Identification Of Microbial Communities Research Articles

Identification of microbial communities and multi-species biofilms contamination in seafood processing environments with different hygiene conditions

Biofilms formed by spoilage and pathogenic bacteria increase microbial persistence, causing an adverse influence on the quality of seafood. The mono-species biofilms are widely reported, however, the contamination of multi-species biofilms and their matrix in food environments are still not fully understood. Here, we assessed the contamination of multi-species biofilms in three seafood processing environments with different hygiene levels by detecting bacterial number and three biofilm matrix components (carbohydrates, extracellular DNA (eDNA), and proteins). Samples comprising seven food matrix surfaces and eight food processing equipment surfaces were collected from two seafood processing plants (XY and XC) and one seafood market (CC). The results showed that the bacterial counts ranged from 1.89 to 4.91 CFU/cm2 and 5.68 to 9.15 BCE/cm2 in these surfaces by cultivation and real-time PCR, respectively. Six biofilm hotspots were identified, including four in CC and two in XY. Among the three processing environments, the amplicon sequence variants (ASVs) of Proteobacteria, Bacteroidetes, and Actinobacteria decreased with improved processing hygiene, while Firmicutes showed a decrease in the four most abundant phyla. The most prevalent bacteria belonged to genera Psychrobacter, Acinetobacter, and Pseudomonas, demonstrating the significant differences and alteration in bacterial community composition during different environments. From the biofilm hotspots, 15 isolates with strong biofilm forming ability were identified, including 7 Pseudomonas, 7 Acinetobacter, and 1 Psychrobacter. The Pseudomonas isolates exhibited the highest production of EPS components and three strong motilities, whose characteristics were positively correlated. Thus, this study verified the presence of multi-species biofilms in seafood processing environments, offering preliminary insights into the diversity of microbial communities during processing. It highlights potential contamination sources and emphasizes the importance of understanding biofilms composition to control biofilms formation in seafood processing environments.

Microbiome analysis of the restricted bacteria in radioactive element-containing water at the Fukushima Daiichi Nuclear Power Station.

In the context of nuclear power station decommissioning, the proliferation of microorganisms within the reactor and piping systems constitutes a formidable challenge. Therefore, the identification of microbial communities in such environments is of paramount importance. In the aftermath of the Fukushima Daiichi Nuclear Power Station accident, microbial community analysis was conducted on environmental samples collected mainly outside the site. However, analyses using samples from on-site areas, including adjacent soil and seawater, were not performed. This study represents the first comprehensive analysis of microbial communities, utilizing meta 16S amplicon sequencing, with a focus on environmental samples collected from the radioactive element-containing water in the torus room, including the surrounding environments. Some of the identified microbial genera are shared with those previously identified in spent nuclear fuel pools in countries such as France and Brazil. Moreover, our discussion in this paper elucidates the correlation of many of these bacteria with metal corrosion.

Identification of Microbial Community in Otomycosis by Metagenomic Next Generation Sequencing (mNGS): Potential Implication of Treatment with Terbinafine.

The present study was designed to identify the microbial community as well as to analyze its diversity by means of metagenomic Next Generation Sequencing (mNGS) in 17 patients with otomycosis treated with terbinafine in the Department of Otolaryngology of Shandong Provincial Hospital from June 2021 to June 2022, so as to evaluate the relationship between microbial community and terbinafine resistance. Those 17 patients were divided into two groups, i.e., Terbinafine Effective Group (TEG, n = 14 cases) and Terbinafine Resistance Group (TRG, n = 3 cases) according to the therapy effect, whose microbial community of secretion of external auditory canal was identified using mNGS. We found that the sequence of bacteria was significantly more than that of fungi and, whereas, the difference between the two groups of bacteria was not significant. There were significant differences in fungal community between the two groups. Aspergillus was the main pathogenic fungus of TEG patients while Malassezia was a dominant fungus in TRG patients. In conclusion, the results from this work indicate that Aspergillus terreusis is the main pathogenic fungus in this cohort of otomycosis patients and MNGS sequencing can offer comprehensive information about the microbial community of otomycosis. The fungus community dominated by Malassezia is more likely to be resistant to terbinafine, which provides certain guidance for clinical treatment of otomycosis with terbinafine.

Characterization of pollutants and identification of microbial communities in the filter media of green infrastructures

Green infrastructure (GI) technologies use natural mechanisms and processes associated with microorganisms, plants, and filter media to facilitate mass circulation and energy flow in the ecosystem. Despite the numerous studies focused on the functions and pollutant treatment performance of nature-based stormwater treatment technologies, studies concerning the effects of filter media characteristics on the diversity and abundance of microorganisms in green stormwater infrastructures are still lacking. In this study, the physico-chemical characteristics of filter media and accumulated sediments in an infiltration trench (IT) and bioretention facility (BI) were investigated. Moreover, the composition and distribution of different microbial communities in GIs designed for stormwater treatment were identified. As compared with BI, higher pollutant concentrations were noted on the filter media and sediments accumulated in IT due to the higher degree of anthropogenic activities in IT's catchment area. Inorganic filter media (i.e., gravel) tend to have greater pollutant trapping efficiency due to the accumulation of sediments in the macropores. On the other hand, organic filter materials (i.e., woodchips) may serve as carbon sources for fueling microbial processes and promote better moisture retention in the facility. Proteobacteria, which constituted 38.6% to 43.0% of the total bacterial population in IT and 37.9% to 41.4% of the total bacterial population in BI, was found to be the most dominant type of bacteria in the facilities. In terms of microbial diversity, BI exhibited a higher diversity index, which is most likely due to the presence of vegetative components forming a symbiotic relationship with microbial colonies. Generally, inorganic filter media are mainly used for improving the GI technologies' drainage and infiltration functions, whereas organic filter media provide suitable growth environments for different bacterial communities involved in important biogeochemical cycles.

Identification of microbial communities and functional genes in an anaerobic-anoxic-oxic (A2O) process in responding to the iron-carbon micro-electrolysis (ICME) pre-treatment of electroplating wastewater based on high-throughput sequencing

Industrial wastewater contains high concentrations of refractory organic carbons, resulting in a low biodegradability difficult for the following biological treatments. The iron-carbon micro-electrolysis (ICME) was developed to break down the larger organic molecules and enhance the biodegradability. Previous ICME pretreatment coupling studies focused primarily on pharmaceutical, dye, and medical wastewater. In this study, the ICME was applied to treat the electroplating wastewater with surfactants, followed by an anaerobic-anoxic-oxic (A2O) biological process. When the ratio of the ICME-treated wastewater was low (10 %), the strike on nutrient removal efficiency (chemical oxidation demand, ammonia, total nitrogen, and total phosphate) was almost negligible. With the increase of ICME-treated wastewater up to 50 %, the removal efficiency gradually decreased, but the effluent water quality still met the discharge standard. Meanwhile, a shift of microbial communities in the three zones was also observed after the 50-day incubation. The abundance of Hydrogenophaga, Chitinophagaceae, and Lentimicrobiaceae all increased, which may be responsible for the degradation of refractory organics in the oxic and anaerobic zones. The functional gene analysis indicated that the adaptation of microbial communities was probably related to cell-to-cell communications and the transportation of molecules across the cell membrane. The microbial community and functional gene analysis revealed the adaptation of the microorganisms to the industrial wastewater. This study provides new insights into the ICME to enhance the biodegradability of electroplating wastewater for A2O treatment.

Identification of microbial community in the urban environment: The concordance between conventional culture and nanopore 16S rRNA sequencing.

Microbes in the built environment have been implicated as a source of infectious diseases. Bacterial culture is the standard method for assessing the risk of exposure to pathogens in urban environments, but this method only accounts for <1% of the diversity of bacteria. Recently, full-length 16S rRNA gene analysis using nanopore sequencing has been applied for microbial evaluations, resulting in a rise in the development of long-read taxonomic tools for species-level classification. Regarding their comparative performance, there is, however, a lack of information. Here, we aim to analyze the concordance of the microbial community in the urban environment inferred by multiple taxonomic classifiers, including ARGpore2, Emu, Kraken2/Bracken and NanoCLUST, using our 16S-nanopore dataset generated by MegaBLAST, as well as assess their abilities to identify culturable species based on the conventional culture results. According to our results, NanoCLUST was preferred for 16S microbial profiling because it had a high concordance of dominant species and a similar microbial profile to MegaBLAST, whereas Kraken2/Bracken, which had similar clustering results as NanoCLUST, was also desirable. Second, for culturable species identification, Emu with the highest accuracy (81.2%) and F1 score (29%) for the detection of culturable species was suggested. In addition to generating datasets in complex communities for future benchmarking studies, our comprehensive evaluation of the taxonomic classifiers offers recommendations for ongoing microbial community research, particularly for complex communities using nanopore 16S rRNA sequencing.

Metagenomic-based surveillance systems for antibiotic resistance in non-clinical settings.

The success of antibiotics as a therapeutic agent has led to their ineffectiveness. The continuous use and misuse in clinical and non-clinical areas have led to the emergence and spread of antibiotic-resistant bacteria and its genetic determinants. This is a multi-dimensional problem that has now become a global health crisis. Antibiotic resistance research has primarily focused on the clinical healthcare sectors while overlooking the non-clinical sectors. The increasing antibiotic usage in the environment - including animals, plants, soil, and water - are drivers of antibiotic resistance and function as a transmission route for antibiotic resistant pathogens and is a source for resistance genes. These natural compartments are interconnected with each other and humans, allowing the spread of antibiotic resistance via horizontal gene transfer between commensal and pathogenic bacteria. Identifying and understanding genetic exchange within and between natural compartments can provide insight into the transmission, dissemination, and emergence mechanisms. The development of high-throughput DNA sequencing technologies has made antibiotic resistance research more accessible and feasible. In particular, the combination of metagenomics and powerful bioinformatic tools and platforms have facilitated the identification of microbial communities and has allowed access to genomic data by bypassing the need for isolating and culturing microorganisms. This review aimed to reflect on the different sequencing techniques, metagenomic approaches, and bioinformatics tools and pipelines with their respective advantages and limitations for antibiotic resistance research. These approaches can provide insight into resistance mechanisms, the microbial population, emerging pathogens, resistance genes, and their dissemination. This information can influence policies, develop preventative measures and alleviate the burden caused by antibiotic resistance.

Metagenomics versus total RNA sequencing: most accurate data-processing tools, microbial identification accuracy and perspectives for ecological assessments.

Metagenomics and total RNA sequencing (total RNA-Seq) have the potential to improve the taxonomic identification of diverse microbial communities, which could allow for the incorporation of microbes into routine ecological assessments. However, these target-PCR-free techniques require more testing and optimization. In this study, we processed metagenomics and total RNA-Seq data from a commercially available microbial mock community using 672 data-processing workflows, identified the most accurate data-processing tools, and compared their microbial identification accuracy at equal and increasing sequencing depths. The accuracy of data-processing tools substantially varied among replicates. Total RNA-Seq was more accurate than metagenomics at equal sequencing depths and even at sequencing depths almost one order of magnitude lower than those of metagenomics. We show that while data-processing tools require further exploration, total RNA-Seq might be a favorable alternative to metagenomics for target-PCR-free taxonomic identifications of microbial communities and might enable a substantial reduction in sequencing costs while maintaining accuracy. This could be particularly an advantage for routine ecological assessments, which require cost-effective yet accurate methods, and might allow for the incorporation of microbes into ecological assessments.

Comparative Study of Different Sampling Methods of Biofilm Formed on Stainless-Steel Surfaces in a CDC Biofilm Reactor.

The formation of biofilms in dairy processing plants can reduce equipment efficiency, contribute to surface deterioration, and contaminate dairy products by releasing the microorganisms they contain, which may cause spoilage or disease. However, a more representative identification of microbial communities and physico-chemical characterization requires to detach and recover adequately the entire biofilm from the surface. The aim of this study is to develop an efficient technique for in-plant biofilm sampling by growing a strain of Pseudomonas azotoformans PFl1A on stainless-steel surface in a dynamic CDC biofilm reactor system using tryptic soy broth (TSB) and milk as growth media. Different techniques, namely, swabbing, scraping, sonic brushing, synthetic sponge, and sonicating synthetic sponge were used and the results were compared to a standard ASTM International method using ultrasonication. Their efficiencies were evaluated by cells enumeration and scanning electron microscopy. The maximum total viable counts of 8.65 ± 0.06, 8.75 ± 0.08, and 8.71 ± 0.09 log CFU/cm2 were obtained in TSB medium using scraping, synthetic sponge, and sonicating synthetic sponge, respectively, which showed no statistically significant differences with the standard method, ultrasonication (8.74 ± 0.02 log CFU/cm2). However, a significantly (p < 0.05) lower cell recovery of 8.57 ± 0.10 and 8.60 ± 0.00 log CFU/cm2 compared to ultrasonication were achieved for swabbing and sonic brushing, respectively. Furthermore, scanning electron microscopy showed an effective removal of biofilms by sonic brushing, synthetic sponge, and sonicating synthetic sponge; However, only the latter two methods guaranteed a superior release of bacterial biofilm into suspension. Nevertheless, a combination of sonication and synthetic sponge ensured dislodging of sessile cells from surface crevices. The results suggest that a sonicating synthetic sponge could be a promising method for biofilm recovery in processing plants, which can be practically used in the dairy industries as an alternative to ultrasonication.

Urinary microbiome profile in men with genitourinary malignancies.

PurposeRecent advances in molecular biology technology have allowed identification of microbial communities in the urinary tract, and urinary microbiome is associated with various urological diseases. In this study, we aimed to characterize the urinary microbiome of genitourinary malignancies.Materials and MethodsMetagenomic analysis of urinary DNA was performed in 85 patients including 30 with bladder cancer (BC), 27 with prostate cancer (PC), 12 with renal cancer (RC), and 16 with non-cancer (NC). 16S rRNA gene sequencing was conducted after amplification of the V3–V4 region.ResultsPC and RC had significantly lower Shannon index than BC, and beta diversity showed significantly different microbiome composition between four groups. We identified six genera of Cutibacterium, Peptoniphilus, Sphingomonas, Staphylococcus, Micrococcus, and Moraxella, which showed significantly different abundance between the four groups. When each of the malignancies were compared to NC at the species level, Micrococcus sp. was significantly increased in BC. We also identified 12 and five species with increased populations in PC and RC, respectively. Of these, Cutibacterium acnes, Cutibacterium granulosum, Peptoniphilus lacydonensis, and Tessaracoccus were significantly increased in both PC and RC.ConclusionsUrinary microbiome composition was different depending on the xlink:type of genitourinary malignancies, and we identified bacteria that are significantly associated with each xlink:type of malignancy. Specifically, several bacterial species were associated both PC and RC, suggesting that PC and RC share a similar pathogenesis-related urinary microbiome.

Fungal Diversity and Dynamics during Grape Wine Fermentations with Different Sulfite Levels and Yeast Inoculations

Microbial communities during grape wine fermentations are diverse and dynamic. High-throughput sequencing (molecular methods enabling precise identification of microbial communities) was used to identify fungal diversity during fermentation of grape juice with different sulfite levels and yeast inoculations. Fermentation (0, 14, and 21 days) was evaluated in two grape varieties, Noble (Vitis rotundifolia) and Vignoles (Vitis hybrid), fermented at three sulfite levels (0, 10, and 20 mg/L) with three yeast inoculations (uninoculated, Saccharomyces cerevisiae, and Torulaspora delbrueckii). Fungal taxonomy of both varieties included six to seven phyla and 115 to 129 genera. The indigenous microbiota was affected by sulfite level and yeast inoculation and varied by grape variety. Sulfite levels had minimal effect on fungal communities but did affect fermentation dynamics. Increasing sulfite additions did not affect the fermentation performance of S. cerevisiae but did affect the fermentation of uninoculated juice and T. delbrueckii-inoculated juice. The primary fungal genera (Podosphaera, Candida, Phialemoniopsis, and Meyerozyma)—those present at a relative abundance >1%—were the same for both varieties but at different relative abundance. Similar fungal diversity patterns were observed for both varieties, with a decrease in diversity at day 14 and an increase at day 21 of fermentation. Juices inoculated with T. delbrueckii were rapidly colonized by Torulaspora spp. at day 0 for both varieties, whereas Saccharomyces spp. dominated by day 14 when inoculated with S. cerevisiae, especially in Noble. The most abundant genera in uninoculated juice were Hanseniaspora and Zygoascus for Noble and Hanseniaspora and Saccharomyces for Vignoles. Understanding grape juice microbial communities and the dynamics of these communities during fermentation provides insight for wine production using spontaneous fermentations or non-Saccharomyces species and information on the effect of sulfur dioxide on these novel fermentations.

Microbial Community Structure Driven by a Volcanic Gradient in Glaciers of the Antarctic Archipelago South Shetland.

It has been demonstrated that the englacial ecosystem in volcanic environments is inhabited by active bacteria. To know whether this result could be extrapolated to other Antarctic glaciers and to study the populations of microeukaryotes in addition to those of bacteria, a study was performed using ice samples from eight glaciers in the South Shetland archipelago. The identification of microbial communities of bacteria and microeukaryotes using 16S rRNA and 18S rRNA high throughput sequencing showed a great diversity when compared with microbiomes of other Antarctic glaciers or frozen deserts. Even the composition of the microbial communities identified in the glaciers from the same island was different, which may be due to the isolation of microbial clusters within the ice. A gradient in the abundance and diversity of the microbial communities from the volcano (west to the east) was observed. Additionally, a significant correlation was found between the chemical conditions of the ice samples and the composition of the prokaryotic populations inhabiting them along the volcanic gradient. The bacteria that participate in the sulfur cycle were those that best fit this trend. Furthermore, on the eastern island, a clear influence of human contamination was observed on the glacier microbiome.

Identification of Microbial Communities in Fermented Food using DNA Barcoding Technique and Development of Novel Method for DNA Isolation from Food Products

Identification of Microbial Communities in Fermented Food using DNA Barcoding Technique and Development of Novel Method for DNA Isolation from Food Products

Comparative Analysis of the Gut Microbiota of Adult Mosquitoes From Eight Locations in Hainan, China.

The midgut microbial community composition, structure, and function of field-collected mosquitoes may provide a way to exploit microbial function for mosquito-borne disease control. However, it is unclear how adult mosquitoes acquire their microbiome, how the microbiome affects life history traits and how the microbiome influences community structure. We analyzed the composition of 501 midgut bacterial communities from field-collected adult female mosquitoes, including Aedes albopictus, Aedes galloisi, Culex pallidothorax, Culex pipiens, Culex gelidus, and Armigeres subalbatus, across eight habitats using the HiSeq 4000 system and the V3−V4 hyper-variable region of 16S rRNA gene. After quality filtering and rarefaction, a total of 1421 operational taxonomic units, belonging to 29 phyla, 44 families, and 43 genera were identified. Proteobacteria (75.67%) were the most common phylum, followed by Firmicutes (10.38%), Bacteroidetes (6.87%), Thermi (4.60%), and Actinobacteria (1.58%). The genera Rickettsiaceae (33.00%), Enterobacteriaceae (20.27%), Enterococcaceae (7.49%), Aeromonadaceae (7.00%), Thermaceae (4.52%), and Moraxellaceae (4.31%) were dominant in the samples analyzed and accounted for 76.59% of the total genera. We characterized the midgut bacterial communities of six mosquito species in Hainan province, China. The gut bacterial communities were different in composition and abundance, among locations, for all mosquito species. There were significant differences in the gut microbial composition between some species and substantial variation in the gut microbiota between individuals of the same mosquito species. There was a marked variation in different mosquito gut microbiota within the same location. These results might be useful in the identification of microbial communities that could be exploited for disease control.

Simple assay for colorimetric quantification of unamplified bacterial 16S rRNA in activated sludge using gold nanoprobes

Domestic and industrial wastewater treatment systems are vital in the protection of natural ecosystems and human health. Identification of microbial communities in the systems is essential to stable treatment performance. However, the current tools of microbial community analysis are labor intensive and time consuming, and require expensive equipment. Therefore, we developed a simple assay for colorimetric quantification of bacterial 16S rRNA extracted from environmental samples. The assay is based on RNA extraction with commercial kits, mixing the unamplified RNA sample with Au-nanoprobes and NaCl, and analyzing the absorbance spectra. Our experimental results confirmed that the assay format was valid. By analyzing the synthesized DNA, we optimized the operational parameters affecting the assay. We achieved adequate capture DNA density by setting the capture DNA probe concentration at 10 μM during the functionalization step. The required incubation time after NaCl addition was 30 min. The binding site of the target had negligible effect on DNA detection. Under the optimized condition, a calibration curve was created using 16S rRNA extracted from activated sludge. The curve was linear above 5.0 × 107 copies/μL of bacterial 16S rRNA concentration, and the limit of detection was 1.17 × 108 copies/μL. Using the calibration curve, the bacterial 16S rRNA concentration in activated sludge samples could be quantified with deviations between 48% and 208% against those determined by RT-qPCR. The findings of our study introduce an innovative tool for the quantification of 16S rRNA concentration as the activity of key bacteria in wastewater treatment processes, achieving stable treatment performance.

Novel approaches for the identification of microbial communities in kimchi: MALDI-TOF MS analysis and high-throughput sequencing

Complex interactions occur within microbial communities during the fermentation process of kimchi. Identification of these microorganisms provides the essential information required to improve food quality and to understand their role in this process. This was the first study to compare two methods for accuracy in the identification of microbial community changes during the fermentation of kimchi by comparing a culture-dependent (MALDI-TOF MS analysis) and a culture-independent method (high-throughput sequencing) of 16S rRNA gene fragment). Members of the Lactobacillus-related genera, Leuconostoc, and Weissella were identified as the predominant microorganisms by both methods. The culture-independent method was able to additionally identify non-lactic acid bacteria and yeasts, such as Kazachstania in kimchi. However, high-throughput sequencing failed to accurately recognize Latilactobacillus sakei, Latilactobacillus curvatus, Lactiplantibacillus plantarum, and W. cibaria, which played an important role in kimchi fermentation, as this method only allowed for identification at the genus level. Conversely, MALDI-TOF MS analysis could identify the isolates at the species level. Also, culture-dependent method could identify predominant species in viable cell communities. The culture-dependent method and culture-independent method provided complementary information by producing a more comprehensive view of the microbial ecology in fermented kimchi.

Biosignature Analysis of Mars Soil Analogs from the Atacama Desert: Challenges and Implications for Future Missions to Mars.

The detection of biosignatures on Mars is of outstanding interest in the current field of astrobiology and drives various fields of research, ranging from new sample collection strategies to the development of more sensitive detection techniques. Detailed analysis of the organic content in Mars analog materials collected from extreme environments on Earth improves the current understanding of biosignature preservation and detection under conditions similar to those of Mars. In this article, we examined the biological fingerprint of several locations in the Atacama Desert (Chile), which include different wet and dry, and intermediate to high elevation salt flats (also named salars). Liquid chromatography and multidimensional gas chromatography mass spectrometry measurement techniques were used for the detection and analysis of amino acids extracted from the salt crusts and sediments by using sophisticated extraction procedures. Illumina 16S amplicon sequencing was used for the identification of microbial communities associated with the different sample locations. Although amino acid load and organic carbon and nitrogen quantities were generally low, it was found that most of the samples harbored complex and versatile microbial communities, which were dominated by (extremely) halophilic microorganisms (most notably by species of the Archaeal family Halobacteriaceae). The dominance of salts (i.e., halites and sulfates) in the investigated samples leaves its mark on the composition of the microbial communities but does not appear to hinder the potential of life to flourish since it can clearly adapt to the higher concentrations. Although the Atacama Desert is one of the driest and harshest environments on Earth, it is shown that there are still sub-locations where life is able to maintain a foothold, and, as such, salt flats could be considered as interesting targets for future life exploration missions on Mars.

Molecular identification of microbial communities in the methane production from vinasse: A review

Sugars, starches, and cellulose materials are used for ethanol production. When producing a liter of alcohol, 10 to 15 liters of liquid waste are generated. This waste is called vinasse, and it generates negative impacts on the environment. The process of storing and disposing vinasse in soils generates emissions to the atmosphere, mainly methane. Anaerobic treatment allows for the capture and generation of more biogas, therefore allowing mitigation of the environmental impacts. The microbial diversity present in the anaerobic digestion (AD) of vinasse is strongly related to the efficiency and quality of methane production. The gene 16s rDNA-based molecular techniques have been the most commonly used techniques for monitoring microbial communities present in the digesters. However, the identification is not enough. Rather, it is necessary to know the metagenomic functionality in this type of habitat. This review provides a comprehensive overview of methods to identify the microorganisms in the anaerobic digestion of vinasse. In addition, microbial community identification in vinasse reactors and their relationship with methane production are reviewed.

Molecular identification of microbial communities in the methane production from vinasse: A review

Sugars, starches, and cellulose materials are used for ethanol production. When producing a liter of alcohol, 10 to 15 liters of liquid waste are generated. This waste is called vinasse, and it generates negative impacts on the environment. The process of storing and disposing vinasse in soils generates emissions to the atmosphere, mainly methane. Anaerobic treatment allows for the capture and generation of more biogas, therefore allowing mitigation of the environmental impacts. The microbial diversity present in the anaerobic digestion (AD) of vinasse is strongly related to the efficiency and quality of methane production. The gene 16s rDNA-based molecular techniques have been the most commonly used techniques for monitoring microbial communities present in the digesters. However, the identification is not enough. Rather, it is necessary to know the metagenomic functionality in this type of habitat. This review provides a comprehensive overview of methods to identify the microorganisms in the anaerobic digestion of vinasse. In addition, microbial community identification in vinasse reactors and their relationship with methane production are reviewed.

Unlocking the biogeochemical role of beaver in state-transition of landscapes in Yellowstone's northern range: Tantalizing insights, initial results, and evolving research design

Extirpation of wolves from the Greater Yellowstone Ecosystem in the 1920s hypothetically triggered a trophic cascade in which herbivores over-browsed riparian zones once released from the fear of wolf (Canis lupus) predation. Eventually, vast meadow-wetland complexes transitioned to grass-lodgepole systems. By 1954, beaver (Castor canadensis) virtually abandoned the Greater Yellowstone Ecosystem. In 2000, Colorado State University established experimental dams with browsing exclosures for Long Term Environmental Research in Biology (LTREB) on three streams in Lamar Valley to compare hydrologic effects of pseudo-beaver dams and browsing on willow (Salix spp.) productivity and state transitions. In 2015, beaver began recolonizing the region. I investigate how the biogeochemical role of beaver versus their hydrologic influence affects the underlying mechanisms of state transition: nutrient cycling, productivity, and stream respiration. Analyses of the 2017 field samples showed that beaver streams trend toward higher nutrient levels and higher variances than the LTREB sites. These trends continued in 2018 and 2019. The data tentatively support the role of beaver as keystone species in state transitions. Interannual modeling of nutrient dynamics, comparisons of stream metabolism, and genetic identification of microbial communities are underway. Similarly, analyses of the repeated measures collected across the month of July 2019 are underway.&#x0D;  &#x0D; Featured photo from figure 1 in report.