 h, in the range from 152 ± 4 to 564 ± 25 ng/ml. None of the B12 treatments had an impact on total bacterial growth, community richness, diversity and total metabolite production, compared to the low B12 control. However, a significant increase of propionate was measured in ExtraB12 compared to NB12. Most taxonomic and metabolite changes compared to control incubations were donor-dependent, implying donor-microbiota-specific changes upon B12 treatments. Our in vitro data suggest that healthy human adult gut microbial communities have the capacity to produce B12 at levels fulfilling their own requirements, independently of the initial B12 content tested in the donor's feces. Further, supplementation of exogenous dietary B12 may have limited impact on the healthy human gut microbial community composition and function.

Microbiome comparison of Dermanyssus gallinae populations from different farm rearing systems and the presence of common endosymbiotic bacteria at developmental stages.

The hematophagous arthropod, Dermanyssus gallinae (Poultry red mite, PRM) can cause remarkable economic losses in the poultry industry across the globe. Although overall composition of endosymbiotic bacteria has been shown in previous studies, how farm habitats influence the microbiome remains unclear. In the present study, we compared the bacterial communities of D. gallinae populations collected from the cage and free-range farms using next-generation sequences targeting the V3-V4 hypervariable region of the 16S rRNA gene. The QIIME2 pipeline was followed in bioinformatic analyses. Proteobacteria represented a great majority of the total bacterial community of D. gallinae from both farming systems. More specifically, Bartonella-like bacteria (40.8%) and Candidatus Cardinium (21.5%) were found to be predominant genera in free-range and cage rearing systems, respectively. However, the microbiome variation based on farming systems was not statistically significant. In addition, the presence of the five common endosymbiotic bacteria (Wolbachia, Cardinium, Rickettsiella, Spiroplasma, and Schineria) was screened in different developmental stages of D. gallinae. Cardinium was detected in all developmental stages of D. gallinae. On the other hand, Wolbachia and Rickettsiella were only found in adults/nymphs, but neither in the eggs nor larvae. To our knowledge, this study provides the first microbiome comparison at genus-level in D. gallinae populations collected from different farm habitats and will contribute to the knowledge of the biology of D. gallinae.