scholarly journals Impacts of Zostera eelgrasses on microbial community structure in San Diego coastal waters

Elem Sci Anth ◽  
2019 ◽  
Vol 7 ◽  
Author(s):  
Sahra J. Webb ◽  
Tia Rabsatt ◽  
Natalia Erazo ◽  
Jeff S. Bowman
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
San Diego ◽  
Pathogenic Bacteria ◽  
Marine Ecosystem ◽  
Rrna Gene ◽  
Microbial Composition ◽  
San Diego Bay ◽  
The Impact

Marine eelgrasses are influential to their surrounding environments through their many ecosystem services, ranging from the provisioning of food and shelter for marine life to serving as a natural defense against pollution and pathogenic bacteria. In the marine waters of San Diego, CA, USA, eelgrass beds comprised of Zostera spp. are an integral part of the coastal ecosystem. To evaluate the impact of eelgrass on bacterial and archaeal community structure we collected water samples in San Diego Bay and sequenced the 16S rRNA gene from paired eelgrass-present and eelgrass-absent sites. To test the hypothesis that microbial community structure is influenced by the presence of eelgrass we applied mixed effects models to these data and to bacterial abundance data derived by flow cytometry. This approach allowed us to identify specific microbial taxa that were differentially present at eelgrass-present and eelgrass-absent sites. Principal coordinate analysis organized the samples by location (inner vs. outer bay) along the first axis, where the first two axes accounted for a 90.8% of the variance in microbial community structure among the samples. Differentially present bacterial taxa included members of the order Rickettsiales, family Flavobacteriaceae, genus Tenacibaculum and members of the order Pseudomonadales. These findings constitute a unique look into the microbial composition of San Diego Bay and examine how eelgrasses contribute to marine ecosystem health, e.g., by supporting specific microbial communities and by filtering and trapping potentially harmful bacteria to the benefit of marine organisms.

scholarly journals Comparative Analysis of Bacterial and Archaeal Community Structure in Microwave Pretreated Thermophilic and Mesophilic Anaerobic Digesters Utilizing Mixed Sludge under Organic Overloading

Water ◽  
2020 ◽  
Vol 12 (3) ◽  
pp. 887 ◽  
Author(s):  
Gokce Kor-Bicakci ◽  
Emine Ubay-Cokgor ◽  
Cigdem Eskicioglu
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
High Throughput Sequencing ◽  
Biogas Production ◽  
Archaeal Community ◽  
Rrna Gene ◽  
Anaerobic Digesters ◽  
Pretreatment Conditions ◽  
The Impact

The effects of microwave (MW) pretreatment were investigated by six anaerobic digesters operated under thermophilic and mesophilic conditions at high organic loading rates (4.9–5.7 g volatile solids/L/d). The experiments and analyses were mainly designed to reveal the impact of MW pretreatment and digester temperatures on the process stability and microbial community structure by correlating the composition of microbial populations with volatile fatty acid (VFA) concentrations. A slight shift from biogas production (with a reasonable methane content) to VFA accumulation was observed in the thermophilic digesters, especially in the MW-irradiated reactors. Microbial population structure was assessed using a high-throughput sequencing of 16S rRNA gene on the MiSeq platform. Microbial community structure was slightly affected by different MW pretreatment conditions, while substantially affected by the digester temperature. The phylum Bacteroidetes proliferated in the MW-irradiated mesophilic digesters by resisting high-temperature MW (at 160 °C). Hydrogenotrophic methanogenesis (mostly the genus of Methanothermobacter) was found to be a key route of methane production in the thermophilic digesters, whereas aceticlastic methanogenesis (mostly the genus of Methanosaeta) was the main pathway in the mesophilic digesters.

scholarly journals Microbial Community Succession is Associated With Corn Straw Degradation in Microbial Consortium M44 During Subculture

2021 ◽  
Author(s):  
Xin ZHANG ◽  
Ge-Er QING ◽  
Ju-Lin GAO ◽  
Xiao-Fang YU ◽  
Shu-Ping HU ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
16S Rrna Gene Sequencing ◽  
Microbial Consortia ◽  
Rrna Gene ◽  
Original Sample ◽  
Microbial Composition ◽  
Endoglucanase Activity ◽  
Rrna Gene Sequencing

Abstract To systematically analyze the succession of functional microbiota that plays an important role during culture of microbial consortia M44 and its relationship with straw degradation characteristics, we determined the straw degradation ratio and activities of cellulose, hemicellulose, lignin enzyme, and VFA content of M44 in different culture periods. We also used 16S rRNA gene sequencing to analyze the change in microbial community structure in M44 and explore the differences in microbial composition in the original sample. The results showed that at 15 ℃ for 21 days, the straw degradation rate, endoglucanase activity, and filter paper enzyme activity of M44 generally decreased with increasing culture age, reaching their highest values at F1. The activities of xylanase, laccase, and lignin peroxidase, as well as VFA content, were the highest at F5, showing a single-peak curve change with first an increase and then decrease. At the phylum level, Proteobacteria, Bacteroidetes, and Firmicutes were dominant in the original samples and in different culture stages. At the genus level, Devosia and Bacillus were dominant in the original sample. During subculture, the dominant bacteria in the first generation (F1) were Pseudomonas, Flavobacterium, Brevundimonas, Achromobacter, Chryseobacterium, and Devosia. The dominant genera in the last generation (F11) were Trichococcus, Acinetobacter, Dyssgonomonas, and Rhizobium. In conclusion, we identified changes in microbial community structure occurring in M44 during subculture, as well as similarities and differences in microbial communities from the original sample.

scholarly journals Antibiotic resistome and microbial community structure during anaerobic co-digestion of food waste, paper and cardboard

2020 ◽  
Vol 96 (2) ◽  
Author(s):  
Kärt Kanger ◽  
Nigel G H Guilford ◽  
HyunWoo Lee ◽  
Camilla L Nesbø ◽  
Jaak Truu ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Solid State ◽  
Food Waste ◽  
Microbial Community Structure ◽  
Microbial Community Composition ◽  
Microbial Community Analysis ◽  
Waste Paper ◽  
Rrna Gene ◽  
Significant Shift

ABSTRACT Solid organic waste is a significant source of antibiotic resistance genes (ARGs) and effective treatment strategies are urgently required to limit the spread of antimicrobial resistance. Here, we studied ARG diversity and abundance as well as the relationship between antibiotic resistome and microbial community structure within a lab-scale solid-state anaerobic digester treating a mixture of food waste, paper and cardboard. A total of 10 samples from digester feed and digestion products were collected for microbial community analysis including small subunit rRNA gene sequencing, total community metagenome sequencing and high-throughput quantitative PCR. We observed a significant shift in microbial community composition and a reduction in ARG diversity and abundance after 6 weeks of digestion. ARGs were identified in all samples with multidrug resistance being the most abundant ARG type. Thirty-two per cent of ARGs detected in digester feed were located on plasmids indicating potential for horizontal gene transfer. Using metagenomic assembly and binning, we detected potential bacterial hosts of ARGs in digester feed, which included Erwinia, Bifidobacteriaceae, Lactococcus lactis and Lactobacillus. Our results indicate that the process of sequential solid-state anaerobic digestion of food waste, paper and cardboard tested herein provides a significant reduction in the relative abundance of ARGs per 16S rRNA gene.

The Impact of Reclaimed Water Irrigation on Soil Microbial Community Structure

2014 ◽  
Vol 955-959 ◽  
pp. 3635-3639 ◽  
Author(s):  
Ji Hua Wang ◽  
Xue Gong ◽  
Jian Fei Guan ◽  
Hui Yan Xing
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
Soil Microbial Community ◽  
Soil Column ◽  
Reclaimed Water ◽  
Soil Microbial Community Structure ◽  
Soil Microbial ◽  
The Impact ◽  
Reclaimed Water Irrigation

The reclaimed water treated in a Harbin recycled water plant has been taken as a target of research, by using microbial traditional culture method and tablet coated counting method, discussing the influence of the reclaimed water irrigation on soil microbial community structure through the method of short-term indoor simulated soil column irrigation. The results shows that the reclaimed water irrigation can significantly increase the quantity of bacteria and actinomycetes in the surface 0-20 cm layer soil, but it has little affect on 20-40 cm and 40-60 cm layer soil. Microbial community structure and diversity were changed relatively with the irrigation of reclaimed water, which embodied the increase or decrease of dominant and subdominant groups, the disappearance of non-dominant groups sensitive to reclaimed water, the appear or disappear of the other part of the occasional groups.

scholarly journals Effects of tobacco–peanut relay intercropping on soil bacteria community structure

2019 ◽  
Vol 69 (13) ◽  
pp. 1531-1536 ◽  
Author(s):  
Lin Gao ◽  
Xin-min Liu ◽  
Yong-mei Du ◽  
Hao Zong ◽  
Guo-ming Shen
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
Soil Bacteria ◽  
Pathogenic Bacteria ◽  
Bacterial Species ◽  
Continuous Cropping ◽  
Soil Microbial ◽  
Relay Intercropping ◽  
Bacteria Community Structure

Abstract Purpose A reasonable cultivation pattern is beneficial to maintain soil microbial activity and optimize the structure of the soil microbial community. To determine the effect of tobacco−peanut (Nicotiana tabacum−Arachis hypogaea) relay intercropping on the microbial community structure in soil, we compared the effects of relay intercropping and continuous cropping on the soil bacteria community structure. Methods We collected soil samples from three different cropping patterns and analyzed microbial community structure and diversity using high-throughput sequencing technology. Result The number of operational taxonomic units (OTU) for bacterial species in the soil was maximal under continuous peanut cropping. At the phylum level, the main bacteria identified in soil were Proteobacteria, Actinobacteria, and Acidobacteria, which accounted for approximately 70% of the total. The proportions of Actinobacteria and Firmicutes increased, whereas the proportion of Proteobacteria decreased in soil with tobacco–peanut relay intercropping. Moreover, the proportions of Firmicutes and Proteobacteria among the soil bacteria further shifted over time with tobacco–peanut relay intercropping. At the genus level, the proportions of Bacillus and Lactococcus increased in soil with tobacco–peanut relay intercropping. Conclusion The community structure of soil bacteria differed considerably with tobacco–peanut relay intercropping from that detected under peanut continuous cropping, and the proportions of beneficial bacteria (the phyla Actinobacteria and Firmicutes, and the genera Bacillus and Lactococcus) increased while the proportion of potentially pathogenic bacteria (the genera Variibacter and Burkholderia) decreased. These results provide a basis for adopting tobacco–peanut relay intercropping to improve soil ecology and microorganisms, while making better use of limited cultivable land.

Comparative Analysis of Gut Microbiota Following Changes in Training Volume Among Swimmers

2020 ◽  
Vol 41 (05) ◽  
pp. 292-299 ◽  
Author(s):  
Jarrad Timothy Hampton-Marcell ◽  
Tifani W. Eshoo ◽  
Marc D. Cook ◽  
Jack A. Gilbert ◽  
Craig A. Horswill ◽  
...  
Keyword(s):  
Body Composition ◽  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
Temporal Dynamics ◽  
Fecal Microbiota ◽  
Future Research ◽  
Training Volume ◽  
Short Term ◽  
Microbial Composition

AbstractExercise can influence gut microbial community structure and diversity; however, the temporal dynamics of this association have rarely been explored. Here we characterized fecal microbiota in response to short term changes in training volume. Fecal samples, body composition, and training logs were collected from Division I NCAA collegiate swimmers during peak training through their in-season taper in 2016 (n=9) and 2017 (n=7), capturing a systematic reduction in training volume near the conclusion of their athletic season. Fecal microbiota were characterized using 16S rRNA V4 amplicon sequencing and multivariate statistical analysis, Spearman rank correlations, and random forest models. Peak training volume, measured as swimming distance, decreased significantly during the study period from 32.6±4.8 km/wk to 11.3±8.1 km/wk (ANOVA, p<0.05); however, body composition showed no significant changes. Coinciding with the decrease in training volume, the microbial community structure showed a significant decrease in overall microbial diversity, a decrease in microbial community structural similarity, and a decrease in the proportion of the bacterial genera Faecalibacterium and Coprococcus. Together these data demonstrate a significant association between short-term changes in training volume and microbial composition and structure in the gut; future research will establish whether these changes are associated with energy balance or nutrient intake.

scholarly journals Assessment of microbial communities in Nakivubo wetland and its catchment areas in Lake Victoria Basin, Uganda

2020 ◽  
Author(s):  
Bernard N. Kanoi ◽  
Maribet Gamboa ◽  
Doris Ngonzi ◽  
Thomas G. Egwang
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Diversity ◽  
Microbial Community Structure ◽  
Lake Victoria ◽  
Rrna Gene ◽  
Lake Victoria Basin ◽  
Structure Changes ◽  
Catchment Areas ◽  
Polluted Sites

AbstractMicrobial community structure changes are key in detecting and characterizing the impacts of anthropogenic activities on aquatic ecosystems. Here, we evaluated the effect of river pollution of industrial and urban sites on the microbial community composition and distribution in the Nakivubo wetland and its catchment areas in Lake Victoria basin, Uganda. Samples were collected from two industrial and one urban polluted sites and the microbial diversity was analyzed based on a 16S rRNA gene clone library. Differences in microbial diversity and community structure were observed at different sampling points. Bacteria associated with bioremediation were found in sites receiving industrial waste, while a low proportion of important human-pathogenic bacteria were seen in urban polluted sites. While Escherichia spp. was the most dominant genus of bacteria for all sites, three unique bacteria, Bacillus sp., Pseudomonas sp., Thermomonas sp., which have been reported to transform contaminants such as heavy metals and hydrocarbons (such as oils) by their metabolic pathways were also identified. Our results may serve as a basis for further studies assessing microbial community structure changes among polluted sites at Nakivubo Water Channel for management and monitoring. The diversity of natural microbial consortia could also be a rich bioprospecting resource for novel industrial enzymes, medicinal and bioactive compounds.

scholarly journals Natural Attenuation of Mn(II) in Metal Refinery Wastewater: Microbial Community Structure Analysis and Isolation of a New Mn(II)-Oxidizing Bacterium Pseudomonas sp. SK3

Water ◽  
2019 ◽  
Vol 11 (3) ◽  
pp. 507 ◽  
Author(s):  
Santisak Kitjanukit ◽  
Kyohei Takamatsu ◽  
Naoko Okibe
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Structure Analysis ◽  
Microbial Community Structure ◽  
Natural Attenuation ◽  
Rrna Gene ◽  
Pseudomonas Sp ◽  
Refinery Wastewater ◽  
Pipe Surface

Natural attenuation of Mn(II) was observed inside the metal refinery wastewater pipeline, accompanying dark brown-colored mineralization (mostly MnIVO2 with some MnIII2O3 and Fe2O3) on the inner pipe surface. The Mn-deposit hosted the bacterial community comprised of Hyphomicrobium sp. (22.1%), Magnetospirillum sp. (3.2%), Geobacter sp. (0.3%), Bacillus sp. (0.18%), Pseudomonas sp. (0.03%), and non-metal-metabolizing bacteria (74.2%). Culture enrichment of the Mn-deposit led to the isolation of a new heterotrophic Mn(II)-oxidizer Pseudomonas sp. SK3, with its closest relative Ps. resinovorans (with 98.4% 16S rRNA gene sequence identity), which was previously unknown as an Mn(II)-oxidizer. Oxidation of up to 100 mg/L Mn(II) was readily initiated and completed by isolate SK3, even in the presence of high contents of MgSO4 (a typical solute in metal refinery wastewaters). Additional Cu(II) facilitated Mn(II) oxidation by isolate SK3 (implying the involvement of multicopper oxidase enzyme), allowing a 2-fold greater Mn removal rate, compared to the well-studied Mn(II)-oxidizer Ps. putida MnB1. Poorly crystalline biogenic birnessite was formed by isolate SK3 via one-electron transfer oxidation, gradually raising the Mn AOS (average oxidation state) to 3.80 in 72 h. Together with its efficient in vitro Mn(II) oxidation behavior, a high Mn AOS level of 3.75 was observed with the pipeline Mn-deposit sample collected in situ. The overall results, including the microbial community structure analysis of the pipeline sample, suggest that the natural Mn(II) attenuation phenomenon was characterized by robust in situ activity of Mn(II) oxidizers (including strain SK3) for continuous generation of Mn(IV). This likely synergistically facilitated chemical Mn(II)/Mn(IV) synproportionation for effective Mn removal in the complex ecosystem established in this artificial pipeline structure. The potential utility of isolate SK3 is illustrated for further industrial application in metal refinery wastewater treatment processes.

scholarly journals Effect of Drought Stress and Developmental Stages on Microbial Community Structure and Diversity in Peanut Rhizosphere Soil

2019 ◽  
Vol 20 (9) ◽  
pp. 2265 ◽  
Author(s):  
Liangxiang Dai ◽  
Guanchu Zhang ◽  
Zipeng Yu ◽  
Hong Ding ◽  
Yang Xu ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Drought Tolerance ◽  
Microbial Communities ◽  
Microbial Community Structure ◽  
Defense Mechanism ◽  
Developmental Stages ◽  
Rrna Gene ◽  
Special Importance ◽  
Arachis Hypogaea L

Background: Peanut (Arachis hypogaea L.), an important oilseed and food legume, is widely cultivated in the semi-arid tropics. Drought is the major stress in this region which limits productivity. Microbial communities in the rhizosphere are of special importance to stress tolerance. However, relatively little is known about the relationship between drought and microbial communities in peanuts. Method: In this study, deep sequencing of the V3-V4 region of the 16S rRNA gene was performed to characterize the microbial community structure of drought-treated and untreated peanuts. Results: Taxonomic analysis showed that Actinobacteria, Proteobacteria, Saccharibacteria, Chloroflexi, Acidobacteria and Cyanobacteria were the dominant phyla in the peanut rhizosphere. Comparisons of microbial community structure of peanuts revealed that the relative abundance of Actinobacteria and Acidobacteria dramatically increased in the seedling and podding stages in drought-treated soil, while that of Cyanobacteria and Gemmatimonadetes increased in the flowering stage in drought-treated rhizospheres. Metagenomic profiling indicated that sequences related to metabolism, signaling transduction, defense mechanism and basic vital activity were enriched in the drought-treated rhizosphere, which may have implications for plant survival and drought tolerance. Conclusion: This microbial communities study will form the foundation for future improvement of drought tolerance of peanuts via modification of the soil microbes.

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